title: T-Cre conditional Tbx1 knockout otic vesicle and periotic mesenchyme tissue at E11.5, biological replicate 2

description:
MestKO2_OVPOM
3 pooled embryos.
Gene expression data from E11.5 otic vesicles and periotic mesenchyme at the stage of dorsoventral elongation.

source_name: E11.5 otic vesicle and periotic mesenchyme, T-Cre conditional Tbx1 knockout

value: T-Cre conditional Tbx1 knockout


title: exp_a_KO

status: Public on Jan 01 2013

type: RNA

city: Rehovot

first: Amit

last: Zeisel

address: Weizmann Institute

department: Physics of complex systems

country: Israel

institute: Weizmann Institute of Science

description: SAMPLE 1

hyb_protocol: According to Affymetrix manual

scan_protocol: According to Affymetrix manual

data_processing:
MAS5 using R microarray suite + lowess correction for each tissue, i.e. samples 1-2, samples 3-6, samples 7-8, using a MATLAB script.
values are in linear scale, p-values are for each probset as calculated by the MAS5 algorithm

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: mouse MII oocytes

label_protocol: According to Affymetrix manual

extract_protocol: QIAGEN miniRNA extraction kit was used.  QIAGEN miniRNA extraction kit was used.

tag: tissue

value: MII oocyte

tag: genotype/variation

value: KO


title: T-Cre conditional Tbx1 heterozygous control otic vesicle at E11.5, biological replicate 3

city: Bronx

first: Tingwei

last: Guo

state: NY

address: 1301 Morris Park Avenue, Room 408

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

description:
Control3_OV
3 pooled embryos.
Gene expression data from E11.5 otic vesicles at the stage of dorsoventral elongation.

hyb_protocol: 10ug of cRNA was hybridized for 16hrs at 45C on Affymetrix Mouse 430_2 arrays.

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

data_processing: Data was analyzed using Affymetrix Expression Console software version 1.1 using Affymetrix default protocols.

molecule: total RNA

source_name: E11.5 otic vesicle, T-Cre conditional heterozygous control

label_protocol: Biotinylated cRNA was prepared according to Affymetrix protocols from 300ng of total RNA.

growth_protocol: Timed matings were dissected at embryonic day 11.5, and periotic tissue was isolated.

extract_protocol: Qiagen RNeasy Micro kit according to the manufacturer's protocol.

treatment_protocol: Periotic tissue was incubated with dispase for 30 min at 37C to remove periotic tissue, folllowed by RNA isolation.

tag: age

tag: genotype

value: T-Cre conditional Tbx1 heterozygote

value: microdissected otic vesicle


title: T-Cre conditional Tbx1 knockout otic vesicle and periotic mesenchyme tissue at E11.5, biological replicate 1

description:
MestKO1_OVPOM
3 pooled embryos.
Gene expression data from E11.5 otic vesicles and periotic mesenchyme at the stage of dorsoventral elongation.

growth_protocol: Timed matings were dissected at embryonic day 11.5, and periotic tissue was isolated, including otic vesicle and perotic mesenchyme. RNA was isolated from the tissue immediately following dissection.

value: microdissected otic vesicle and periotic mesenchyme


title: T-Cre conditional Tbx1 knockout otic vesicle and periotic mesenchyme tissue at E11.5, biological replicate 3

description:
MestKO3_OVPOM
3 pooled embryos.
Gene expression data from E11.5 otic vesicles and periotic mesenchyme at the stage of dorsoventral elongation.


title: T-Cre conditional Tbx1 heterozygous control otic vesicle at E11.5, biological replicate 1

description:
Control1_OV
3 pooled embryos.
Gene expression data from E11.5 otic vesicles at the stage of dorsoventral elongation.


title: Patient, biopsy M13

city: Boston

first: Matija

last: Snuderl

state: MA

address: 55 Fruit St.

department: Pathology

institute: MAssachusetts General Hospital

hyb_protocol: Hybridization reactions were performed according to manufacturer’s instructions

scan_protocol: A high density scan (600 fields of view) was performed

data_processing: The raw data was normalized to technical controls included by NanoString Technologies, then normalized to endogenous control genes ACTB, GAPDH, and LDHA (Northcott et al, 2011).

organism: Homo sapiens

source_name: Tumor tissue

extract_protocol: Total RNA was extraced from 2x 30um thick FFPE sections per sample using Citasolv and Qiagen Rneasy FFPE kit (cat.73504).

tag: disease state

value: Medulloblastoma


title: Patient, biopsy M3


title: T-Cre conditional Tbx1 knockout otic vesicle tissue at E11.5, biological replicate 3

description:
MestKO3_OV
3 pooled embryos.
Gene expression data from E11.5 otic vesicles at the stage of dorsoventral elongation.

source_name: E11.5 otic vesicle, T-Cre conditional Tbx1 knockout


title: T-Cre conditional Tbx1 knockout otic vesicle tissue at E11.5, biological replicate 1

description:
MestKO1_OV
3 pooled embryos.
Gene expression data from E11.5 otic vesicles at the stage of dorsoventral elongation.


title: T-Cre conditional Tbx1 heterozygous control otic vesicle at E11.5, biological replicate 2

description:
Control2_OV
3 pooled embryos.
Gene expression data from E11.5 otic vesicles at the stage of dorsoventral elongation.


title: T-Cre conditional Tbx1 knockout otic vesicle tissue at E11.5, biological replicate 2

description:
MestKO2_OV
3 pooled embryos.
Gene expression data from E11.5 otic vesicles at the stage of dorsoventral elongation.


title: mESCs at d17 of differentiation with DCI treatment

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 94°C for 35 minutes in Fragmentatin buffer of the compnay.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen, Hilden, Germany) with DNAse digestion using the manufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: cell type

value: mESCs

tag: treatment

tag: strain


title: mESCs at d17 of differentiation with KGF treatment


title: mESCs at d24 of differentiation (Control)

value: d24 of differentiation (Control)


title: Stimulated Gli2R Tg CD4 T cells, rep2

city: London

first: Anna

last: Furmanski

address: 30 Guilford Street

country: United Kingdom

institute: ICH UCL

description: Gene expression data from splenic CD4+ T cells with stimulation by anti-CD3 and -CD28 for 6h from Gli2R Tg mice

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip Expression Analysis Technical Manual)

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

data_processing: summarization by the mas5 algorithm the R/Bioconductor package affy.

source_name: Stimulated, splenic CD4 T cells from Gli2R mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were harvested from spleen of indicated mice (9-15wks old)

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

treatment_protocol: CD4 cells were immediately extracted by magnetic bead purification. Total RNA was extracted using the Stratagene Absolutely RNA miniprep kit

value: CD4 T cells

value: Stimulated with anti-CD3/CD28

value: Gli2R Tg

tag: genetic background


title: mESCs at d8 of differentiation (Control)

value: d8 of differentiation (Control)


title: mESCs at d24 of differentiation with KGF and DCI treatment


title: OSCC microRNA 530

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: FOM

hyb_protocol: Standard Agilent protocol

scan_protocol: Standard Agilent protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using protocol miRNA_107_Sep09

source_name: OSCC

label_protocol: Standard Agilent protocol

extract_protocol: Tri-reagent (Sigma)

tag: gender

value: M

tag: source tissue

value: FOM

value: Oral cavity squamous cell carcinoma tumor

tag: case


title: mESCs at d24 of differentiation with DCI treatment


title: mESCs at d17 of differentiation with KGF and DCI treatment


title: mESCs at d8 of differentiation with KGF treatment


title: Stimulated Gli2A Tg CD4 T cells, rep2

description: Gene expression data from splenic CD4+ T cells with stimulation by anti-CD3 and -CD28 for 6h from Gli2A Tg mice

source_name: Stimulated, splenic CD4 T cells from Gli2A Tg mice

value: Gli2A Tg


title: Stimulated Gli2R Tg CD4 T cells, rep1


title: Stimulated Gli2R Tg CD4 T cells, rep3


title: OSCC microRNA 575

description: Alveolar

value: Alveolar


title: OSCC microRNA 394

description: FOM


title: OSCC microRNA 364

description: Alveolar


title: Stimulated Gli2A Tg CD4 T cells, rep3


title: Stimulated Gli2A Tg CD4 T cells, rep1


title: OSCC microRNA 201

description: FOM


title: Stimulated WT CD4 T cells, rep1

description: Gene expression data from splenic CD4+ T cells with stimulation by anti-CD3 and -CD28 for 6h from WT mice

source_name: Stimulated, splenic CD4 T cells from WT mice

value: WT


title: OSCC microRNA 449

description: Tongue

value: Tongue


title: OSCC microRNA 592

description: Tongue


title: Stimulated WT CD4 T cells, rep2


title: OSCC microRNA 537

description: Buccal

value: Buccal


title: OSCC microRNA 180

description: Tongue

value: F


title: Stimulated WT CD4 T cells, rep3


title: mESCs at d17 of differentiation (Control)

value: d17 of differentiation (Control)


title: OSCC microRNA 169

description: FOM


title: OSCC microRNA 281

description: Tongue


title: OSCC microRNA 288

description: Tongue


title: Unstimulated Gli2R Tg CD4 T cells, rep2

description: Gene expression data from splenic CD4+ T cells without stimulation from Gli2R Tg mice

source_name: Unstimulated, splenic CD4 T cells from Gli2R mice

value: Unstimulated


title: Unstimulated Gli2A Tg CD4 T cells, rep3

description: Gene expression data from splenic CD4+ T cells without stimulation from Gli2A Tg mice

source_name: Unstimulated, splenic CD4 T cells from Gli2A Tg mice


title: OSCC microRNA 298

description: Tongue


title: OSCC microRNA 489

description: FOM


title: OSCC microRNA 37

description: FOM


title: Unstimulated Gli2A Tg CD4 T cells, rep2


title: OSCC microRNA 513

description: Tongue


title: OSCC microRNA 331

description: FOM


title: Unstimulated Gli2A Tg CD4 T cells, rep1


title: Unstimulated Gli2R Tg CD4 T cells, rep1


title: OSCC microRNA 350

description: Tongue


title: OSCC microRNA 229

description: FOM


title: OSCC microRNA 238

description: Tongue


title: OSCC microRNA 234

description: Tongue


title: OSCC microRNA 562

description: Tongue


title: inv_mutant_v_wt_rep_2

city: Edinburgh

first: Donald

last: Dunbar

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

hyb_protocol: Hybridisation to FL002 arrays: Hybridisation to amino-modified long oligonucleotide arrays using Genomics Solutions hybridisation station with Biosolutions hybridisation buffer (see http://www.flychip.org.uk/protocols/gene_expression/hyb_oligoMWG.php).

scan_protocol: Scanning was with Genepix 4000B dual laser scanner (see http://www.flychip.org.uk/protocols/gene_expression/scanning2.php).

data_processing: Spot quantification via the Dapple package. Data normalised with the vsn (variance stabilisation normalisation) Bioconductor package.

organism: Drosophila melanogaster

label_protocol: Klenow Labelling: Between 3 to 5µg total RNA are reverse transcribed to cDNA [anchored oligo (dT)23 (Sigma), Superscript III (Invitrogen)] and second strand synthesis is then performed [Second strand buffer (Invitrogen), DNA Polymerase I (Invitrogen), RNaseH (New England Biolabs), E. coli DNA ligase (GE Healthcare)] to obtain double stranded DNA. Random primers are annealed to this denatured DNA template and extended by Klenow fragment using the Bioprime DNA Labeling System (Invitrogen) while fluorescent dyes Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated. (http://www.flychip.org.uk/protocols/gene_expression/klenow_v2.php) - used 5 ug total RNA starting material and labelled 500ng cDNA with the Klenow kit.

growth_protocol: Fly stocks were maintained at 25 degrees Celcius

extract_protocol: RNA extraction using Trizol (see http://www.flychip.org.uk/protocols/gene_expression/standard_extraction.php)

value: Inv mutant 4Y7

tag: developmental stage

value: larva

value: Wild-type (Canton S)


title: Unstimulated WT CD4 T cells, rep2

description: Gene expression data from splenic CD4+ T cells without stimulation from WT mice

source_name: Unstimulated, splenic CD4 T cells from WT mice

value: CD4 T cells


title: inv_mutant_v_wt_rep_3


title: inv_mutant_v_wt_rep_4


title: Unstimulated WT CD4 T cells, rep3


title: OSCC microRNA 481

description: Tongue


title: Unstimulated WT CD4 T cells, rep1


title: Liver_healthy_control_animal-23

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: Expression profiles of porcine liver tissues were studied to indentify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same heard.

hyb_protocol: The slides were hybridized in a Discovery XT hybridization station (Ventana Discovery Systems, Tucson, AZ, USA). Transfer Chip Prep-2 from 4 ºC to room temperature 1 hour before use. Prepare ChipSpread by mixing equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and B (formamide; 2 mg/mL SDS) and incubate at room temperature for 1 hour before use. A total of 2.5 mL is needed per slide. Print labels, trim them and place them on the slides. Mix the Chip Map reagents (Chip Prep-1, -2 and - 3) by inversion, remove the cap and place the reagents in the Discovery. Place the slides in the machine and initiate the run. Cover slide with 2.5 mL ChipSpread when the message appears (after few minutes). The machine now runs for app. 1.5 hours to pre-hybridize the slides. Heat a waterbath to 90°C or use a PCR machine. Mix the Chiphybe80, add 200 µL to the sample (<20 µL) and mix carefully. Heat the sample mixture at 90°C for 3 minutes and mix carefully by pipetting. Press the button on the machine which then prepares the slides for hybridization. When the message appears apply the samples onto the slides and press the button and the machine hybridizes at 48 ºC for 6 hours. Wipe oil from backside of slides using a clean-room napkin and place slides in the slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. If processing more than 20 slides, place equal number of slides in two slide-holders and continue in parallel. Transfer the slide-holder to a HTW filled with RiboWash and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with RiboWash and repeat the wash. Dip the slide-holder in 2x SSC filled in a mTub (200 mL 20x SSC, Elga H2O + 1800 mL water). Transfer the slide-holder to a HTW filled with 2x SSC and wash for 2 min with magnetic stirring at 700 rpm. Refill the HTW with 2x SSC and repeat the wash. Dip the slide-holder 10 times in 0.1x SSC filled in a mTub (5 mL 20x SSC, Elga H2O + 995 mL water) and leave the holder submerged in 0.1x SSC. Transfer the slides to a mBox slide holder placed in a mTub filled with Elga H2O. Dry arrays by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro (version 6.0.1.27, Molecular Devices) using FeatureType = Irregular Filled and MorphologicalClosingFollowedByOpening as background measurement.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.8.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.16.4) which is part of the Bioconductor project. Probes classified as “not found” by GenePix, positive control probes, probes with a SNR value below 1, and probes with more than 50 % of saturated pixels were weighted “0” before the log2-transformed ratios of Alexa-555 to Alexa-647 (not background corrected) were normalized within-slide using global-loess with default parameters utilising the matrix of binary probe weights as implemented in Limma [6]. This was followed by a scale normalisation between arrays to compensate for different spreads of M-values. All control probes were weighted “0” before further analysis. The individual probes were furthermore filtrated based on their representation across the arrays, such that probes not represented by at least four (in the control group) and eight (in the challenge group) non-zero weighted measurements were excluded from the statistical analysis. Finally, probe pairs were excluded if one of the duplicates did not pass the filtration. The exclusions were performed by sub-setting the objects containing the normalised data. The normalized log-ratios were analyzed in Limma to identify genes being significantly differentially expressed between tissue of uninfected control animals and tissue of infected animals. The relative reliability of each array was estimated using the arrayWeights function of Limma. The function measures how well the expression values for the individual arrays follow the linear model. The matrix of spot weights was multiplied by the obtained vector of array weights to generate a final weight matrix which was applied to the statistical analysis. A pooled correlation estimate was used to take the duplicated elements into account. The false discovery rate was controlled using the method of Benjamini and Hochberg as implemented in Limma and a corrected P-value below 0.05 was considered significant.

organism: Sus scrofa

extract_protocol: RNeasy Midi Kit with DNase treatment following the enclosed protocol (Qiagen)

treatment_protocol: Pigs assigned as healthy non-inoculated control animals were killed and sampled prior to inoculation of the infected group. Samples of approximately 500 mg were taken from liver tissue, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use. Pigs assigned as infected animals, were inoculated with Actinobacillus pleuropneumoniae 5b (strain L20) by dripping 1 ml bacterial suspension, (McFarland 0.5, mixed 1:1 with Brain Heart Infusion + 0.1 % NAD) containing approximately 0.7 x107 CFU, in each nostril during inhalation. Culture of bacteria as well as inoculation procedures has previously been described by (Kristensen et al., Vet. Microbiol. 98, 243-249, 2004). Animals were killed 14 – 18 hours post inoculation by means of captive bolt pistol followed by pitching and exsanguinations. All animal procedures were approved by the Danish Animal Experiments Inspectorate. Immediately after killing, lungs were inspected for sizes and numbers of pulmonary lesions. To verify the infection, samples from lung, liver, tonsil and spleen were cultivated on PPLO agar (BD, Brøndby, Denmark) to re-isolate the inoculation strain, which hereafter was serotyped using latex agglutination (Giese et al., Acta. Vet. Scand. 34, 223-225, 1993). From the infected animals, samples of approximately 500 mg were taken from liver tissue, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use.

tag: breed

value: Danish Landrace/Yorkshire/Duroc cross

tag: herd

value: high health free from A. pleuropneumoniae

value: castrated males

value: 8-10 weeks

value: healthy control

tag: sample

value: liver

source_name: Reference, pool of equal amount of total-RNA from all liver samples balanced with respect to control and challenged animals.

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany). The labelled reference samples were mixed and divided into aliquots before combining it with a labelled sample.

value: Reference, pool of equal amount of total-RNA from all liver samples in experiment


title: OSCC microRNA 392

description: Tongue

value: M

value: Oral cavity squamous cell carcinoma tumor


title: Unstimulated Gli2R Tg CD4 T cells, rep3

value: Gli2R Tg


title: OSCC microRNA 327

description: Tongue

value: Tongue


title: inv_mutant_v_wt_rep_1


title: OSCC microRNA 600

description: Tongue


title: Liver_challenged_animal-28

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the common reference samples and red spike-in RNA was added to the samples. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany).

value: AP serotype 5b infected


title: Liver_challenged_animal-34


title: mESCs at d24 of differentiation with KGF treatment

value: mESCs


title: Liver_challenged_animal-33


title: OSCC microRNA 353

description: Tongue


title: OSCC microRNA 391

description: Tongue


title: Liver_challenged_animal-26


title: OSCC microRNA 258

description: Tongue

value: F


title: Liver_healthy_control_animal-21


title: OSCC microRNA 478

description: Tongue


title: OSCC microRNA 385

description: Tongue


title: Liver_challenged_animal-31


title: OSCC microRNA 325

description: Tongue


title: Liver_challenged_animal-25


title: Liver_challenged_animal-32


title: OSCC microRNA 266

description: Tongue


title: Liver_challenged_animal-27


title: OSCC microRNA 388

description: Tongue


title: Liver_healthy_control_animal-20


title: Liver_challenged_animal-30


title: OSCC microRNA 578

description: Tongue


title: OSCC microRNA 367

description: Tongue


title: OSCC microRNA 447

description: Tongue


title: Liver_healthy_control_animal-22


title: Liver_healthy_control_animal-24


title: OSCC microRNA 347

description: Tongue


title: E. amylovora Ea1189_amyR OE_pear_rep2

city: Vernon Hills

first: DONGPING

last: WANG

state: IL

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

hyb_protocol: 1. Add 20 μl water to dissolve the dried labeled-cDNA (600ng); 2. Add 5 μl 10 × Blocking Agent; 3. Add 25 μl 2 × GE × Hybridization Buffer H1-RPM. Mix well by pipetting to reduce bubble formation. Spin for 1 min and place on ice.  Prepare the hybridization assembly: 1. Load a clean gasket slide into the Agilent Suretlyb chamber base with the label facing up; 2. Slowly dispense 40 μl hybridization samples onto the gasket well. To minimize bubble formation; 3. Slowly place an array active side (Agilent facing down) onto the gasket slide; 4. Place the SureHyb chamber clamp cover on the sandwiched slides and slide the clamp assembly onto both pieces; 5. Hand-tighten the clamp on to the chamber. Rotate the gasket slide when tightening; 6. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles; 7. Place assembled slide chamber in a hybridization oven set to 65°C, 15 rpm; 8. Hybridize at 65°C for 17 h.  Washing: This step is performed under dark conditions. 1. Add Triton into the X-102 to Gene Expression washing buffer 1 and 2; 2. Pre-warm gene expression wash buffer 2 in a 37°C water bath O/N; 3. Dessemble the hybridization chamber, put gaskets and slide into Washing Buffer 1. Use a tweezer to separate the slide from the cover slide; 4. Put the slide into the washing container and array side facing out. Wash for 1 min; 5. Transfer the slide into another container containing Washing Buffet 2 and wash for another min; 6. Remove the slide slowly to minimize the attachment of water. Put the slide into a 50 ml tubes in dark places.

scan_protocol: Slides were scanned using an Agilent Scanner (Agilent technologies, Santa Clara, CA, USA) at 5-µm resolution. All slides were scanned using 100% laser power; PMT voltages were automatically adjusted using the GenePix Pro 6.0 software acquisition system to obtain maximal signal intensities with <0.02% probe saturation. The resulting 16 bit images were processed using the GenePix Pro 6.0 image analysis software (v6.0.1.26).

data_processing:
Microarray data normalization: Microarray normalization is carried out using maanova function in R program version 2.2.1. Eight arrays in one slide were globally normalized using glowess method; 1. library(maanova) go to the directory: setwd(C:\\Documents and Settings\\Wang\\Desktop\\Erwinia in vivo\\rcsC MBMA); 2. Read data: Data = read.madata(NormInput.txt, designfile=Designfile1.txt, header=TRUE, spotflag=TRUE, metarow=1, metacol=2, row=3, col=4, geneID=5, pmt=6); 3. Log transformation: LogData = createData(Data, n.rep=1, log.trans=TRUE); 4. Normalization by Glowess method: NormalData=transform.madata(LogData, method=c(glowess)); 5. Save the plot files: postscript(file=PlotRawData.ps), riplot(LogData, onScreen=FALSE), postscript(file=PlotGLOWESS.ps), riplot(NormalData, onScreen=FALSE); 6. close the graph: graphics.off() norm.temp<-cbind(NormalData$metarow, NormalData$metacol,NormalData$row, NormalData$col, NormalData$geneID, NormalData$data); 7. output: write.table(norm.temp, file=Normal_Data.csv, sep=,, row.names=FALSE, col.names=TRUE, quote=FALSE)

Data selection: Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. A modified t-test (p-value) was computed to measure the significance associated with each differential expression value. A gene expression value was decided to be significantly different in the mutant and over-expression strains when the p-value was less than 0.05 (except otherwise mentioned) and the expression ratio was ≥ 2.0or ≤ 0.5.

The Samples grown in MBMA medium were normalized separately from the Samples grown on pear.

label: Alexa Fluor 555

organism: Erwinia amylovora

source_name: E. amylovora Ea1189 amyR over-expressing cells, pear

label_protocol:
cDNA labeling was carried out using the FairPlay III Microarray Labeling Kit from Agilent.

Reverse transcription: 10 μ g total RNA was used to generate cDNA. Add 1 μl of 500 ng/ μl random primers into the 10 μg total RNA which is dissolved in 12 μl RNase free water. Incubate at 70°C for 10 min in a PCR machine. Cool samples immediately on ice until ready for use. Combine the following components in a sterile, RNase and DNase free tube: 2 μl 10 × AffinityScript RT Buffer; 1 μl 20 × dNTP mix; 1.5 μl 0.1 M DTT; 0.5 μl 40 U/ul RNase Block. Add the annealed primers and RNA into the mixture. Add 3 μl of AffinityScript RT and incubate at 42°C for 60 min. Add 10 μl of 1 M NaOH and incubate at 70°C for 10 min to hydrolyzed RNA. Cool to room temperature and add 10 μl 1 M HCL to neutralize the solution.

cDNA purification: Add 4 μl of 3 M sodium acetate pH 5.5 to the reaction. Add 1 μl of 20 mg/ml glycogen to the reaction. Add 100 μl ice cold 100% ethanol and incubate at -20°C overnight. Spin the reaction at 13.2 rpm for 15 min at 4°C and decant the supernatant (You should see some white pellet at the bottom of the tube). Wash with 200 μl ice cold 70% ethanol and spin 5 min. Decant supernatant carefully and allow for air dry for about 30 min to eliminate ethanol.

cDNA labeling with a reaction fluorescence dye: Prepare the amine-modified cDNA. Thoroughly dissolve the amine-modified DNA in 5 μl of nuclease-free water, warm in a 42°C water bath for 5 min. Prepare labeling buffer: 2.5 g sodium bicarbonate in 100 ml water. Add 3 μl labeling buffer to the amine-labeled cDNA. Dissolve one vial of dye in 2 μl of high quality DMSO, vortex for 10 s. Add the 8 ul amine-modified cDNA into the dissolved dye. Incubate the reaction in dark for 1 h.

Purification of dye-labeled cDNA using QIAquick PCR Purification column: Add 8 μl of nuclease-free water and 2 μl 3 M sodium acetate pH 5.5 to the reaction mixture. Add 100 μl buffer PB to the mixture. Apply the sample to the QIAquick column and centrifuge for 60 s. Discard flow-through and place the QIAquick column back into the same tube. To wash, add 0.75 ml buffer PE to the column and centrifuge for 60 s. Centrifuge in a 2 ml collection tube for 1 min. Place QIAquick column in a clean 1.5 ml tube. Add 50 μl buffer EB and centrifuge for 1 min.

growth_protocol: Bacterial strains were grown overnight in LB media supplemented with or without antibiotic and diluted in 5 ml MBMA media at an OD600 of 0.005. After 18 hours growth at MBMA medium at 28°C, 2 ml of RNA Protect Reagent (Qiagen) was added to 1 ml bacterial cultures (at OD600 of about 0.5-0.8) to stabilize RNA. For in vivo condition, bacterial strains were grown overnight in LB media and bacterial cells were collected by centrifugation. The cells were resuspended in PBS, adjusted to an OD600 to 0.2 to 0.3 and inoculated onto immature pear fruit surface by cutting the fruit in half.  After incubation at 28°C for up to 18 h with high humidity, bacterial cells were collected by washing with a solution containing 2 ml RNA Protect Reagent (Qiagen) and 1 ml RNase-free water.

extract_protocol:
Add 100 μl 1 mg/ml lysozyme buffer (TE buffer: 10 mM Tris-HCL, 1 mM EDTA pH=8.0 containing 1 mg/ml lysozyme). Vortex for 10 s and incubate at RT for at least 15 min. Add 350 μl Buffer RLT and vortex vigorously. Add 250 μl 100% ethanol, mix by pipetting.
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C.

tag: strain/background

value: amyR over-expressor

tag: growing condition

value: pear fruits

tag: Stage

value: logarithmic phase


title: OSCC microRNA 166

description: Tongue

tag: tissue


title: E. amylovora Ea1189_amyR mutant_pear_rep1

source_name: E. amylovora Ea1189 amyR mutant cells, pear

tag: genotype/variation

value: amyR mutant


title: E. amylovora Ea1189_WT_pear_rep1

source_name: E. amylovora Ea1189 cells, pear

value: wild type


title: E. amylovora Ea1189_amyR mutant_MBMA_rep3

source_name: E. amylovora Ea1189 amyR mutant cells, MBMA

value: MBMA minimal medium


title: E. amylovora Ea1189_WT_pear_rep2


title: E. amylovora Ea1189_amyR OE_pear_rep1


title: E. amylovora Ea1189_amyR_OE_MBMA_rep3

source_name: E. amylovora Ea1189 amyR over-expressing cells, MBMA


title: E. amylovora Ea1189_amyR mutant_pear_rep2


title: E. amylovora Ea1189_amyR_OE_MBMA_rep2


title: E. amylovora Ea1189_amyR_OE_MBMA_rep1


title: Liver_challenged_animal-36

value: Danish Landrace/Yorkshire/Duroc cross

value: high health free from A. pleuropneumoniae

value: castrated males

tag: age

value: 8-10 weeks


title: OSCC microRNA 43

description: Tongue

value: M


title: E. amylovora Ea1189_amyR mutant_MBMA_rep1


title: OSCC microRNA 139

description: Tongue

value: Oral cavity squamous cell carcinoma tumor


title: E. amylovora Ea1189_amyR mutant_MBMA_rep2


title: E. amylovora Ea1189_WT_MBMA_rep2

source_name: E. amylovora Ea1189 cells, MBMA


title: E. amylovora Ea1189_WT_MBMA_rep1


title: OSCC microRNA 193

description: Buccal

value: Buccal


title: Liver_healthy_control_animal-24

description: Expression profiles of porcine liver tissues were studied to identify genes being significantly affected by bacterial infection of the lungs. Samples were taken from liver tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same herd. Samples were investigated for changes in gene expression by means of global cDNA microarrays.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.8.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.16.4) which is part of the Bioconductor project. Probes classified as “not found” by GenePix, positive control probes, probes with a SNR value below 1, and probes with more than 50 % of saturated pixels were weighted “0” before the log2-transformed ratios of Alexa-555 to Alexa-647 (not background corrected) were normalized within-slide using global-loess with default parameters utilising the matrix of binary probe weights as implemented in Limma [6]. This was followed by a scale normalisation between arrays to compensate for different spreads of M-values. All control probes were weighted “0” before further analysis. The individual probes were furthermore filtrated based on their representation across the arrays, such that probes not represented by at least four (in the control group) and eight (in the challenge group) non-zero weighted measurements were excluded from the statistical analysis. Finally, probe pairs were excluded if one of the duplicates did not pass the filtration. The exclusions were performed by sub-setting the objects containing the normalised data. The two sets of normalized log-ratios were analyzed using Globaltest [7,8] as implemented in the Globaltest R-package (version 4.12.0) to identify gene sets being significantly associated with response to infection. The two sets of normalized log-ratios were furthermore analyzed in Limma to identify genes being significantly differentially expressed between tissue of uninfected control animals and tissue of infected animals. The relative reliability of each array was estimated using the arrayWeights function of Limma. The function measures how well the expression values for the individual arrays follow the linear model. The matrix of spot weights was multiplied by the obtained vector of array weights to generate a final weight matrix which was applied to the statistical analysis. A pooled correlation estimate was used to take the duplicated elements into account. The false discovery rate was controlled using the method of Benjamini and Hochberg as implemented in Limma and a corrected P-value below 0.05 was considered significant.

source_name: Liver, healthy control

treatment_protocol: Pigs assigned as healthy non-inoculated control animals were killed and sampled prior to inoculation of the infected group. Samples of approximately 500 mg were taken from liver and tracheobronchial lung lymph node tissues, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use. Pigs assigned as infected animals, were inoculated with Actinobacillus pleuropneumoniae 5b (strain L20) by dripping 1 ml bacterial suspension, (McFarland 0.5, mixed 1:1 with Brain Heart Infusion + 0.1 % NAD) containing approximately 0.7 x107 CFU, in each nostril during inhalation. Culture of bacteria as well as inoculation procedures has previously been described by (Kristensen et al., Vet. Microbiol. 98, 243-249, 2004). Animals were killed 14 – 18 hours post inoculation by means of captive bolt pistol followed by pitching and exsanguinations. All animal procedures were approved by the Danish Animal Experiments Inspectorate. Immediately after killing, lungs were inspected for sizes and numbers of pulmonary lesions. To verify the infection, samples from lung, liver, tonsil and spleen were cultivated on PPLO agar (BD, Brøndby, Denmark) to re-isolate the inoculation strain, which hereafter was serotyped using latex agglutination (Giese et al., Acta. Vet. Scand. 34, 223-225, 1993). From the infected animals, samples of approximately 500 mg were taken from liver and tracheobronchial lung lymph node tissues, snap frozen in liquid nitrogen and stored at minus 80 degrees until further use.

value: healthy control

source_name: Reference, liver

tag: reference

value: pool of equal amount of total-RNA from all liver samples in experiment


title: OSCC microRNA 91

description: Tongue

value: Tongue


title: Liver, challenged animal

source_name: Liver, challenged animal

tag: treatment

value: AP serotype 5b infected


title: Liver_challenged_animal-32


title: Liver_challenged_animal-25


title: Lung_lymph_node_challenged_animal-36

description: Expression profiles of porcine tracheobronchial lung lymph node tissues were studied to identify genes being significantly affected by bacterial infection of the lungs. Samples were taken from tracheobronchial lung lymph node tissues in pigs experimentally infected with A. pleuropneumoniae, serotype 5b, and from healthy non-inoculated control pigs from the same herd. Samples were investigated for changes in gene expression by means of global cDNA microarrays.

source_name: Lung lymph node, challenged animal

source_name: Reference, lung lymph node

value: pool of equal amount of total-RNA from all tracheobronchial lung lymph node samples in experiment


title: Lung_lymph_node_challenged_animal-31


title: Liver_challenged_animal-26


title: Liver_challenged_animal-33


title: Lung_lymph_node_challenged_animal-32


title: Lung_lymph_node_healthy_control_animal-20

source_name: Lung lymph node, healthy control


title: Liver_challenged_animal-28


title: Lung_lymph_node_challenged_animal-33


title: Liver_healthy_control_animal-22


title: Lung_lymph_node_challenged_animal-30


title: Lung_lymph_node_challenged_animal-25


title: Lung_lymph_node_challenged_animal-26


title: Liver_challenged_animal-27


title: Lung_lymph_node_challenged_animal-34


title: Lung_lymph_node_challenged_animal-27


title: Liver_healthy_control_animal-20


title: Lung_lymph_node_challenged_animal-28


title: Lung_lymph_node_healthy_control_animal-23


title: Lung_lymph_node_healthy_control_animal-22


title: Liver_challenged_animal-36


title: Liver_healthy_control_animal-21


title: Liver_challenged_animal-34


title: Lung_lymph_node_healthy_control_animal-24


title: Liver_challenged_animal-31


title: Liver_healthy_control_animal-23


title: Lung_lymph_node_healthy_control_animal-21


title: LC24_exercise

city: Tucson

first: Dawn

middle: K

last: Coletta

state: AZ

address: 1501 N. Campbell Ave

department: Medicine

institute: UNIVERSITY OF ARIZONA

description:
Gene expression after exercise
US92200302_251485067006_S01_GE1_105_Jan09_1_2

hyb_protocol: Cy3-labeled aRNA was fragmented using Agilent Gene Expression Hybridization kit and hybidized to 4x44K Whole Human Genome Microarray at 65C for 17 hours

scan_protocol: After washing, slides were scanned with an Agilent DNA microarray scanner

data_processing: Feature extraction software version 10.5.1.1 (Agilent) was used for analysis.

source_name: skeletal muscle, post exercise

label_protocol: Total RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA amplification kit and quantified for Cy3 dye labeled aRNA concentration, RNA absorbance ratio, A260, Adye, and dye/probe values.

extract_protocol: Muscle biopsy specimens were homogenized in RNAStat solution using a Polytron homogenizer, and the total RNA was purified with RNeasy and DNase I treatment.

treatment_protocol: volunteers had muscle biopsies at rest and 30 minutes after an exercise bout, and muscle biopsies were frozen in liquid nitrogen.

value: female

tag: insulin sensitivity - m value

value: skeletal muscle

tag: exercise status

value: after exercise


title: SV34_exercise

description:
Gene expression after exercise
US92200302_251485067007_S01_GE1_105_Jan09_1_2

tag: gender

value: male


title: P61

city: Atlanta

first: Gregory

last: Doho

state: GA

address: 1365B Clifton Rd NE

institute: Emory University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: BeadChips were scanned using Illumina HiScan

data_processing: The data were normalized using quantile-normalization with GenomeStudio V2010.3

source_name: PBMC

label_protocol: PCR product was prepared with standard Illumina protocol for arrays

extract_protocol: Total RNA was isolated using RNeasy kits (QIAGEN, Valencia, CA) according to manufacturer instructions.

treatment_protocol: Total RNA was isolated from the peripheral blood mononuclear cells (PBMC) obtained from the women (n=61) with Stage 0-III breast cancer treated with or without chemotherapy.

tag: treatment (chemo)

value: No Chemo

tag: breast cancer stage

value: IA

tag: processing batch

value: Batch 2

tag: cell type

value: PBMC


title: HR36_rest

description:
Gene expression before exercise
US92200302_251485067007_S01_GE1_105_Jan09_1_3

source_name: skeletal muscle, resting

value: before exercise


title: RM27_rest

description:
Gene expression before exercise
US92200302_251485067010_S01_GE1_105_Jan09_1_3


title: AC30_rest

description:
Gene expression before exercise
US92200302_251485067006_S01_GE1_105_Jan09_1_3


title: LC24_rest

description:
Gene expression before exercise
US92200302_251485067006_S01_GE1_105_Jan09_1_1


title: P60

value: IIB


title: RB26_exercise

description:
Gene expression after exercise
US92200302_251485058130_S01_GE1_105_Jan09_1_2


title: SV34_rest

description:
Gene expression before exercise
US92200302_251485067007_S01_GE1_105_Jan09_1_1


title: Muscle_longissimus_dorsi_Animal_339_vs_Animal_288

description: The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. We used a direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays.

data_processing: Statistical analysis was carried out in the R computing environment (version 2.6.1 for Windows) using the package Linear Models for Microarray Analysis (Limma, version 2.12.0) which is part of the Bioconductor project. The log2-transformed ratios of Alexa-647 to Alexa-555 (background corrected using the Edwards method) were normalized within-slide using printtip-loess with default parameters as implemented in Limma. The set of normalized log-ratios were analyzed in Limma to identify genes being significantly differentially expressed between samples with high versus low intramuscular fat (IMF). The false discovery rate was controlled using the method of Benjamini and Hochberg as implemented in Limma and a corrected P-value below 0.05 was considered significant. The features of the arrays were mapped to a LocusLink identifier and an annotation package was built using the Bioconductor package AnnBuilder (version 1.9.14). A test for significantly (P < 0.05) overrepresentation of gene ontology (GO) terms among both induced and repressed genes was conducted using the GOHyperG function of the Bioconductor package GOstats (ver 2.4.0).

source_name: Porcine muscle longissimus dorsi, Animal: 339, IMF: 0.8 %, Family: D

label_protocol: 20 µg total RNA was labelled by using the Superscript Direct cDNA Labeling System (Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the labelling reactions. Green spike-in RNA was added to the samples labelled with Alexa-555 and red spike-in RNA was added to the samples  labelled with Alexa-647. The fluorescently labelled cDNA was purified using the NucleoSpin 96 Extract II PCR Clean-up kit (Macherey-Nagel, Düren, Germany).

growth_protocol: Samples from the longissimus dorsi muscle were taken at the slaughter line at a live weight of 108-115 kg, immediately snap frozen in liquid nitrogen and then stored at -80°C.

extract_protocol: RNeasy Maxi Kit with DNase treatment following the enclosed protocol (Qiagen)

treatment_protocol: The animals included in the study are the F2 offspring of a cross between five Duroc boars and five Norwegian Landrace sows. These two races are known to differ in meat quality traits like intramuscular fat content. Animals were selected based on high and low intramuscular fat content (IMF %), with emphasis on getting the largest possible contrast, and put into two separate groups for comparison. In total there were 14 animals with high IMF and 14 animals with low IMF. Intramuscular fat recordings were performed using the Foss-Let method (Woodward et al.1976, Br J Nutr 36, 567-570) on longissimus dorsi muscle samples taken at slaughtering (live weight 108-115 kg). Prior to slaughtering, the animals were raised in similar pens and given the same diet.

tag: Breed

source_name: Porcine muscle longissimus dorsi, Animal: 288, IMF: 2.4 %, Family: E


title: Muscle_longissimus_dorsi_Animal_360_vs_Animal_262

source_name: Porcine muscle longissimus dorsi, Animal: 360, IMF: 2.8 %, Family: A

value: crossbred population of Landrace x Yorkshire/Landrace x Duroc

source_name: Porcine muscle longissimus dorsi, Animal: 262, IMF: 0.9 %, Family: E


title: Muscle_longissimus_dorsi_Animal_312_vs_Animal_237

source_name: Porcine muscle longissimus dorsi, Animal: 312, IMF: 3.2 %, Family: B

source_name: Porcine muscle longissimus dorsi, Animal: 237, IMF: 0.9 %, Family: D


title: Muscle_longissimus_dorsi_Animal_367_vs_Animal_314

source_name: Porcine muscle longissimus dorsi, Animal: 367, IMF: 0.8 %, Family: A

source_name: Porcine muscle longissimus dorsi, Animal: 314, IMF: 3.5 %, Family: B


title: RM27_exercise

description:
Gene expression after exercise
US92200302_251485067010_S01_GE1_105_Jan09_1_4


title: KA33_exercise

description:
Gene expression after exercise
US92200302_251485058130_S01_GE1_105_Jan09_1_4


title: HR36_exercise

description:
Gene expression after exercise
US92200302_251485067007_S01_GE1_105_Jan09_1_4


title: Muscle_longissimus_dorsi_Animal_356_vs_Animal_122

source_name: Porcine muscle longissimus dorsi, Animal: 356, IMF: 3.1 %, Family: B

source_name: Porcine muscle longissimus dorsi, Animal: 122, IMF: 0.8 %, Family: C


title: Muscle_longissimus_dorsi_Animal_195_vs_Animal_151

source_name: Porcine muscle longissimus dorsi, Animal: 195, IMF: 0.9 %, Family: E

source_name: Porcine muscle longissimus dorsi, Animal: 151, IMF: 2.5 %, Family: D


title: AC30_exercise

description:
Gene expression after exercise
US92200302_251485067006_S01_GE1_105_Jan09_1_4


title: P59

value: Chemo

value: IB


title: KA33_rest

description:
Gene expression before exercise
US92200302_251485058130_S01_GE1_105_Jan09_1_3


title: Muscle_longissimus_dorsi_Animal_34_vs_Animal_146

source_name: Porcine muscle longissimus dorsi, Animal: 34, IMF: 2.8 %, Family: A

source_name: Porcine muscle longissimus dorsi, Animal: 146, IMF: 0.8 %, Family: D


title: Muscle_longissimus_dorsi_Animal_302_vs_Animal_152

source_name: Porcine muscle longissimus dorsi, Animal: 302, IMF: 1.0 %, Family: D

source_name: Porcine muscle longissimus dorsi, Animal: 152, IMF: 2.7 %, Family: D


title: Muscle_longissimus_dorsi_Animal_357_vs_Animal_189

source_name: Porcine muscle longissimus dorsi, Animal: 357, IMF: 1.1 %, Family: A

source_name: Porcine muscle longissimus dorsi, Animal: 189, IMF: 2.5 %, Family: D


title: Muscle_longissimus_dorsi_Animal_397_vs_Animal_306

source_name: Porcine muscle longissimus dorsi, Animal: 397, IMF: 0.9 %, Family: C

source_name: Porcine muscle longissimus dorsi, Animal: 306, IMF: 2.4 %, Family: B


title: Muscle_longissimus_dorsi_Animal_177_vs_Animal_157

source_name: Porcine muscle longissimus dorsi, Animal: 177, IMF: 1.0 %, Family: E

source_name: Porcine muscle longissimus dorsi, Animal: 157, IMF: 3.6 %, Family: D


title: Muscle_longissimus_dorsi_Animal_460_vs_Animal_124

source_name: Porcine muscle longissimus dorsi, Animal: 460, IMF: 2.4 %, Family: C

source_name: Porcine muscle longissimus dorsi, Animal: 124, IMF: 1.1 %, Family: C


title: Muscle_longissimus_dorsi_Animal_12_vs_Animal_301

source_name: Porcine muscle longissimus dorsi, Animal: 12, IMF: 3.2 %, Family: B

source_name: Porcine muscle longissimus dorsi, Animal: 301, IMF: 0.6 %, Family: D


title: Muscle_longissimus_dorsi_Animal_67_vs_Animal_176

source_name: Porcine muscle longissimus dorsi, Animal: 67, IMF: 4.4 %, Family: C

source_name: Porcine muscle longissimus dorsi, Animal: 176, IMF: 1.0 %, Family: E


title: P57

source_name: PBMC


title: JN32_exercise

description:
Gene expression after exercise
US92200302_251485058335_S01_GE1_105_Jan09_1_4

source_name: skeletal muscle, post exercise


title: RB26_rest

description:
Gene expression before exercise
US92200302_251485058130_S01_GE1_105_Jan09_1_1

source_name: skeletal muscle, resting


title: JG34_rest

description:
Gene expression before exercise
US92200302_251485047035_S01_GE1_105_Jan09_1_1


title: JN32_rest

description:
Gene expression before exercise
US92200302_251485058335_S01_GE1_105_Jan09_1_3


title: HG34_rest

description:
Gene expression before exercise
US92200302_251485058137_S01_GE1_105_Jan09_1_1


title: AK23_exercise

description:
Gene expression after exercise
US92200302_251485047035_S01_GE1_105_Jan09_1_4


title: P56


title: RL26_exercise

description:
Gene expression after exercise
US92200302_251485058335_S01_GE1_105_Jan09_1_2


title: AK23_rest

description:
Gene expression before exercise
US92200302_251485047035_S01_GE1_105_Jan09_1_3


title: GC48_rest

description:
Gene expression before exercise
US92200302_251485047036_S01_GE1_105_Jan09_1_3


title: RL26_rest

description:
Gene expression before exercise
US92200302_251485058335_S01_GE1_105_Jan09_1_1


title: JG34_exercise

description:
Gene expression after exercise
US92200302_251485047035_S01_GE1_105_Jan09_1_2


title: HG34_exercise

description:
Gene expression after exercise
US92200302_251485058137_S01_GE1_105_Jan09_1_2


title: P47


title: P55

value: IIA


title: MM29_exercise

description:
Gene expression after exercise
US92200302_251485047036_S01_GE1_105_Jan09_1_2


title: P53


title: GC48_exercise

description:
Gene expression after exercise
US92200302_251485047036_S01_GE1_105_Jan09_1_4


title: P49


title: P48


title: P51


title: P58


title: P44


title: P52


title: MM29_rest

description:
Gene expression before exercise
US92200302_251485047036_S01_GE1_105_Jan09_1_1


title: P46


title: P45


title: P54


title: P50

value: IIIB


title: P38


title: P39


title: P41


title: P43


title: GW0742_0h_rep3

city: Chicago

first: Jie

last: Zhou

state: ILLINOIS

address: 900 East 57th Street, KCBD 10100

institute: University of Chicago IGSB

description: 0h control / before treatment

hyb_protocol: Hybridization was done according to manufacturer recommendations.

scan_protocol: Hybridized microarrays were scanned using a GenePix 4000B scanner (Molecular Devices) at 5 µm resolution.

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

source_name: MCF7 Control for GW0742

label_protocol: Total RNA samples were labeled by direct incorporation of cyanine 3-labeled CTP using the Agilent Low RNA Input Linear Amplification Kit PLUS (One-Color) (Agilent Technologies)

growth_protocol: MCF-7 cells were cultured for 48 hours in medium with 10% charcoal-stripped FBS before treatment.

extract_protocol: Total mRNA were extracted from cells using Qiagen Rneasy Kit

treatment_protocol: MCF7 cells were treated with each NR ligand for 24h before collection and processing for microarrays. Three biological replicates were collected and processed for both control and treatment.

tag: ligand

value: Control

tag: ligand concentration


title: P40


title: GW0742_24h_rep3

description: 10nM GW0742 treatment for 24h

source_name: MCF7 GW0742 Treatment


title: GW0742_0h_rep2

description: 0h control / before treatment


title: GW0742_24h_rep2

description: 10nM GW0742 treatment for 24h


title: P42


title: DEX_24h_rep1

description: 100nM DEX treatment for 24h

source_name: MCF7 DEX treatment

value: DEX


title: DEX_24h_rep2

description: 100nM DEX treatment for 24h


title: DEX_24h_rep3

description: 100nM DEX treatment for 24h


title: GW0742_24h_rep1

description: 10nM GW0742 treatment for 24h


title: P36


title: P34


title: GW0742_0h_rep1

description: 0h control / before treatment


title: R5020_24h_rep3

description: 10nM R5020 treatment for 24h

source_name: MCF7 R5020 treatment


title: P37


title: P32


title: P35


title: R5020_24h_rep2

description: 10nM R5020 treatment for 24h


title: P29

value: Batch 1-2


title: R5020_24h_rep1

description: 10nM R5020 treatment for 24h


title: R5020_DEX_Control_rep3

description: 0h control / before treatment

source_name: MCF7 Control for R5020 DEX


title: gbdR rep2

city: Hanover

first: Thomas

middle: H

last: Hampton

state: NH

address: North College Street

department: Pharm/Tox

institute: Dartmouth Medical School

description: Static biofilm culture grown on plastic

hyb_protocol: cDNA was hybridized to Affymetrix Pseudomonas GeneChips according to manufacturer’s instructions

scan_protocol: GeneChips were scanned with GeneChip scanner 3000 7G (Affymetrix) in the Dartmouth Genomics and Microarray Laboratory

data_processing: We used the BioConductor Affymetrix library to read in CEL file data, and data were normalized using RMA in BioConductor

organism: Pseudomonas aeruginosa PAO1

source_name: PA01 gbd deletion mutant

label_protocol: RNA was converted into cDNA using (NS)5 primers, cDNA was fragemented, and terminally labeled with biotinylated-ddUTP according to the manufacturer’s instructions.

growth_protocol: Bacteria were grown in MOPS defined medium containing 10 mM glucose, 2mM pyruvate, 3% Survanta (Abbott Nutrition) which contains 11.0-15.5 mg/mL disaturated phosphatidylcholine, and 8µM additional ferric chloride and incubated at 37˚C with aeration. Cells were harvested during mid-exponential phase.

extract_protocol: RNA was isolated by use of an RNeasy Kit (Qiagen). Contaminating DNA was removed through 1-hour RQ1 DNase (Promega) treatments and semi-quantitative PCR with the RNA was performed to ensure the absence of contaminating DNA.

treatment_protocol: Three strains were used in these studies. P. aeruginosa PAO1 strain delta-plcHR and delta-gbdR mutants were constructed previously: Wargo MJ, Szwergold BS, Hogan DA: Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J Bacteriol 2008, 190(8):2690-2699 and Shortridge VD, Lazdunski A, Vasil ML: Osmoprotectants and phosphate regulate expression of phospholipase C in Pseudomonas aeruginosa. Mol Microbiol 1992, 6(7):863-871.

tag: genotype

value: delta-gbdR


title: R5020_DEX_Control_rep2

description: 0h control / before treatment


title: P31


title: P33


title: P30


title: WT rep2

description: Static biofilm culture grown on plastic

source_name: PA01 wild type

value: wild type


title: P21


title: CD437_24h_rep2

description: 100nM CD437 treatment for 24h

source_name: MCF7 CD437 treatment


title: P26


title: P24


title: gbdR rep1

description: Static biofilm culture grown on plastic


title: CD437_24h_rep3

description: 100nM CD437 treatment for 24h


title: P27


title: plchR rep2

description: Static biofilm culture grown on plastic

source_name: PA01 plcH deletion mutant

value: delta-plcHR


title: plchR rep1

description: Static biofilm culture grown on plastic


title: P23

value: No Chemo


title: P28


title: WT rep1

description: Static biofilm culture grown on plastic


title: P25

value: IA


title: R5020_DEX_Control_rep1

description: 0h control / before treatment


title: P19


title: P20


title: P17


title: ATRA_24h_rep3

description: 100nM ATRA treatment for 24h

source_name: MCF7 ATRA treatment

value: ATRA


title: CD437_24h_rep1

description: 100nM CD437 treatment for 24h


title: P18

value: PBMC


title: P22


title: P14

value: Batch 1-1


title: ATRA_24h_rep2

description: 100nM ATRA treatment for 24h


title: PA2206 mutant_H2O2_10mins_rep3

city: Cork

first: Fergal

last: O'Gara

address: University College Cork

department: Microbiology

country: Ireland

institute: BIOMERIT Research Centre

description: Gene expression data from PA2206 mutant strain.

hyb_protocol: Carried out at DNAVISION, Belgium, according to manufacturer's (Affymetrix) guidelines.

data_processing: The probe set data were generated using Microarray suite 5.0. The raw data was normalised using the robust multiarray average (RMA) algorithm (Irizarry et al,. 2003) and pairwise comparison (t-test, P < 0.05) was carried out to generate a list of genes with significantly altered expression between the test strains (PA2206- pBBR1MCS5-PA2206 and PA2206-) greater than 1.5 fold. The p-value was then assessed for each gene by controlling the false discovery rate using the Benjamini Hochberg method (Benjamini and Hochberg, 1995). A gene was considered as differentially expressed (i) when the corrected p-value was < 0.05, and (ii) when this gene was significantly expressed in at least two pairwise comparisons.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PA2206 mutant_1mM H2O2_10mins_rep3

extract_protocol: Total RNA was extracted using the Qiagen™ RNeasy® Mini RNA extraction kit in accordance with the manufacturer’s guidelines. The RNA was treated with Ambion® TURBO™ DNase at 37˚C for 1 hour and the RNA pellet was then resuspended in sterile diethylpyrocarbonate (DEPC)-treated water (1 ml of 0.1% DEPC added to 1000ml distilled H2O) to a final volume of 25 µl.

tag: strain

value: PA2206 mutant


title: ATRA_24h_rep1

description: 100nM ATRA treatment for 24h


title: PA2206 complemented strain_H2O2_10mins_rep3

description: Gene expression data from PA2206  complemented strain.

scan_protocol: Carried out at DNAVISION, Belgium, according to manufacturer's (Affymetrix) guidelines.

source_name: P. aeruginosa PA2206 complemented strain_1mM H2O2_10mins_rep3

value: PA2206 complemented


title: PA2206 complemented strain_H2O2_10mins_rep2

source_name: P. aeruginosa PA2206 complemented strain_1mM H2O2_10mins_rep2

label_protocol: Carried out at DNAVISION, Belgium, according to manufacturer's (Affymetrix) guidelines.


title: P15

value: Chemo

value: III


title: P16


title: AM580_24h_rep3

description: 100nM AM580 treatment for 24h

source_name: MCF7 AM580 treatment


title: AM580_24h_rep2

description: 100nM AM580 treatment for 24h


title: P13

source_name: PBMC


title: P11


title: AM580_24h_rep1

description: 100nM AM580 treatment for 24h


title: PA2206 mutant_H2O2_10mins_rep2

source_name: P. aeruginosa PA2206 mutant_1mM H2O2_10mins_rep2


title: P12

value: IIB


title: P09

value: IIA


title: SkMel30 cells with HOXA1 5

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: SkMel30 cells transduced with HOXA1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on U133_Plus2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and quantile normalization method.

source_name: SkMel30 cells transduced with HOXA1

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

growth_protocol: All cell lines were propagated at 37°C and 5% CO2 in humidified atmosphere in RPMI 1640 Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.

treatment_protocol: Full-length cDNA encoding HOXA1 (NM_005522.4) was obtained from the human ORFeome collection and transferred to viral vectors via Gateway recombination. The SkMel30 melanoma cell lines was transduced with either control or HOXA1 vector.

tag: cell line

tag: transduction


title: PA2206 mutant_H2O2_10mins_rep1

source_name: P. aeruginosa PA2206 mutant_1mM H2O2_10mins_rep1


title: P05


title: P02


title: P10

value: IIIA


title: P08


title: P06


title: CD_AM_Control_rep3

description: 0h control / before treatment

source_name: MCF7 Contron for CD437 AM580 ATRA

value: Control


title: P04


title: P03


title: Colon INDO#4

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

description: Biological replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with Illumina GenomeStudio software.

#4 replicates were normalized in a separate batch from the other replicates.

source_name: Human fetal colon INDO

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

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and then purified on QIAgen RNeasy columns.

tag: tissue

value: fetal colon

tag: gestional age

value: 18 weeks


title: E2_24h_rep3

description: 10nM E2 treatment for 24h

source_name: MCF7 E2 treatment


title: CD_AM_Control_rep1

description: 0h control / before treatment


title: CD_AM_Control_rep2

description: 0h control / before treatment


title: SkMel30 cells with HOXA1 6

description: SkMel30 cells transduced with HOXA1


title: Colon INDO#3

description: Biological replicate 3

value: 17 weeks


title: SkMel30 cells with GFP/control 2

description: SkMel30 cells transduced with GFP control

value: GFP control


title: E2_24h_rep1

description: 10nM E2 treatment for 24h


title: SkMel30 cells with GFP/control 3

source_name: SkMel30 cells transduced with GFP control


title: Colon INDO#2

description: Biological replicate 2


title: E2_24h_rep2

description: 10nM E2 treatment for 24h


title: SkMel30 cells with HOXA1 4

description: SkMel30 cells transduced with HOXA1


title: Colon INDO#1

description: Biological replicate 1


title: P01

value: rIIIC


title: E2_Control_rep3

description: 0h control / before treatment

source_name: MCF7 Control for E2 Treament


title: Colon Ctrl#4

description: Biological replicate 4

source_name: Human fetal colon control


title: E2_Control_rep2

description: 0h control / before treatment


title: Colon Ctrl#3

description: Biological replicate 3


title: SkMel30 cells with GFP/control 1


title: Colon Ctrl#2

description: Biological replicate 2


title: Colon Ctrl#1

description: Biological replicate 1


title: duod8

description: fresh-frozen resected, untreated periampullary adenocarcinomas pancreaticoduodenectomies were identified from The University of Texas MD Anderson Cancer Center (UTMDACC) frozen tumor bank from 2002 to 2009

hyb_protocol: Samples were amplified, labeled, and 10μg of cDNA was hybridized to the HG-U133 Plus 2.0 Affymetrix GeneChip array according the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

scan_protocol: GeneArray Scanne using Microarray Suit software.

data_processing: RMA (Robust Multichip Average) algorithm is used for quantification of the data.

extract_protocol: Total RNA was extracted using the TRIzol method (Invitrogen, Carlsbad, CA). RNA was purified using the RNeasy mini-kit (Qiagen, Alameda, CA) and the quality of RNA was assessed on an Agilent 2100 Bioanalyzer and quantified using Nano Drop ND-1000 (Nano Drop, Wilmington, DE).

treatment_protocol: untreated

value: duodenal adenocarcinomas


title: panc8

source_name: fresh-frozen resected, untreated periampullary adenocarcinomas

label_protocol: Samples were amplified, labeled, and 10μg of cDNA was hybridized to the HG-U133 Plus 2.0 Affymetrix GeneChip array according the manufacturer’s protocol (Affymetrix, Santa Clara, CA).

value: pancreatic adenocarcinomas


title: Ileum INDO#4

description: Biological replicate 4

source_name: Human fetal ileum INDO

value: fetal ileum


title: Ileum INDO#3

description: Biological replicate 3


title: Ileum Ctrl#4

description: Biological replicate 4

source_name: Human fetal ileum control


title: E2_Control_rep1

description: 0h control / before treatment


title: panc6


title: PA2206 complemented strain_H2O2_10mins_rep1

source_name: P. aeruginosa PA2206 complemented strain_1mM H2O2_10mins_rep1


title: Ileum Ctrl#2

description: Biological replicate 2


title: NCCIT-Mock-rep1

city: LA

first: jueng soo

last: You

state: CA

address: 1441 Eastlake Ave

department: Norris Comprehensive Cancer Center

institute: USC

description: replicate 1

data_processing: The data were normalized using quantile normalization with R package lumi

source_name: human pluripotent cells

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment and Quality control experiment performed

treatment_protocol: For differentiation RA was treated, For SNF5 level change we generated stable cell line for kd and transfected SNF5 for oe.

value: NCCIT

value: human pluripotent cells

tag: protocol

value: Mock


title: Ileum INDO#2

description: Biological replicate 2


title: panc5


title: Ileum Ctrl#3

description: Biological replicate 3


title: panc3


title: panc7


title: NCCIT-SNF5oe-rep2

description: replicate 2

value: exogenous SNF5 overexpression


title: NCCIT-SNF5oe-rep1

description: replicate 1


title: panc4


title: Ileum INDO#1

description: Biological replicate 1


title: NCCIT-SNF5sh-rep2

description: replicate 2

value: SNF5 shRNA infenction


title: Ileum Ctrl#1

description: Biological replicate 1


title: NCCIT-Mock-rep2

description: replicate 2


title: panc2


title: FtCtx_hu_HIV_Meth_4

city: La Jolla

first: Erick

middle: T

last: Tatro

address: 9500 Gilman Dr

department: Psychiatry

institute: University of California San Diego

data_processing: Real-time TaqMan assays were run on low-density array setting, raw data in SDS files were uploaded into RQ manager. Threshold of 0.2 and auto baseline setting were used. Data Assist Software from Applied Biosystems was used to generate Cycle Threshold (CT) values for each miRNA and sample, which is reported here; along with the ΔΔCT values. MiR's which did not amplify are labeled as null.

label: FAM

extract_protocol: miRVANA (Applied Biosystems)

treatment_protocol: Flash frozen

tag: Sex

value: Male

tag: hiv status

value: HIV+

tag: age

tag: meth-use-history

value: PAST

tag: plasma-loghiv-rna

tag: csf-loghiv-rna

tag: wkmem-ds

tag: memoryds

tag: verbal-ds

tag: global-ds

tag: motor-ds


title: FtCtx_hu_HIV_Meth_5-2


title: FtCtx_hu_HIV_Meth_4-2


title: FtCtx_hu_HIV_Meth_3-2


title: NCCIT-Consh-rep1

description: replicate 1

tag: cell type

value: Control shRNA infection


title: panc1


title: FtCtx_hu_HIV_Meth_5


title: NCCIT-Consh-rep2

description: replicate 2

tag: cell line


title: duod7


title: NCCIT-RA-rep1

description: replicate 1

value: Retinoeic Acid


title: FtCtx_hu_HIV_Meth_2-2


title: NCCIT-SNF5sh-rep1

description: replicate 1


title: fibroblast_100 µM genistein_48h_rep5

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

description: replicate 5

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio software package  (gene expression module version 1.9.0).

source_name: fibroblast_100 µM genistein_48h

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrepAmp Kit for Illumina arrays

growth_protocol: Fibroblasts were cultured from cryo-preserved cells in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% antibiotic/antimycotic solution at 37 oC in a humidified atmosphere of 5% CO2. 10E5 cells were seeded in 6-well plates and grown to a confluence of approximately 80 %.

extract_protocol: Total RNA was extracted from cells using the High Pure RNA Isolation Kit in accordance with the prescribed protocol, quantified with Quant iT RiboGreen Assay Kit

treatment_protocol: The medium was replaced by fresh medium non-supplemented, containing dimethyl sulfooxide (DMSO) added to a final concentration of 0.05%, or genistein at 30, 60 and 100 µM concentrations, with 0.05% DMSO. The experimental treatment was carried out for 1h, 24 h and 48 h period.

value: HDFa

value: fibroblasts


title: fibroblast_60 µM genistein_48h_rep5

description: replicate 5

source_name: fibroblast_60 µM genistein_48h


title: duod5


title: fibroblast_K1_0.05%DMSO_24h_rep5

description: replicate 5


title: fibroblast_100 µM genistein_24h_rep5

description: replicate 5

source_name: fibroblast_100 µM genistein_24h


title: fibroblast_K1_0.05%DMSO_48h_rep5

description: replicate 5


title: duod4


title: duod2


title: FtCtx_hu_HIV_Meth_3


title: duod6


title: fibroblast_30 µM genistein_48h_rep5

description: replicate 5

source_name: fibroblast_30 µM genistein_48h


title: P07

source_name: PBMC

tag: treatment (chemo)

value: No Chemo

tag: breast cancer stage

tag: processing batch

value: Batch 1-1

value: PBMC


title: FtCtx_hu_HIV_Meth_1-2


title: FtCtx_hu_HIV_Meth_1


title: FtCtx_hu_HIV_Meth_2


title: fibroblast_K1_0.05%DMSO_1h_rep5

description: replicate 5


title: FtCtx_hu_Neg_5-2

value: Neg


title: fibroblast_60 µM genistein_24h_rep5

description: replicate 5

source_name: fibroblast_60 µM genistein_24h


title: fibroblast_30 µM genistein_24h_rep5

description: replicate 5

source_name: fibroblast_30 µM genistein_24h


title: duod3

tag: tissue

value: duodenal adenocarcinomas


title: fibroblast_K1_0.05%DMSO_48h_rep4

description: replicate 4


title: fibroblast_60 µM genistein_48h_rep4

description: replicate 4


title: fibroblast_30 µM genistein_48h_rep4

description: replicate 4


title: fibroblast_100 µM genistein_1h_rep5

description: replicate 5

source_name: fibroblast_100 µM genistein_1h


title: cholang2

value: extrahepatic biliary adenocarcinomas


title: cholang1


title: fibroblast_100 µM genistein_48h_rep4

description: replicate 4


title: FtCtx_hu_Neg_5

tag: Sex


title: fibroblast_30 µM genistein_1h_rep5

description: replicate 5

source_name: fibroblast_30 µM genistein_1h


title: fibroblast_60 µM genistein_1h_rep5

description: replicate 5

source_name: fibroblast_60 µM genistein_1h


title: fibroblast_100 µM genistein_24h_rep4

description: replicate 4


title: amp13

value: ampullary adenocarcinomas


title: fibroblast_30 µM genistein_24h_rep4

description: replicate 4


title: duod1


title: fibroblast_K1_0.05%DMSO_24h_rep4

description: replicate 4


title: amp14


title: fibroblast_60 µM genistein_24h_rep4

description: replicate 4


title: amp11


title: FtCtx_hu_Neg_4-2

tag: hiv status


title: fibroblast_100 µM genistein_1h_rep4

description: replicate 4


title: FtCtx_hu_Neg_3

tag: age


title: FtCtx_hu_Neg_4

tag: meth-use-history


title: FtCtx_hu_Neg_3-2


title: FtCtx_hu_Neg_2-2


title: amp12


title: NCCIT-RA-rep2

description: replicate 2

value: NCCIT

value: human pluripotent cells

tag: protocol


title: fibroblast_K1_0.05%DMSO_48h_rep3

description: replicate 3


title: fibroblast_K1_0.05%DMSO_1h_rep4

description: replicate 4


title: fibroblast_60 µM genistein_1h_rep4

description: replicate 4


title: FtCtx_hu_Neg_1-2


title: amp10


title: fibroblast_100 µM genistein_48h_rep3

description: replicate 3


title: fibroblast_30 µM genistein_24h_rep3

description: replicate 3


title: fibroblast_60 µM genistein_48h_rep3

description: replicate 3


title: fibroblast_30 µM genistein_48h_rep3

description: replicate 3


title: fibroblast_60 µM genistein_24h_rep3

description: replicate 3


title: fibroblast_100 µM genistein_24h_rep3

description: replicate 3


title: fibroblast_K1_0.05%DMSO_24h_rep3

description: replicate 3


title: fibroblast_30 µM genistein_1h_rep4

description: replicate 4


title: amp8


title: FtCtx_hu_Neg_1


title: amp9


title: FtCtx_hu_Neg_2


title: FtCtx_hu_HIV_6-2

tag: plasma-loghiv-rna

tag: csf-loghiv-rna


title: amp6


title: FtCtx_hu_HIV_6

tag: wkmem-ds

tag: memoryds


title: amp5


title: FtCtx_hu_HIV_5

tag: verbal-ds

tag: global-ds


title: FtCtx_hu_HIV_4-2

tag: motor-ds


title: fibroblast_60 µM genistein_1h_rep3

description: replicate 3

tag: cell line

tag: cell type


title: FtCtx_hu_HIV_3-2


title: FtCtx_hu_HIV_4


title: fibroblast_30 µM genistein_1h_rep3

description: replicate 3


title: FtCtx_hu_HIV_3


title: FtCtx_hu_HIV_5-2


title: FtCtx_hu_HIV_2-2


title: FtCtx_hu_HIV_2


title: fibroblast_100 µM genistein_1h_rep3

description: replicate 3


title: fibroblast_K1_0.05%DMSO_1h_rep3

description: replicate 3


title: FtCtx_hu_HIV_1-2


title: amp7


title: amp2


title: LPJ128b Tumor B-cells

first: Michael

middle: R

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: Hybridized overnight according to the manufacturer's protocol using an Affymetrix GeneChip Hybridization Oven 640

scan_protocol: Scanned according to the manufacturer's protocol using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were RMA normalized using the "ExpressionFileCreator" module of GenePattern with the default settings.

label: Biotin

source_name: Follicular Lymphoma B-cells, Relapse

label_protocol: Labeled according to the manufacturer's protocol.

extract_protocol: RNA and DNA were extracted using a Qiagen AllPrep kit

tag: patient identifier

tag: gender

value: Female

tag: type

value: Follicular Lymphoma

tag: subset

value: Relapse Tumor B-cells


title: LPJ128a CD20hi B-cells

source_name: CD20hi Follicular Lymphoma B-cells

value: CD20hi B-cells


title: Genotype MR-insecticide Rep.Biol A vs Genotype MR-water Rep Biol C

city: Valdivia

first: Andrea

last: Silva

state: Valdivia

address: Isla teja s/n

department: Ciencias Ambientales y Evolutivas

country: Chile

institute: Universidad Austral de Chile

description: Technical replicate: Biological replicate A, genotype MR. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.

hyb_protocol: The labeled aRNA was fragmented at 60 °C for 30 min and stopped by the addition of 2× GEx Hybridization Buffer HI-RPM as described in the Agilent two-color microarray-based gene expression analysis protocol

scan_protocol: All the hybridizations, washed, and scans of microarrays were performed in the Cornell University Life Sciences Core Laboratories Center (http://cores.lifesciences.cornell.edu)

data_processing: Microarray data analysis was performed using the LIMMA library for the statistical package R with Bayesian inference using a lineal model. Normalization within each array was performed using LOESS method, whereas model adjustment was performed using the lmFit function for each genotype. The overall statistical analysis was performed using the eBayes function.

organism: Myzus persicae

source_name: adult wingless aphids

label_protocol: The Amino Allyl MessageAmp™ II with Cy™3/Cy™5 kit (Ambion) was used to prepare RNA samples for array hybridization. In brief, a reverse transcription from 1.2 mg of total RNA was carried out in each sample using the T7 oligo-dT primer provided in the kit, followed by a second strand cDNA synthesis. Then, double-stranded DNA (dsDNA) was purified with a cDNA filter cartridge and used as template for in vitro transcription with the incorporation of aminoallyl modified UTP, which resulted in amplified RNA (aRNA) containing modified UTP. The aRNA was purified with an aRNA filter cartridge and 5 µg were coupled to Cy3 or Cy5 dyes

growth_protocol: Four hundred synchronized adult wingless aphids were placed in groups of 20 individuals on a pepper leaf-disc in Petri dishes containing 2% agar.

extract_protocol: Total RNA was isolated separately for each experimental condition (genotypes, biological replicates and treatments) from ~ 40 frozen aphids using the RNeasy Plant Mini Kit (Qiagen, Cat no. 74904)

treatment_protocol: 10 dishes, by genotype,were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water) using a Potter-Precision laboratory spray tower (Burkhard) that ensures a homogeneous application.

tag: genotype

value: Genotype multiple resistant (MR)

tag: treatment

value: Insecticide

value: Seven days

tag: tissue

value: whole organism

value: Acetone plus water


title: Genotype S-insecticide Rep.Biol C vs Genotype S-water Rep Biol C

description: Biological replicate C, genotype S. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.

value: Genotype sensitive (S)

tag: age


title: Genotype SR-water Rep.Biol B vs Genotype SR-insecticide Rep Biol B

description: Biological replicate B, genotype SR. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.

value: Genotype simple resistant (SR)


title: LPJ108 CD20int B-cells

source_name: CD20int Follicular Lymphoma B-cells

value: Male

value: CD20int B-cells


title: LPJ114 CD20int B-cells


title: LPJ128a CD20int B-cells


title: Genotype S-water Rep.Biol B vs Genotype S-insecticide Rep Biol B

description: Biological replicate B, genotype S. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.


title: LPJ114 CD20hi B-cells


title: Genotype S-insecticide Rep.Biol A vs Genotype S-water Rep Biol A

description: Biological replicate A, genotype S. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.


title: amp4

source_name: fresh-frozen resected, untreated periampullary adenocarcinomas


title: amp3


title: Genotype SR-insecticide Rep.Biol A vs Genotype SR-water Rep Biol A

description: Biological replicate A, genotype SR. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.


title: H.influenzae R2846 110-4

city: Oklahoma City

first: Timothy

middle: M

last: VanWagoner

state: OK

address: 940 SL Young Blvd, BMS340

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description: Biological replicate 3, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

hyb_protocol: Arrays were pre-hybridized in NimbleGen hybridization chamber at 45°C for two hours with gentle rotation using a buffer containing 100mg/ml herring sperm DNA (Promega Corporation, Madison, WI) 50mM MES, 1M NaCl, 10mM EDTA, 0.005% Tween-20 for fifteen minutes. The prehybe solution was replaced with a 350ml volume of the same composition as the pre-hybridization buffer but supplemented with 4mg of labeled prokaryotic cDNA and 1nM labeled control oligonucleotide. The array was hybridized overnight at 45°C with gentle rotation. Following hybridization, the arrays were removed from the hybridization and washed three times, at room temperature, in a buffer containing 6X SSPE, 0.01% (v/v) Tween-20 and then six times in a buffer containing 100mM MES, 26mM NaCl, 0.01% (v/v) Tween-20 at 45°C. Arrays were stained) in a buffer containing 50mM MES, pH 6.6, 1M NaCl, 0.005% Tween-20, and 1:1000 dilution of Streptavidin-Cy3 (GE Healthcare) for ten minutes with gentle agitation, then washed twice in 6X SSPE, 0.01% (v/v) Tween-20 at room temperature, dried under argon and stored desiccated.

scan_protocol: update

data_processing: RMA normalized using quantile normalization and gene calls generated using the RMA algorithm

organism: Haemophilus influenzae

source_name: H. influenzae R2846 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 3

label_protocol: Total prokaryotic RNA is converted to cDNA by random primed reverse transcription with SuperScript II (Invitrogen Corporation, Carlsbad, CA) in a reaction containing 10mg RNA, 1mg random hexamer, 1200U SuperScript II, 1X SuperScript first strand buffer, 20mM DTT, 500mM dNTPs in a total volume of 60ml. Following incubation, residual RNA was enzymatically degraded with the addition of 1U RNase H and 1mg RNase A. Reactions were purified by extraction with phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation.in the presence of 1ml of Pellet Paint Co-Precipitant (EMD Biosciences, Madison WI). cDNA was enzymatically fragmented with 0.2U Dnase I in a 40ml reaction volume for 15 minutes at 37°C. Dnase I was inactivated by incubation at 99°C for ten minutes. Fragmented cDNA was end-labeled by the catalytic addition of 3’ biotin-N6-ddATP (Perkin-Elmer, Boston, MA) with terminal deoxynucleotidyl transferase (Promega Corporation, Madison, WI). The biotin-labeled reaction products were purified by centrifugal concentration through a Centricon YM-10 Concentrator (Millipore Corporation, Billerica, MA).

growth_protocol: H. influenzae R2846 was used to inoculate 5 ml of brain heart infusion broth (BHI) containing 10ug/ml NAD and 2.0ug/ml hemin. These cultures were grown at 37C for 3 hours, collected by centrifugation, washed once in PBS with 0.1% gelatin, and resuspended in PBS-gelatin. The cultures were adjusted to an OD(605)=0.5. 5 ml of the cultures were inoculated into 60 ml of BHI broth containing NAD and 150uM deferoxamine to a final concentration of ~2x10^7 cfu/ml.

extract_protocol: RNA was prepared using Trizol (as described by the manufacturer). Residual genomic DNA was removed by treatment with RNase-free DNase (Invitrogen) as directed by the manufacturer and confirmed by q-rt-PCR analysis. RNA samples were then precipitated using LiCl and samples resolved by PAGE to ensure sample integrity.

treatment_protocol: 20 ml samples were taken after 90 minutes growth and transfered into an equal volume of RNAProtect reagent. Iron (500 uM FeCl3) and hemin (10ug/ml) were added to the remaining 40 ml and the cultures allowed to continue incubation at 37C for an additional 20 minutes post supplementation and 20 ml samples collected as abov

tag: strain

value: 90 minutes in FeHm deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes


title: Genotype MR-water Rep.Biol B vs Genotype MR-insecticide Rep Biol B

description: Biological replicate B, genotype MR. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.


title: H.influenzae R2846 110-3

description: Biological replicate 2, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

source_name: H. influenzae R2846 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 2


title: Genotype MR-insecticide Rep.Biol A vs Genotype MR-water Rep Biol A

description: Biological replicate A, genotype MR. Aphid were sprayed with 1 ml of pirimicarb (20 ppm in acetone plus water). After 24 hours living aphids were quickly frozen in liquid nitrogen and stored at -70°C until RNA extraction.


title: FtCtx_hu_HIV_1

tag: Sex

tag: hiv status

value: HIV+

tag: meth-use-history

tag: plasma-loghiv-rna

tag: csf-loghiv-rna


title: LPJ108 CD20hi B-cells


title: H.influenzae R2846 110-2

description: Biological replicate 1, 90 minutes in FeHm Deplete BHI, followed by supplementation with Fe and Heme and growth for 20 minutes

source_name: H. influenzae R2846 grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 1


title: LPJ103 CD20int B-cells


title: H.influenzae R2846 90-3

description: Biological replicate 2, 90 minutes in FeHm deplete BHI

source_name: H. influenzae R2846 grown in iron and heme deplete media for 90 minutes, replicate 2

value: 90 minutes in FeHm deplete BHI


title: 7d_SN_3

city: Shanghai

first: Guohui

last: Ding

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences

description: Gene expression at 7d following sciatic nerve resection in SN

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA) with default settings，Dye channel: Green, Scan resolution = 5μm, PMT 100%，10%，16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA).

organism: Rattus norvegicus

source_name: SN_sciatic nerve resection_7d

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

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s instructions. The quality of the purified RNA was assessed using a BioAnalyzer 2100 (Agilent Technology, Santa Clara, CA). The purified RNA was quantified by determining the absorbance at 260nm using a Nanodrop ND-1000 spectrophotometer (Infinigen Biotechnology Inc., City of Industry, CA).

treatment_protocol: Thirty adult, male Sprague-Dawley (SD) rats (180-220g, supplied by the Experimental Animal Center of Nantong University) were randomly divided into five groups of six rats each. Each animal was anaesthetized by an intraperitoneal injection of complex narcotics (85mg/kg trichloroac etaldehyde monohydrate, 42mg/kg magnesium sulfate, 17mg/kg sodium pentobarbital), and the sciatic nerve was exposed and lifted through an incision on the lateral aspect of the mid-thigh of the left hind limb. A 1cm long segment of sciatic nerve was then resected at the site just proximal to the division of tibial and common peroneal nerves, and the incision sites were then closed. To minimize discomfort and possible painful mechanical stimulation, the rats were housed in large cages with sawdust bedding after surgery. L4-6 DRG tissues and SN tissues (0.5cm) were collected at different time points after injury, respectively. All the experimental procedures involving animals were conducted in accordance with Institutional Animal Care guidelines and ethically approved by the Administration Committee of Experimental Animals, Jiangsu Province, China (Approval ID: SYXK(SU)2007-0021).

value: Sprague-Dawley

value: proximal sciatic nerve (SN)


title: LPJ103 CD20hi B-cells

value: Female

value: Follicular Lymphoma


title: H.influenzae R2846 90-4

description: Biological replicate 3, 90 minutes in FeHm deplete BHI

source_name: H. influenzae R2846 grown in iron and heme deplete media for 90 minutes, replicate 3


title: 7d_SN_2


title: H.influenzae 86028 110-4

source_name: H. influenzae 86-028NP grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 3

growth_protocol: H. influenzae 86-028NP was used to inoculate 5 ml of brain heart infusion broth (BHI) containing 10ug/ml NAD and 2.0ug/ml hemin. These cultures were grown at 37C for 3 hours, collected by centrifugation, washed once in PBS with 0.1% gelatin, and resuspended in PBS-gelatin. The cultures were adjusted to an OD(605)=0.5. 5 ml of the cultures were inoculated into 60 ml of BHI broth containing NAD and 150uM deferoxamine to a final concentration of ~2x10^7 cfu/ml.


title: 7d_SN_1


title: H.influenzae R2846 90-2

description: Biological replicate 1, 90 minutes in FeHm deplete BHI

source_name: H. influenzae R2846 grown in iron and heme deplete media for 90 minutes, replicate 1


title: H.influenzae 86028 90-2

source_name: H. influenzae 86-028NP grown in iron and heme deplete media for 90 minutes, replicate 2


title: H.influenzae 86028 90-1

source_name: H. influenzae 86-028NP grown in iron and heme deplete media for 90 minutes, replicate 1


title: H.influenzae 86028 90-4

source_name: H. influenzae 86-028NP grown in iron and heme deplete media for 90 minutes, replicate 3


title: H.influenzae 86028 110-1

source_name: H. influenzae 86-028NP grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 1


title: SA2 Centi-pool Cohort - mAdbID:100368

city: Baltimore

first: Nevil

middle: John

last: Singh

state: MD

address: 685 W Baltimore Street

department: Microbiology & Immunology

institute: UMB

description: mAdb experiment ID: 100368

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45103101

data_processing: Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. Gene expression analysis was performed using NCI BRB-Array Tools developed by the NCI Biometric Research Branch Bethesda, MD). FeatureExtractor_Version: 10.1.1.1. The mAdb arrays have 37,558 probes. The data we submitted is filtered using BRBArray Tools and the following criteria: 1. Exclude spots with intensities below 30; 2. Exclude spots below 10; 3. Exclude probes missing in more than 80% of the arrays; 4. Reduce multiple probes per gene to one

source_name: SA2 Centi-pool Cohort

label_protocol:
Ambion MessageAmp II Protocol - Cy5
Other: Total RNA was used to generate antisense RNA (aRNA) using the Amino Allyl MessageAmp II aRNA Kit (Ambion) following manufacturer's instructions.

extract_protocol:
Agilent RNA Extraction
Other: not available

value: B10.A, PCC+,Vbeta3+,TCRalpha+/-

tag: source tissue

value: Blood

value: Polyclonal Vbeta3+,TCRalpha+/- T cells

tag: trait

value: "deletor" Quantitative Trait value 22.60

tag: genotype/variation

tag: comment

value: Centi-Pool Generation Protocol Polyclonal Vbeta3+,TCRalpha+/- T cells from PCC+ mice were FACS sorted and 100 cells per well were seeded into 24 well plates and expanded in vitro. A million expanded T cells were injected to PCC+,CD3epsilon-/- mice. Seven days later, a million 5C.C7,Ly5.1 T cells were injected. Starting 40 days later, the recipient mice were euthanized and the remaining 5C.C7 T cells in the spleen and lymph nodes enumerated. A representative spectrum of centi pools with high "deletor" activity (mice with low 5C.C7 survival) to low "deletor" activity (mice with high 5C.C7 survival) were sorted and RNA isolated for microarray quantitative trait analysis.

source_name: Pooled Reference Sample

label_protocol:
Ambion MessageAmp II Protocol - Cy3
Other: Total RNA was used to generate antisense RNA (aRNA) using the Amino Allyl MessageAmp II aRNA Kit (Ambion) following manufacturer's instructions.

value: T cells

tag: sample type

value: Mouse RNA Sample Pooling RNA from Mouse T cells (Naïve, Memory, and Tolerant) were mixed in equal proportion.


title: LPJ041b Tumor B-cells

city: Houston

source_name: Tumor Follicular Lymphoma B-cells

label_protocol: Labelled according to the manufacturer's protocol.

tag: patient identifier

tag: gender

tag: type

value: Follicular Lymphoma Relapse

value: Tumor B-cell


title: H.influenzae 86028 110-2

source_name: H. influenzae 86-028NP grown in iron and heme deplete media for 90 minutes, then supplemented with Fe and Heme, replicate 2

tag: treatment


title: LPJ041a CD20int B-cells

source_name: CD20int Follicular Lymphoma B-cells

label_protocol: Labelled according to Affymetrix manufacturers protocol

tag: subset

value: CD20int B-cell


title: 7d_DRG_2

description: Gene expression at 7d following sciatic nerve resection in DRG

source_name: DRG_sciatic nerve resection_7d

tag: tissue

value: dorsal root ganglia (DRG)


title: 4d_SN_3

description: Gene expression at 4d following sciatic nerve resection in SN

source_name: SN_sciatic nerve resection_4d

tag: strain


title: 7d_DRG_3


title: SA1 Centi-pool Cohort - mAdbID:100367

description: mAdb experiment ID: 100367

source_name: SA1 Centi-pool Cohort

tag: cell type

value: "deletor" Quantitative Trait value 0.80


title: PD4 Centi-pool Cohort - mAdbID:100362

description: mAdb experiment ID: 100362

source_name: PD4 Centi-pool Cohort

value: "deletor" Quantitative Trait value 6.97


title: LPJ040 CD20hi B-cells

source_name: CD20hi Follicular Lymphoma B-cells

value: Male

tag: age

value: CD20hi B-cell


title: LPJ041a CD20hi B-cells

value: Female


title: 7d_DRG_1

value: Sprague-Dawley


title: 4d_SN_2

value: proximal sciatic nerve (SN)


title: LPJ040 CD20int B-cells

value: Follicular Lymphoma


title: PC3 Centi-pool Cohort - mAdbID:100364

description: mAdb experiment ID: 100364

source_name: PC3 Centi-pool Cohort

value: B10.A, PCC+,Vbeta3+,TCRalpha+/-

value: Blood

value: Polyclonal Vbeta3+,TCRalpha+/- T cells

value: "deletor" Quantitative Trait value 5.25


title: PD5 Centi-pool Cohort - mAdbID:100361

description: mAdb experiment ID: 100361

source_name: PD5 Centi-pool Cohort

value: "deletor" Quantitative Trait value 29.97

value: Centi-Pool Generation Protocol Polyclonal Vbeta3+,TCRalpha+/- T cells from PCC+ mice were FACS sorted and 100 cells per well were seeded into 24 well plates and expanded in vitro. A million expanded T cells were injected to PCC+,CD3epsilon-/- mice. Seven days later, a million 5C.C7,Ly5.1 T cells were injected. Starting 40 days later, the recipient mice were euthanized and the remaining 5C.C7 T cells in the spleen and lymph nodes enumerated. A representative spectrum of centi pools with high "deletor" activity (mice with low 5C.C7 survival) to low "deletor" activity (mice with high 5C.C7 survival) were sorted and RNA isolated for microarray quantitative trait analysis.

value: T cells

value: Mouse RNA Sample Pooling RNA from Mouse T cells (Naïve, Memory, and Tolerant) were mixed in equal proportion.


title: LPJ023 CD20hi B-cells


title: PD3 Centi-pool Cohort - mAdbID:100363

description: mAdb experiment ID: 100363

source_name: PD3 Centi-pool Cohort

value: "deletor" Quantitative Trait value 19.40


title: LPJ023 CD20int B-cells

value: CD20int B-cell


title: PA1 Centi-pool Cohort - mAdbID:100360

description: mAdb experiment ID: 100360

source_name: PA1 Centi-pool Cohort

value: "deletor" Quantitative Trait value 1.17


title: 4d_SN_1


title: PB4 Centi-pool Cohort - mAdbID:100358

description: mAdb experiment ID: 100358

source_name: PB4 Centi-pool Cohort

value: "deletor" Quantitative Trait value 10.60


title: PA3 Centi-pool Cohort - mAdbID:100359

description: mAdb experiment ID: 100359

source_name: PA3 Centi-pool Cohort

value: "deletor" Quantitative Trait value 1.73


title: 1d_SN_3

description: Gene expression at 1d following sciatic nerve resection in SN

source_name: SN_sciatic nerve resection_1d


title: 1d_SN_2


title: PB5 Centi-pool Cohort - mAdbID:100357

description: mAdb experiment ID: 100357

source_name: PB5 Centi-pool Cohort

value: "deletor" Quantitative Trait value 0.02


title: 1d_SN_1

value: Sprague-Dawley