title: wild type mid-log phase

description: Normalized log10 intensity of X_INT/Y_INT (sample/reference) averaged over dye flip between sample and reference RNA.

source_name: Δura3 knockout at OD600 = 0.3788

tag: genotype

tag: temperature

tag: od

source_name: Halobacterium salinarum NRC-1 reference sample


title: Episomal hiPSC in FMM, rep1

status: Public on Mar 03 2014

type: RNA

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

country: USA

institute: Fate Therapeutics

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe intensities were normalized according to a log-scale robust multi-array analysis (RMA) method in Expression Console (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: induced pluripotent stem cells, small molecule medium FMM

label_protocol: Biotinylated cRNA were prepared using the Message Amp II kit two-round protocol from 100 ng total RNA.

growth_protocol: Pluripotent lines were cultured in FMM, SMC4 or Conventional medium as indicated above and in the manuscript. Cultures were maintained on either feeder cells or matrigel.

extract_protocol: Total RNA was isolated post incubation with the PicoPure RNA Isolation kit.

treatment_protocol: Somatic cells were reprogrammed by either lentiviral- or episomal-induced ectopic expression of various genes including OCT4, NANOG and SOX2. The reprogrammed cells were selected by FACS and directly sorted into 96-well plates. Each clone was expanded in various culture conditions and asessed for pluripotent properties.

tag: cell type

value: induced pluripotent stem cells

tag: culture medium

value: FMM


title: Human_embryonic_stem_cells_rep1

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

description: Total RNA isolated from human embryonic stem cells

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.14.1). It was vst transformed and quantile normalized.

label_protocol: standard as recommended by illumina

extract_protocol: Qiagen's AllPrep DNA/RNA/Protein Mini kit

value: Human embryonic stem cells


title: Biofilm +E. coli K12 vs Mixed Reference 2

city: San Francisco

first: Emily

middle: Patricia

last: Fox

address: 600 16th Street, GH - N374

department: Biochemistry and Biophysics

institute: University of California, San Francisco

description: Biofilm +E. coli K12 vs Mixed Reference

hyb_protocol: 0.4 mg Cy3-labelled cDNA and 0.4 mg Cy5-labelled cDNA were hybridized onto custom Agilent 8*15k microarrays (AMADID #020166)

scan_protocol: Scanned on a 4000B Axon Instrument Scanner

data_processing: Arrays were gridded with Gene Pix Pro software version 7, Lowess normalization was performed using a Goulphar script for R

organism: Candida albicans

source_name: Biofilm C. albicans +E. coli K12 (replicate 2)

label_protocol: cDNA was synthesized from 8 mg total RNA using Superscript II Reverse Transcriptase (Invitrogen, 18064-014), according to the manufacturer’s instruction, and using a mixture of 0.5 mM 3:2 aminoally-dUTP (Ambion 8437):dNTPs. cDNA was dye coupled to either Cy3 or Cy5 (GE Healthcare PA23001 or PA25001)

growth_protocol: C. albicans was grown alone or with bacteria, in biofilms or suspension cultures, in Bovine Heart Infusion Media +5% FBS, at 37degC

extract_protocol: Total RNA extracted using Ambion RiboPure Yeast RNA Kit (AM1926)

tag: source strain background

tag: strain

source_name: Mixed reference pool#2: cDNA from 252016610051-blocks1 - 6


title: Human_embryonic_stem_cells_rep3


title: Biofilm +water vs Mixed Reference 2

description: Biofilm +water vs Mixed Reference

source_name: Biofilm C. albicans +water (replicate 2)


title: Biofilm +media vs Mixed Reference 2

description: Biofilm +media vs Mixed Reference

source_name: Biofilm C. albicans +media (replicate 2)


title: mouse cerebellum at P30 knockout 3

city: Helsinki

first: Tarja

middle: Hannele

last: Joensuu

address: Haartmaninkatu 8 (PO Box 63)

department: Folkhälsan Institute of Genetics

institute: Folkhälsan Research Center

description:
P30 KO3.CEL
Gene expression data from symptomatic Cstb-/- mouse cerebellum.

hyb_protocol: The sample preparation and hybridzation of each cRNAs on Affymetrix GeneChip® Mouse Genome 430 2.0 arrays based on manufacturer's instruction.

scan_protocol: The quality control of each microarray was inspected using the Affymetrix GeneChip® Operating Software (GCOS) v1.4.

data_processing: The raw data were imported to GeneSpring GX software and expression signal values were generated using the RMA (Robust Multiarray Average) algorithm (Irizarry et al., 2003) for background adjustment, quantile-normalization and summarization. Filtering of the probe sets was based on the expression with lower and upper cutoff 20 and 100 percentile, and on the fold-change (FC) with cutoff 1.3. In overall statistics of differentially expressed genes, t-test unpaired equal variance with corrected p-value ≤ 0.05 (cerebella) and p-value ≤ 0.01 (CGCs), with Benjamini and Hochberg multiple testing correction was used.

organism: Mus musculus

source_name: CSTB KO_cerebellum at P30

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

growth_protocol: Cstb-/- and wild type mice were grown under standard conditions in animal facilities. Cerebella from P5 pups were dissected and meninges removed in HHGN (1x HBSS, 2.5 mM HEPES, 35 mM glucose, 4 mM NaCO3). Intact cerebella were trypsinated in 10 mg/ml trypsin, 200 U/ml DNase in HHGN for 20 min at RT and triturated in 200 U/ml DNase in BME (Basal Medium Eagle). Cells were cultured in BME, 10% calf serum, 25 mM HCl. After 16-20 h from plating, 10 μM AraC (cytosine 1-β-d-arabinofuranoside) was added to prevent glial proliferation. Cells were harvested at DIV2.

extract_protocol: Total RNA was extracted using the ABI Prism 6100 Nucleic Acid PrepStation and PerfectPure RNA Cultured Cell kit according to the manufacturer’s instructions from cerebella and CGCs, respectively.

treatment_protocol: Mice were anesthetized with CO2 and sacrificed by decapitation. The dissected cerebella were homogenized using Lysing Matrix D tubes and FastPrep® FP120 Instrument with Proteinase K digestion (20 mg/ml, >30U/mg) according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: cystatin B (CSTB)-deficient (Cstb-/-)

tag: gender

value: male

tag: developmental stage

value: postnatal day 30 (P30)

tag: tissue

value: cerebellum


title: mouse cerebellum at P30 knockout 1

description:
P30 KO1.CEL
Gene expression data from symptomatic Cstb-/- mouse cerebellum.

value: female


title: Biofilm +E. faecalis vs Mixed Reference 1

description: Biofilm +E. faecalis vs Mixed Reference

source_name: Biofilm C. albicans +E. faecalis (replicate 1)

source_name: Mixed reference pool#1: cDNA from 252016610034-blocks1 - 6


title: mouse cerebellum at P30 knockout 2

description:
P30 KO2.CEL
Gene expression data from symptomatic Cstb-/- mouse cerebellum.


title: Biofilm +K. pneumoniae vs Mixed Reference 1

source_name: Biofilm C. albicans +K. pneumoniae (replicate 1)


title: mouse cerebellum at P7 wild type 4

description:
P7 WT4.CEL
Gene expression data from wild type mouse cerebellum.

source_name: WT_cerebellum at P7

value: wild type

value: postnatal day 7 (P7)


title: hSKP pro-inflammatory condition, biological rep3

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology and Dermato-Cosmetology

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description:
hSKP_INFL-03
Gene expression data from pro-inflammatory stimulated hSKP

hyb_protocol: 12.5 μg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, summarization (median polish) and normalization (quantile) were done with Robust Multi-array Analysis (RMAExpress v1.0.5).

source_name: hSKP at 18h with pro-inflammatory stimulation

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip 3’ IVT Express Kit following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Approximately two weeks after isolation, hSKP spheroids were broken down to single cells using Liberase DH at 37 °C. They were subsequently cultivated in hSKP growth medium supplemented with 5 % (v/v) FBS to promote adherence of the cells to the plastic. The next day, the attached hSKP were washed and further cultivated in hSKP growth medium without FBS until further use.

extract_protocol: Total mRNA was extracted using the TriPure Isolation ReagentTM (Roche Applied Science) according to the manufacturer's instructions.

treatment_protocol: hSKP were stimulated for 18 h using a cocktail of pro-inflammatory cytokines: 25 ng/mL IL-1β, 1 x 103 U/mL IFN-γ, 50 ng/mL TNFα and 3 x 103 U/mL IFN-α.

tag: age

value: 1 year

value: foreskin

value: human skin-derived precursor cells (hSKP)

tag: passage

value: passage 4

tag: stimulated with

value: pro-inflammatory cytokine cocktail for 18hr


title: Neural_Stem_Cells_rep2

description: Total RNA isolated from Neural Stem Cells

value: Human embryonic stem cells derived Neural Stem Cells


title: Neural_Crest_Cells_derived_under_NOTCH_inhibitor_rep2

description: Total RNA isolated from Neural Crest Cells derived under NOTCH inhibitor

value: Human embryonic stem cells derived Neural Crest Cells differentiated under NOTCH inhibitor


title: hSKP pro-inflammatory condition, biological rep2

description:
hSKP_INFL-02
Gene expression data from pro-inflammatory stimulated hSKP

value: 7 years


title: hSKP pro-inflammatory condition, biological rep1

description:
hSKP_INFL-01
Gene expression data from pro-inflammatory stimulated hSKP


title: mouse cerebellum at P7 wild type 1

description:
P7 WT1.CEL
Gene expression data from wild type mouse cerebellum.


title: mouse cerebellum at P7 wild type 2

description:
P7 WT2.CEL
Gene expression data from wild typel mouse cerebellum.


title: Biofilm +E. coli clinical vs Mixed Reference 1

source_name: Biofilm C. albicans +E. coli clinical isolate (replicate 1)


title: hSKP control condition, biological rep1

description:
hSKP_CTL-01
Gene expression data from untreated hSKP

source_name: hSKP at 18h without pro-inflammatory stimulation

value: none (control)


title: Biofilm +E. coli K12 vs Mixed Reference 1

description: Biofilm +E. coli K12 vs Mixed Reference

source_name: Biofilm C. albicans +E. coli K12 (replicate 1)


title: hSKP control condition, biological rep3

description:
hSKP_CTL-03
Gene expression data from untreated hSKP


title: hASC clone_1.10-ASC

type: genomic

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

country: Spain

institute: Oviedo University-HUCA

description: healthy sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2.  The non_normalized data matrix (available on Series records) contains Unmethylated (Signal A) and methylated (Singal B) signal intensities.

label: Cy3, Cy5

molecule: genomic DNA

source_name: human adipose mesecnchimal stem cell clone

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: sample type

value: single cell clone

tag: cell line id


title: Neural_Stem_Cells_rep1


title: Neural_Crest_Cells_derived_under_NOTCH_inhibitor_rep3


title: mouse cerebellum at P7 wild type 3

description:
P7 WT3.CEL
Gene expression data from wild type mouse cerebellum.


title: hSKP control condition, biological rep2

description:
hSKP_CTL-02
Gene expression data from untreated hSKP


title: Biofilm +media vs Mixed Reference 1

description: Biofilm +media vs Mixed Reference

source_name: Biofilm C. albicans +media (replicate 1)


title: mouse cerebellum at P7 knockout 5

description:
P7 KO5.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellum.

source_name: CSTB KO_cerebellum at P7

value: cystatin B (CSTB)-deficient (Cstb-/-)


title: Neural_Crest_Cells_rep2

description: Total RNA isolated from Neural Crest Cells

value: Human embryonic stem cells derived Neural Crest Cells


title: Human_embryonic_stem_cells_rep2

description: Total RNA isolated from human embryonic stem cells

value: Human embryonic stem cells


title: CTR12950_1045790

first: Bahram

last: Valamehr

address: 3535 General Atomics Court Tte 200

institute: Fate Therapeutics Inc.

description: This CGH experiment is designed to detect deletion, insertion, amplification, etc. in the sample relative to the reference.

hyb_protocol: The labeled DNA is prepared for hybridization with human DNA and placed on the Sureprint G3 human CGH + SNP 4x180k microarray and hybridized at 65ºC for ~ 24hours.

scan_protocol: The arrays are washed and scanned at 3μM resolution on an Agilent C Scanner.

data_processing: Data was processed and analyzed through Agilent’s CytoGenomics software version 2.7.

source_name: FTC7 6,24 Clone 9 p10

label_protocol: Samples were labeled according to Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis

growth_protocol: FTC007 was cultured in fibroblast medium while FTC007 hiPSC clones were cultured in FMM

extract_protocol: Genomic DNA was isolated using QIAamp DNA Mini Kit and Proteinase K digestion

tag: cell line

value: hiPSC

source_name: Agilent Male Reference

value: Agilent Male Reference


title: Biofilm +water vs Mixed Reference 1

description: Biofilm +water vs Mixed Reference

source_name: Biofilm C. albicans +water (replicate 1)


title: mouse cerebellum at P7 knockout 3

description:
P7 KO3.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellum.

value: male

value: cerebellum


title: hASC clone_1.7-ASC

description: healthy sample


title: Neural_Crest_Cells_rep1


title: hASC clone_1.22-ASC

description: healthy sample


title: hASC clone_3.10-ASC

description: healthy sample


title: Planktonic +C. perfringens vs Planktonic_rep1

source_name: Planktonic C. albicans +C. perfringens (replicate 1)

source_name: Planktonic C. albicans (replicate 1)


title: Planktonic +C. perfringens vs Planktonic_rep2

source_name: Planktonic C. albicans +C. perfringens (replicate 2)

source_name: Planktonic C. albicans (replicate 2)


title: CTR12949_1045788

source_name: FTC7 6,24 Clone 7 p10


title: mouse cerebellum at P7 knockout 2

description:
P7 KO2.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellum.

value: postnatal day 7 (P7)


title: LymphNode_Spleen_CD4+ T cells_LAT__Act_4h_rep3

status: Public on Mar 02 2014

description: Activated Lat- T cells from mouse lymph nodes and spleen

hyb_protocol: Samples were hybridized to GeneChip Mouse Gene 1.1 ST 24 plate with specific protocols for using the GeneTitran Hybridization Module for WT Array Plates (P/N 901621).

scan_protocol: GeneTitan Instrument was used to scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control the GeneTitan hybridization process and in summarizing probe cell intensity data.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

source_name: mouse lymph node and spleen CD4+hDTR_ T cells, LAT-, Activated

label_protocol: 100 ng of total RNA was used as a starting material for sample preparation. Samples were processed with Ambion WT Expression kit for Affymetrix Whole Transcript Expression Arrays (P/N 4411974), according to manufactures protocol. Sample concentration was checked with Nanodrop ND-2000 and sample quality was controlled by BioRad's Experion electrophoresis station.

extract_protocol: Total RNA was extracted with RNeasy mini kit (Qiagen) according to manufacturers instructions. In-column DNase (RNase-Free Dnase Set, Qiagen) treatment was performed. RNA was eluted in dH2O.

value: lymph nodes and spleen

value: T cells

value: LAT- and Activated


title: LymphNode_Spleen_CD4+ T cells_LAT__Act_4h_rep2


title: CTR12947_1045784

source_name: FTC7 p7

value: fibroblast


title: LymphNode_Spleen_CD4+ T cells_LAT__rep3

description: Lat- T cells from mouse lymph nodes and spleen

source_name: mouse lymph node and spleen CD4+hDTR_ T cells, LAT-

value: LAT-


title: mouse cerebellum at P7 knockout 1

description:
P7 KO1.CEL
Gene expression data from pre-symptomatic Cstb-/- mouse cerebellum.


title: hASC clone_3.5-ASC

description: healthy sample


title: CTR12948_1045786

source_name: FTC7 4,24 Clone 10 p8


title: LymphNode_Spleen_CD4+ T cells_LAT__Act_4h_rep1


title: LymphNode_Spleen_CD4+ T cells_LAT__rep2


title: LymphNode_Spleen_CD4+ T cells_LAT+_Act_4h_rep1

description: Activated Lat+ T cells from mouse lymph nodes and spleen

source_name: mouse lymph node and spleen CD4+hDTR+ T cells, LAT+, Activated

value: LAT+ and Activated


title: LymphNode_Spleen_CD4+ T cells_LAT+_rep2

description: Lat+ T cells from mouse lymph nodes and spleen

source_name: mouse lymph node and spleen CD4+hDTR+ T cells, LAT+

value: LAT+


title: LymphNode_Spleen_CD4+ T cells_LAT+_Act_4h_rep2


title: LymphNode_Spleen_CD4+ T cells_LAT+_Act_4h_rep3


title: LymphNode_Spleen_CD4+ T cells_LAT__rep1


title: LymphNode_Spleen_CD4+ T cells_LAT+_rep3


title: LymphNode_Spleen_CD4+ T cells_LAT+_rep1


title: HTL0132

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

description: Gene expression data from human pancreatic islets

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized onto the GeneChip® Human Gene 1.0 ST whole transcript based assay overnight in the GeneChip® Hybridization oven 6400 using standard procedures. The arrays were washed and stained in a GeneChip® Fluidics Station 450.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: The array data was summarized and normalized with Robust Multi-array Analysis (RMA) method using the oligo package from bioconductor. Batch correction using COMBAT function from SVA package from bioconductor. Annotation using annotate package from bioconductor and hugene10sttranscriptcluster.db annotation data.

source_name: pancreatic islets

label_protocol: Briefly, 100-200 ng total RNA was processed as indicated by GeneChip® Expression 3’-Amplification Reagents Onecycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) was used to produce double-stranded cDNA. This was used as a template to generate biotintargeted cRNA following the manufacturer’s specifications.

growth_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to RNA preparation.

extract_protocol: Total RNA was isolated with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 bioanalyzer (Bio-Rad, Hercules, CA, USA) and a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

value: pancreatic islets


title: HTL0130


title: HTL0129


title: HTL0131


title: HTL0128


title: HTL0126


title: HTL0125


title: HTL0127


title: HTL0121


title: HTL0124


title: HTL0118


title: HTL0122


title: HTL0123


title: HTL0119


title: HTL0114


title: HTL0111


title: HTL0117


title: HTL0115


title: HTL0116


title: HTL0109


title: HTL0112


title: HTL0108


title: HTL0110


title: HTL0107


title: HTL0103


title: HTL0102


title: HTL0113


title: HTL0104


title: HTL0105


title: HTL0098


title: HTL0097


title: HTL0100


title: HTL0096


title: HTL0106


title: HTL0093


title: HTL0092


title: HTL0094


title: HTL0089


title: HTL0095


title: HTL0101


title: HTL0090


title: HTL0088


title: HTL0091


title: HTL0085


title: HTL0087


title: HTL0084


title: HTL0083


title: HTL0086


title: HTL0078


title: HTL0079


title: HTL0076


title: HTL0077


title: HTL0074


title: HTL0082


title: HTL0080


title: HTL0071


title: HTL0072


title: HTL0070


title: HTL0066


title: HTL0073


title: HTL0067


title: HTL0068


title: HTL0065


title: HTL0075


title: HTL0059


title: HTL0063


title: HTL0058


title: HTL0062


title: HTL0064


title: HTL0069


title: HTL0056


title: HTL0061


title: HTL0057


title: HTL0054


title: HTL0060


title: HTL0051


title: HTL0055


title: BATF_KO_P14_D3_Effector_rep4

city: Boston

first: R. Anthony

last: Barnitz

state: MA

address: 450 Brookline Ave.

department: Department of Pediatric Oncology

institute: Dana-Farbert Cancer Institute, Harvard Medical School

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.  The chips are transferred to a Fludics Station 450 that performs washes and staining with Affymetrix Hybe/Wash/Stain (cat # 900720) to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: The arrays were scanned on the GeneChip Scanner 3000 7G using AGCC (Affymetrix Gene Command Console) for the image proccessing.

data_processing: The data were processed using GenePattern (RMA) and custom scripts (differential expression, collapsing probes to genes, etc).

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements.  The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Primary P14 TCR transgenic CD8+ T cells were isolated from wild-type or BATF-/- mice using CD8 negative selection magnetic-activated cell sorting (MACS) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 10mM HEPES, 50 U/ml of Penicillin, 50 mg/ml of Streptomycin, and 50 mM b-mercaptoethanol.

extract_protocol: RNA extraction was performed using the RNeasy Mini kit (Qiagen).  Concentrations of total RNA were determined using a Nanodrop spectrophotometer (Wilmington, DE).  RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Naïve CD8+ T cells were stimulated with plate-bound anti-CD3 (4 mg/ml, clone 2C11, BD Pharmingen) and anti-CD28 (4 mg/ml, clone 37.51, BD Pharmingen) in the presence of recombinant human IL-2 (100 U/ml, R&D Systems) for 3 days to generate in vitro effector CD8+ T cells.

value: BATF-/- P14 TCR transgenic C57Bl/6

tag: cell state

value: Day 3 in vitro effector CD8+ T cells


title: BATF_KO_P14_D3_Effector_rep2


title: HTL0053


title: BATF_KO_P14_D3_Effector_rep3


title: WT_P14_D3_Effector_rep4

value: P14 TCR transgenic C57Bl/6


title: HTL0050


title: WT_P14_D3_Effector_rep2


title: BATF_KO_P14_D3_Effector_rep1


title: HTL0052


title: BATF_KO_P14_Naive_rep1

value: Day 0 Naïve CD8+ T cells


title: HTL0043


title: HTL0047


title: HTL0046


title: WT_P14_D3_Effector_rep1


title: BATF_KO_P14_Naive_rep3


title: HTL0048


title: BATF_KO_P14_Naive_rep2


title: HTL0042


title: WT_P14_D3_Effector_rep3


title: HTL0044


title: UT33_CD44 Low

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description:
Gene expression data from UT33 cells not in the top 5% highest CD44 expression (cancer stem cell depleted)
CD44 Low_UT33

hyb_protocol: Target preparation for Affymetrix Human Exon 1.0 ST Arrays was performed using 5μg of amplified cDNA following the manufacturer’s recommendations. Hybridization, washing and staining performed with the Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.

source_name: UT33 cell line cultured in plastic flasks, Sorted to exclude cells with the top 5% highest CD44 expression

label_protocol: RNA was amplified and labeled using the Affymetrix WT terminal labeling kit  following the manufacturer’s recommendations

growth_protocol: The cells were cultured in Dulbecco's modified Eagle's medium, supplemented with 2 mM glutamine, 1% nonessential amino acids, 100 IU/mL penicillin, 50 μg/mL streptomycin, and 10% fetal bovine serum in humidified air with 5% CO2 at 37°C. Cells were grown in T75 flasks to 75% confluence and harvested for flow cytometry sorting.

extract_protocol: RNA was isolated from the fresh frozen tissue using the Qiagen Rneasy Plus Micro Kit according to the manufacturer's protocols.

treatment_protocol: Sorting protocols are detailed in Wilson et al (http://www.ncbi.nlm.nih.gov/pubmed/23108794).

tag: isolation method

value: CD44 expression

tag: cancer stem cell population

value: Cancer stem cell depleted


title: HTL0049


title: UT16A_CD44 Low

description:
Gene expression data from UT16A cells not in the top 5% highest CD44 expression (cancer stem cell depleted)
CD44 Low_UT16A

source_name: UT16A cell line cultured in plastic flasks, Sorted to exclude cells with the top 5% highest CD44 expression


title: HTL0045


title: UT24A_CD44 Low

description:
Gene expression data from UT24A cells not in the top 5% highest CD44 expression (cancer stem cell depleted)
CD44 Low_UT24A

source_name: UT24A cell line cultured in plastic flasks, Sorted to exclude cells with the top 5% highest CD44 expression


title: UT30_CD44 Low

description:
Gene expression data from UT30 cells not in the top 5% highest CD44 expression (cancer stem cell depleted)
CD44 Low_UT30

source_name: UT30 cell line cultured in plastic flasks, Sorted to exclude cells with the top 5% highest CD44 expression


title: WT_P14_Naive_rep2


title: HTL0040


title: HTL0041


title: HTL0039


title: WT_P14_Naive_rep1


title: UT14_CD44 Low

description:
Gene expression data from UT14 cells not in the top 5% highest CD44 expression (cancer stem cell depleted)
CD44 Low_UT14

source_name: UT14 cell line cultured in plastic flasks, Sorted to exclude cells with the top 5% highest CD44 expression


title: HTL0036


title: HTL0037


title: UT30_CD44 High

description:
Gene expression data from UT30 cells with the top 5% highest CD44 expression (cancer stem cell enriched)
CD44 High_UT30

source_name: UT30 cell line cultured in plastic flasks, Sorted for cells with the top 5% highest CD44 expression

value: Cancer stem cell enriched


title: HTL0038


title: UT33_CD44 High

description:
Gene expression data from UT33 cells with the top 5% highest CD44 expression (cancer stem cell enriched)
CD44 High_UT33

source_name: UT33 cell line cultured in plastic flasks, Sorted for cells with the top 5% highest CD44 expression


title: UT16A_CD44 High

description:
Gene expression data from UT16A cells with the top 5% highest CD44 expression (cancer stem cell enriched)
CD44 High_UT16A

source_name: UT16A cell line cultured in plastic flasks, Sorted for cells with the top 5% highest CD44 expression


title: HTL0035


title: UT24A_CD44 High

description:
Gene expression data from UT24A cells with the top 5% highest CD44 expression (cancer stem cell enriched)
CD44 High_UT24A

source_name: UT24A cell line cultured in plastic flasks, Sorted for cells with the top 5% highest CD44 expression


title: UT14_CD44 High

description:
Gene expression data from UT14 cells with the top 5% highest CD44 expression (cancer stem cell enriched)
CD44 High_UT14

source_name: UT14 cell line cultured in plastic flasks, Sorted for cells with the top 5% highest CD44 expression


title: HTL0033


title: HTL0032


title: UT33_Not Side Population

description:
Gene expression data from UT33 cancer stem cell depleted cells not in side population
Not SidePop_UT33

source_name: UT33 cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for cells not in side population

value: Side population by Hoescht 33342 exclusion


title: UT30_Not Side Population

description:
Gene expression data from UT30 cancer stem cell depleted cells not in side population
Not SidePop_UT30

source_name: UT30 cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for cells not in side population


title: HTL0028


title: HTL0030


title: HTL0027


title: HTL0024


title: HTL0034


title: HTL0023


title: HTL0029


title: UT24A_Not Side Population

description:
Gene expression data from UT24A cancer stem cell depleted cells not in side population
Not SidePop_UT24A

source_name: UT24A cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for cells not in side population


title: ctrsi-mix

city: Takasaki

first: Kinuko

last: Ohneda

state: Gunma

address: 60 Nakaorui machi

country: Japan

institute: Takasaki Univ Health Welfare

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: Bone marrow-derived mast cells

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Bone marrow mononuclear cells isolated from femurs and tibiae were cultured for 2 weeks in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS and penicillin-streptomycin in the presence of 10 ng/mL recombinant murine IL-3 (Peprotech), and subsequently cultured for two weeks with IL-3 and 10 ng/mL recombinant murine stem cell factor (Peprotech).

extract_protocol: RNA was extracted using NucleoSpin RNA II (TAKARA) following manufacturer's instructions

tag: transfection

value: control


title: HTL0025


title: UT16A_Not Side Population

description:
Gene expression data from UT16A cancer stem cell depleted cells not in side population
Not SidePop_UT16A

source_name: UT16A cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for cells not in side population


title: UT14_Not Side Population

description:
Gene expression data from UT14 cancer stem cell depleted cells not in side population
Not SidePop_UT14

source_name: UT14 cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for cells not in side population


title: activated CD8+ T lymphocyte [Tem]

city: La Jolla

first: John

last: Chang

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: Test, single-cell

data_processing: The Ct values in the Matrix non-normalized were exported from the BioMark software.  The Ct values are single-cell gene expression measurements, therefore were not normalized.  Fold-changes were not calculated.

label: TaqMan

source_name: splenocytes

label_protocol: Reverse transcriptase was activated by heating to 95°C for 2 minutes.  In the same tube, sequence-specific amplification was performed on the cDNA by denaturing at 95°C for 15 seconds, then annealing and amplification at 60°C for 4 minutes for 18 cycles.  Preamplified products were diluted 5-fold prior to analysis with Universal PCR Master Mix and inventoried TaqMan gene expression assays in 96.96 Dynamic Arrays on a BioMark System (Fluidigm).  Ct values were calculated from the system’s software.

extract_protocol: Inventoried TaqMan DNA probes (Life Technologies) were pooled to a final concentration of 0.2X for each of the 94 gene expression assays.  Single CD8+ T cells were sorted directly into RT-PreAmp Master Mix (Life Technologies) containing the pooled assays.  Cell lysis and sequence-specific reverse transcription was performed at 50C for 20 minutes.

tag: cell type

value: CD8+ T cell

tag: activation agent

value: Recombinant Listeria monocytogenes expressing ovalbumin

tag: time

value: 45 days


title: activated CD8+ T lymphocyte [Tcm]

description: Test, single-cell

tag: strain


title: HTL0020

source_name: pancreatic islets


title: HTL0021


title: HTL0081


title: UT33_Side Population

description:
Gene expression data from UT33 side population cancer stem cell enriched cells
SidePop_UT33

source_name: UT33 cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for side population cells


title: G1si-mix

value: GATA1 siRNA


title: HTL0015

description: Gene expression data from human pancreatic islets


title: activated CD8+ T lymphocyte [Day 7 bulk]

description: Test, single-cell

value: 7 days


title: HTL0022


title: HTL0016


title: UT30_Side Population

description:
Gene expression data from UT30 side population cancer stem cell enriched cells
SidePop_UT30

source_name: UT30 cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for side population cells


title: activated CD8+ T lymphocyte [Day 7 Tsle]

description: Test, single-cell


title: activated CD8+ T lymphocyte [Day 5 bulk]

description: Test, single-cell

value: 5 days


title: activated CD8+ T lymphocyte [Day 7 Tmp]

description: Test, single-cell


title: HTL0012


title: HTL0013


title: activated CD8+ T lymphocyte [Day 5 Tsle]

description: Test, single-cell


title: UT30_ALD negative

description:
Gene expression data from UT30 ALD negative cancer stem cell depleted cells
Not ALD_UT30

source_name: UT30 cell line cultured in plastic flasks, Sorted for ALD negative cells

value: Aldefluor staining


title: activated CD8+ T lymphocyte [Day 5 Tmp]

description: Test, single-cell


title: HTL0011

value: pancreatic islets


title: HTL0014


title: HTL0026


title: HTL0019


title: HTL0008


title: activated CD8+ T lymphocyte [Day 3 bulk]

description: Test, single-cell

value: 3 days


title: UT14_Side Population

description:
Gene expression data from UT14 side population cancer stem cell enriched cells
SidePop_UT14

source_name: UT14 cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for side population cells


title: activated CD8+ T lymphocyte [Prox]

description: Test, single-cell

value: 2 days


title: UT24A_ALD negative

description:
Gene expression data from UT24A ALD negative cancer stem cell depleted cells
Not ALD_UT24A

source_name: UT24A cell line cultured in plastic flasks, Sorted for ALD negative cells


title: UT16A_Side Population

description:
Gene expression data from UT16A side population cancer stem cell enriched cells
SidePop_UT16A

source_name: UT16A cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for side population cells


title: activated CD8+ T lymphocyte [FirstDiv]

description: Test, single-cell


title: UT14_ALD negative

description:
Gene expression data from UT14 ALD negative cancer stem cell depleted cells
Not ALD_UT14

source_name: UT14 cell line cultured in plastic flasks, Sorted for ALD negative cells


title: UT16A_ALD negative

description:
Gene expression data from UT16A ALD negative cancer stem cell depleted cells
Not ALD_UT16A

source_name: UT16A cell line cultured in plastic flasks, Sorted for ALD negative cells


title: UT24A_Side Population

description:
Gene expression data from UT24A side population cancer stem cell enriched cells
SidePop_UT24A

source_name: UT24A cell line cultured in plastic flasks, Sorted by Hoescht 33342 exclusion for side population cells


title: HTL0007


title: activated CD8+ T lymphocyte [Distal]

description: Test, single-cell


title: HTL0006


title: HTL0010


title: UT30_ALD positive

description:
Gene expression data from UT30 ALD positive cancer stem cell enriched cells
ALD_UT30

source_name: UT30 cell line cultured in plastic flasks, Sorted for ALD positive cells


title: unactivated CD8+ T lymphocyte [Naïve]

description: Test, single-cell

value: unactivated

value: day 0


title: HTL0005


title: UT24A_ALD positive

description:
Gene expression data from UT24A ALD positive cancer stem cell enriched cells
ALD_UT24A

source_name: UT24A cell line cultured in plastic flasks, Sorted for ALD positive cells


title: HTL0009


title: HTL0004


title: UT14_ALD positive

description:
Gene expression data from UT14 ALD positive cancer stem cell enriched cells
ALD_UT14

source_name: UT14 cell line cultured in plastic flasks, Sorted for ALD positive cells


title: HTL0001


title: HTL0002


title: Vk2/E6E7 cells_HIV gp120_rep3

status: Public on Mar 01 2014

city: Mumbai

first: Atmaram

last: Bandivdekar

state: Maharashtra

address: Jehangir Merwanji Street

department: Division of Biochemistry

country: India

institute: National Institute for Research in Reproductive Health, Indian Council of Medical Research

description: Gene expression after 24hr in HIV gp120 treated vaginal epithelial cells

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Human 8x60k (AMADID No: 027114). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX V 11.

source_name: Vk2/E6E7 epithelial cells_HIV gp120_replicate3

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

growth_protocol: The human vaginal epithelial cell line Vk2/E6E7 was employed in the study. Briefly, cells were grown in keratinocyte serum free medium (K-SFM) supplemented with 0.1 ng/ml EGF, 50 µg/ml bovine pituitary extract (Invitrogen, Carlsbad, CA) and 0.4 mM CaCl2 (Sigma, St. Louis, MO), at 37°C and 5% CO2. Cells were split 1:3 at 60% confluence, for passaging the cells.

extract_protocol: TRIzol Method following the manufacturer's recommendations

treatment_protocol: Vk2/E6E7 cells were grown in six well plates (BD Falcon, US) to 100% confluence for the experiments. Confluent monolayers were treated with HIV gp120 (83nM) for a time course of 24 hr. Untreated cells served as a control.

value: human vaginal epithelial


title: Vk2/E6E7 cells_HIV gp120_rep1

source_name: Vk2/E6E7 epithelial cells_HIV gp120_replicate1


title: HTL0003


title: E12.5_17LHS

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

country: United Kingdom

institute: University of Oxford

description: Brain of E12.5 dpc left hemispheres mouse embryo replicate4

hyb_protocol: Illumina Direct Hybridization Assay used for Whole-genome gene expression profilling

scan_protocol: Illumina BeadArray Reader used to capture immages with default setting

data_processing:
Illumina GenomeStudio were used to generate raw non-normalized data
Illumina GenomeStudio were used to generate background subtracted normalized data

label_protocol: Illumina TotalPrep-96 RNA Amplification kit from Ambion # 4393543 used

extract_protocol: QIAGEN Rneasy kit were used for Total RNA extraction

treatment_protocol: Brain Right/left Heamispheres were separated along the midline dissected from mouse embryonic head

value: brain

tag: Stage

tag: hemisphere

value: left


title: E8.5_16LHS

description: Brain of E8.5 dpc left hemispheres mouse embryo replicate4

tag: tissue


title: Vk2/E6E7 cells_HIV gp120_rep2

source_name: Vk2/E6E7 epithelial cells_HIV gp120_replicate2


title: E12.5_19LHS

description: Brain of E12.5 dpc leftt hemispheres mouse embryo replicate2


title: UT33_ALD negative

description:
Gene expression data from UT33 ALD negative cancer stem cell depleted cells
Not ALD_UT33

source_name: UT33 cell line cultured in plastic flasks, Sorted for ALD negative cells

value: Cancer stem cell depleted


title: E10.5_25LHS

description: Brain of E10.5 dpc left hemispheres mouse embryo replicate2


title: UT16A_ALD positive

description:
Gene expression data from UT16A ALD positive cancer stem cell enriched cells
ALD_UT16A

source_name: UT16A cell line cultured in plastic flasks, Sorted for ALD positive cells

value: Cancer stem cell enriched


title: HTL0031

description: Gene expression data from human pancreatic islets

source_name: pancreatic islets


title: E8.5_1LHS

description: Brain of E8.5 dpc left hemispheres mouse embryo replicate3


title: Vk2/E6E7 cells_control_rep1

description: Gene expression after 24hr in control vaginal epithelial cells


title: E12.5_4LHS

description: Brain of E12.5 dpc left hemispheres mouse embryo replicate1


title: Vk2/E6E7 cells_control_rep3


title: E10.5_15LHS

description: Brain of E10.5 dpc left hemispheres mouse embryo replicate3


title: E10.5_22LHS

description: Brain of E10.5 dpc left hemispheres mouse embryo replicate4


title: E12.5_1LHS

description: Brain of E12.5 dpc left hemispheres mouse embryo replicate3


title: Vk2/E6E7 cells_control_rep2


title: E10.5_21LHS

description: Brain of E10.5 dpc left hemispheres mouse embryo replicate1


title: E8.5_9LHS

description: Brain of E8.5 dpc left hemispheres mouse embryo replicate1


title: E10.522RHS

description: Brain of E10.5 dpc right hemispheres mouse embryo replicate4

value: right


title: E12.5_17RHS

description: Brain of E12.5 dpc righthemispheres mouse embryo replicate4


title: E8.5_16RHS

description: Brain of E8.5 dpc right hemispheres mouse embryo replicate4


title: E10.5_15RHS

description: Brain of E10.5 dpc right hemispheres mouse embryo replicate3


title: E12.5_1RHS

description: Brain of E12.5 dpc right hemispheres mouse embryo replicate3


title: E12.5_4RHS

description: Brain of E12.5 dpc right hemispheres mouse embryo replicate1


title: E12.5_19RHS

description: Brain of E12.5 dpc right hemispheres mouse embryo replicate2


title: E8.5_9RHS

description: Brain of E8.5 dpc right hemispheres mouse embryo replicate1


title: WT vs sigA (G336C) rep1

city: Ithaca

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

institute: Cornell University

hyb_protocol: Equal amounts (100-150 pmol) of labeled cDNA were combined plus hybridization buffer (2X = 50% formamide, 10X SSC, 0.1% SDS). cDNA mix was denatured at 95°C and hybridized 16-18 hours at 42°C to DNA microarray slides which had been prehybridized for at least 30 min at 42°C in 1% bovine serum albumin, 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate (SDS), washed in water and dried. Following hybridization the slides were washed sequentially in: 2X SSC + 0.1% SDS for 5 min at 42°C, 2X SSC + 0.1% SDS for 5 min at room temperature, 2X SSC for 5 min at room temperature, 0.2X SSC for 5 min at room temperature, and finally dipped in water and spun until dry.

scan_protocol: Arrays were scanned using a GenePixTM 4000B array scanner (Axon Instruments, Inc.) Raw data files were produced from the scanned images using the GenePix Pro 6.0 software package (GPR files).

data_processing: Red/green fluorescence intensity values were normalized  using the GenePix Pro 6.0 software package such that the ratio of medians of all features was equal to 1. Fold changes equal to average of mutant/average of wild type. Ave represents the average of medians for duplicate spots (minus median of background).

label: Alexa Fluor 555

organism: Bacillus subtilis

source_name: WT

label_protocol: cDNA synthesis was performed using the SuperScriptTM Plus Indirect cDNA labeling System (Invitrogen) as per the manufacturer’s instructions using 20 microgram of total RNA. Total cDNA was labeled overnight with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen)

extract_protocol: The cell cultures were grown to an OD600 of 0.4 in LB broth with agitation. RNA isolation was performed using the RNeasy mini kit (Qiagen). RNA was subsequently DNase treated with TURBO DNA-freeTM (Ambion) and precipitated overnight. The RNA was dissolved in RNase free water and quantified using a NanoDrop spectrophotometer (Nanodrop Tech. Inc., Wilmington, DE).

tag: genotype/variation

value: WT

label: Alexa Fluor 647

source_name: sigA (G336C)

value: sigA (G336C)


title: E10.5_25RHS

description: Brain of E10.5 dpc right hemispheres mouse embryo replicate2


title: WT vs sigA (G336C) rep1 dye-swap

description: rep1 dye-swap


title: WT vs sigA (G336C) rep2 dye-swap

description: rep2 dye-swap


title: E8.5_1RHS

description: Brain of E8.5 dpc right hemispheres mouse embryo replicate3


title: E8.5_17LHS

description: Brain of E8.5 dpc left hemispheres mouse embryo replicate2


title: E10.5_21RHS

description: Brain of E10.5 dpc right hemispheres mouse embryo replicate1


title: WT vs sigA (G336C) rep2


title: E8.5_17RHS

description: Brain of E8.5 dpc right hemispheres mouse embryo replicate2


title: SD_week 1_replicate 3

city: college park

first: rongshuang

last: lin

state: MD

address: Plant Sci building

department: Plant sci

institute: Univ Maryland

description: Expression data for bark tissues under SD treatment for 1 week, replicate 3

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed using RMA function  in the affy package in R.

organism: Populus trichocarpa

source_name: Bark from plants  under 1-week SD for replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT expression kit mannual).

growth_protocol: Plants were grown in a controlled environment change under LD photoperiod (16 h light/8 h dark) and 20°C for 6 weeks after which the photoperiod was shifted to SD (8 h light/16 h dark) at the same temperature for 6 weeks.

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy plant mini kit with Qiacube with modifications.

value: Bark

tag: genotype

value: Nisqually

tag: treatment

value: SD

value: 1 week

tag: replicate


title: SD_week 4_replicate 3

description: Expression data for bark tissues under SD treatment for 4 week, replicate 3

source_name: Bark from plants  under 4-week SD for replicate 3

treatment_protocol: Plants were grown in a controlled environment change under LD photoperiod (16 h light/8 h dark) and 20°C for 6 weeks after which the photoperiod was shifted to SD (8 h light/16 h dark) at the same temperature for 6 weeks.

value: 4 week


title: SD_week 2_replicate 3

description: Expression data for bark tissues under SD treatment for 2 week, replicate 3

source_name: Bark from plants  under 2-week SD for replicate 3

value: 2 week


title: SD_week 3_replicate 2

description: Expression data for bark tissues under SD treatment for 3 week, replicate 2

source_name: Bark from plants  under 3-week SD for replicate 2

value: 3 week


title: SD_week 2_replicate 2

description: Expression data for bark tissues under SD treatment for 2 week, replicate 2

source_name: Bark from plants  under 2-week SD for replicate 2


title: LD_replicate 2

description: Expression data for bark tissues under LD right before being transferred to SD, replicate 2

source_name: Bark from LD-grown plants right before SD treatment for replicate 2

value: LD


title: SD_week 5_replicate 1

description: Expression data for bark tissues under SD treatment for 5 week, replicate 1

source_name: Bark from plants  under 5-week SD for replicate 1

value: 5 week


title: SD_week 6_replicate 2

description: Expression data for bark tissues under SD treatment for 6 week, replicate 2

source_name: Bark from plants  under 6-week SD for replicate 2

value: 6 week


title: SD_week 5_replicate 3

description: Expression data for bark tissues under SD treatment for 5 week, replicate 3

source_name: Bark from plants  under 5-week SD for replicate 3


title: SD_week 2_replicate 1

description: Expression data for bark tissues under SD treatment for 2 week, replicate 1

source_name: Bark from plants under 2-week SD for replicate 1


title: SD_week 5_replicate 2

description: Expression data for bark tissues under SD treatment for 5 week, replicate 2

source_name: Bark from plants  under 5-week SD for replicate 2


title: LD_replicate 1

description: Expression data for bark tissues under LD right before being transferred to SD, replicate 1

source_name: Bark from LD-grown plants right before SD treatment for replicate 1


title: SD_week 4_replicate 1

description: Expression data for bark tissues under SD treatment for 4 week, replicate 1

source_name: Bark from plants  under 4-week SD for replicate 1


title: SD_week 4_replicate 2

description: Expression data for bark tissues under SD treatment for 4 week, replicate 2

source_name: Bark from plants  under 4-week SD for replicate 2


title: LD_replicate 3

description: Expression data for bark tissues under LD right before being transferred to SD, replicate 3

source_name: Bark from LD-grown plants right before SD treatment for replicate 3


title: LD regrowth week 2_replicate 3

description: Expression data for bark tissues under LD regrowth for 2 week, replicate 3

source_name: Bark from plants under 2-week LD regrowth for replicate 3

extract_protocol: Extraction of total RNA was performed using Qiangen RNeasy plant mini kit with Qiacube with modifications.

treatment_protocol: LD (16 h light/8 h dark) -grown plants were transferred to growth chamber under SD (8 h light/16 h dark) for 8 weeks at 20°C and then under SD and low temperature (10°C/4°C; day/night) for 12 weeks. The plants were then moved to LD, 20°C for regrowth.


title: SD_week 3_replicate 3

description: Expression data for bark tissues under SD treatment for 3 week, replicate 3

source_name: Bark from plants  under 3-week SD for replicate 3


title: SD_week 6_replicate 3

description: Expression data for bark tissues under SD treatment for 6 week, replicate 3

source_name: Bark from plants  under 6-week SD for replicate 3


title: SD_week 1_replicate 1

description: Expression data for bark tissues under SD treatment for 1 week, replicate 1

source_name: Bark from plants under 1-week SD for replicate 1


title: LD regrowth week 3_replicate 3

description: Expression data for bark tissues under LD regrowth for 3 week, replicate 3

source_name: Bark from plants  under 3-week LD regrowth for replicate 3

growth_protocol: LD (16 h light/8 h dark) -grown plants were transferred to growth chamber under SD (8 h light/16 h dark) for 8 weeks at 20°C and then under SD and low temperature (10°C/4°C; day/night) for 12 weeks. The plants were then moved to LD, 20°C for regrowth


title: SD_week 3_replicate 1

description: Expression data for bark tissues under SD treatment for 3 week , replicate 1

source_name: Bark from plants  under 3-week SD for replicate 1


title: SD_week 6_replicate 1

description: Expression data for bark tissues under SD treatment for 6 week, replicate 1

source_name: Bark from plants  under 6-week SD for replicate 1


title: LD regrowth_week 1_replicate 3

description: Expression data for bark tissues under LD regrowth for 1 week, replicate 3

source_name: Bark from plants under 1-week LD regrowth for replicate 3


title: LD regrowth week 2_replicate 2

description: Expression data for bark tissues under LD regrowth for 2 week, replicate 2

source_name: Bark from plants under 2-week LD regrowth for replicate 2


title: SD_LT_dormancy release, replicate 3

description: Expression data for bark tissues from plants released from dormancy, replicate 3

source_name: Bark from plants released from dormancy for replicate 3

value: SD-LT

value: 8 week-12 week


title: LD regrowth week 3_replicate 2

description: Expression data for bark tissues under LD regrowth for 3 week, replicate 2

source_name: Bark from plants  under 3-week LD regrowth for replicate 2


title: UT33_ALD positive

description:
Gene expression data from UT33 ALD positive cancer stem cell enriched cells
ALD_UT33

source_name: UT33 cell line cultured in plastic flasks, Sorted for ALD positive cells

value: Aldefluor staining


title: atg7 Mopholino biological replicate 1

city: Dallas

first: James

last: Amatruda

state: TX

address: 5323 Harry Hines Boulevard

department: Pediatrics and Molecular Biology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Hybridization was carried out according to Affymetrix protocol 701027 rev 5, using Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the Affymetrix GeneChip Scanner 3000 using default parameters

data_processing: Probeset-level normalization was achieved using the MAS5.0 algorithm. Data analysis and linear modeling were performed in the R programming language, utilizing functions from Linear Models for Microarray Data. For each probe, a moderated t-statistic (with standard errors moderated across genes) was computed using a Bayesian model. For each transcript, signal-to-noise ratios (SNR) were computed for each respective morphant compared to the control group

organism: Danio rerio

source_name: Zebrafish embryo hearts a 3 days post-fertilization

label_protocol: Biotinylated cRNA were prepared  from 5 ug total RNA using the GeneChip IVT labeling kit,  according to the manufacturer's instructions (#702232 rev 2, Afymetrix, Inc., Santa Clara, CA).

growth_protocol: Embryos were injected at the 1-cell stage and raised under standard conditions

extract_protocol: Total RNA was extracted from tumors using Trizol reagent according to the manufacturer's instructions.

treatment_protocol: Hearts were purified from 3 dpf zebrafish as described in Burns CG, MacRae CA. Purification of hearts from zebrafish embryos. Biotechniques 2006; 40:278-81; PMID:16568816.  Total RNA was extracted with the Trizol method

value: heart

tag: age

value: 3 days post-fertilization


title: atg5 Mopholino biological replicate 2


title: LD regrowth week 3_replicate 1

description: Expression data for bark tissues under LD regrowth for 3 week, replicate 1

source_name: Bark from plants  under 3-week LD regrowth for replicate 1


title: atg5 Mopholino biological replicate 1


title: atg7 Mopholino biological replicate 2


title: LD regrowth_week 1_replicate 1

description: Expression data for bark tissues under LD regrowth for 1 week, replicate 1

source_name: Bark from plants under 1-week LD regrowth for replicate 1


title: LD regrowth_week 1_replicate 2

description: Expression data for bark tissues under LD regrowth for 1 week, replicate 2

source_name: Bark from plants under 1-week LD regrowth for replicate 2


title: LD regrowth week 2_replicate 1

description: Expression data for bark tissues under LD regrowth for 2 week, replicate 1

source_name: Bark from plants under 2-week LD regrowth for replicate 1


title: Uninjected control biological replicate 2


title: SD_LT_dormancy release, replicate 2

description: Expression data for bark tissues from plants released from dormancy, replicate 2

source_name: Bark from plants released from dormancy for replicate 2


title: SD_LT_dormancy release, replicate 1

description: Expression data for bark tissues from plants released from dormancy, replicate 1

source_name: Bark from plants released from dormancy for replicate 1


title: becn1 Mopholino biological replicate 2


title: Uninjected control biological replicate 3


title: becn Mopholino biological replicate 3


title: atg5 Mopholino biological replicate 3


title: Control Morpholino biological replicate 2


title: Uninjected control biological replicate 1


title: FcgKO Non stim 2

city: New Haven

first: Ruslan

last: Medzhitov

state: CT

address: PO Box 208011 300 Cedar Street TAC S660

department: Immunobiology

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol with Cy3-SAV

scan_protocol: Standard Illumina scanning protocol using HiScan System

data_processing: The data were analysed in Genome Studio Illumina Software

source_name: FcgKO Non stim 2

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina® TotalPrepTM RNA Amplification Kit

growth_protocol: Peritoneal MF were isolated from naïve euthanized mouse and plated in 24-well TC dishes into complete RPMI media, with 10% FBS and 15% L929 conditional sup containing MCSF o/n to allow MF adherence. Floaters (B cells, T cells etc) were discarded, fresh pre-warmed media was added over MF and cells stimulated with IFNg for 6hrs before RNA collection

extract_protocol: Total RNA from stimulated or control peritoneal MF was isolated using Qiagen RNEasy Kit. DNA was removed using Qiagen Dnase protocol.

value: Fcg-chain KO

value: Peritoneal MF


title: Control Mopholino biological replicate 3


title: FcgKO Unstimulated 1

source_name: Peritoneal MF

growth_protocol: Peritoneal MF were isolated from naïve euthanized mouse and plated in 24-well TC dishes into complete RPMI media, with 10% FBS and 15% L929 conditional sup containing MCSF o/n to allow MF adherence. Floaters (B cells, T cells etc) were discarded, fresh pre-warmed media was added over MF and cells stimulated with IL4 for 6hrs before RNA collection


title: FcgKO Unstimulated 2


title: WT IL4 stim 2

treatment_protocol: Peritoneal MF were stimulated with recombinant IL4 (10 ng/ml) for 6hrs.

value: WT


title: FcgKO IFNg stim 2

source_name: FcgKO IFNg stim 2

treatment_protocol: Peritoneal MF were stimulated with recombinant IFNg (10 ng/ml) for 6hrs.


title: FcgKO Non stim 1

source_name: FcgKO Non stim 1


title: SD_week 1_replicate 2

description: Expression data for bark tissues under SD treatment for 1 week, replicate 2

source_name: Bark from plants  under 1-week SD for replicate 2

value: Bark

value: Nisqually


title: WT Non stim 2

source_name: WT Non stim 2


title: WT Non stim 1

source_name: WT Non stim 1


title: WT IL4 stim 1


title: WT Unstimulated 2


title: WT IFNg stim 2

source_name: WT IFNg stim 2


title: IFNg 2

source_name: BMMF

growth_protocol: Total BM cells after red blood cell lysis were plated at 6x10^6 cells in 15 cm Petri dish in 20 ml MF growth media (complete RPMI, 20% FBS, 30% L929 conditional sup containing MCSF). Cells were fed with additional 20 ml of growth media on day 4. On day 7, cells were lifted using cold PBS + 5m MEDTA and replated in non-TC dishes in MF replating media (complete RPMI, 10% FBS, 15% L929 conditional sup containing MCSF).  On day 8 cells were stimulated as indicated.

extract_protocol: Total RNA from stimulated or control BMMF was isolated using Qiagen RNEasy Kit. DNA was removed using Qiagen Dnase protocol.

treatment_protocol: BMMF were stimulated with recombinant IFNg (10 ng/ml),  SRBC-IgG2a ops (10:1 SRBC:BMMF ratio ) or both for 6hrs.

value: bone marrow macrophage


title: WT Unstimulated 1


title: SRBC-IgG2a ops 2


title: WT IFNg stim 1

source_name: WT IFNg stim 1


title: FcgKO IFNg stim 1

source_name: FcgKO IFNg stim 1


title: IFNg+SRBC-IgG2a ops 1


title: IFNg+SRBC-IgG2a ops 2


title: Non stim 2


title: FcgKO IL4 stim 2


title: FcgKO IL4 stim 1


title: IFNg 1


title: SRBC-IgG2a ops 1


title: Non stim 1


title: MCF10A + Dox

city: London

first: Susana

last: Godinho

state: State...

address: Charterhouse Square

department: Centre for Molecular Oncology

institute: Barts Cancer Institute

description: Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array

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

scan_protocol: Affymetrix standard procedure.

data_processing: SNP array data was processed with the Nexus Copy Number Software (BioDiscovery; http://www.biodiscovery.com/software/nexus-copy-number/), using the “Matched Paired Analysis” module.

source_name: MCF10A cell line

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: MCF10A cells were grown 4 days in 3-D cultures of matrigel. Cells were recovered using dispase and DNA was extracted using DNA purification kit form Qiagen.

extract_protocol: Genomic DNA was extracted from MCF10A cells using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: See specific treatments above.

tag: cell line

value: non-transformed mammary epithelial cells

tag: treated with

value: Doxycyclin to induce Plk4 overexpression and centrosome amplification prior to plating in 3D cultures


title: HCT116 replicate 3

city: Stockholm

first: Cinzia

last: Bersani

address: Cancer Center Karolinska, R8:04

institute: Karolinska Institutet

hyb_protocol: Labeled reaction were hybridized onto the arrays for 18–40 h at 65 °C. Following hybridization, microarrays were washed in a series of four solutions containing 2×SSC with 0.03% SDS, 2×SSC, 1×SSC, and 0.2×SSC, respectively. The first wash was performed for 5 minutes at 65°C. The subsequent washes were performed at room temperatures for 5 minutes each. Following the last wash the microarrays were dried by centrifugation in a low-ozone environment (<5 ppb) to prevent destruction of Cy dyes. Once dry, the microarrays were kept in a low-ozone environment during storage and scanning.

scan_protocol: Microarrays were scanned using GenePix Professional 4200A (Axon Instruments) and data was collected using GenePix Pro 6.0 (Molecular Devices).

data_processing: Arrays were normalized computationally by the Stanford Microarray Database (SMD) [62]. The data were filtered for signal over background of greater than 2 and included for further analysis. A second filtering was done on the basis of data values including only genes whose Log(base2) of R/G Normalized Ratio (Mean) is > 2 for at least 2 of the 3 arrays. Data were retrieved and exported into Microsoft Excel.

label_protocol: 30μg total RNA was mixed with 1μl Anchored oligo dT primer 4-5μg/μl (Operon, HPLC purified), 1μl Random Hexamer (Amersham), 1μl Cy5 or Cy3 mRNA Doping Control Mix (Ambion/Stratagene) to the sample treated with siControl or siWig-1, respectively. The volume was adjusted to 18.4μl with DEPC treated ddH2O. Samples were mixed by quick vortexing and incubated at 70ºC for 10 min followed by 10 min on ice. Next, 5μl 5X superscript II first strand buffer, 3μl 0.1 M DTT, 0.6μl 50X aa-dUPT ((50μl of 100 mM dATP/dCTP/dGTP, 25μl of 100 mM dTTP, 50μl of 50mM aa-dUTP (Ambion 8439)), 2μl Superscript II (Gibco) was added to the samples. cDNA synthesis were carried out at 42ºC for 2 hours. RNA was degradated by addition of 13μl 1M NaOH and 1μl 0.5M EDTA and incubation at 65°C for 10 min followed by neutralization by addition of 50μl 1M HEPES. The reaction were subsequently purified with the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer's instructions using buffer ERC (Qiagen) and eluting the DNA off the columns using two times 12.5μl 10mM Na-Phosphate pH 8.5. Amplified cDNA was fluorescently labeled with NHSmonoester Cy5 or Cy3 (Amersham RPN5661). Unincorporated dyes were removed with QIAquick PCR Purification Kit according to the manufacturer's instructions. Purified cDNA was diluted into in a 55µl solution containing 2μl of 10μg/μl Human Cot1 DNA (Invitrogen), 2μl of 10μg/μl polyA RNA (Sigma), 2μl of 10μg/μl yeast tRNA (Invitrogen), 1.32μl HEPES, 9.35μl 20XSSC and 1.65μl 10%SDS. The sample was incubated 2 min at 100°C followed by 37°C for 20-25 min, then it was spun at 14,000 rpm for 10 minutes and kept at RT for 15-20 min.

growth_protocol: HCT116 cells  were grown in Iscove's modified Dulbeccos medium supplemented with 10% fetal bovine serum (GIBCO), 1% L-glutamine and 2.5μg/mL Plasmocin (InvivoGen) in 5% CO2 at 37°C.

extract_protocol: Total RNA from HCT116 cells was extracted using TRIzol® reagent (Invitrogen)

treatment_protocol: Cell were transfected with 10nM Hs_WIG1_1 siRNA (siW1)  or AllStars Negative Control siRNA (siC) (Qiagen) using HiPerFect (Qiagen) according to manufacturers protocol.

tag: modification

value: Wig-1 protein knockdown

source_name: siControl


title: HCT116 replicate 2


title: MCF10A -Dox


title: Heart_KO_Rep2

city: San Antonio

first: Haihui

last: Pan

state: Texas

address: 8403 Floyd Curl Dr.

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

hyb_protocol: MouseRef-8 version 2.0, Illumina

scan_protocol: BeadChips were scanned on a BeadArrayTM Reader (Illumina) using BeadScan software (version 3.2, Illumina)

data_processing: the scanned data were uploaded into GenomeStudio® software (version 1.1, Illumina) via the gene expression module (Direct Hyb).

label_protocol: TotalPrepTM RNA amplification kit (Ambion, Cat. #AMIL1791)

growth_protocol: Regular Chow

extract_protocol: miRNeasy mini kit (Qiagen, Cat. #217004)

treatment_protocol: fasting for 5 hours

tag: strain background

tag: gender

value: female

value: 20 wks

value: Nelf-b f/f; CreER


title: Heart_KO_Rep1


title: MCF10A siRNA MCAK

tag: cell type

value: siRNA against MCAK to induce aneuploidy 48hrs prior to plating in 3-D cultures


title: Phytophthora parasitica infection of A. thaliana roots_6h_rep2

city: Sophia Antipolis

first: Gourgues

last: Mathieu

address: 400 routes des Chappes, BP167

department: UMR Institut Sophia Agrobiotech

country: France

institute: University of Nice Sophia Antipolis

description: Phytophthora parasitica infection of A. thaliana roots_samples recovered 6 hours after inoculation

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: RMA normalization. Nimblescan software.

organism: Phytophthora nicotianae INRA-310

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol:
The pathosystem involving A. thaliana and Phytophthora parasitica was described in Attard A, Gourgues M, Callemeyn-Torre N, Keller H. 2010. The immediate activation of defense responses in Arabidopsis roots is not sufficient to prevent Phytophthora parasitica infection. The New phytologist 187: 449–460.
The protocol for recovery of RNA from purified appressoria was described in Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre JY, Gourgues M. 2010. Cellular and molecular characterization of Phytophthora parasitica appressorium-mediated penetration. New Phytol 185: 248–257.

extract_protocol: RNA extraction from inoculated plant tissues was performed as described by Laroche-Raynaland coworkers (Laroche-Raynal M, Aspart L, Delseny M, Penon Phytophthora 1984. Plant Science 35: 139–146). Phytophthora parasitica RNA was extracted using Trizol reagent (Invitrogen, France).

value: Wild type

value: roots

tag: sample time

value: 6 hr after inoculation


title: becn1 Mopholino biological replicate 1

source_name: Zebrafish embryo hearts a 3 days post-fertilization

value: heart

value: 3 days post-fertilization


title: Heart_KO_Rep3


title: Heart_Ctrl_Rep2

value: Nelf-b f/f


title: Phytophthora parasitica infection of A. thaliana roots_30h_rep2

description: Phytophthora parasitica infection of A. thaliana roots_samples recovered 30 hours after inoculation

value: 30 hr after inoculation


title: Phytophthora parasitica infection of A. thaliana roots_30h_rep1

source_name: Phytophthora parasitica infection of A. thaliana roots_samples recovered 30 hours after inoculation


title: Phytophthora parasitica infection of A. thaliana roots_6h_rep1

source_name: Phytophthora parasitica infection of A. thaliana roots_samples recovered 6 hours after inoculation


title: 1485V092011_unstim_20121201_n104_01_05.RCC

city: Cambridge

first: Nir

last: Hacohen

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: Lysates in Qiagen RLT buffer were hybridized for 12-24 hours with custom nCounter Gene Expression CodeSets.

scan_protocol: Nanostring nCounter system (Nanostring; Seattle, WA) was used to digitally count transcripts in a multiplex reaction.

data_processing: The raw data is first scaled by positive spike-ins, shifted by negative spike-ins, and a negative binomial is fit using DESeq based on the scale parameter estimated from the positive spike-ins

growth_protocol: Monocyte-derived dendritic cells from each donor were cultured for 7 days in RPMI supplemented with 10% FBS, 100 ng/mL GM-CSF and 40 ng/mL IL-4.

extract_protocol: Total RNA was isolated using Qiagen RNeasy columns.

treatment_protocol: MoDCs were stimulated with 15 ng/mL LPS for 2.5 h or 5 h, influenza virus for 10 h, 100 U/mL IFNβ for 6.5 h, or left unstimulated.

tag: stimulation

value: unstim

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: F

tag: age (years)

tag: ethnicity

value: African-American

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Phytophthora parasitica germinated cycts with appressoria_rep1

tag: genotype

tag: tissue

value: germinated cycts with appressoria


title: Heart_Ctrl_Rep1

tag: strain background

tag: gender

tag: age

tag: genotype/variation


title: Phytophthora parasitica infection of A. thaliana roots_10h_rep1

description: Phytophthora parasitica infection of A. thaliana roots_samples recovered 10 hours after inoculation

tag: sample time

value: 10 hr after inoculation


title: Heart_Ctrl_Rep3


title: Phytophthora parasitica mycelium_rep1

description: Phytophthora parasitica mycelium

source_name: Phytophthora parasitica mycelium

value: mycelium


title: Phytophthora parasitica infection of A. thaliana roots_10h_rep2

source_name: Phytophthora parasitica infection of A. thaliana roots_samples recovered 10 hours after inoculation


title: 1350V092011_unstim_20121201_n104_01_01.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

value: East Asian


title: 1477V092011_unstim_20121201_n104_01_02.RCC

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)


title: 1465V092011_unstim_20121201_n104_01_04.RCC

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: 1459V092011_unstim_20121201_n104_01_03.RCC

tag: gender

value: M


title: Phytophthora parasitica germinated cycts with appressoria_rep2

tag: genotype

tag: tissue


title: Phytophthora parasitica infection of A. thaliana roots_2,5h_rep1

description: Phytophthora parasitica infection of A. thaliana roots_ samples recovered 2,5 hours after inoculation

tag: sample time

value: 2.5 hr after inoculation


title: Phytophthora parasitica mycelium_rep2

description: Phytophthora parasitica mycelium


title: Phytophthora parasitica zoospores_rep1

description: Phytophthora parasitica zoospores

source_name: Phytophthora parasitica zoospores

value: zoospores


title: Phytophthora parasitica infection of A. thaliana roots_2,5h_rep2

description: Phytophthora parasitica infection of A. thaliana roots_samples recovered 2,5 hours after inoculation

value: Wild type


title: 1097V091511_unstim_20121201_n103_01_12.RCC

tag: stimulation

tag: hours

tag: plate


title: Phytophthora parasitica zoospores_rep2

description: Phytophthora parasitica zoospores


title: 1470V091511_unstim_20121201_n103_01_11.RCC

tag: cartridge

tag: lane

tag: date of visit


title: 1328V091511_unstim_20121201_n103_01_10.RCC

tag: time of visit

tag: age (years)

tag: ethnicity


title: 1391V091511_unstim_20121201_n103_01_08.RCC

tag: million pbmc

tag: million dcs

tag: height (cm)


title: 0824V091511_unstim_20121201_n103_01_09.RCC

value: Caucasian

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: 1031V091411_unstim_20121201_n103_01_04.RCC

tag: gender

value: MULTI-RACIAL


title: 1048V091411_unstim_20121201_n103_01_06.RCC


title: 1280V091411_unstim_20121201_n103_01_05.RCC


title: 0948V091411_unstim_20121201_n103_01_07.RCC


title: 0381V091411_unstim_20121201_n103_01_03.RCC


title: 1262V090811_unstim_20121201_n103_01_02.RCC


title: 1148V090811_unstim_20121201_n102_01_12.RCC


title: 1090V090811_unstim_20121201_n103_01_01.RCC


title: 1415V091311_unstim_20121201_n102_01_11.RCC


title: 1229V062811_unstim_20121201_n102_01_06.RCC


title: 1011V091311_unstim_20121201_n102_01_08.RCC


title: 1446V062811_unstim_20121201_n102_01_05.RCC


title: 1421V091311_unstim_20121201_n102_01_07.RCC


title: 1168V062811_unstim_20121201_n102_01_04.RCC


title: 1340V062311_unstim_20121201_n101_01_10.RCC


title: 1344V062811_unstim_20121201_n102_01_03.RCC


title: 0668V062311_unstim_20121201_n101_01_09.RCC


title: 0313V062811_unstim_20121201_n102_01_02.RCC


title: 1266V062311_unstim_20121201_n102_01_01.RCC


title: 1222V062311_unstim_20121201_n101_01_12.RCC


title: 0517V062211_unstim_20121201_n101_01_07.RCC


title: 0570V062211_unstim_20121201_n101_01_05.RCC


title: 0332V062211_unstim_20121201_n101_01_06.RCC


title: 0447V062211_unstim_20121201_n101_01_08.RCC


title: 0533V062111_unstim_20121201_n101_01_03.RCC


title: 0773V062111_unstim_20121201_n101_01_02.RCC


title: 0688V062211_unstim_20121201_n101_01_04.RCC


title: 1317V091311_unstim_20121201_n102_01_09.RCC


title: 0987V091311_unstim_20121201_n102_01_10.RCC


title: 1605V021412_LPS_20121130_n97_01_11.RCC

value: LPS


title: 1356V061511_unstim_20121201_n101_01_01.RCC


title: 1680V020912_LPS_20121130_n97_01_10.RCC


title: 1330V021412_LPS_20121130_n97_01_12.RCC


title: 1474V020912_LPS_20121130_n97_01_09.RCC


title: 1361V062311_unstim_20121201_n101_01_11.RCC


title: 1681V020812_LPS_20121130_n97_01_08.RCC


title: 1349V020712_LPS_20121130_n97_01_06.RCC


title: 1359V020712_LPS_20121130_n97_01_05.RCC


title: 1112V110911_LPS_20121130_n96_01_05.RCC


title: 1406V111511_LPS_20121130_n96_01_11.RCC


title: 1399V111011_LPS_20121130_n96_01_08.RCC


title: 1622V020112_LPS_20121130_n97_01_03.RCC


title: 1559V111511_LPS_20121130_n97_01_01.RCC


title: 1205V111511_LPS_20121130_n96_01_12.RCC


title: 0916V111011_LPS_20121130_n96_01_07.RCC


title: 1314V110911_LPS_20121130_n96_01_06.RCC


title: 0708V111611_LPS_20121130_n97_01_02.RCC


title: 0490V111011_LPS_20121130_n96_01_09.RCC


title: 0880V110811_LPS_20121130_n96_01_04.RCC


title: 0896V111511_LPS_20121130_n96_01_10.RCC


title: 1567V020712_LPS_20121130_n97_01_04.RCC


title: 0481V110811_LPS_20121130_n96_01_02.RCC


title: 1411V110311_LPS_20121130_n96_01_01.RCC


title: 1492V020812_LPS_20121130_n97_01_07.RCC


title: 1538V110211_LPS_20121130_n95_01_09.RCC


title: 1472V110311_LPS_20121130_n95_01_12.RCC


title: 1419V110111_LPS_20121130_n95_01_05.RCC


title: 1282V110811_LPS_20121130_n96_01_03.RCC


title: 1272V110111_LPS_20121130_n95_01_04.RCC


title: 0266V110211_LPS_20121130_n95_01_06.RCC


title: 0719V110211_LPS_20121130_n95_01_07.RCC


title: 0800V110211_LPS_20121130_n95_01_08.RCC


title: 1387V110211_LPS_20121130_n95_01_10.RCC


title: 1195V110311_LPS_20121130_n95_01_11.RCC


title: 1131V102711_LPS_20121130_n95_01_02.RCC


title: 1268V102711_LPS_20121130_n95_01_01.RCC


title: HCT116 replicate 1

tag: cell line

tag: modification

value: Wig-1 protein knockdown


title: 0308V012412_IFNb_20121130_n94_01_08.RCC

tag: stimulation

value: IFNb

tag: hours


title: 1672V012412_IFNb_20121130_n94_01_10.RCC

tag: plate

tag: cartridge


title: 1686V022212_IFNb_20121130_n94_01_04.RCC

tag: lane

tag: date of visit


title: 1542V102611_LPS_20121130_n94_01_12.RCC

tag: time of visit

tag: age (years)


title: 1646V012412_IFNb_20121130_n94_01_06.RCC

tag: ethnicity

tag: million pbmc


title: 0744V012412_IFNb_20121130_n94_01_09.RCC

tag: million dcs

tag: height (cm)


title: 1349V020712_IFNb_20121130_n94_01_02.RCC

tag: weight (kg)

tag: systolic/diastolic


title: 1156V061511_unstim_20121130_n100_01_10.RCC

tag: gender

tag: bmi


title: 1647V012412_IFNb_20121130_n94_01_05.RCC


title: 1660V012412_IFNb_20121130_n94_01_07.RCC


title: 1331V012412_IFNb_20121130_n94_01_11.RCC


title: 1547V110111_LPS_20121130_n95_01_03.RCC


title: 0825V061511_unstim_20121130_n100_01_11.RCC


title: 1359V020712_IFNb_20121130_n94_01_01.RCC


title: 1357V061511_unstim_20121130_n100_01_12.RCC


title: 0218V061511_unstim_20121130_n100_01_09.RCC


title: 1282V110811_LPS_20121130_n100_01_03.RCC


title: 1622V020112_LPS_20121130_n100_01_04.RCC


title: 1538V110211_LPS_20121130_n100_01_02.RCC


title: 1542V102611_LPS_20121130_n100_01_01.RCC


title: 1343V061411_unstim_20121130_n100_01_08.RCC


title: 1416V021612_LPS_20121130_n100_01_05.RCC


title: 0744V012412_LPS_20121130_n100_01_06.RCC


title: 1323V061411_unstim_20121130_n100_01_07.RCC


title: 1026V022112_IFNb_20121129_n93_01_12.RCC


title: 1687V021512_IFNb_20121130_n94_01_03.RCC


title: 1625V022112_IFNb_20121129_n93_01_10.RCC


title: 1342V021612_IFNb_20121129_n93_01_08.RCC


title: 1416V021612_IFNb_20121129_n93_01_09.RCC


title: 1237V021512_IFNb_20121129_n93_01_06.RCC


title: 1654V022112_IFNb_20121129_n93_01_11.RCC


title: 1684V021612_IFNb_20121129_n93_01_07.RCC


title: 1687V021512_IFNb_20121129_n93_01_04.RCC


title: 1688V021512_IFNb_20121129_n93_01_05.RCC


title: 1605V021412_IFNb_20121129_n93_01_01.RCC


title: 1627V021412_IFNb_20121129_n93_01_03.RCC


title: 1474V020912_IFNb_20121129_n92_01_11.RCC


title: 1540V020812_IFNb_20121129_n92_01_08.RCC


title: 1681V020812_IFNb_20121129_n92_01_10.RCC


title: 1589V020812_IFNb_20121129_n92_01_07.RCC


title: 1349V020712_IFNb_20121129_n92_01_05.RCC


title: 1680V020912_IFNb_20121129_n92_01_12.RCC


title: 1683V020712_IFNb_20121129_n92_01_02.RCC


title: 1567V020712_IFNb_20121129_n92_01_03.RCC


title: 1492V020812_IFNb_20121129_n92_01_06.RCC


title: 1359V020712_IFNb_20121129_n92_01_04.RCC


title: 0888V111511_IFNb_20121128_n91_01_07.RCC


title: 1559V111511_IFNb_20121128_n91_01_10.RCC


title: 1406V111511_IFNb_20121128_n91_01_08.RCC


title: 1205V111511_IFNb_20121128_n91_01_09.RCC


title: 0708V111611_IFNb_20121128_n91_01_12.RCC


title: 0980V111611_IFNb_20121128_n91_01_11.RCC


title: 1266V111511_IFNb_20121128_n91_01_06.RCC


title: 1399V111011_IFNb_20121128_n91_01_03.RCC


title: 1330V021412_IFNb_20121129_n93_01_02.RCC


title: 0490V111011_IFNb_20121128_n91_01_04.RCC


title: 0896V111511_IFNb_20121128_n91_01_05.RCC


title: 1478V020812_IFNb_20121129_n92_01_09.RCC


title: 1622V020112_IFNb_20121129_n92_01_01.RCC


title: 0916V111011_IFNb_20121128_n91_01_02.RCC


title: 1314V110911_IFNb_20121128_n90_01_11.RCC


title: 1437V110911_IFNb_20121128_n90_01_12.RCC


title: 0013V110911_IFNb_20121128_n91_01_01.RCC


title: 1242V110311_IFNb_20121128_n90_01_04.RCC


title: 1282V110811_IFNb_20121128_n90_01_08.RCC


title: 0481V110811_IFNb_20121128_n90_01_07.RCC


title: 1112V110911_IFNb_20121128_n90_01_10.RCC


title: 1411V110311_IFNb_20121128_n90_01_06.RCC


title: 1472V110311_IFNb_20121128_n90_01_03.RCC


title: 1231V110211_IFNb_20121128_n90_01_01.RCC


title: 0880V110811_IFNb_20121128_n90_01_09.RCC


title: 0760V110211_IFNb_20121128_n89_01_12.RCC


title: 1436V110311_IFNb_20121128_n90_01_05.RCC


title: 1195V110311_IFNb_20121128_n90_01_02.RCC


title: 0800V110211_IFNb_20121128_n89_01_09.RCC


title: 0266V110211_IFNb_20121128_n89_01_07.RCC


title: 1419V110111_IFNb_20121128_n89_01_06.RCC


title: 1538V110211_IFNb_20121128_n89_01_10.RCC


title: 1547V110111_IFNb_20121128_n89_01_04.RCC


title: 0719V110211_IFNb_20121128_n89_01_08.RCC


title: 1542V102611_IFNb_20121128_n89_01_01.RCC


title: 1131V102711_IFNb_20121128_n89_01_03.RCC


title: 1387V110211_IFNb_20121128_n89_01_11.RCC


title: 1272V110111_IFNb_20121128_n89_01_05.RCC


title: 0752V022112_IFNb_20121128_n88_01_12.RCC


title: 1366V102611_IFNb_20121128_n88_01_07.RCC


title: 1290V120611_IFNb_20121128_n88_01_10.RCC


title: 0679V120611_IFNb_20121128_n88_01_11.RCC


title: 1597V120611_IFNb_20121128_n88_01_09.RCC


title: 1563V120611_IFNb_20121128_n88_01_08.RCC


title: 1512V102511_IFNb_20121128_n88_01_03.RCC


title: 0277V102511_IFNb_20121128_n88_01_04.RCC


title: 1268V102711_IFNb_20121128_n89_01_02.RCC


title: 0615V102511_IFNb_20121128_n88_01_01.RCC


title: 1277V102511_IFNb_20121128_n88_01_02.RCC


title: 1360V102011_IFNb_20121123_n87_01_11.RCC


title: 1008V101911_IFNb_20121123_n87_01_09.RCC


title: 1077V101911_IFNb_20121123_n87_01_10.RCC


title: 1327V102011_IFNb_20121123_n87_01_12.RCC


title: 1302V101911_IFNb_20121123_n87_01_07.RCC


title: 1370V101311_IFNb_20121123_n87_01_01.RCC


title: 1331V012412_dNS1_20121123_n86_01_12.RCC


title: 1519V101311_IFNb_20121123_n87_01_02.RCC


title: 0641V101811_IFNb_20121123_n87_01_04.RCC


title: 1660V012412_dNS1_20121123_n86_01_08.RCC


title: 1672V012412_dNS1_20121123_n86_01_11.RCC


title: 0744V012412_dNS1_20121123_n86_01_10.RCC


title: 1274V102611_IFNb_20121128_n88_01_06.RCC


title: 1509V101811_IFNb_20121123_n87_01_05.RCC


title: 0308V012412_dNS1_20121123_n86_01_09.RCC


title: 0752V022112_dNS1_20121123_n86_01_04.RCC


title: 1380V101911_IFNb_20121123_n87_01_06.RCC


title: 1293V101911_IFNb_20121123_n87_01_08.RCC


title: 1686V022212_dNS1_20121123_n86_01_05.RCC


title: 1646V012412_dNS1_20121123_n86_01_07.RCC


title: 1026V022112_dNS1_20121123_n86_01_03.RCC


title: 1342V021612_dNS1_20121122_n85_01_11.RCC


title: 1625V022112_dNS1_20121123_n86_01_01.RCC


title: 1647V012412_dNS1_20121123_n86_01_06.RCC


title: 1627V021412_dNS1_20121122_n85_01_06.RCC


title: 1684V021612_dNS1_20121122_n85_01_10.RCC


title: 1330V021412_dNS1_20121122_n85_01_05.RCC


title: 1687V021512_dNS1_20121122_n85_01_07.RCC


title: 1605V021412_dNS1_20121122_n85_01_04.RCC


title: 1654V022112_dNS1_20121123_n86_01_02.RCC


title: 1349V020712_dNS1_20121122_n84_01_07.RCC


title: 1681V020812_dNS1_20121122_n84_01_12.RCC


title: 1679V020912_dNS1_20121122_n85_01_02.RCC


title: 1680V020912_dNS1_20121122_n85_01_03.RCC


title: 1474V020912_dNS1_20121122_n85_01_01.RCC


title: 1348V102611_IFNb_20121128_n88_01_05.RCC


title: 1589V020812_dNS1_20121122_n84_01_09.RCC


title: 1478V020812_dNS1_20121122_n84_01_11.RCC


title: 1416V021612_dNS1_20121122_n85_01_12.RCC


title: 1359V020712_dNS1_20121122_n84_01_06.RCC


title: 1540V020812_dNS1_20121122_n84_01_10.RCC


title: 1683V020712_dNS1_20121122_n84_01_04.RCC


title: 1492V020812_dNS1_20121122_n84_01_08.RCC


title: 1237V021512_dNS1_20121122_n85_01_09.RCC


title: 1105V111511_dNS1_20121122_n83_01_11.RCC


title: 1559V111511_dNS1_20121122_n83_01_12.RCC


title: 1688V021512_dNS1_20121122_n85_01_08.RCC


title: 1406V111511_dNS1_20121122_n83_01_09.RCC


title: 1567V020712_dNS1_20121122_n84_01_05.RCC


title: 0708V111611_dNS1_20121122_n84_01_02.RCC


title: 0980V111611_dNS1_20121122_n84_01_01.RCC


title: 0888V111511_dNS1_20121122_n83_01_08.RCC


title: 1622V020112_dNS1_20121122_n84_01_03.RCC


title: 0013V110911_dNS1_20121122_n83_01_02.RCC


title: 0896V111511_dNS1_20121122_n83_01_06.RCC


title: 1437V110911_dNS1_20121122_n83_01_01.RCC


title: 1399V111011_dNS1_20121122_n83_01_04.RCC


title: 0916V111011_dNS1_20121122_n83_01_03.RCC


title: 1282V110811_dNS1_20121122_n82_01_09.RCC


title: 1314V110911_dNS1_20121122_n82_01_12.RCC


title: 1436V110311_dNS1_20121122_n82_01_06.RCC


title: 1211V110811_dNS1_20121122_n82_01_10.RCC


title: 1472V110311_dNS1_20121122_n82_01_04.RCC


title: 1411V110311_dNS1_20121122_n82_01_07.RCC


title: 1205V111511_dNS1_20121122_n83_01_10.RCC


title: 1242V110311_dNS1_20121122_n82_01_05.RCC


title: 1195V110311_dNS1_20121122_n82_01_03.RCC


title: 1231V110211_dNS1_20121122_n82_01_02.RCC


title: 0760V110211_dNS1_20121122_n82_01_01.RCC


title: 0481V110811_dNS1_20121122_n82_01_08.RCC


title: 0490V111011_dNS1_20121122_n83_01_05.RCC


title: 1266V111511_dNS1_20121122_n83_01_07.RCC


title: 1387V110211_dNS1_20121122_n81_01_12.RCC


title: 0880V110811_dNS1_20121122_n82_01_11.RCC


title: 1538V110211_dNS1_20121122_n81_01_11.RCC


title: 1268V102711_dNS1_20121122_n81_01_03.RCC


title: 0719V110211_dNS1_20121122_n81_01_09.RCC


title: 0266V110211_dNS1_20121122_n81_01_08.RCC


title: 1419V110111_dNS1_20121122_n81_01_07.RCC


title: 1547V110111_dNS1_20121122_n81_01_05.RCC


title: 1542V102611_dNS1_20121122_n81_01_02.RCC


title: 0800V110211_dNS1_20121122_n81_01_10.RCC


title: 1272V110111_dNS1_20121122_n81_01_06.RCC


title: 1131V102711_dNS1_20121122_n81_01_04.RCC


title: 0308V012412_LPS_20121122_n80_01_10.RCC


title: 0744V012412_LPS_20121122_n80_01_11.RCC


title: 1660V012412_LPS_20121122_n80_01_09.RCC


title: 1646V012412_LPS_20121122_n80_01_08.RCC


title: 0752V022112_LPS_20121122_n80_01_05.RCC


title: 1686V022212_LPS_20121122_n80_01_06.RCC


title: 1647V012412_LPS_20121122_n80_01_07.RCC


title: 1416V021612_LPS_20121122_n80_01_01.RCC


title: 1026V022112_LPS_20121122_n80_01_04.RCC


title: 1331V012412_LPS_20121122_n81_01_01.RCC


title: 1672V012412_LPS_20121122_n80_01_12.RCC


title: 1237V021512_LPS_20121121_n79_01_10.RCC


title: 1342V021612_LPS_20121121_n79_01_12.RCC


title: 1688V021512_LPS_20121121_n79_01_09.RCC


title: 1684V021612_LPS_20121121_n79_01_11.RCC


title: 1627V021412_LPS_20121121_n79_01_07.RCC


title: 1654V022112_LPS_20121122_n80_01_03.RCC


title: 1687V021512_LPS_20121121_n79_01_08.RCC


title: 1605V021412_LPS_20121121_n79_01_05.RCC


title: 1330V021412_LPS_20121121_n79_01_06.RCC


title: 1679V020912_LPS_20121121_n79_01_03.RCC


title: 1680V020912_LPS_20121121_n79_01_04.RCC


title: 1474V020912_LPS_20121121_n79_01_02.RCC


title: 1681V020812_LPS_20121121_n79_01_01.RCC


title: 1589V020812_LPS_20121121_n78_01_10.RCC


title: 1625V022112_LPS_20121122_n80_01_02.RCC


title: 1492V020812_LPS_20121121_n78_01_09.RCC


title: 1349V020712_LPS_20121121_n78_01_08.RCC


title: 1478V020812_LPS_20121121_n78_01_12.RCC


title: 1540V020812_LPS_20121121_n78_01_11.RCC


title: 1567V020712_LPS_20121121_n78_01_06.RCC


title: 1683V020712_LPS_20121121_n78_01_05.RCC


title: 1105V111511_LPS_20121121_n77_01_12.RCC


title: 1205V111511_LPS_20121121_n77_01_11.RCC


title: 0980V111611_LPS_20121121_n78_01_02.RCC


title: 0708V111611_LPS_20121121_n78_01_03.RCC


title: 1406V111511_LPS_20121121_n77_01_10.RCC


title: 0888V111511_LPS_20121121_n77_01_09.RCC


title: 1266V111511_LPS_20121121_n77_01_08.RCC


title: 0490V111011_LPS_20121121_n77_01_06.RCC


title: 1399V111011_LPS_20121121_n77_01_05.RCC


title: 0896V111511_LPS_20121121_n77_01_07.RCC


title: 0013V110911_LPS_20121121_n77_01_03.RCC


title: 1314V110911_LPS_20121121_n77_01_01.RCC


title: 1359V020712_LPS_20121121_n78_01_07.RCC


title: 0880V110811_LPS_20121121_n76_01_10.RCC


title: 1559V111511_LPS_20121121_n78_01_01.RCC


title: 0481V110811_LPS_20121121_n76_01_07.RCC


title: 1622V020112_LPS_20121121_n78_01_04.RCC


title: 1282V110811_LPS_20121121_n76_01_08.RCC


title: 1411V110311_LPS_20121121_n76_01_06.RCC


title: 1242V110311_LPS_20121121_n76_01_04.RCC


title: 1472V110311_LPS_20121121_n76_01_03.RCC


title: 1210V110911_LPS_20121121_n76_01_11.RCC


title: 1112V110911_LPS_20121121_n76_01_12.RCC


title: 0760V110211_LPS_20121121_n75_01_12.RCC


title: 1387V110211_LPS_20121121_n75_01_11.RCC


title: 1530V101811_IFNb_20121123_n87_01_03.RCC


title: 1195V110311_LPS_20121121_n76_01_02.RCC


title: 1436V110311_LPS_20121121_n76_01_05.RCC


title: 1211V110811_LPS_20121121_n76_01_09.RCC


title: 1231V110211_LPS_20121121_n76_01_01.RCC


title: 1437V110911_LPS_20121121_n77_01_02.RCC


title: 0800V110211_LPS_20121121_n75_01_09.RCC


title: 0719V110211_LPS_20121121_n75_01_08.RCC


title: 1538V110211_LPS_20121121_n75_01_10.RCC


title: 0266V110211_LPS_20121121_n75_01_07.RCC


title: 1272V110111_LPS_20121121_n75_01_05.RCC


title: 1547V110111_LPS_20121121_n75_01_04.RCC


title: 1419V110111_LPS_20121121_n75_01_06.RCC


title: 1268V102711_LPS_20121121_n75_01_02.RCC


title: 1131V102711_LPS_20121121_n75_01_03.RCC


title: 1542V102611_LPS_20121121_n74_01_12.RCC


title: 1672V012412_unstim_20121121_n74_01_10.RCC


title: 1654V022112_unstim_20121121_n74_01_01.RCC


title: 0308V012412_unstim_20121121_n74_01_08.RCC


title: 1026V022112_unstim_20121121_n74_01_02.RCC


title: 1331V012412_unstim_20121121_n74_01_11.RCC


title: 0744V012412_unstim_20121121_n74_01_09.RCC


title: 0752V022112_unstim_20121121_n74_01_03.RCC


title: 1686V022212_unstim_20121121_n74_01_04.RCC


title: 1625V022112_unstim_20121121_n73_01_12.RCC


title: 1647V012412_unstim_20121121_n74_01_05.RCC


title: 1646V012412_unstim_20121121_n74_01_06.RCC


title: 1687V021512_unstim_20121121_n73_01_05.RCC


title: 1688V021512_unstim_20121121_n73_01_06.RCC


title: 1605V021412_unstim_20121121_n73_01_02.RCC


title: 1680V020912_unstim_20121121_n73_01_01.RCC


title: 1627V021412_unstim_20121121_n73_01_04.RCC


title: 1330V021412_unstim_20121121_n73_01_03.RCC


title: 1679V020912_unstim_20121121_n72_01_12.RCC


title: 1660V012412_unstim_20121121_n74_01_07.RCC


title: 1474V020912_unstim_20121121_n72_01_11.RCC


title: 1548V102611_LPS_20121121_n75_01_01.RCC


title: 1681V020812_unstim_20121121_n72_01_10.RCC


title: 1478V020812_unstim_20121121_n72_01_09.RCC


title: 1651V021512_unstim_20121121_n73_01_08.RCC


title: 1684V021612_unstim_20121121_n73_01_09.RCC


title: 1237V021512_unstim_20121121_n73_01_07.RCC


title: 1540V020812_unstim_20121121_n72_01_08.RCC


title: 1589V020812_unstim_20121121_n72_01_07.RCC


title: 1349V020712_unstim_20121121_n72_01_05.RCC


title: 1359V020712_unstim_20121121_n72_01_04.RCC


title: 1492V020812_unstim_20121121_n72_01_06.RCC


title: 1623V020212_unstim_20121120_n71_01_11.RCC


title: 1677V020112_unstim_20121120_n71_01_09.RCC


title: 1567V020712_unstim_20121121_n72_01_03.RCC


title: 1617V020212_unstim_20121120_n71_01_12.RCC


title: 1568V020212_unstim_20121121_n72_01_01.RCC


title: 1610V020112_unstim_20121120_n71_01_06.RCC


title: 1683V020712_unstim_20121121_n72_01_02.RCC


title: 1632V020112_unstim_20121120_n71_01_08.RCC


title: 1611V020112_unstim_20121120_n71_01_07.RCC


title: 1613V020112_unstim_20121120_n71_01_10.RCC


title: 1622V020112_unstim_20121120_n71_01_05.RCC


title: 1559V111511_unstim_20121120_n71_01_02.RCC


title: 1205V111511_unstim_20121120_n70_01_12.RCC


title: 0888V111511_unstim_20121120_n70_01_10.RCC


title: 1406V111511_unstim_20121120_n70_01_11.RCC


title: 1105V111511_unstim_20121120_n71_01_01.RCC


title: 0896V111511_unstim_20121120_n70_01_08.RCC


title: 0490V111011_unstim_20121120_n70_01_07.RCC


title: 0708V111611_unstim_20121120_n71_01_04.RCC


title: 1266V111511_unstim_20121120_n70_01_09.RCC


title: 1399V111011_unstim_20121120_n70_01_06.RCC


title: 0916V111011_unstim_20121120_n70_01_05.RCC


title: 0980V111611_unstim_20121120_n71_01_03.RCC


title: 1314V110911_unstim_20121120_n70_01_02.RCC


title: 1437V110911_unstim_20121120_n70_01_03.RCC


title: 0013V110911_unstim_20121120_n70_01_04.RCC


title: 1112V110911_unstim_20121120_n70_01_01.RCC


title: 0481V110811_unstim_20121120_n69_01_08.RCC


title: 1411V110311_unstim_20121120_n69_01_07.RCC


title: 1472V110311_unstim_20121120_n69_01_04.RCC


title: 1282V110811_unstim_20121120_n69_01_09.RCC


title: 1211V110811_unstim_20121120_n69_01_10.RCC


title: 1436V110311_unstim_20121120_n69_01_06.RCC


title: 1242V110311_unstim_20121120_n69_01_05.RCC


title: 1210V110911_unstim_20121120_n69_01_12.RCC


title: 0760V110211_unstim_20121120_n69_01_01.RCC


title: 0800V110211_unstim_20121120_n68_01_10.RCC


title: 1387V110211_unstim_20121120_n68_01_12.RCC


title: 0266V110211_unstim_20121120_n68_01_08.RCC


title: 1538V110211_unstim_20121120_n68_01_11.RCC


title: 1419V110111_unstim_20121120_n68_01_07.RCC


title: 1272V110111_unstim_20121120_n68_01_06.RCC


title: 1548V102611_unstim_20121120_n68_01_02.RCC


title: 1547V110111_unstim_20121120_n68_01_05.RCC


title: 0719V110211_unstim_20121120_n68_01_09.RCC


title: 1195V110311_unstim_20121120_n69_01_03.RCC


title: 1131V102711_unstim_20121120_n68_01_04.RCC


title: 1231V110211_unstim_20121120_n69_01_02.RCC


title: 1268V102711_unstim_20121120_n68_01_03.RCC


title: 0880V110811_unstim_20121120_n69_01_11.RCC


title: 1542V102611_unstim_20121120_n68_01_01.RCC


title: 1498V102011_IFNb_20121120_n67_01_12.RCC


title: 1370V101311_IFNb_20121120_n67_01_06.RCC


title: 1498V102011_IFNb_20121120_n67_01_11.RCC


title: 1370V101311_IFNb_20121120_n67_01_09.RCC


title: 0731V012412_LPS_20121120_n67_01_04.RCC


title: 0374V121311_LPS_20121120_n67_01_05.RCC


title: 1498V102011_IFNb_20121120_n67_01_08.RCC


title: 1519V101311_IFNb_20121120_n67_01_10.RCC


title: 1519V101311_IFNb_20121120_n67_01_07.RCC


title: 1501V011112_LPS_20121120_n67_01_02.RCC


title: 0272V011012_LPS_20121120_n66_01_09.RCC


title: 0312V011012_LPS_20121120_n66_01_11.RCC


title: 1650V011012_LPS_20121120_n66_01_10.RCC


title: 1350V011012_LPS_20121120_n66_01_12.RCC


title: 1224V011112_LPS_20121120_n67_01_01.RCC


title: 1505V121511_LPS_20121120_n66_01_07.RCC


title: 0330V121511_LPS_20121120_n66_01_06.RCC


title: 0775V121511_LPS_20121120_n66_01_08.RCC


title: 1142V121411_LPS_20121120_n66_01_05.RCC


title: 0374V121311_LPS_20121120_n66_01_01.RCC


title: 0638V121311_LPS_20121120_n66_01_02.RCC


title: 1467V121411_LPS_20121120_n66_01_03.RCC


title: 0514V120711_IFNb_20121120_n65_01_12.RCC


title: 1488V121411_LPS_20121120_n66_01_04.RCC


title: 1652V011912_LPS_20121120_n67_01_03.RCC


title: 1248V121311_LPS_20121120_n65_01_11.RCC


title: 0501V120811_LPS_20121120_n65_01_10.RCC


title: 1594V120811_LPS_20121120_n65_01_07.RCC


title: 1575V120711_LPS_20121120_n65_01_02.RCC


title: 1607V120811_LPS_20121120_n65_01_06.RCC


title: 1297V120711_LPS_20121120_n65_01_05.RCC


title: 1580V120811_LPS_20121120_n65_01_08.RCC


title: 1502V120811_LPS_20121120_n65_01_09.RCC


title: 1573V120711_LPS_20121120_n65_01_03.RCC


title: 1491V120711_LPS_20121120_n64_01_12.RCC


title: 1603V120711_LPS_20121120_n65_01_01.RCC


title: 1319V120611_LPS_20121120_n64_01_10.RCC


title: 0679V120611_LPS_20121120_n64_01_09.RCC


title: 0916V111011_LPS_20121121_n77_01_04.RCC


title: 1416V021612_unstim_20121121_n73_01_11.RCC


title: 1597V120611_LPS_20121120_n64_01_07.RCC


title: 1348V102611_LPS_20121120_n64_01_05.RCC


title: 1512V102511_LPS_20121120_n64_01_03.RCC


title: 1277V102511_LPS_20121120_n64_01_02.RCC


title: 1563V120611_LPS_20121120_n64_01_06.RCC


title: 0615V102511_LPS_20121120_n64_01_01.RCC


title: 1498V102011_LPS_20121119_n63_01_12.RCC


title: 1360V102011_LPS_20121119_n63_01_10.RCC


title: 1077V101911_LPS_20121119_n63_01_09.RCC


title: 0514V120711_LPS_20121120_n65_01_04.RCC


title: 1008V101911_LPS_20121119_n63_01_08.RCC


title: 1327V102011_LPS_20121119_n63_01_11.RCC


title: 1370V101311_LPS_20121119_n63_01_02.RCC


title: 1302V101911_LPS_20121119_n63_01_07.RCC


title: 0641V101811_LPS_20121119_n63_01_04.RCC


title: 0697V120611_LPS_20121120_n64_01_11.RCC


title: 1380V101911_LPS_20121119_n63_01_06.RCC


title: 1290V120611_LPS_20121120_n64_01_08.RCC


title: 1509V101811_LPS_20121119_n63_01_05.RCC


title: 1256V101311_LPS_20121119_n63_01_01.RCC


title: 1489V101211_LPS_20121119_n62_01_11.RCC


title: 1214V101211_LPS_20121119_n62_01_10.RCC


title: 0627V101311_LPS_20121119_n62_01_12.RCC


title: 1515V101111_LPS_20121119_n62_01_09.RCC


title: 1511V100611_LPS_20121119_n62_01_08.RCC


title: 0731V012412_IFNb_20121119_n62_01_07.RCC


title: 0277V102511_LPS_20121120_n64_01_04.RCC


title: 1652V011912_IFNb_20121119_n62_01_06.RCC


title: 1342V021612_unstim_20121121_n73_01_10.RCC


title: 1530V101811_LPS_20121119_n63_01_03.RCC


title: 1501V011112_IFNb_20121119_n62_01_05.RCC


title: 1350V011012_IFNb_20121119_n62_01_03.RCC


title: 0775V121511_IFNb_20121119_n61_01_11.RCC