title: Leaves_uninfected_line37_dye_swap

city: Stellenbosch

last: Alexandersson

address: Victoria Street

country: South Africa

institute: IWBT, Stellenbosch University

hyb_protocol: Pre-hybridization was done under lifterslips (Erie Scientific, Portsmouth, NH, USA) with a pre-warmed solution containing 5X SSC (from 20X SSC: 3 M NaCl, 1.5 M sodium citrate, pH 7.0), 0.1% SDS and 1% BSA at 42°C for at least 30 min. Following pre-hybridization, the slides were washed in five washes of deionized water and finally briefly submerged in ethanol before short centrifugation. The combined Cy-labeled probes (28 µL) were mixed with 30 µL of a 2X hybridization buffer (50% formamide, 5X SSC and 0.2% SDS), 1 µL each of COT1 DNA (1 µg/µL) and poly(A)-DNA (12 µg/µL) added, for a total volume of 60 µL. The mixture was denatured at 90°C for 3 min, and subsequently applied to the slide using lifterslips. Slides were incubated for 16 h at 42°C in hybridization chambers (ArrayIt, Telechem International, Sunnyvale, CA, USA) and successively washed in low stringency (2X SSC, 0.5% SDS; heated to 55°C), medium stringency (0.5X SSC) and high stringency (0.05X SSC) wash buffers for 5 min each and then briefly submerged in ethanol prior to short centrifugation.

scan_protocol: An Axon GenePix 4000A scanner was used, optimizing the photomultiplier tube (PMT) settings during pre-scans to obtain equal output from the red and green channels before proceeding to full scans using the GenePix 5.1 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Result files were analyzed using the Limma package in R 2.9.1. Spots flagged as “bad” by the GenePix software were removed from further analysis. Background correction was done by the normexp method with an offset of 50 to avoid negative or zero corrected intensities and normalization was then done by print-tip loess. The duplicateCorrelation function was used to estimate a common value for within-array duplicated spots. Finally, fold changes and standard errors were obtained by fitting a linear model to each gene and standard errors were smoothed by empirical Bayes. Genes with a p-value below 0.05 after false discovery rate (FDR) control were regarded as significant.

organism: Nicotiana tabacum

source_name: Transgenic Vvpgip1 line 37

label_protocol: Twenty-five µg RNA was used in each cDNA synthesis reaction in a total volume of 30 µL. Before denaturation at 70°C for 10 min, 2 µL of oligo d(T) primers (500 µg/mL) were added. Following denaturation, first strand buffer and DTT were added according to the manufacturer’s recommendation (Invitrogen, Carlsbad, CA, USA). A 2:3 (aa-dUTP:dTTP) aminoallyl-dNTP (Ambion, Austin, TX, USA) mix was added to a 1X concentration (0.5 mM each of dATP, dCTP and dGTP; 0.2 mM aa-dUTP and 0.3 mM dTTP) before incubation at 46°C for 2 min, after which 200 U of SuperScript III Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) was added. The same amount of enzyme was added following incubation for 4 h at 46°C, after which cDNA synthesis proceeded overnight.  RNA was hydrolyzed by 10 µL 1 M NaOH and 0.5 M EDTA and incubated at 65°C for 15 min. To neutralize the pH, 10 µL 1 M HCl solution was added following hydrolysis. Unincorporated aminoallyl dUTP and free amines were removed using the RNeasy Mini Kit. cDNA was quantified using a Nanodrop and dried down to volumes of less than 1 µL in a vacuum dryer. Five µL of 0.1 M Na2CO3, pH 9.0, was added to the cDNA, and mixture incubated at 37°C for 10 min. Cy3 or Cy5 (Amersham Biosciences, Buckinghamshire, UK) ester was added and the coupling allowed to proceed for 1 h in the dark at room temperature. Uncoupled dyes were removed by purification with the RNeasy Mini Kit. Probe labeling efficiency of Cy-esters was estimated by measuring the absorbance at 550 nm and 650 nm. Similar amounts of labeled samples were hybridized on TIGR 10K potato microarrays (version 3).

growth_protocol: Transgenic Vvpgip1 line 37 and 45 described in Joubert et al. (2006) were used. Wild-type and transgenic Nicotiana tabacum SR1 (Petit Havana) plants were grown in a soil and peat moss (Jiffy Products International AS, Norway) mixture in a growth room at 24°C and 55% relative humidity. Plants were supplemented with a commercially available liquid organic fertilizer every two weeks (Nitrosol®, Fleuron (Pty) Ltd, South Africa). A light intensity of 120 µmol m2 s-1 was maintained over a 16 h light period.

extract_protocol: RNA was extracted using a sodium perchlorate-based method. 0.5 to 1 g of plant material was finely ground in liquid nitrogen, allowed to thaw in an extraction buffer (5 M sodium perchlorate, 0.3 M Tris-HCl pH 8.3, 8.5% polyvinylpolypyrollidone (PVPP), 2.0% PEG 4000, 1.0% β-mercapto-ethanol and 1.0% SDS) and then shaken for 30 min at room temperature. Following centrifugation, plant debris was removed by passing the supernatant through a syringe plugged with cotton wool. Several phenol/chloroform extractions were performed before precipitating the RNA with 2.5 M LiCl at -20°C overnight. The pellet was washed with 70% ethanol and the resuspended RNA was purified using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany).

treatment_protocol: All samples were collected under normal growth conditions in the abscence of plant pathogens

tag: cultivar

value: Petite Havana SR1

tag: plant line

value: Transgenic Vvpgip1 line 37

value: leaves

source_name: untransformed WT

value: untransformed WT


title: 6H_seedling_rep2

status: Public on Dec 08 2011

type: RNA

city: Yokohama

first: Jianwei

last: Tang

state: Kanagawa

address: 641-12 Maioka-cho, Totsuka-ku

department: Kihara Institute for Biological Research

country: Japan

institute: Yokohama City University

description: Hordeum vulgare cv. Betzes chromosome 6 addition line of Triticum aestivum cv. Chinese Spring, replicate 2

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Li 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent Agilent Technologies) using default parameters(protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Triticum aestivum

source_name: Barley chromosome addition line of common wheat

label_protocol: A Cy3 labeled cRNA probe were prepared using a Low RNA Input Linear Amp Kit (Agilent Technologies), and microarray hybridization was performed following the recommended protocol.

growth_protocol: Seeds were germinated and grown on soil at 22 ºC under 16 hr light and 8 hr dark conditions for 2 weeks.

extract_protocol: Total RNA was extracted using an RNeasy Plant Mini kit (Qiagen). Total RNA quality was checked with an Agilent 2100 Bioanalyzer.

tag: line

tag: tissue

value: Leaf


title: 5H_seedling_rep2

description: Hordeum vulgare cv. Betzes chromosome 5 addition line of Triticum aestivum cv. Chinese Spring, replicate 2


title: retina TAA day 7 bio rep3

city: Davis

first: Zeljka

last: Smit-McBride

state: CA

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

country: USA

institute: University of California, Davis Eye Center

description:
Gene expression data at day 7 from the eyes intravitreally injected with TAA at day 0
TAA-12 Ret

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX 11 using RMA algorhitm as analysis and normalization method.

label: biotin

organism: Mus musculus

source_name: retina TAA treatment day 7

label_protocol: Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 0.100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were 2 months old, kept at normal 12/12 light/dark conditions, feed ad libitum

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Animals were sacrificed within CO2 chamber, eyes were enucleated, disected, retinal tissue was removed and quicky immersed into 300ul RNALater. Samples were stored in RNALater at -20C till the total RNA isolation step.

tag: strain

tag: gender

value: males

tag: organ

value: eye

value: retina


title: Mouse 591 ileum

city: Gothenburg

first: Erik

last: Larsson

address: Bruna stråket 16

department: Wallenberg Laboratory

country: Sweden

institute: University of Gothenburg

description: RMA expression value derived from Expression Console software; gene level analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the Uppsala Array Platform microarray core facility (Sweden).

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

data_processing: Raw data were processed with the Expression Console software (Affymetrix) for background correction and normalization. Downstream data analysis and statistical evaluations were performed using customized matlab scripts.

source_name: Healthy male, autoclaved chow diet

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

extract_protocol: RNA was isolated using the RNeasy mini kit or the RNeasy Lipid tissue mini kit (QIAGEN), according to the manufacturer's instructions.

value: ileum

value: CONV-R

tag: genotype

value: WT


title: retina BSS day 30 bio rep1

description:
Gene expression data at day 30 from the eyes intravitreally injected with BSS at day 0
Con-13 Ret

source_name: retina BSS control day 30


title: Mouse 592 ileum


title: 1HS_seedling_rep3

description: Hordeum vulgare cv. Betzes chromosome 1 short arm addition line of Triticum aestivum cv. Chinese Spring, replicate 3


title: Leaves_uninfected_line45

source_name: Transgenic Vvpgip1 line 45

value: Transgenic Vvpgip1 line 45


title: Leaves_uninfected_line37


title: Mouse 588 ileum


title: 1HS_seedling_rep2

description: Hordeum vulgare cv. Betzes chromosome 1 short arm addition line of Triticum aestivum cv. Chinese Spring, replicate 2


title: Mouse 589 ileum


title: 7H_seedling_rep2

description: Hordeum vulgare cv. Betzes chromosome 7 addition line of Triticum aestivum cv. Chinese Spring, replicate 2


title: retina DEX day 7 bio rep3

description:
Gene expression data at day 7 from the eyes intravitreally injected with DEX at day 0
Dex-08 Ret

source_name: retina DEX treatment day 7


title: retina DEX day 7 bio rep1

description:
Gene expression data at day 7 from the eyes intravitreally injected with DEX at day 0
Dex-06 Ret


title: retina TAA day 7 bio rep1

description:
Gene expression data at day 7 from the eyes intravitreally injected with TAA at day 0
TAA-09 Ret


title: retina DEX day 7 bio rep2

description:
Gene expression data at day 7 from the eyes intravitreally injected with DEX at day 0
Dex-07 Ret


title: Mouse 583 ileum


title: Mouse 584 ileum


title: retina TAA day 7 bio rep2

description:
Gene expression data at day 7 from the eyes intravitreally injected with TAA at day 0
TAA-11 Ret


title: 6H_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 6 addition line of Triticum aestivum cv. Chinese Spring, replicate 1


title: retina BSS day 7 bio rep1

description:
Gene expression data at day 7 from the eyes intravitreally injected with BSS at day 0
Con-01 Ret

source_name: retina BSS control day 7


title: 2H_seedling_rep2

description: Hordeum vulgare cv. Betzes chromosome 2 addition line of Triticum aestivum cv. Chinese Spring, replicate 2


title: retina BSS day 7 bio rep2

description:
Gene expression data at day 7 from the eyes intravitreally injected with BSS at day 0
Con-02 Ret


title: 4H_seedling_rep2

description: Hordeum vulgare cv. Betzes chromosome 4 addition line of Triticum aestivum cv. Chinese Spring, replicate 2


title: 7H_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 7 addition line of Triticum aestivum cv. Chinese Spring, replicate 1


title: Mouse 587 ileum


title: CS_seedling_rep1

description: Triticum aestivum cv. Chinese Spring, replicate 1

source_name: Common wheat

value: Triticum aestivum cv. Chinese Spring


title: Mouse 601 proximal colon

description: RMA expression value derived from Expression Console software; gene level analysis

value: proximal colon

value: GF


title: Mouse 586 ileum


title: 3H_seedling_rep2

description: Hordeum vulgare cv. Betzes chromosome 3 addition line of Triticum aestivum cv. Chinese Spring, replicate 2


title: FRC3

city: London

first: Caroline

middle: Emma

last: Johnston

address: 125 Coldharbour Lane

country: United Kingdom

institute: Kings College London

description:
4613963049_F
REST KO replicate 3

E14Tg2a line: See Hooper et al., 1987, Nature, 326, 292-295 (PMID 3821905).

hyb_protocol: Standard Illumina hybridization protocol to Illumina Mouse Ref-8 v2 BeadArrays.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization using the Bioconductor BeadArray library in R. Differential expression was calculated using the limma library.

source_name: FloResCre

label_protocol: RNA was labelled using a TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: ESCs and EBs were cultured and differentiated as described previously (Wiles et al., Exp Cell Res 1999;247:241-8). Neural induction using SB431542 (Cambridge Bioscience) was adapted from earlier protocols (Ying et al., Nat. Biotechnol. 2003; 21:183-6; Chambers et al., Nat Biotechnol 2009;27:275-80). Briefly, ESCs were plated on fibronectin-coated coverslips or gelatin-coated 6-well clusters at a density to achieve 80-90% confluence after a further 24h, after which growth medium was d with N2B27 medium containing 5uM SB431542. RG-NSCs were generated according to Conti et al. (PloS Biol 2005;3:e283) and differentiated using either a tri-potential differentiation protocol (Glaser et al., PloS One 2007;2:e298) or for astrocyte differentiation, in NS-A/Euroclone medium (Cadama) supplemented with 10% FCS or 20ng/ml BMP4.

extract_protocol: Total RNA isolation, reverse transcription and PCR analyses were carried out as previously described (Johnson et al., PLoS Biol, 2008;6:e256).

tag: cell line

value: REST KO


title: Mouse 585 ileum


title: Mouse 600 proximal colon


title: retina BSS day 7 bio rep3

description:
Gene expression data at day 7 from the eyes intravitreally injected with BSS at day 0
Con-03 Ret


title: FRC1

description:
4613963049_D
REST KO replicate 1

E14Tg2a line: See Hooper et al., 1987, Nature, 326, 292-295 (PMID 3821905).


title: Mouse 602 proximal colon


title: 5H_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 5 addition line of Triticum aestivum cv. Chinese Spring, replicate 1


title: FR3

description:
4613963049_C
Control replicate 3

E14Tg2a line: See Hooper et al., 1987, Nature, 326, 292-295 (PMID 3821905).

source_name: FloRes

value: control


title: Mouse 599 proximal colon


title: FRC2

description:
4613963049_E
REST KO replicate 2

E14Tg2a line: See Hooper et al., 1987, Nature, 326, 292-295 (PMID 3821905).


title: FR2

description:
4613963049_B
Control replicate 2

E14Tg2a line: See Hooper et al., 1987, Nature, 326, 292-295 (PMID 3821905).


title: Ebi3 –/– Il10 –/–  Treg rep3

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. An addtive correctin of 20 was then added to the signal before natural log transformation to stabilize the data. batch correction was applied to some data using Partek Genomics Suite 6.4

label: Biotin

source_name: FACS purified T cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 1 ug of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

growth_protocol: Freshly isolated cells were utilized

extract_protocol: Qiagen Rneasy Plus Mini kit was used to extract RNA according to the manufacturer's protocol

treatment_protocol: No treatment of cells; Freshly isolated cells were used

value: Ebi3 –/– Il10 –/–  Treg

tag: batch

tag: cell type

value: T cell


title: CRSsNP 3

city: Wuhan

first: zhang

last: xinhao

address: 1095 Jiefang Avenue

country: China

institute: Tongji Hospital

hyb_protocol: The Hy5™ fluorescent labeled miRNAs were hybridized to Exiqon miRCURY locked nucleic acid (LNA) array (version 9.2) (Exiqon, Vedbaek, Denmark) at 52ºC for overlight.

scan_protocol: Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent®, Santa Clara, CA, USA) by Exiqon® (Vedbaek, Denmark).

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain “normalized data”, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

organism: Homo sapiens

source_name: sinasal mucosa

label_protocol: 2 μg of total RNA from each sample was fluorochrome labeled  Exiqon®, Vedbaek, Denmark using the miRCURY™ LNA microRNA Power labeling kit.

extract_protocol: Total RNA was extracted using TRIzol® Reagent (Invitrogen) according to the manufacturer’s protocol.

value: eosinophilic CRSsNP from sinonasal mucosa

tag: disease state

value: CRSsNP


title: Il10 –/–  Treg rep3

value: Il10 –/–  Treg


title: CRSsNP 2


title: Mouse 596 proximal colon


title: Ebi3 –/– Il10 –/–  Treg rep2


title: Ebi3 –/– Treg rep3

value: Ebi3 –/– Treg


title: Wild type Treg rep3

value: Wild type Treg


title: Mouse 597 proximal colon


title: Mouse 598 proximal colon


title: FR1

description:
4613963049_A
Control replicate 1

E14Tg2a line: See Hooper et al., 1987, Nature, 326, 292-295 (PMID 3821905).


title: Il10 –/–  Treg rep2


title: P2 fat tissue

city: new york

first: kivanc

last: birsoy

address: 1230 Rockefeller University

institute: Rockefeller University

description: Developing mouse adipose tissue pooled from at least 3 embryos

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: developing adipose tissue

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

extract_protocol: RNA from each sample was labeled using the Illumina TotalPrep RNA Amplification kit (Ambion) and cRNA was hybridized to Illumina's MouseRef-8 Expression BeadChips (Illumina). The arrays were washed, blocked, and then hybridized. Image processing and data extraction were performed using BeadStudio (Illumina).

treatment_protocol: RNA isolated from developing WAT was pooled from four independent embryos at eight different embryonic and early postnatal time points. The RNA was then labeled and hybridized to Illumina Mouse Ref8 BeadChips.

value: developing adipose tissue

tag: developmental stage


title: 4H_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 4 addition line of Triticum aestivum cv. Chinese Spring, replicate 1

value: Leaf


title: P0 fat tissue


title: 1HS_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 1 short arm addition line of Triticum aestivum cv. Chinese Spring, replicate 1


title: CRSsNP 1


title: 3H_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 3 addition line of Triticum aestivum cv. Chinese Spring, replicate 1


title: 2H_seedling_rep1

description: Hordeum vulgare cv. Betzes chromosome 2 addition line of Triticum aestivum cv. Chinese Spring, replicate 1


title: CRSwNP 3

value: eosinophilic CRSwNP from sinonasal mucosa

value: CRSwNP


title: P12 fat tissue


title: Ebi3 –/– Treg rep2


title: Wild type Treg rep2


title: P5 fat tissue


title: CRSwNP 2


title: Mouse 595 proximal colon


title: Mouse 594 proximal colon


title: CRSwNP 1


title: Mouse 591 proximal colon

value: CONV-R

value: WT


title: Il10 –/–  Treg rep1


title: e18.5 fat tissue


title: Mouse 593 proximal colon

value: proximal colon


title: control 3

value: sinonasal mucosa


title: control 2


title: e17.5 fat tissue


title: Mouse 592 proximal colon


title: e16.5 fat tissue


title: e15.5 fat tissue


title: control 1


title: Mouse 590 proximal colon


title: Mouse 587 proximal colon


title: Wild type Treg rep1


title: Ebi3 –/– Il10 –/–  Treg rep1


title: Mouse 589 proximal colon


title: Mouse 586 proximal colon


title: Ebi3 –/– Treg rep1


title: Mouse 585 proximal colon


title: IL15 thymic NKT 2

city: Nashville

first: Joyce

last: Sebastian

address: A-4223 Medical Centre North

department: Department of Microbiology and Immunology

institute: Vanderbilt University School of Medicine

description: Gene expression of sorted thymic IL15ko NKT cells

hyb_protocol: Hybridizations were performed using One-colour hybridization on SurePrint G3 Mouse GE 60k Microarray (Agilent)

scan_protocol: Slides were scanned using a GenePix 4000B Microarray scanner (Molecular Devices)

data_processing: Images were processed with Agilent Feature Extraction software to generate raw probe intensity data, which was subsequently normalised by the quantile method.  Differential expression analysis was carried out with an empirical Bayes approach on linear model using limma package.

source_name: Sorted NKT cells replicate 2

label_protocol: standard Agilent protocol

growth_protocol: Frest isolated NKT cells from indicated mouse strains

extract_protocol: RNA was isolated using a Qiagen Qiashredder followed by the Qiagen RNeasy kit according to the manufacturer's instructions. RNA yield was quantified spectrophotometrically (Nanodrop ND-1000) and aliquots electrophoresed to determine sample purity and concentration (Agilent 2100 Bioanalyzer).

treatment_protocol: Single cell suspensions from 10 pooled thymi were enriched for T cells by MACS using PanT cell isolation kit (Miltenyi).  NKT cells (CD3e+CD1d tetramer+) were then purified by flow sorting (FACSAria, Becton-Dickinson) from the enriched T cells.

tag: genetic background

tag: source organ

value: thymus

value: NKT cells


title: spxA1-null mutant of Streptococcus sanguinis mixed with wild type SK36, replicate 1

city: Tianjin

first: Lei

last: Chen

address: 92 Weijin Rd

institute: Tianjin University

description: Biological replicate 1 of RNA mixture from Streptococcus sanguinis ΔspxA1 and the wild type SK36.

hyb_protocol: Hybridization at 42C for 16-20 hrs was performed following the protocol at http://pfgrc.jcvi.org/index.php/microarray/protocols.html.

scan_protocol: Scanned on a GenePix 4000A scanner. Images were analyzed using the program Spotfinder (v321win).

data_processing: Data were LOWESS normalized and background subtracted using Midas (v2.20). Processed Red signal/processed Green signal ratios were calculated using Excel.

organism: Streptococcus sanguinis

source_name: Streptococcus sanguinis wild type

label_protocol: Microbial RNA Aminoallyl Labeling was performed following the protocol at http://pfgrc.jcvi.org/index.php/microarray/protocols.html.

growth_protocol: S. sangunis SK36 was grown in brain heart infusion broth (BHI; Difco Inc., Detroit, MI) under microaerobic conditions at 37 °C. Overnight culture was diluted into fresh BHI broth by 1% inoculation and cultured further for 5 hours.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) following manufacturer's instructions.

value: wild type

source_name: Streptococcus sanguinis ΔspxA1

growth_protocol: S. sangunis ΔspxA1 was grown in brain heart infusion broth (BHI; Difco Inc., Detroit, MI) under microaerobic conditions at 37 °C. Overnight culture was diluted into fresh BHI broth by 1% inoculation and cultured further for 5 hours.


title: spxA1-null mutant of Streptococcus sanguinis mixed with wild type SK36, replicate 3

description: Biological replicate 3 of RNA mixture from Streptococcus sanguinis ΔspxA1 and the wild type SK36.


title: spxA1-null mutant of Streptococcus sanguinis mixed with wild type SK36, replicate 2

description: Biological replicate 2 of RNA mixture from Streptococcus sanguinis ΔspxA1 and the wild type SK36.


title: IL15 thymic NKT 1

source_name: Sorted NKT cells replicate 1


title: Mouse 588 proximal colon

description: RMA expression value derived from Expression Console software; gene level analysis


title: Mouse 584 proximal colon


title: Mouse 583 proximal colon


title: B6 thymic NKT 1

description: Gene expression of sorted thymic wildtype NKT cells

value: wt


title: Tumor Macrophage Irradiated d7 rep1

status: Public on Dec 07 2011

city: Portland

first: Michael

last: Gough

state: OR

address: 4805 NE Glisan St

department: Earle A Chiles Research Institute

institute: Providence Cancer Center

hyb_protocol: Mouse Genome 430 2.0 GeneChip array (3’IVT array assay)

scan_protocol: Image processing and expression analysis were performed using Affymetrix GeneChip Command Console (AGCC) v. 2.0.0.1029 and Affymetrix Expression Console v. 1.1 software, respectively.

source_name: Tumor macrophage

label_protocol: NuGEN Nano Ovation v.2 w/ Encore protocol

growth_protocol: Tumors were innoculated s.c. in the right leg below the knee at a dose of 2x105 Panc02 cells and allowed to establish for 14-17 days before initiation of treatment. At harvest, the tumor was dissected into approximately 2mm fragments followed by agitation in 1mg/mL collagenase (Invitrogen), 100µg/mL hyaluronidase (Sigma), and 20mg/mL DNase (Sigma) in PBS for 1hr at room temperature. The digest was filtered through 100µm nylon mesh to remove macroscopic debris. Cell suspensions were stained with antibodies specific for CD11b, IA (MHC class II) and Gr1 and CD11b+ IA+ cells were FACS sorted using a BD FACSAria Cell Sorter to greater than 98% purity.

extract_protocol: Total RNA was prepared from FACS sorted CD11b+IA+ cells using a PrepEase RNA Spin Kit (Affymetrix, Cleveland, OH).

treatment_protocol: Three daily 20Gy treatment fractions were given using an Elekta Synergy linear accelerator (Atlanta, GA) with 6MV photons incorporating a half beam block to minimize dose to the torso

value: tumor macrophage

tag: treatment

value: irradiated

tag: time

value: day 7

tag: tumor source

value: Panc02 cell line


title: Tumor Macrophage Irradiated d7 rep2

data_processing: Image processing and expression analysis were performed using Affymetrix GeneChip Command Console (AGCC) v. 2.0.0.1029 and Affymetrix Expression Console v. 1.1 software, respectively.


title: Tumor Macrophage Untreated d7 rep1

value: untreated


title: B6 thymic NKT 2


title: Tumor Macrophage Irradiated d1 rep2

value: day 1


title: B6 thymic NKT 3

source_name: Sorted NKT cells replicate 3


title: Tumor Macrophage Untreated d7 rep2


title: Tumor Macrophage Irradiated d1 rep1


title: Tumor Macrophage Untreated d1 rep2


title: Tumor Macrophage Untreated d1 rep1


title: 132 L1 SC rep2

city: Takatsuki

first: Akira

last: Imoto

state: Osaka

institute: Osaka Medical College

description: Gene expression data from lumbar cord of SC model

hyb_protocol: The procedures for target hybridization, washing, and staining with signal amplification were conducted according to the supplier’s protocols (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing:
The intensity of each feature of the array was calculated using GeneChip Operating Software v1.1.1 (Affymetrix). The mean intensity was standardized to the target intensity, which was set to 1,000, to reliably compare variable multiple arrays.
The values were log transformed and median centered. GeneSpring (Agilent Technologies, Inc., Santa Clara, CA, http://www.agilent.com) and Excel (Microsoft, Redmond, WA, http://www.microsoft.com) were used for gene selection.

source_name: lumbar cord of SC model

label_protocol: Target cRNA was generated from 100 ng total RNA from each sample using Two-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Male severe combined immunodeficiency (SCID) mice (Clea Japan, Tokyo, 9 weeks old) were housed in a light- and temperature-controlled room and fed standard food ad libitum (irradiated CMF; Oriental Yeast, Tokyo, Japan).

extract_protocol: The specimens were dissolved in TRIzol reagent, were homogenized using a Multi-beads shocker (Yasui Kikai), and total RNA was extracted according to the manufacturer's instructions.

value: SCID mouse

value: male

tag: age

value: 15 weeks old

value: lumbar cord


title: 119 L1 N-inv rep1

description: Gene expression data from lumbar cord of N-inv model

source_name: lumbar cord of N-inv model


title: 130 L1 SC rep1


title: 111 L1 PBS rep1

description: Gene expression data from lumbar cord of PBS model

source_name: lumbar cord of PBS model


title: 123 L1 N-inv rep2


title: 112 L1 PBS rep2


title: Mm OE ICAM1-negative-2

city: Berkeley

first: Russell

last: Fletcher

department: MCB, Functional Genomics Lab

institute: UC Berkeley

description: FACS purified ICAM1-positive cells

hyb_protocol: Hybridized to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (http://www.affymetrix.com).

scan_protocol: Affymetrix standard protocols

data_processing: Microarray data were normalized using GCRMA.

source_name: ICAM1 (-) cells

label_protocol: Labeled to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (http://www.affymetrix.com).

extract_protocol: The olfactory epithelia from P21-P25 CD1 mice (Charles River Laboratories, Wilmington, MA), were isolated, dissociated, and then purified by FACS using a FITC-conjugated antibody for ICAM1 (CD54).  ICAM1-positive and negative cell populations were collected and compared.  RNA was purified with TRIzol reagent .

value: Olfactory epithelium

tag: cell population


title: genotype: Faris acid lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Mature (50 mm diameter, very juicy, pale-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 4.0, and juice vesicle tissue was excised and frozen in liquid nitrogen

hyb_protocol: Standard Affymetrix protocols; Affy-Oven320

scan_protocol: Standard Affymetrix protocols; Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Citrus x limon

source_name: juice sac (genotype: Faris acid lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,)

label_protocol: Standard Affymetrix protocols; Affy-Eukaryotic Target Preparation for mRNA

growth_protocol: Environmental Conditions:  Field conditions in Riverside, CA USA

extract_protocol: TRIzol-Qiagen

tag: Faris sweet lemon (Germplasm Name); PO:0006013 juice sac, (Organism Part); PO:0007050 FR.03 late stage of fruit ripening (Development Stage); field soil (Growth Media).


title: genotype: Faris acid lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep2

description: Young (33 mm diameter, slightly juicy, green or yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH between 3.5 and 4.5, and juice vesicle tissue was excised and frozen in liquid nitrogen

source_name: juice sac (genotype: Faris acid lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,)

tag: Faris sweet lemon (Germplasm Name); PO:0006013 juice sac, (Organism Part); PO:0007009 FF.01 fruit size 30% (Development Stage); field soil (Growth Media).


title: Mm OE ICAM1-negative-3

description: FACS purified ICAM1-positive cells

tag: tissue

tag: strain


title: genotype: Frost Lisbon lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep2

description: Young (28 mm diameter, slightly juicy, yellow-green rind) fruit of Frost Lisbon lemon were harvested, cut, determined to have juice pH about 3.5, and juice vesicle tissue was excised and frozen in liquid nitrogen

source_name: juice sac (genotype: Frost Lisbon lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,)

tag: Frost Lisbon lemon (Germplasm Name); PO:0006013 juice sac, (Organism Part); PO:0007009 FF.01 fruit size 30% (Development Stage); field soil (Growth Media).


title: genotype: Frost Lisbon lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep3

description: Young (31 mm diameter, slightly juicy, yellow-green rind) fruit of Frost Lisbon lemon were harvested, cut, determined to have juice pH about 3.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Frost Lisbon lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep1

description: Mature (51 mm diameter, very juicy, yellow-green rind) fruit of Frost Lisbon lemon were harvested, cut, determined to have juice pH about 3.5, and juice vesicle tissue was excised and frozen in liquid nitrogen

source_name: juice sac (genotype: Frost Lisbon lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,)

tag: Frost Lisbon lemon (Germplasm Name); PO:0006013 juice sac, (Organism Part); PO:0007050 FR.03 late stage of fruit ripening (Development Stage); field soil (Growth Media).


title: genotype: Faris acid lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep3

description: Young (32 mm diameter, slightly juicy, pale-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH between 3.5 and 4.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Faris acid lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep2

description: Mature (54 mm diameter, very juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 4.0, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Frost Lisbon lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep1

description: Young (29 mm diameter, slightly juicy, yellow-green rind) fruit of Frost Lisbon lemon were harvested, cut, determined to have juice pH about 3.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: Mm OE ICAM1-positive-3

description: FACS purified ICAM1-negative cells

source_name: ICAM1 (+) cells


title: genotype: Frost Lisbon lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep2

description: Mature (46 mm diameter, very juicy, yellow-green rind) fruit of Frost Lisbon lemon were harvested, cut, determined to have juice pH about 3.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: Mm OE ICAM1-negative-1

description: FACS purified ICAM1-positive cells


title: Mm OE ICAM1-positive-2

description: FACS purified ICAM1-negative cells


title: genotype: Faris sweet lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep2

description: Mature (54 mm diameter, very juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 6.0, and juice vesicle tissue was excised and frozen in liquid nitrogen

source_name: juice sac (genotype: Faris sweet lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening,)


title: genotype: Frost Lisbon lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep3

description: Mature (48 mm diameter, very juicy, yellow-green rind) fruit of Frost Lisbon lemon were harvested, cut, determined to have juice pH about 3.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: Mm OE ICAM1-positive-1

description: FACS purified ICAM1-negative cells


title: genotype: Faris acid lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep1

description: Mature (48 mm diameter, very juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 4.0, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: Si-2 HISC medium

city: Dresden

first: Daniel

middle: E.

last: Stange

address: Fetscherstr. 74

country: Germany

institute: University Clinic Dresden

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved and data normalized using Feature Extraction Software (V.9.5.3, Agilent Technologies). Normalized ratios are given in Log10.

source_name: human small intestine organoid

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Human intestinal organoids were grown with HISC medium in Matrigel.

extract_protocol: RNA was isolated using the RNeasy Micro kit (Qiagen)

value: human small intestinal organoid patient_2

source_name: human reference RNA (Stratagene)

value: human reference RNA (Stratagene)


title: Si Crypts

source_name: human small intestinal crypts

value: human freshly isolated small intestinal crypts


title: Colon HISC medium

source_name: human colon organoid

value: human colon organoid


title: Si Villi

source_name: human small intestinal villus

value: human freshly isolated small intestinal villus


title: genotype: Faris acid lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep1

description: Young (29 mm diameter, slightly juicy, green or yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH between 3.5 and 4.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Faris sweet lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep3

description: Mature (50 mm diameter, very juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 5.5, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Faris sweet lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep3

description: Young (37 mm diameter, slightly juicy, yellow-green rind) fruit of Ferris sweet lemon were harvested, cut, determined to have juice pH about 6.0, and juice vesicle tissue was excised and frozen in liquid nitrogen

source_name: juice sac (genotype: Faris sweet lemon - developmental stage: PO:0007009 FF.01 fruit size 30%,)


title: genotype: Faris sweet lemon - developmental stage: PO:0007050 FR.03 late stage of fruit ripening, - rep1

description: Mature (48 mm diameter, very juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 6.0, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Faris sweet lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep2

description: Young (31 mm diameter, slightly juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 6.0, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: genotype: Faris sweet lemon - developmental stage: PO:0007009 FF.01 fruit size 30%, - rep1

description: Young (30 mm diameter, slightly juicy, yellow-green rind) fruit of Faris sweet lemon were harvested, cut, determined to have juice pH about 6.0, and juice vesicle tissue was excised and frozen in liquid nitrogen


title: Si-1 HISC medium

value: human small intestinal organoid patient_1


title: P1.5C swap

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description: This research was approved by Ethic Committee of the Medical and Research Center - Hospital A. C. Camargo number 764/06. Twenty-four sporadic and favorable histology advanced (Stage III or IV) Wilms tumor (WT) samples from Children Oncology Group (NWTSG), four human differentiated kidneys , and four temporal stages of kidney differentiation in mouse (E15.5, E17.5, P1.5 and P7.5) were used for this study. Metanephric blastema cells from four temporal differentiation stages, from E15.5 to the fully differentiated kidney in mouse, and blastemal cells of WT and differentiated kidneys in human were used for RNA extraction and amplification. RNA were extracted with PicoPure™ RNA Isolation kit (Arcturus Engineering #KT0204) and treated with RNase-Free DNase Set (Qiagen #79254; Qiagen-Germantown MD USA).  Amplification methodology used RiboAmpTM RNA amplification KIT0201 and RiboAmpTM HS Plus KIT0505 (ARCTURUS) for human and mouse samples, respectively. A pool of RNAs obtained from 15 distinct human cell lines was amplified in the presence of SuperScript III and oligo dT(24)-T7. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Cy3 or Cy5-labeled dCTP. Dye-swap was performed for each sample as control for dye bias and used as replicate.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Esperma de salmao,  Formamida 25%. / Temperature:14 a 24 hs / Time:42 C / Touch Down: Washing - Round 1 - Solution: SSC2X / Temperature:42ºC / Time:15' / Washing Number: 1 Washing - Round 2 - Solution: SSC0,1X-SDS0,1% / Temperature:42ºC / Time:15' / Washing Number: 2 Washing - Round 3 - Solution: SSC0,1X / Temperature:42ºC / Time:15' / Washing Number: 2

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: R version 2.9.2 (2009-08-24), Lowess-normalized signal intensity, log2 test/reference

source_name: Reference

label_protocol: Labeled cDNA was generated in a reverse transcriptase reaction using 7mg of amplified RNA (aRNA), random hexamer primer (Invitrogen), Cy3- or Cy5-labeled dCTP (Amersham, Biosciences) and SuperScript II (Invitrogen).For reference, 4mg of aRNA were Cy3- or Cy5-labeled dCTP (Amersham, Biosciences) in the presence of SuperScript II (Invitrogen).

extract_protocol: Trizol

tag: reference

value: pool of 15 human cell lines

tag: cell line

value: Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))

extract_protocol: kit Pico Pure RNA Isolation Kit

value: mouse kidney blastemal cells

value: 1 day old


title: A1 unstimulated

city: Seattle

first: Deanna

last: Santer

address: 1959 NE Pacific St Health Science Bldg BB561 Campus Box 356428

institute: University of Washington

scan_protocol: BeadChips were scanned on an Illumina BeadArray Reader

data_processing: The data was background subtracted and quantile normalized using the Bioconductor package, lumi, with a small factor added to each signal intensity to bring all values above zero, then transformed to log2 scale

source_name: PBMC

label_protocol: Illumina TotalPrep RNA Amplification Kit (Applied Biosystems)

extract_protocol: RNA was isolated using a Qiagen RNeasy kit with on column DNase digestion as per the manufacturer's instructions. Quality control was done using an Agilent Bioanalyzer.

treatment_protocol: Total human PBMCs were isolated via Ficoll-Paque and were left untreated or treated as described above for 5 hours before RNA isolation

tag: donor

value: Donor 1

tag: cell type

value: PBMC

value: unstimulated


title: P1.5C control

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)


title: L1 unstimulated

source_name: Purified CD14+ Monocytes

treatment_protocol: CD14+ monocytes were isolated from PBMCs using CD14 magnetic beads and were left untreated or treated as described above for 5 hours before RNA isolation

value: Donor 2


title: J5 unstimulated


title: L4 C1q alone


title: J6 immune complex

value: immune complex


title: P1.5B swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)


title: A2 immune complex

value: Donor 1


title: DK12 control

value: human differentiated kidney

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: L3 immune complex + C1q

value: Donor 2

value: immune complex + C1q


title: A4 C1q alone

value: PBMC


title: J4 C1q alone


title: DK06 control

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)


title: J3 immune complex + C1q


title: DK12 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)


title: DK06 swap

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: human differentiated kidney


title: P1.5B control

value: mouse kidney blastemal cells

value: 1 day old

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: P1.5A control

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)


title: P1.5A swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)


title: DK16 swap

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)


title: DK16 control

value: human differentiated kidney

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)


title: DK02 control

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)


title: FK swap

value: T98G (glioblastoma multiform))

source_name: FK

value: pool of human fetal kidneys (Clontech)


title: FK control

tag: sample

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: DU 145 (prostate carcinoma)


title: E17.5C swap

source_name: E17.5C swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: FaDu (pharynx squamous cell carcinoma)

value: mouse kidney blastemal cells


title: J2 immune complex

value: Donor 1

value: immune complex


title: E17.5D swap

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)


title: E17.5C

source_name: E17.5C control

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: E17.5D control

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: DU 145 (prostate carcinoma)


title: J7 immune complex + C1q

value: Donor 2

value: PBMC

value: immune complex + C1q


title: A3 immune complex + C1q

value: Donor 1


title: L2 immune complex

value: immune complex


title: E15.5G control

value: mouse kidney blastemal cells

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)


title: E17.5B control

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)


title: J8 C1q alone


title: E15.5G swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: WT BC-28 control

tag: wilms tumor sample

value: relapse tumor

tag: Stage

value: IV

tag: gender

value: female

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DU 145 (prostate carcinoma)


title: E17.5B swap

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: mouse kidney blastemal cells


title: WT BC-28 swap

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)


title: WT BC-27 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: no-relapse tumor

value: male


title: WT BC-27 control

value: IV

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: T98G (glioblastoma multiform))


title: J1 unstimulated

value: Donor 1

tag: treatment

value: unstimulated


title: WT BC-29 swap

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: female


title: WT BC-29 control

value: DLD-1 (colorectal adenocarcinoma)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)


title: WT BC-25 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: DU 145 (prostate carcinoma)

value: no-relapse tumor

value: IV


title: WT BC-23 swap

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: T98G (glioblastoma multiform))

value: relapse tumor


title: WT BC-23 control

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)


title: WT BC-22 swap

value: DLD-1 (colorectal adenocarcinoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: male


title: WT BC-25 control

value: female

value: DU 145 (prostate carcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)


title: WT BC-22 control

value: IV

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)


title: WT BC-21 control

value: relapse

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: T98G (glioblastoma multiform))


title: WT BC-21 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)


title: WT BC-15 swap

value: DLD-1 (colorectal adenocarcinoma)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: no-relapse

value: III


title: WT BC-15 control

value: male

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)


title: WT BC-13 control

value: female

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: GM-637 (fibroblast)

value: T98G (glioblastoma multiform))


title: WT BC-13 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)


title: WT BC-08 swap

value: DLD-1 (colorectal adenocarcinoma)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: relapse


title: WT BC-17 control

value: no-relapse

value: III

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: SK-MEL-28 (melanoma)


title: WT BC-17 swap

value: GM-637 (fibroblast)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))

value: female


title: WT BC-14 control

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)


title: WT BC-16 control

value: DLD-1 (colorectal adenocarcinoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)


title: WT BC-18 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)


title: WT BC-18 control

value: no-relapse

value: III

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)


title: WT BC-16 swap

value: GM-637 (fibroblast)

value: SK-MEL-28 (melanoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: WT BC-09 swap

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: relapse

value: female


title: WT BC-19 swap

value: pool of 15 human cell lines

value: DLD-1 (colorectal adenocarcinoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: IV


title: WT BC-12 swap

value: Daudi (Burkitt's lymphoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: no-relapse


title: WT BC-12 control

value: III

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: SK-MEL-28 (melanoma)


title: WT BC-10 swap

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))

value: female


title: WT BC-19 control

value: relapse

value: IV

value: DLD-1 (colorectal adenocarcinoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)


title: WT BC-14 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: no-relapse


title: WT BC-10 control

value: III

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: SK-MEL-28 (melanoma)


title: WT BC-09 control

value: relapse

value: female

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: WT BC-08 control

value: DLD-1 (colorectal adenocarcinoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)


title: WT BC-07 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: male


title: WT BC-06 swap

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: III


title: WT BC-07 control

value: relapse

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: H-146 (small cell lung carcinoma)

value: SK-MEL-28 (melanoma)


title: WT BC-06 control

value: female

value: DLD-1 (colorectal adenocarcinoma)

value: HT-1080 (fibrosarcoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: WT BC-05 control

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)


title: WT BC-04 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: male


title: WT BC-03 swap

value: DU 145 (prostate carcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: relapse

value: III


title: P7.5A control

value: mouse kidney blastemal cells

tag: age

value: 1 week old

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: H-146 (small cell lung carcinoma)

value: SK-MEL-28 (melanoma)


title: P7.5A swap

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: Jurkat (acute T cell leukemia)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: P7.5B control

value: DU 145 (prostate carcinoma)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)


title: WT BC-02 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: relapse

value: male


title: WT BC-05 swap

value: DLD-1 (colorectal adenocarcinoma)

value: H-146 (small cell lung carcinoma)

value: III

value: female


title: P7.5C control

value: mouse kidney blastemal cells

value: 1 week old

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: SK-MEL-28 (melanoma)


title: P7.5B swap

value: pool of 15 human cell lines

value: DU 145 (prostate carcinoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: WT BC-04 control

value: relapse

value: male

value: DLD-1 (colorectal adenocarcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)


title: WT BC-03 control

value: III

value: female

value: pool of 15 human cell lines (Daudi (Burkitt's lymphoma)

value: HT-1080 (fibrosarcoma)


title: P7.5C swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: HB4a (normal mammary luminal epithelium)

value: HEK293 (human embryonic kidney)

value: SK-MEL-28 (melanoma)

value: mouse kidney blastemal cells

value: 1 week old


title: WT BC-02 control

value: relapse

value: DU 145 (prostate carcinoma)

value: Jurkat (acute T cell leukemia)

value: Saos-2 (osteosarcoma)

value: SK-BR-3 (breast adenocarcinoma)

value: T24 (bladder transitional cell carcinoma)

value: T98G (glioblastoma multiform))


title: 4T1-TB_1

city: Buffalo

first: song

last: liu

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: The labeled probes were then mixed with hybridization reagents and hybridized overnight to the MouseWG-6 v2 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files are analyzed with Illumina’s GenomeStudio gene expression module (V1.6.0)

source_name: Splenic CD11b+Gr-1high cell populations

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA from highly purified splenic CD11b+Gr-1high cells from the different experimental groups was quantified by a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific) and evaluated for degradation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples requirements were as follows: RIN >7, an OD 260:280 of 1.9-2.0, and an OD 260/230 >1.8.

value: BALB/c

value: female

tag: experimental group

value: 4T1-TB (tumor-bearing)

value: lymphoid

value: Splenic CD11b+Gr-1high cell populations


title: DK02 swap

value: pool of 15 human cell lines

value: Daudi (Burkitt's lymphoma)

value: DLD-1 (colorectal adenocarcinoma)

value: FaDu (pharynx squamous cell carcinoma)

value: GM-637 (fibroblast)

value: H-146 (small cell lung carcinoma)

value: HT-1080 (fibrosarcoma)

value: HB4a (normal mammary luminal epithelium)

value: human differentiated kidney


title: Mtb infected-16w-1

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: Public Health Research Institute at UMDNJ

description: Biological replicate

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for advanced genomics of the Public Health Research Institute of UMDNJ was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing:
Microarray data from the scanned images were extracted using the software from Agilent technologies and normalization/downstream analysis was performed using Partek Genomic Suite version 6.5 software.
Lowess-error-normalised log2 ratio for significant difference in fold change in gene expression was calculated and represented as Mtb infected at Tx/T0.

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

growth_protocol: New Zealand White rabbits were infected aerogenically with Mtb HN878 at 3.2log10 (on day 0).  Lung tissues from rabbits were isolated at Day0, 2,4, and 16 weeks post infection and used for total RNA isolation.

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: Mtb HN878

tag: time point

value: 16 wks post infection

value: Uninfected


title: Mtb infected-16w-4

description: Technical replicate


title: 4T1-TB_2

value: BALB/c

tag: tissue


title: Mtb infected-16w-2

description: Biological replicate


title: GCSF_2

tag: strain

value: female

value: G-CSF-treated


title: Mtb infected-4w-7

description: Technical replicate

value: 4 wks post infection


title: Mtb infected-16w-3

description: Technical replicate


title: RD cell line H3K4me3 replicate 2

type: genomic

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

hyb_protocol: Hybridization was performed by NimbleGen using standard Nimblegen protocols

scan_protocol: Scanning was performed by NimbleGen using standard Nimblegen protocols

data_processing: Log2 transformed Control and immunoprecipitation data files were processed with the R Smudgekit version 2.4 software to remove potential chip hybridization artifacts. The average values of the two replicate oligonucleotide probes on each array was used for all processing. All available  control data was quantile normalized together, and the median value for each probe was used as the input value.  The log2 difference (ChIP/control) is reported.

molecule: genomic DNA

source_name: RD H3K4me3 ChIP DNA

label_protocol: Labelling was performed by NimbleGen using standard Nimblegen protocols

extract_protocol: 1% formaldehyde was added to ~1 × 10^8 cells for 10 min at 37°C. Cells were washed twice in cold phosphate-buffered saline with protease inhibitors and then placed in hypotonic buffer for 20 min, followed by Dounce homogenization to isolate cross-linked nuclei. Nuclei were placed in sodium dodecyl sulfate lysis buffer for 30 min and then sonicated on ice with 21 10-s pulses, each followed by a 10-s rest period. Samples were diluted and then precleared at 4°C for 60 min with protein A- or G- agarose beads. Samples were immunoprecipitated for 12 to 18 h on a rotating platform at 4°C. Antibodies utilized for immunoprecipitation included histone 3 monomethyl lysine 27 (H3K27me1, Upstate 07-448), histone 3 tri-methyl lysine 4 (H3K4me3, ABCAM, ab8580), and nonspecific rabbit IgG (Santa Cruz, sc-2091). Antibody-bound DNA-protein complexes were collected using protein A- or G-agarose beads, washed, eluted from the beads, and cross-linking of DNA-protein adducts reversed by incubation at 65 °C for 4 h. DNA was cleaned with the QIAquick PCR purification kit (Qiagen) according to manufacturer’s instructions and amplified with the GenomePlex Whole Genome Amplification kit (Sigma) according to manufacturer’s instructions. Amplified DNA was cleaned using the QIAquick PCR purification kit (Qiagen) before amplification, labeling, and hybridization to arrays.

value: muscle

value: RD

tag: antibody

tag: vendor

value: Abcam

tag: catalog #

source_name: RD H3K4me3 control DNA


title: GCSF_1

value: lymphoid

value: Splenic CD11b+Gr-1high cell populations


title: Mtb infected-4w-6

description: Biological replicate


title: Mtb infected-4w-4

description: Technical replicate


title: liver-hdac6ko dex-biological rep 2

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.10.0) / Bioconductor (version 2.5) package affy using the CDF environment MoGene-1_0-st-v1.r3.cdf (as provided by Bioconductor) and annotation from Netaffx (www.netaffx.com) (as provided in the attached file).
probe group file: CDF environment MoGene-1_0-st-v1.r3.cdf as provided by http://bioconductor.org/biocLite.R

source_name: knockout liver

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).

growth_protocol: fed ad libitum,  constant 12h day/night cycle, constant room temperature

extract_protocol: mice were killed, dissected, livers extracted and immediately snap frozen in liquid Nitrogen. Total RNA from livers was extracted using the Qiagen RNEasy Mini Kit

treatment_protocol: 1mg/kg dexamethasone or vehicle respectively i.p. injected over 3 weeks

value: C57Bl/6 HDAC6 Y/-

value: male

value: liver

tag: genotype

value: HDAC6 Y/-

value: dexamethasone


title: liver-hdac6ko vehicle-biological rep 3

value: vehicle


title: WT_2

value: wild type (non-tumor-bearing control)


title: WT_1


title: liver-hdac6ko vehicle-biological rep 1


title: RD cell line H3K4me3 replicate 1

tag: cell line


title: liver-hdac6ko dex-biological rep 1


title: liver-hdac6ko dex-biological rep 3


title: liver-hdac6ko vehicle-biological rep 2


title: Mtb infected-4w-5

description: Biological replicate

value: Uninfected

value: Mtb HN878


title: Mtb infected-4w-3

description: Technical replicate


title: liver-wild-type dex-biological rep 2

source_name: wildtype liver

value: wild-type


title: RD cell line H3K27me1 replicate 2

source_name: RD H3K27me1 ChIP DNA

tag: cell type

value: Upstate

source_name: RD H3K27me1 control DNA


title: Mtb infected-4w-1

description: Biological replicate

value: 4 wks post infection


title: liver-wild-type dex-biological rep 1


title: SY5Y cell line H3K4me3 replicate 3

source_name: SY5Y H3K4me3 ChIP DNA

value: neural

source_name: SY5Y H3K4me3 control DNA


title: Mtb infected-4w-8

description: Technical replicate


title: RD cell line H3K27me1 replicate 3

value: muscle

value: RD


title: Mtb infected-4w-2

description: Biological replicate


title: SY5Y cell line H3K4me3 replicate 1

value: Abcam


title: liver-wild-type dex-biological rep 3


title: RD cell line H3K4me3 replicate 3


title: liver-wild-type vehicle-biological rep 2


title: Mtb infected-2w-3

description: Biological replicate

value: 2 wks post infection


title: K562 cell line H3K4me3 replicate 1

source_name: K562 H3K4me3 ChIP DNA

value: erythroid

source_name: K562 H3K4me3 control DNA


title: liver-wild-type vehicle-biological rep 3

value: male


title: liver-wild-type vehicle-biological rep 1

value: liver


title: Mtb infected-2w-2

description: Biological replicate


title: Mtb infected-2w-4

description: Biological replicate


title: K562 cell line H3K27me1 replicate 3

source_name: K562 H3K27me1 ChIP DNA

source_name: K562 H3K27me1 control DNA


title: SY5Y cell line H3K4me3 replicate 2


title: Mtb infected-2w-1

description: Biological replicate


title: laeA mutant +PAA aerobic glucose limited chemostat steady state (TV57)-2

status: Public on Dec 06 2011

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: aerobic glucose limited chemostat culture with PAA

hyb_protocol: Acquisition and quantification of array images were performed using Affymetrix GeneChip Operating Software (GCOS version 1.2). Before comparison, all arrays were globally scaled to a target value of 100 using the average signal from all gene features. To the 15,531 transcript features on the arrays, a filter was applied to extract 13,746 open reading frames of which there were 13,485 different genes. This discrepancy was due to several genes being represented more than once. To represent the variation in triplicate measurements, the coefficient of variation (S.D. divided by the mean) was calculated. When the genes were ranked according to increasing average intensity, the average coefficient of variation showed a sharp increase for the genes with the lowest expression. Therefore, all genes in which the average expression in all conditions was below 12 were removed from the dataset. Subsequently all remaining values below 12 were set to a value of 12. To assess differential expression, the Significance Analysis of Microarrays (SAM version 1.21) add-in to MicrosoftTM Excel was used for comparisons of replicate array experiments. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene-specific t tests. Each gene is assigned a score on the basis of its change in gene expression relative to the standard deviation of repeated measurements for that gene. Genes with scores greater than a threshold are deemed potentially significant. The percentage of such genes identified by chance is the false discovery rate (FDR). To estimate the FDR, nonsense genes are identified by analyzing permutations of the measurements. The threshold can be adjusted to identify smaller or larger sets of genes, and FDRs are calculated for each set. Here internal SAM parameters for fold-change threshold and the false discovery rate values were set at 2 and 1% respectively.   The genes with significantly changed expression in one of the comparisons were arranged in groups via overlapping them in MicrosoftTM Excel.

scan_protocol: Scanning of the Affymetrix Genechip® microarrays was performed with The Affymetrix scanner 3000 following Affymetrix instructions

data_processing: Data were processed with the GeneChip® Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity was scaled to 100 with GCOS 1.2

organism: Penicillium chrysogenum

source_name: aerobic glucose limited chemostat steady state 14

label_protocol: Double stranded cDNA synthesis was carried out using 10 µg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, USA). The double-stranded cDNA was purified with the GeneChip Sample Cleanup Module (Affymetrix/Qiagen) followed by in vitro transcription and labelling using the GeneChip IVT labeling Kit (Affymetrix). Finally, labelled cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix/Qiagen) prior to fragmentation. 15 µg of fragmented, biotinylated cRNA was hybridised to Affymetrix custom-made Penicillium chrysogenum GeneChip® microarrays (array code DSM_PENa520255F) at 45ºC for 16 h as described in the Affymetrix users' manual. Washing and staining of arrays were performed using the GeneChip® Fluidics Station 400 and scanning with the Affymetrix GeneArray Scanner 3000.

growth_protocol: Chemostat experiments were performed with the industrial high penicillin production strain Penicillium chrysogenum DS17690, kindly donated by DSM Anti-Infectives (Delft, The Netherlands), the DS63171 (velA delta) and the DS67261 (laeA delta). Cultivation medium was prepared as described earlier (van Gulik et al., 2000) and contained 0.25 Cmol/L glucose in presence or absence of 4 mM PAA and was used for the batch and chemostat phase of fermentations, allowing a biomass concentration of about 3 gDW/L.  Glucosel-limited chemostat cultivations were performed according to Harris et al. (2009) in a 7 L turbine stirred reactor with a working volume of 1.8 L under aerobic conditions (DO > 70%) and a dilution rate of 0.03 h-1 at 25°C and pH 6.5.  Sampling for transcriptome measurements  was performed at steady state.  Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RA, Pronk JT, Daran JM. Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics. 2009 Feb 10;10:75.

extract_protocol: For total RNA extraction, half of the pellet was grounded by mortar and pestle under constant cooling with liquid nitrogen. The powder was dissolved in 5 mL of Trizol reagent (Invitrogen) and 1 mL chloroform (Sigma) and mixed well. The two phases were separated by centrifugation (4600 g, 15 min). Total RNA was isolated using a phenol-chloroform extraction method, which consisted of two extraction steps in acid-phenol/chloroform/isoamyl alcohol (5:1, pH 4.8, Ambion, Foster City, USA), followed by a chloroform extraction step. Each time the phases were separated by centrifugation (4600 g, 15 min). Total RNA was precipitated for 30 min at -20ºC in 96% ethanol and 0.3 M sodium acetate. The RNA was collected by centrifugation at 23000 g for 15 min and dissolved in RNAse free H2O.

treatment_protocol: 60 mL of culture broth was sampled and rapidly filtered over a glass fiber filter (Type A/E, Pall Life Sciences, East Hills, USA). The filter with mycelium was wrapped in aluminium foil, quenched in liquid nitrogen and stored at -80ºC until further use.

tag: genotype/variation

value: laeA mutant

tag: paa

value: +PAA


title: RD cell line H3K27me1 replicate 1


title: SY5Y cell line H3K27me1 replicate 2

source_name: SY5Y H3K27me1 ChIP DNA

source_name: SY5Y H3K27me1 control DNA


title: K562 cell line H3K27me1 replicate 1


title: SY5Y cell line H3K27me1 replicate 3


title: laeA mutant -PAA aerobic glucose limited chemostat steady state (TV22)-1

description: aerobic glucose limited chemostat culture w/o PAA

source_name: aerobic glucose limited chemostat steady state 11

value: -PAA


title: DS17690 +PAA aerobic glucose limited chemostat steady state (IS75)-2

source_name: aerobic glucose limited chemostat steady state 5

value: wild type high penicillin production strain


title: SY5Y cell line H3K27me1 replicate 1


title: laeA mutant -PAA aerobic glucose limited chemostat steady state (TV25)-2

source_name: aerobic glucose limited chemostat steady state 12


title: K562 cell line H3K27me1 replicate 2


title: velA mutant +PAA aerobic glucose limited chemostat steady state (TV32)-2

source_name: aerobic glucose limited chemostat steady state 10

value: velA mutant


title: Tbx5  48-3

city: keelung

first: jenn-kan

last: Lu

address: 2 Pei-Ning Road,Keelung

department: Aquaculture

country: Taiwan

hyb_protocol: The cDNA was then pretreated with GEx hybridization buffer (HI263 PRM; Aglient Technologies) before transferring to hybridization chamber gasket slides for the hybridization reaction.

scan_protocol: The slide was scanned with an Axon Instruments GenePix 4000B scanner (Molecular Devices, Silicon Valley, CA, USA)

data_processing: In our cDNA microarray analysis, the microarray data was normalized by using Genespring 265 GX10.0. software (Aglient Technologies).  The MO Tbx5 anti-sense RNA treatment and control (WT) were used in our microarray analsysis. The each sample labeled with Cy5 and Cy3 fluorescent dyes (Amersham Pharmacia Biotech; Piscataway, NJ) and run in paired hybridizations on the arrays. The Lowess normalization was performed after subtracting the median background. Genes with a negative log ratio in green are down-regulated by Tbx5 gene 1.5X knockdown filtered on expression (-10.868 - -0.584) in the normalized data.

organism: Danio rerio

source_name: zebrafish embryo (tbx5 -MO)

label_protocol: Coupling the fluorescent  dye using indirect cDNA labeling with a microarray kit (Invitrogen), the cDNA was hydrolyzed and  neutralized using NaOH and HCl.

extract_protocol: The quality was confirmed using an Aglient 2100 Bioanalyzer (Aglient Technologies,  Santa Cruz, CA, USA). Purified RNA was reverse-transcribed into complementary (c)DNA using SuperScrip TM III RT (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Isolated total zebrafish embryo RNA was purified using an RNeasy® 257 Mini Kit (QIAGEN, Hilden,   Germany)

tag: development stage

value: whole embryo

value: AB strain

source_name: zebrafish embryo (Control wilde-type)


title: velA mutant -PAA aerobic glucose limited chemostat steady state (TV54)-2

source_name: aerobic glucose limited chemostat steady state 8


title: velA mutant +PAA aerobic glucose limited chemostat steady state (TV27)-1

source_name: aerobic glucose limited chemostat steady state 9


title: DS17690 +PAA aerobic glucose limited chemostat steady state (IS73)-1

source_name: aerobic glucose limited chemostat steady state 4


title: DS17690 -PAA aerobic glucose limited chemostat steady state (IS80)-3

source_name: aerobic glucose limited chemostat steady state 3


title: Tbx5  48-1


title: velA mutant -PAA aerobic glucose limited chemostat steady state (TV43)-1

source_name: aerobic glucose limited chemostat steady state 7


title: DS17690 +PAA aerobic glucose limited chemostat steady state IS79)-3

source_name: aerobic glucose limited chemostat steady state 6


title: Tbx5  48-2


title: Tbx5  24-2


title: Tbx5  24-1


title: lung_tumor_resection_3574T

city: Boston

first: Yen-Tsung

last: Huang

address: 665 Huntington Avenue

institute: Harvard School of Public Health

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: CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. The data table contains the normalized expression values produced by that algorithm.

source_name: lung tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from tumor tissue from non-small cell lung cancer patients at surgery using the Promega Qiagen DNA Extraction Kit. DNA quality and quantity was assessed using OD measure and agarose gel electrophoresis.

tag: smoking packyears

tag: Stage

tag: histology


title: Tbx5  30-2


title: DS17690 -PAA aerobic glucose limited chemostat steady state (IS76)-2

source_name: aerobic glucose limited chemostat steady state 2


title: Tbx5  30-1


title: lung_tumor_resection_3423T


title: rice leaf, biological rep 3

city: Mississippi State

first: Feng

last: Tan

state: MS

address: Dorman Hall 402

department: Biochemistry and Molecular Biology

institute: Mississippi State University

description: gene expression data from rice matured leaf

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 C on Affymetrix Rice Genome Array. GeneChips were washed and stained in the Affymetrix GCS3000.

scan_protocol: GeneChips were scanned using the Alpha Innotech AlphaScan.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Oryza sativa

source_name: rice matured leaf

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice immatured seed after 7-8 days pollination were harvested and the embryo was removed.

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

value: leaf


title: lung_tumor_resection_4600T


title: rice leaf, biological rep 2


title: lung_tumor_resection_1415T


title: lung_tumor_resection_1174T


title: lung_tumor_resection_5219T


title: DS17690 -PAA aerobic glucose limited chemostat steady state (IS74)-1

source_name: aerobic glucose limited chemostat steady state 1


title: lung_tumor_resection_3187T


title: lung_tumor_resection_Y02


title: rice leaf, biological rep 1


title: lung_tumor_resection_DB558


title: lung_tumor_resection_1167T


title: rice endosperm, biological rep 2

description: gene expression data from rice endosperm 7-8 days after pollitation

source_name: rice immatured seeds 7-8 days after pollination

value: endosperm


title: 318369

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
BCPAP TSA M4 vs. BCPAP CTL M4
Date:2007/11/20

hyb_protocol: Agilent : 750.0 ng at 48 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: BCPAP, TSA, M4

label_protocol: Ulysis + MirVana

extract_protocol: Total RNA was extracted using TRIZOL reagent.

treatment_protocol: Cultured in the presence of 330nM TSA for 16h in fresh complete medium.

value: BCPAP

value: papillary thyroid carcinoma

tag: treatment

value: TSA

tag: label

value: BCPAP TSA M4

tag: extract

tag: sample

tag: subject

tag: tissue derivation

value: thyroid

tag: replicate

source_name: BCPAP, CTL, M4

treatment_protocol: Cultured in the absence of TSA for 16h in fresh complete medium.

value: BCPAP CTL M4


title: 314004

description:
BCPAP CTL M1 vs. BCPAP TSA M1
Date:2007/11/20

source_name: BCPAP, CTL, M1

value: BCPAP CTL M1

source_name: BCPAP, TSA, M1

value: BCPAP TSA M1


title: lung_tumor_resection_Y14


title: 318367

description:
BCPAP CTL M4 vs. BCPAP TSA M4
Date:2007/11/20


title: laeA mutant +PAA aerobic glucose limited chemostat steady state (TV33)-1

source_name: aerobic glucose limited chemostat steady state 13

tag: strain

value: laeA mutant


title: 314282

description:
BCPAP TSA M2 vs. BCPAP CTL M2
Date:2007/11/21

source_name: BCPAP, TSA, M2

value: BCPAP TSA M2

source_name: BCPAP, CTL, M2

value: BCPAP CTL M2


title: lung_tumor_resection_DB500


title: rice endosperm, biological rep 1

tag: tissue


title: lung_tumor_resection_DB360


title: lung_tumor_resection_DB496


title: lung_tumor_resection_DB398


title: 314283

description:
BCPAP CTL M2 vs. BCPAP TSA M2
Date:2007/11/20

tag: cell line


title: rice endosperm, biological rep 3


title: lung_tumor_resection_DB348


title: 314002

description:
BCPAP TSA M1 vs. BCPAP CTL M1
Date:2007/11/20

tag: cell type


title: HRG 24h replicate 1

city: Uppsala

first: Sonia

last: Tugues

address: dag hammarsjöldsväg 20

department: Genetics and pathology

institute: Uppsala University

description: gene expression data from peritoneal macrophages cultured for 24 h. In RPMI/5%FCS and treated with HRG (1ug/ml)

hyb_protocol: GeneChip ST Arrays (GeneChip Mouse Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

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

data_processing: Subsequent analysis of the gene expression data was carried out in the freely available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). The raw data was normalized in the Affymetrix provided software Expression Console using the robust multi-array average (RMA) method. In order to search for the differentially expressed genes between the hrg-/- samples and the wt samples group an empirical Bayes moderated t-test was then applied, using the ‘limma’ package. To address the problem with multiple testing, the p-values were adjusted using the method of Benjamini and Hochberg

source_name: peritoneal macrophages isolated from C57/BL6 mice

label_protocol: 250 nanograms of total RNA/sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit

growth_protocol: isolated peritoneal macrophages incubated overnight in RPMI/5% FCS

extract_protocol: total RNA from macrophages was extracted using an Rneasy Mini kit from Qiagen

treatment_protocol: Treatment of peritoneal macrophages with 1 ug/ml of recombinant histidine-rich glycoprotein during 6 and 24 hours.

tag: sample type

value: peritoneal macrophages isolated from wt C57/Bl6 mice by peritoneal lavage

value: peritoneal macrophage

tag: genetic background

value: HRG

tag: time


title: lung_tumor_resection_DB306

tag: smoking packyears


title: Basal 24h replicate 1

description: gene expression data from peritoneal macrophages cultured for 24 h. In RPMI/5%FCS

value: untreated


title: HRG 24h replicate 2


title: lung_tumor_resection_DB174

tag: Stage


title: lung_tumor_resection_DB322

tag: histology


title: lung_tumor_resection_DB202


title: HRG 6h replicate 1

description: gene expression data from peritoneal macrophages cultured for 6 h. In RPMI/5%FCS and treated with HRG (1ug/ml)

tag: treatment

value: 6 h


title: Basal 24h replicate 2


title: Basal 6h replicate 1

description: gene expression data from peritoneal macrophages cultured for 6 h. In RPMI/5%FCS


title: lung_tumor_resection_DB568


title: HRG 6h replicate 2


title: lung_tumor_resection_1393T


title: lung_tumor_resection_1555T


title: lung_tumor_resection_DB564


title: ETV4 KD Hypoxia Replicate 2

city: Zürich

middle: Philipp

last: Stiehl

address: Winterthurerstr. 190

department: Physiology

institute: University of Zurich

hyb_protocol: 300 ng of Cy3-labelled cRNA mixed with 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol dye/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
Agilent Feature Extraction software
Differential expression was computed using the Bioconductor package limma.

source_name: shNTC hypo 2

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: lentiviral infection was used to generate shNTC and shETV4 PC-3 cells, respectively. Efficient knock down was verified by measuring ETV4 and control transcript levels by quantitative PCR and immunoblotting. Fresh batches of cells with verified target knock down were used for biological replicates as ETV4 knock down ceased in pool of cells over time.

extract_protocol: total RNA was extracted using Qiagen RNeasy colums according to the manufactures protocol (Quiagen AG, CH-8634 Hombrechtikon, Switzerland).

treatment_protocol: shNTC and shETV4 cell pools were cultured at 20% or 0.2% oxygen for 24 hours using a Ruskinn invivo2 hypoxic workstation. Biological replicates were completely independent cultures at different days.

tag: knockdown

value: shNTC control

tag: treatement

value: 0.2% Oxygen

source_name: shETV4 hypo 2


title: lung_tumor_resection_DB542


title: ETV4 KD Normoxia Replicate 3

source_name: shNTC normox 3

value: 20% Oxygen

source_name: shETV4 normox 3


title: lung_tumor_resection_DB554

source_name: lung tumor


title: lung_tumor_resection_DB540


title: ETV4 KD Normoxia Replicate 1

source_name: shNTC normox 1

source_name: shETV4 normox 1


title: lung_tumor_resection_DB482


title: ETV4 KD Normoxia Replicate 2

source_name: shNTC normox 2

source_name: shETV4 normox 2


title: ETV4 KD Hypoxia Replicate 3

source_name: shNTC hypo 3

source_name: shETV4 hypo 3


title: lung_tumor_resection_DB466


title: Basal 6h replicate 2


title: lung_tumor_resection_DB458


title: lung_tumor_resection_DB414


title: lung_tumor_resection_DB546


title: DCs ID75 non-infected rep_2

city: Montreal

first: luis

last: Barreiro

state: Quebec

address: 3175 Chemin de la Côte Sainte-Catherine

country: Canada

institute: luis

hyb_protocol: As recommended by Illumina.

scan_protocol: As recommended by Illumina.

data_processing: Bioconductor software package lumi. The data provided is log2 transformed.

source_name: Human dendritic cells

label_protocol: As recommended by Illumina.

growth_protocol: Blood monocytes were purified from PBMCs by positive selection with magnetic CD14 MicroBeads. In order to derive dendritic cells, monocytes were cultured for 5 days in RPMI 1640  supplemented with 10% heat-inactivated FCS , L-glutamina, GM-CSF (20 ng/ml; Immunotools), and IL-4 (20 ng/ml; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.

extract_protocol: Total RNA was extracted from the non-infected DCs and the MTB-infected DCs using the miRNeasy kit (Qiagen).

treatment_protocol: We infected DCs with an MTB strain expressing green-fluorescent protein (H37Rv)

tag: gender

value: Male

tag: sample

tag: infection status

value: non-infected


title: DCs ID78 non-infected rep_2

tag: replicate


title: lung_tumor_resection_DB464


title: lung_tumor_resection_DB478


title: DCs ID80 non-infected rep_2


title: DCs ID77 MTB-infected rep_2

value: MTB-infected


title: DCs ID77 non-infected rep_2


title: DCs ID74 non-infected rep_2


title: ETV4 KD Hypoxia Replicate 1

source_name: shNTC hypo 1

source_name: shETV4 hypo 1


title: lung_tumor_resection_DB418


title: DCs ID75 MTB-infected rep_2


title: lung_tumor_resection_DB380


title: DCs ID74 MTB-infected rep_2


title: lung_tumor_resection_DB326


title: lung_tumor_resection_DB314


title: DCs ID80 MTB-infected rep_2


title: DCs ID78 MTB-infected rep_2


title: DCs ID73 MTB-infected rep_2


title: lung_tumor_resection_DB270


title: lung_tumor_resection_DB272


title: lung_tumor_resection_DB334


title: lung_tumor_resection_DB488


title: DCs ID74 MTB-infected rep_1


title: DCs ID73 non-infected rep_2


title: lung_tumor_resection_DB412


title: lung_tumor_resection_DB312


title: lung_tumor_resection_DB268


title: DCs ID73 MTB-infected rep_1


title: lung_tumor_resection_DB244


title: DCs ID72 MTB-infected rep_1


title: DCs ID71 MTB-infected rep_1


title: lung_tumor_resection_DB238


title: lung_tumor_resection_DB232


title: DCs ID72 non-infected rep_1


title: lung_tumor_resection_DB222


title: DCs ID73 non-infected rep_1


title: lung_tumor_resection_DB248


title: DCs ID71 non-infected rep_1


title: DCs ID70 MTB-infected rep_1


title: DCs ID72 MTB-infected rep_2


title: DCs ID70 non-infected rep_1


title: DCs ID69 MTB-infected rep_1


title: DCs ID69 non-infected rep_1


title: lung_tumor_resection_DB188


title: lung_tumor_resection_DB198


title: lung_tumor_resection_DB236


title: DCs ID72 non-infected rep_2


title: lung_tumor_resection_DB106


title: DCs ID71 MTB-infected rep_2


title: lung_tumor_resection_DB228


title: lung_tumor_resection_DB226


title: lung_tumor_resection_DB124


title: lung_tumor_resection_DB218


title: lung_tumor_resection_DB122


title: lung_tumor_resection_DB102


title: lung_tumor_resection_DB128


title: lung_tumor_resection_DB136


title: DCs ID71 non-infected rep_2


title: DCs ID70 MTB-infected rep_2


title: DCs ID74 non-infected rep_1


title: DCs ID69 non-infected rep_2


title: lung_tumor_resection_DB098


title: DCs ID70 non-infected rep_2


title: DCs ID88 MTB-infected rep_1


title: lung_tumor_resection_DB088


title: DCs ID87 non-infected rep_1


title: DCs ID88 non-infected rep_1


title: DCs ID69 MTB-infected rep_2


title: lung_tumor_resection_DB028


title: DCs ID87 MTB-infected rep_1


title: DCs ID86 MTB-infected rep_1


title: lung_tumor_resection_Y03


title: lung_tumor_resection_5192T


title: DCs ID86 non-infected rep_1


title: DCs ID85 non-infected rep_1


title: DCs ID85 MTB-infected rep_1


title: DCs ID84 MTB-infected rep_1


title: DCs ID84 non-infected rep_1


title: lung_tumor_resection_5283T


title: lung_tumor_resection_DB020


title: lung_tumor_resection_DB022


title: lung_tumor_resection_DB080


title: lung_tumor_resection_4460T


title: lung_tumor_resection_5198T


title: lung_tumor_resection_4135T


title: lung_tumor_resection_4585T


title: DCs ID85 MTB-infected rep_2


title: DCs ID86 non-infected rep_2


title: DCs ID85 non-infected rep_2


title: lung_tumor_resection_3446T


title: DCs ID86 MTB-infected rep_2


title: DCs ID83 non-infected rep_1


title: DCs ID83 MTB-infected rep_1


title: lung_tumor_resection_3522T


title: lung_tumor_resection_3491T


title: lung_tumor_resection_3336T


title: lung_tumor_resection_3324T


title: DCs ID83 non-infected rep_2


title: lung_tumor_resection_3415T


title: lung_tumor_resection_3314T


title: DCs ID84 MTB-infected rep_2


title: DCs ID83 MTB-infected rep_2


title: DCs ID84 non-infected rep_2


title: DCs ID82 non-infected rep_2


title: lung_tumor_resection_2903T


title: lung_tumor_resection_3156T


title: DCs ID82 non-infected rep_1


title: lung_tumor_resection_2312T


title: lung_tumor_resection_1479T


title: DCs ID82 MTB-infected rep_1


title: DCs ID81 non-infected rep_2


title: DCs ID81 MTB-infected rep_2


title: DCs ID82 MTB-infected rep_2


title: lung_tumor_resection_3416T


title: lung_tumor_resection_DB026


title: DCs ID81 non-infected rep_1


title: lung_tumor_resection_1226T


title: lung_tumor_resection_1649T


title: lung_tumor_resection_1265T


title: lung_tumor_resection_1238T


title: lung_tumor_resection_Y23