title: Lower Internal part of stem,  rep bio 2,  rep tech 2

city: Villeneuve d'Ascq

first: Stephane

last: Fenart

address: Cité Scientifique

department: Biology

country: France

institute: University Lille 1

hyb_protocol: standard NimbleGen protocol

scan_protocol: standard NimbleGen protocol

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). Processed data then consist of log2(intensities) files  (.calls files).

organism: Linum usitatissimum

source_name: Greenhouse sample

label_protocol: standard NimbleGen protocol

growth_protocol: all plant material were grown in greenhouse

extract_protocol: Total RNA was extracted using the NuceloSpin RNA Plant (Macherey-Nagel). RNA quality and concentration was determined by analysis with an Experion bioanalyzer (Biorad) using RNA Std chips.

tag: tissue

value: Lower Internal part of stem


title: Noto-GFP_positive_sort_rep2

status: Public on Oct 01 2011

type: RNA

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

country: USA

institute: University of Wisconsin-Madison

description: replicate 2: posterior regions dissected and pooled from 39 embryos; ~4300 Noto-GFP positive cells sorted

hyb_protocol: Samples were hybridized to Affymetrix MOE430v2 arrays using the manufacturer's protocols

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Data was analyzed using GCOS software v1.4

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Noto-GFP positive cells sorted from the posterior of E8.5 mouse embryos

label_protocol: Total RNA was amplified and labeled using the AFFYMETRIX GeneChip® Two-Cycle Target Labeling Kit

growth_protocol: Litters of heterozygous Noto-GFP embryos (mixed 129S3;ICR background) were collected at embryonic day (E) 8.5 (median somite number 6; ~25-50 embryos per experiment)

extract_protocol: Small-scale RNA extraction was performed using Trizol or Trizol LS as per the manufacturer's instructions. Sigma GeneElute linear polyacrylamide was used as carrier

treatment_protocol: The region posterior to the SI-SII somite boundary was dissected, pooled, and dissociated using 1% trypsin in PBS. Noto-GFP+ cells were sorted from Noto-GFP- cells and both populations were collected (~2600-6600 cells per experiment)

tag: STRAIN

tag: GENDER

value: MIXED


title: Lower External part of stem,  rep bio 1,  rep tech 2

value: Lower External part of stem


title: Lower Internal part of stem,  rep bio 2,  rep tech 1


title: Middle Internal part of stem,  rep bio 2,  rep tech 2

value: Middle Internal part of stem


title: Middle Internal part of stem,  rep bio 1,  rep tech 1


title: Lower Internal part of stem,  rep bio 1,  rep tech 1


title: Noto-GFP_positive_sort_rep1

description: replicate 1: posterior regions dissected and pooled from 23 embryos; ~2600 Noto-GFP positive cells sorted


title: Middle Internal part of stem,  rep bio 2,  rep tech 1


title: Middle External part of stem,  rep bio 2,  rep tech 1

value: Middle External part of stem


title: Lower External part of stem,  rep bio 2,  rep tech 1


title: Middle Internal part of stem,  rep bio 1,  rep tech 2


title: Lower External part of stem,  rep bio 1,  rep tech 1


title: Lower Internal part of stem,  rep bio 1,  rep tech 2


title: Lower External part of stem,  rep bio 2,  rep tech 2


title: Middle External part of stem,  rep bio 2,  rep tech 2


title: Upper Internal part of stem,  rep bio 2,  rep tech 2

value: Upper Internal part of stem


title: Middle External part of stem,  rep bio 1,  rep tech 2


title: Upper Internal part of stem,  rep bio 1,  rep tech 2


title: Upper Internal part of stem,  rep bio 1,  rep tech 1


title: Middle External part of stem,  rep bio 1,  rep tech 1


title: Upper External part of stem,  rep bio 1,  rep tech 2

value: Upper External part of stem


title: Upper Internal part of stem,  rep bio 2,  rep tech 1


title: Upper External part of stem,  rep bio 2,  rep tech 1


title: Internal part of whole stem,  rep bio 2,  rep tech 2

value: Internal part of whole stem


title: Internal part of whole stem,  rep bio 1,  rep tech 2


title: Upper External part of stem,  rep bio 1,  rep tech 1


title: Upper External part of stem,  rep bio 2,  rep tech 2


title: Internal part of whole stem,  rep bio 1,  rep tech 1


title: Internal part of whole stem,  rep bio 2,  rep tech 1


title: External part of whole stem,  rep bio 2,  rep tech 1

value: External part of whole stem


title: External part of whole stem,  rep bio 1,  rep tech 2


title: External part of whole stem,  rep bio 1,  rep tech 1


title: External part of whole stem,  rep bio 2,  rep tech 2


title: 988-012_Peripheral_L_POP_entire_28MAR2007_BWR-0261

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: Gene expression profiling of peripheral plaque. 290 subjects from CISTER study

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

organism: Homo sapiens

source_name: Peripheral plaque

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: Peripheral plaque

tag: sample id


title: 880-006_Peripheral_L_AT_mid_05MAR2007_BWR-0212


title: 980-005_Peripheral_R_SFA_prox_29MAR2007_BWR-0263


title: 901-006_Peripheral_R_SFA_dist_09APR2007_BWR-0287


title: 951-009_Peripheral_L_SFA_prox_23MAR2007_BWR-0237


title: 988-002_Peripheral_L_SFA_entire_08FEB2007_BWR-0094


title: 988-012_Peripheral_L_SFA_prox_28MAR2007_BWR-0260


title: 119-043_Peripheral_L_SFA_dist_30MAR2007_BWR-0305


title: 880-004_Peripheral_L_POP_entire_06FEB2007_BWR-0131


title: 880-005_Peripheral_L_PER_prox_07FEB2007_BWR-0134


title: 985-008_Peripheral_R_SFA_11APR2007_BWR


title: 880-009_Peripheral_R_PT_entire_03APR2007_BWR-0347


title: 119-034_Peripheral_L_SFA_mid_06MAR2007_BWR-0184


title: 988-015_Peripheral_L_POP_02MAY2007_BWR


title: 988-013_Peripheral_L_SFA_29MAR2007_BWR


title: 985-006_Peripheral_L_SFA_10APR2007_BWR


title: 119-026_Peripheral_R_SFA_prox_23FEB2007_BWR-0156


title: 985-005_Peripheral_L_SFA_10APR2007_BWR


title: 901-027_Peripheral_L_POP_04MAY2007_BWR


title: 985-007_Peripheral_L_SFA_11APR2007_BWR


title: 951-009_Peripheral_L_POP_23MAR2007_BWR


title: 901-021_Peripheral_R_SFA_02MAY2007_BWR


title: 980-006_Peripheral_L_SFA_05APR2007_BWR


title: 901-023_Peripheral_L_CFA_03MAY2007_BWR


title: 901-029_Peripheral_L_SFA_07MAY2007_BWR


title: 901-013_Peripheral_R_AT_19APR2007_BWR


title: 901-020_Peripheral_L_CFA_01MAY2007_BWR


title: 980-002_Peripheral_L_SFA_22FEB2007_BWR


title: 901-010_Peripheral_L_SFA_12APR2007_BWR


title: 901-031_Peripheral_L_POP_08MAY2007_BWR


title: 901-006_Peripheral_R_PT_09APR2007_BWR


title: 901-012_Peripheral_R_SFA_18APR2007_BWR


title: 901-009_Peripheral_L_POP_12APR2007_BWR


title: 901-003_Peripheral_L_SFA_05APR2007_BWR


title: 901-002_Peripheral_L_POP_04APR2007_BWR


title: 901-002_Peripheral_L_SFA_04APR2007_BWR


title: 901-001_Peripheral_R_SFA_23MAR2007_BWR


title: 880-011_Peripheral_R_SFA_26APR2007_BWR


title: 880-007_Peripheral_R_SFA_07MAR2007_BWR


title: 880-010_Peripheral_R_SFA_09APR2007_BWR


title: 880-009_Peripheral_R_SFA_03APR2007_BWR


title: 880-010_Peripheral_L_SFA_09APR2007_BWR


title: 880-006_Peripheral_L_SFA_05MAR2007_BWR


title: 880-005_Peripheral_R_SFA_21FEB2007_BWR


title: 880-012_Peripheral_R_SFA_01MAY2007_BWR


title: 880-008_Peripheral_L_SFA_13MAR2007_BWR


title: 880-005_Peripheral_R_POP_21FEB2007_BWR


title: 880-005_Peripheral_L_SFA_07FEB2007_BWR


title: 119-027_Peripheral_L_SFA_27FEB2007_BWR


title: 901-002_Peripheral_L_AT_04APR2007_BWR


title: 840-019_Peripheral_L_SFA_30APR2007_BWR


title: 880-005_Peripheral_L_POP_07FEB2007_BWR


title: 880-001_Peripheral_L_SFA_11JAN2007_BWR


title: 880-004_Peripheral_L_OTH_06FEB2007_BWR


title: 840-014_Peripheral_L_SFA_28FEB2007_BWR


title: 119-048_Peripheral_L_SFA_10APR2007_BWR


title: 114-025_Peripheral_R_SFA_30MAR2007_BWR


title: 988-011_Peripheral_R_SFA_26MAR2007_BWR


title: 057-003_Peripheral_L_POP_01MAY2007_BWR


title: 951-006_Peripheral_R_SFA_16JAN2007_BWR


title: 988-006_Peripheral_L_SFA_22MAR2007_BWR


title: 986-001_Peripheral_R_SFA_02MAY2007_BWR


title: 962-004_Peripheral_R_SFA_20APR2007_BWR


title: 980-003_Peripheral_L_SFA_08FEB2007_BWR


title: 951-009_Peripheral_R_SFA_04MAY2007_BWR


title: 114-027_Peripheral_L_SFA_04APR2007_BWR


title: 962-005_Peripheral_R_SFA_20APR2007_BWR


title: 980-001_Peripheral_L_SFA_20FEB2007_BWR


title: 985-003_Peripheral_L_POP_20MAR2007_BWR


title: 988-005_Peripheral_R_SFA_28FEB2007_BWR


title: 962-006_Peripheral_L_SFA_20APR2007_BWR


title: 050-003_Peripheral_R_POP_11APR2007_BWR


title: 962-001_Peripheral_L_SFA_27MAR2007_BWR


title: 988-003_Peripheral_R_SFA_09FEB2007_BWR


title: 920-008_Peripheral_L_SFA_19MAR2007_BWR


title: 988-010_Peripheral_L_SFA_16MAR2007_BWR


title: 920-008_Peripheral_R_SFA_23MAR2007_BWR


title: 951-008_Peripheral_L_SFA_09MAR2007_BWR


title: 920-007_Peripheral_L_POP_13FEB2007_BWR


title: 951-004_Peripheral_L_SFA_05JAN2007_BWR


title: 951-005_Peripheral_R_SFA_16FEB2007_BWR


title: 920-007_Peripheral_L_SFA_13FEB2007_BWR


title: 901-028_Peripheral_L_POP_04MAY2007_BWR


title: 880-011_Peripheral_R_POP_26APR2007_BWR


title: 901-022_Peripheral_R_SFA_02MAY2007_BWR


title: 920-004_Peripheral_L_SFA_25JAN2007_BWR


title: 901-011_Peripheral_L_SFA_18APR2007_BWR


title: 901-019_Peripheral_R_SFA_01MAY2007_BWR


title: 901-017_Peripheral_L_SFA_30APR2007_BWR


title: 901-007_Peripheral_R_SFA_10APR2007_BWR


title: 901-004_Peripheral_L_SFA_06APR2007_BWR


title: 901-005_Peripheral_R_SFA_09APR2007_BWR


title: 900-006_Peripheral_L_SFA_22FEB2007_BWR


title: 900-007_Peripheral_L_SFA_26FEB2007_BWR


title: 901-013_Peripheral_R_SFA_19APR2007_BWR


title: 901-008_Peripheral_R_CFA_10APR2007_BWR


title: 901-025_Peripheral_R_TPT_03MAY2007_BWR


title: 900-002_Peripheral_L_POP_09FEB2007_BWR


title: 901-027_Peripheral_L_SFA_04MAY2007_BWR


title: 840-020_Peripheral_L_SFA_04MAY2007_BWR


title: 901-015_Peripheral_R_SFA_19APR2007_BWR


title: 900-012_Peripheral_R_SFA_25APR2007_BWR


title: 901-025_Peripheral_R_CFA_03MAY2007_BWR


title: 900-001_Peripheral_R_POP_07FEB2007_BWR


title: 900-003_Peripheral_L_SFA_23FEB2007_BWR


title: 900-004_Peripheral_R_SFA_14FEB2007_BWR


title: 840-013_Peripheral_L_SFA_21FEB2007_BWR


title: 840-009_Peripheral_L_SFA_30JAN2007_BWR


title: 840-012_Peripheral_R_SFA_20FEB2007_BWR


title: 820-057_Peripheral_L_SFA_02MAY2007_BWR


title: 820-055_Peripheral_L_SFA_02MAY2007_BWR


title: 820-054_Peripheral_R_SFA_25APR2007_BWR


title: 820-053_Peripheral_R_SFA_11APR2007_BWR


title: 840-017_Peripheral_L_SFA_13APR2007_BWR


title: 820-056_Peripheral_L_SFA_02MAY2007_BWR


title: 820-050_Peripheral_R_SFA_04APR2007_BWR


title: 820-052_Peripheral_R_SFA_04APR2007_BWR


title: 820-048_Peripheral_R_SFA_08MAR2007_BWR


title: 820-036_Peripheral_R_SFA_14DEC2006_BWR


title: 820-046_Peripheral_R_SFA_07MAR2007_BWR


title: 820-040_Peripheral_L_SFA_18JAN2007_BWR


title: 820-045_Peripheral_L_SFA_07MAR2007_BWR


title: 820-034_Peripheral_L_SFA_11DEC2006_BWR


title: 820-045_Peripheral_R_SFA_25APR2007_BWR


title: 820-037_Peripheral_R_SFA_15DEC2006_BWR


title: 820-036_Peripheral_R_TPT_14DEC2006_BWR


title: 800-015_Peripheral_L_POP_01FEB2007_BWR


title: 820-041_Peripheral_L_SFA_08FEB2007_BWR


title: 820-044_Peripheral_L_SFA_05MAR2007_BWR


title: 820-038_Peripheral_R_SFA_21DEC2006_BWR


title: 820-032_Peripheral_L_SFA_07DEC2006_BWR


title: 119-050_Peripheral_R_SFA_17APR2007_BWR


title: 820-033_Peripheral_R_POP_11DEC2006_BWR


title: 119-058_Peripheral_L_SFA_04MAY2007_BWR


title: 800-001_Peripheral_R_SFA_30MAR2007_BWR


title: 820-035_Peripheral_L_SFA_14DEC2006_BWR


title: 119-055_Peripheral_L_SFA_26APR2007_BWR


title: 119-057_Peripheral_R_SFA_27APR2007_BWR


title: 119-056_Peripheral_L_SFA_27APR2007_BWR


title: 119-039_Peripheral_R_SFA_23MAR2007_BWR


title: 119-036_Peripheral_R_SFA_13MAR2007_BWR


title: 119-040_Peripheral_L_SFA_27MAR2007_BWR


title: 119-046_Peripheral_R_SFA_06APR2007_BWR


title: 119-031_Peripheral_R_SFA_06MAR2007_BWR


title: 119-025_Peripheral_UNK_SFA_22FEB2007_BWR


title: 119-029_Peripheral_R_SFA_28FEB2007_BWR


title: 119-029_Peripheral_UNK_SFA_28FEB2007_BWR


title: 119-049_Peripheral_L_SFA_13APR2007_BWR


title: 119-028_Peripheral_L_SFA_27FEB2007_BWR


title: 119-024_Peripheral_L_SFA_16FEB2007_BWR


title: 119-030_Peripheral_UNK_SFA_02MAR2007_BWR


title: 119-019_Peripheral_L_SFA_13FEB2007_BWR


title: 119-017_Peripheral_UNK2_SFA_06FEB2007_BWR


title: 119-022_Peripheral_L_SFA_16FEB2007_BWR


title: 119-015_Peripheral_R_SFA_02FEB2007_BWR


title: 119-018_Peripheral_L_SFA_08FEB2007_BWR


title: 119-006_Peripheral_L_SFA_16JAN2007_BWR


title: 119-004_Peripheral_R_SFA_16JAN2007_BWR


title: 119-009_Peripheral_R_SFA_26JAN2007_BWR


title: 119-003_Peripheral_R_SFA_16JAN2007_BWR


title: 119-013_Peripheral_R_SFA_02FEB2007_BWR


title: 119-002_Peripheral_R_CFA_13FEB2007_BWR


title: 119-011_Peripheral_L_SFA_30JAN2007_BWR


title: 119-010_Peripheral_L_SFA_29JAN2007_BWR


title: 119-002_Peripheral_R_SFA_13FEB2007_BWR


title: 114-037_Peripheral_R_SFA_02MAY2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 6

city: St John's

first: Tiago

last: Hori

state: NL

address: 0 Marine Lab Rd

department: Ocean Sciences Centre

country: Canada

institute: Memorial University of Newfoundland

description: Biological replicate 5 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

hyb_protocol: Arrays were prehybridized at 42°C in Nexterion Oligo Prehyb Buffer (Schott Nexterion cat. nr 1116889) for at least 2 hours. Arrays were washed at room temperature for with 0.1% SDS for 5 minutes, followed by 3 5-minute washes with water. Slides were dried by spinning them for 5 minutes at 200x g and kept at 42°C. LifterSlips were prepared by washing them sequentially with water, water, 70% ethanol and 100% ethanol and drying them using compressed air. For each array two labeled cDNAs were combined (one sample, one reference) and 2 μl of LNA blocker (Genisphere) and 40 μl of prewarmed 2x formamide-based hybridization buffer (Genisphere) was added. These samples were incubated at 80°C for 10 minutes and then kept at 42°C. Pre-warmed arrays were put in Corning hybridization chambers, LifterSlips were applied and the samples were loaded under the LifterSlips. Hybridizations were performed overnight for ~16 hours in a water bath at 42°C. After hybridization, arrays were washed at room temperature for 15 minutes with 2xSSC/0.2% SDS which was pre-warmed at 42°C. Next slides were washed  at room temperature for 15 minutes with 2xSSC, followed by 2 15-minute washes with 0.2xSSC. Slides were dried by spinning them for 5 minutes at 200x g.

scan_protocol: Arrays were scanned at a resolution of 10 μm using a ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin Elmer).

data_processing: Signal intensity data was extracted from tiff images using Imagene v7.5. In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot  was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (average background + 2* SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene. Logratios of duplicate spots were averaged.

label: ALEXA 647

organism: Gadus morhua

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 6

label_protocol: 5 ug of DNAse-treated column-purified total RNA was labeled using Invitrogen SuperScript Direct cDNA Labeling kit according to the manufacturer's protocol. Test samples were always labeled with AlexaFluor 647, the common reference was always labeled with AlexaFluor 555.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) following manufacturer's instructions. Total RNA was treated with DNAse I and column-purified using the RNeasy Mi-Elute Cleanup kit (Qiagen) following manufacturer's instructions.

treatment_protocol: At sampling time fish were euthanized by a lethal dose (0.4 g/l) of tricaine methanesulphonate and spleens were collected in RNAse-free 1.5 ml tubes, flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Spleen

tag: developmental stage

value: Naïve juveniles

tag: population

value: New Brunswick Atlantic cod

tag: treatment protocol

value: Exposed to chronic temperature increases and subsequently injected with pIC

label: ALEXA 555

source_name: Common Reference

value: Pool with equal contribution of RNA from every individual involved in the microarray experiment


title: p62_wild_type

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Human Bone marrow

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.  cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Human bone marrow mononuclear cells transduced with p62-EV, p62WT, p62P392L, retroviral expression vectors.

extract_protocol: Total RNA isolated from above treated pre-osteoclast cells.

treatment_protocol: Stimulated with M-CSF and RANKL for 48 h.

tag: tissue origin

value: normal human bone marrow

tag: cell type

value: mononuclear cells


title: p62_P392L


title: 119-007_Peripheral_R_SFA_23JAN2007_BWR


title: 119-001_Peripheral_L_SFA_12JAN2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 5

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 5


title: pIC injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 4

description: Biological replicate 4 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 4


title: p62_empty_vector

description: EV


title: 114-033_Peripheral_L_SFA_25APR2007_BWR


title: 114-036_Peripheral_L_SFA_02MAY2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 1

description: Biological replicate 1 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 1


title: pIC injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 2

description: Biological replicate 2 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 2


title: 114-024_Peripheral_L_SFA_28MAR2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 3

description: Biological replicate 3 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 3


title: 114-022_Peripheral_L_SFA_22MAR2007_BWR


title: Measles Virus Nucleocapsid Protein

growth_protocol: Human bone marrow mononuclear cells transduced with EV, MVNP retroviral expression vectors.

value: bone marrow


title: Empty Vector


title: 114-030_Peripheral_R_CFA_18APR2007_BWR


title: 114-019_Peripheral_L_SFA_16MAR2007_BWR


title: PBS injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 4

description: Biological replicate 4 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 4

value: Exposed to chronic temperature increases and subsequently injected with PBS


title: PBS injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 3

description: Biological replicate 3 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 3


title: PBS injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 5

description: Biological replicate 5 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 5


title: PBS injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 6

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 6


title: 114-015_Peripheral_R_SFA_08MAR2007_BWR


title: 114-016_Peripheral_R_SFA_14MAR2007_BWR


title: 114-006_Peripheral_R_SFA_21FEB2007_BWR


title: 114-008_Peripheral_R_SFA_21FEB2007_BWR


title: 114-020_Peripheral_L_SFA_21MAR2007_BWR


title: PBS injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 2

description: Biological replicate 2 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 2


title: pIC injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 6

description: Biological replicate 6 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 6

value: Held at 10°C and subsequently injected with pIC


title: 114-005_Peripheral_L_SFA_08FEB2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 5

description: Biological replicate 5 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 5


title: 114-003_Peripheral_L_CFA_05FEB2007_BWR


title: 820-031_Peripheral_L_SFA_30NOV2006_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 4

description: Biological replicate 4 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 4


title: 114-004_Peripheral_L_SFA_05FEB2007_BWR

source_name: Peripheral plaque


title: PBS injected fish exposed to chronic increases in temperature and sampled 24 hours post injection- - rep 1

description: Biological replicate 1 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 24 hours post injection- - replicate 1


title: 114-002_Peripheral_R_PRO_02FEB2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 3

description: Biological replicate 3 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 3

source_name: Common Reference


title: 057-003_Peripheral_R_SFA_09APR2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 2

description: Biological replicate 2 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 2


title: 050-009_Peripheral_L_SFA_01MAY2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 1

description: Biological replicate 1 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 1


title: 057-001_Peripheral_L_SFA_26MAR2007_BWR

description: Gene expression profiling of peripheral plaque. 290 subjects from CISTER study


title: PBS injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 5

description: Biological replicate 5 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 5

value: Held at 10°C and subsequently injected with PBS


title: PBS injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 3

description: Biological replicate 3 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 3


title: PBS injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 6

description: Biological replicate 6 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 6


title: PBS injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 1

description: Biological replicate 1 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 1


title: 034-002_Peripheral_L_SFA_12APR2007_BWR


title: 013-006_Peripheral_L_SFA_20APR2007_BWR


title: PBS injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 4

description: Biological replicate 4 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 4


title: 039-002_Peripheral_UNK_SFA_18APR2007_BWR


title: 013-005_Peripheral_L_SFA_16APR2007_BWR


title: PBS injected fish held at 10C prior to injection and sampled at 24 hours post injection - rep 2

description: Biological replicate 2 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 24 hours post injection - replicate 2


title: 050-006_Peripheral_R_SFA_17APR2007_BWR


title: 013-003_Peripheral_R_SFA_06APR2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 6

description: Biological replicate 5 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 6


title: 988-014_Peripheral_L_SFA_11APR2007_BWR


title: PBS injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 6

description: Biological replicate 5 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 6


title: 988-016_Peripheral_R_SFA_27APR2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 1

description: Biological replicate 1 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 1


title: pIC injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 5

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 5


title: pIC injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 2

description: Biological replicate 2 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 2


title: 988-004_Peripheral_L_SFA_20FEB2007_BWR

source_name: Peripheral plaque


title: 342770_gal_TS_wtCy5_ccpACy3

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman TG et al., 2006b

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of copY mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Net intensity (tr.mean) {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to transition (TS) phase in CDM medium with galactose as the sole carbon source

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from Four replicate cultures.

tag: genotype/variation

value: Wild type

source_name: Net intensity (tr.mean) {B}

value: ccpA mutant


title: 342704_gal_TS_wtCy5_ccpACy3

description: Sample 1


title: 985-002_Peripheral_R_SFA_07MAR2007_BWR


title: PBS injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 5

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 5

source_name: Common Reference


title: 988-008_Peripheral_R_POP_09MAR2007_BWR


title: 186055_gal_M_wtCy3-ccpACy5

description: Sample 3

growth_protocol: Cells were grown to MID-log phase in CDM medium with Galactose as the sole carbon source


title: pIC injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 4

description: Biological replicate 4 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 4


title: 985-004_Peripheral_L_SFA_20MAR2007_BWR


title: pIC injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 3

description: Biological replicate 3 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with pIC

source_name: pIC injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 3


title: 962-003_Peripheral_L_CFA_19APR2007_BWR


title: 186053_gal_M_wtCy5-ccpACy3

description: Sample 2


title: 980-004_Peripheral_L_SFA_29MAR2007_BWR


title: 962-002_Peripheral_L_SFA_12APR2007_BWR


title: 953-002_Peripheral_L_SFA_19APR2007_BWR


title: 920-009_Peripheral_R_SFA_23APR2007_BWR


title: 186051_gal_M_wtCy5-ccpACy3

description: Sample 1


title: 185698_gluc_TS_wtCy3_ccpACy5

description: Sample 2

growth_protocol: Cells were grown to transition (TS) phase in CDM medium with glucose as the sole carbon source


title: 185719_gluc_TS_wtCy3_ccpACy5

description: Sample 3


title: 185519_gluc_TS_wtCy5_ccpACy3

description: Sample 1


title: 186049_gluc_M_wtCy5-ccpACy3

description: Sample 3

growth_protocol: Cells were grown to MID-log phase in CDM medium with Glucose as the sole carbon source


title: 920-009_Peripheral_L_SFA_09APR2007_BWR


title: 185720_gluc_M_wtCy3-ccpACy5

description: Sample 2


title: 920-005_Peripheral_L_SFA_26JAN2007_BWR


title: PBS injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 4

description: Biological replicate 4 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 4


title: 901-018_Peripheral_L_SFA_01MAY2007_BWR


title: 901-026_Peripheral_R_CFA_04MAY2007_BWR


title: PBS injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 3

description: Biological replicate 3 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 3


title: 901-030_Peripheral_R_SFA_07MAY2007_BWR


title: 185716_gluc_M_wtCy3-ccpACy5

description: Sample 1


title: PBS injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 1

description: Biological replicate 1 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 1


title: PBS injected fish exposed to chronic increases in temperature and sampled 6 hours post injection- - rep 2

description: Biological replicate 2 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days) and subsequently injected with PBS

source_name: PBS injected fish that were exposed to chronic inccreases in temperature and sampled 6 hours post injection- - replicate 2


title: pIC injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 6

description: Biological replicate 6 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 6


title: 901-016_Peripheral_L_SFA_20APR2007_BWR

description: Gene expression profiling of peripheral plaque. 290 subjects from CISTER study


title: 920-006_Peripheral_R_SFA_01FEB2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 4

description: Biological replicate 4 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 4


title: pIC injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 3

description: Biological replicate 3 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 3


title: 901-014_Peripheral_R_SFA_19APR2007_BWR


title: 900-003_Peripheral_R_SFA_12FEB2007_BWR


title: 901-009_Peripheral_L_CFA_12APR2007_BWR


title: 900-005_Peripheral_L_SFA_21FEB2007_BWR


title: 900-001_Peripheral_L_SFA_23FEB2007_BWR


title: 900-011_Peripheral_L_SFA_20APR2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 5

description: Biological replicate 5 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 5


title: 900-010_Peripheral_L_POP_10APR2007_BWR


title: 840-016_Peripheral_L_SFA_03APR2007_BWR


title: 900-009_Peripheral_L_SFA_23MAR2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 2

description: Biological replicate 2 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 2


title: 900-001_Peripheral_L_POP_23FEB2007_BWR


title: PBS injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 5

description: Biological replicate 5 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 5


title: 840-011_Peripheral_L_SFA_13FEB2007_BWR

source_name: Peripheral plaque


title: PBS injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 6

description: Biological replicate 6 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 6


title: 840-010_Peripheral_R_SFA_06FEB2007_BWR


title: pIC injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 1

description: Biological replicate 1 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with pIC.

source_name: pIC injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 1


title: Pre-injected fish exposed to chronic increases in temperature  - rep 6

description: Biological replicate 6 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days)

source_name: Pre-injected fish that were exposed to chronic inccreases in temperature  - replicate 6

value: Exposed to chronic temperature increases


title: 840-014_Peripheral_R_SFA_14MAR2007_BWR


title: 820-049_Peripheral_L_SFA_28MAR2007_BWR


title: PBS injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 3

description: Biological replicate 3 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 3

source_name: Common Reference


title: PBS injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 2

description: Biological replicate 2 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 2


title: PBS injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 1

description: Biological replicate 1 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 1


title: 119-047_Peripheral_L_SFA_06APR2007_BWR


title: 119-044_Peripheral_R_SFA_03APR2007_BWR


title: Pre-injected fish exposed to chronic increases in temperature  - rep 5

description: Biological replicate 5 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days)

source_name: Pre-injected fish that were exposed to chronic inccreases in temperature  - replicate 5


title: PBS injected fish held at 10C prior to injection and sampled at 6 hours post injection - rep 4

description: Biological replicate 4 of 6. Control fish that were held at 10C for the duration of the experiment and subsequently injected with PBS.

source_name: PBS injected fish that were held at 10C prior to injection and sapled at 6 hours post injection - replicate 4


title: 840-018_Peripheral_R_SFA_24APR2007_BWR


title: 760-002_Peripheral_R_SFA_27APR2007_BWR


title: 820-043_Peripheral_L_SFA_01MAR2007_BWR


title: Pre-injected fish exposed to chronic increases in temperature  - rep 3

description: Biological replicate 3 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days)

source_name: Pre-injected fish that were exposed to chronic inccreases in temperature  - replicate 3


title: Pre-injected fish exposed to chronic increases in temperature  - rep 4

description: Biological replicate 4 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days)

source_name: Pre-injected fish that were exposed to chronic inccreases in temperature  - replicate 4


title: 800-002_Peripheral_R_SFA_11APR2007_BWR


title: Pre-injected fish exposed to chronic increases in temperature  - rep 2

description: Biological replicate 2 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days)

source_name: Pre-injected fish that were exposed to chronic inccreases in temperature  - replicate 2


title: Pre-injected fish held at 10C - rep 5

description: Biological replicate 5 of 6. Control fish that were held at 10C for the duration of the experiment.

source_name: Pre-injected fish held at 10C - replicate 5

value: Held at 10°C


title: Pre-injected fish exposed to chronic increases in temperature  - rep 1

description: Biological replicate 1 of 6. Experimental fish that were exposed to chronic temperature increases (~1°C every 5 days)

source_name: Pre-injected fish that were exposed to chronic inccreases in temperature  - replicate 1


title: 119-021_Peripheral_L_SFA_16FEB2007_BWR

description: Gene expression profiling of peripheral plaque. 290 subjects from CISTER study


title: 119-037_Peripheral_R_SFA_13MAR2007_BWR


title: Pre-injected fish held at 10C - rep 4

description: Biological replicate 4 of 6. Control fish that were held at 10C for the duration of the experiment.

source_name: Pre-injected fish held at 10C - replicate 4


title: 119-014_Peripheral_R_SFA_02FEB2007_BWR


title: 114-016_Peripheral_R_POP_14MAR2007_BWR


title: 119-008_Peripheral_L_SFA_26JAN2007_BWR


title: 114-031_Peripheral_L_SFA_19APR2007_BWR


title: 114-018_Peripheral_R_SFA_15MAR2007_BWR


title: Pre-injected fish held at 10C - rep 2

description: Biological replicate 2 of 6. Control fish that were held at 10C for the duration of the experiment.

source_name: Pre-injected fish held at 10C - replicate 2


title: Embryo E. tarda immersed rep2

city: Amsterdam

first: Oliver

last: Stockhammer

state: NH

address: Meibergdreef 15

department: Medical Microbiology

institute: AMC

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 2 of 3: Zebrafish embryos infected with E. tarda

hyb_protocol: The dual colour hybridization of the microarray chips was performed at ServiceXS (ServiceXS, Leiden, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling.

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos used for the bacterial immersion assay were dechorionated with pronase (2 mg/ml) at 24 hpf. At 25 hpf they were immersed in bacterial suspensions of E. tarda (1E8 CFU/ml), E. coli (1E8 CFU/ml), Pseudomonas aeruginosa PAO1 (1E9 CFU/ml) or P. aeruginosa PA14 (1E9 CFU/ml) for 5 h after which the embryos were quenched in liquid nitrogen.

tag: comment

value: 24 hpf embryos were dechorionated with pronase (2 mg/ml) and at 25 hpf immersed for 5 hours in pure eggwater (60 µg/ml Instant Ocean salts) or eggwater containing 1E8 CFU/ml of E. tarda or E. coli or 1E9 CFU/ml of P. aeruginosa PAO1 or PA14. Embryos were then quenched in liquid nitrogen and stored at -80˚C prior to RNA extraction. This sample is a mixture of all RNA samples used in this study.

tag: sample type

value: pooled common reference

value: embryo

tag: time point

value: 30 hpf

tag: infection

value: 1E8 CFU/ml of E. tarda


title: Embryo Non-infected rep2

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 2 of 3: Non-infected zebrafish embryos


title: 114-034_Peripheral_L_SFA_25APR2007_BWR

source_name: Peripheral plaque

value: Peripheral plaque


title: Pre-injected fish held at 10C - rep 1

description: Biological replicate 1 of 6. Control fish that were held at 10C for the duration of the experiment.

source_name: Pre-injected fish held at 10C - replicate 1

value: Spleen

value: Naïve juveniles

value: New Brunswick Atlantic cod

value: Pool with equal contribution of RNA from every individual involved in the microarray experiment


title: Embryo Non-infected rep3

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 3 of 3: Non-infected zebrafish embryos


title: Embryo E. tarda immersed rep3

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 3 of 3: Zebrafish embryos infected with E. tarda


title: Pre-injected fish held at 10C - rep 3

description: Biological replicate 3 of 6. Control fish that were held at 10C for the duration of the experiment.

source_name: Pre-injected fish held at 10C - replicate 3


title: 114-013_Peripheral_L_SFA_08MAR2007_BWR


title: 114-010_Peripheral_L_SFA_26FEB2007_BWR


title: Embryo PA14 immersed rep2

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 2 of 2: Zebrafish embryos infected with Pseudomonas aeruginosa PA14

value: 1E9 CFU/ml of P. aeruginosa PA14


title: Embryo Non-infected rep1

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 1 of 3: Non-infected zebrafish embryos


title: Embryo E. coli immersed rep3

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 3 of 3: Zebrafish embryos infected with E. coli

value: 1E8 CFU/ml of E. coli


title: Sulfate-repetition3-dye swap

city: Thiverval-Grignon

first: Jean-Marie

last: Beckerich

address: Campus Agroparistech

institute: INRA

description: originally submitted ratio value represents µM/mM

hyb_protocol: hybridizations were performed for 17h at 65°C in dedicated micro-chambers with 80pmol of the different labelled samples.hybridization buffer was from Agilent (ref 5188-5242)

scan_protocol: Agilent G2565 Scanner in extended dynamic range with a resolution of 5nm per pixel

data_processing:
intensity-dependent normalization was performed with the LOESS procedure followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio using the anapuce package of R. Differential analysis was performed with the varmixt package of R.
the raw P values were adjustred by the Benjamini-Hochberg method
genes with both a P-value < 0,05 and a ratio higher than 2 were considered as diffrentially expressed

organism: Kluyveromyces lactis

source_name: growth on 0,1mM sulfate

label_protocol: RNA was labeled using the Superscript indirect cDNA labeling system kit (Invitrogen) with anchored oligo(dT)20 primer according to manufacturer's instructions

growth_protocol: K. lactis cells were grown in exponential growth for ten generations thanks to transfer on fresh medium. The growth medium is a chemically defined medium according to Mansour et al. Appl. Env. Microbiol. (2008) 74:6505-6512.

extract_protocol: Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)

tag: growth medium

value: 0.1mM sulfate

source_name: growth on 0,1µM sulfate

value: 0.1µM sulfate


title: Embryo PAO1 immersed rep1

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Zebrafish embryos infected with Pseudomonas aeruginosa PAO1

value: 1E9 CFU/ml of P. aeruginosa PAO1


title: Embryo PA14 immersed rep1

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 1 of 2: Zebrafish embryos infected with Pseudomonas aeruginosa PA14


title: Sulfate-repetition3

description: originally submitted ratio value represents mM/µM


title: Sulfate-repetition2-dye swap


title: Sulfate-repetition2


title: Embryo E. coli immersed rep2

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 2 of 3: Zebrafish embryos infected with E. coli


title: F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

description: Raw data file: slide7-3_1.txt

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Interslide scaling based on average intensity of the slide was performed in PostPrep

organism: Lactiplantibacillus plantarum

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: pH controlled Batch cultivation 2*CDM-broth

extract_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer  1.For each sample prepare a tube with Extraction Mixture  2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture  3.Mix and store the sample at -40°C  4.Centrifuge cells at -20°C at 9000 rpm for 10 minutes (Centrifuge RC5B)  5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture  6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand  7.Freeze the tube immediately in liquid nitrogen  8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  12.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  13.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   14.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

treatment_protocol: sampled at OD600 of 1

tag: strain


title: 114-009_Peripheral_L_SFA_21FEB2007_BWR

description: Gene expression profiling of peripheral plaque. 290 subjects from CISTER study


title: F09 : 0.3M NaCl,1.1*AA, 28C,pH5.2,N2 over F10 : 0M NaCl,2*AA, 37C,pH6.4,O2 (slide7-3_2.txt)

description: Raw data file: slide7-3_2.txt


title: Embryo E. coli immersed rep1

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 1 of 3: Zebrafish embryos infected with E. coli


title: 114-007_Peripheral_L_SFA_21FEB2007_BWR


title: 057-002_Peripheral_L_SFA_27MAR2007_BWR


title: 102-001_Peripheral_R_SFA_04MAY2007_BWR


title: F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 over F18 : 0M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide7-4_1.txt


title: F02 : 0.3M NaCl,2*AA, 37C,pH5.2,N2 over F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 (slide7-2_2.txt)

description: Raw data file: slide7-2_2.txt


title: F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide7-2_1.txt


title: 050-008_Peripheral_R_POP_01MAY2007_BWR


title: F15 : 0M NaCl,2*AA, 28C,pH6.4,N2 over F14 : 0.3M NaCl,1.1*AA, 37C,pH6.4,N2 (slide7-4_2.txt)

description: Raw data file: slide7-4_2.txt


title: 050-007_Peripheral_R_SFA_18APR2007_BWR


title: F18 : 0M NaCl,2*AA, 37C,pH5.8,N2 over F29 : 0M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide7-1_1.txt


title: Embryo E. tarda immersed rep1

description:
The CR (common reference) was composed by combining RNA from each sample of the immersion experiment
Biological replicate 1 of 3: Zebrafish embryos infected with E. tarda


title: F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 over F29 : 0M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide7-1_2.txt


title: Sulfate-repetition1


title: Cystine-repetition3-dye swap

source_name: growth on 1mM cystine

value: 1mM cystine

source_name: growth on 1µM cystine

value: 1µM cystine


title: Sulfate-repetition1-dye swap


title: F29 : 0M NaCl,2*AA, 28C,pH5.8,O2 over F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2

description: Raw data file: slide6-4_1.txt


title: F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2 over F18 : 0M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide6-3_2.txt


title: Cystine-repetition3


title: Cystine-repetition2


title: Cystine-repetition2-dye swap


title: F29 : 0M NaCl,2*AA, 28C,pH5.8,O2 over F27 : 0M NaCl,1.1*AA, 28C,pH5.8,N2

description: Raw data file: slide6-3_1.txt


title: F18 : 0M NaCl,2*AA, 37C,pH5.8,N2 over F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2

description: Raw data file: slide6-4_2.txt


title: F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2 over F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide6-2_2.txt


title: 050-002_Peripheral_L_SFA_10APR2007_BWR


title: F29 : 0M NaCl,2*AA, 28C,pH5.8,O2 over F25 : 0M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide6-2_1.txt


title: F29 : 0M NaCl,2*AA, 28C,pH5.8,O2 over F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2

description: Raw data file: slide6-1_2.txt


title: F28 : 0.3M NaCl,1.1*AA, 28C,pH5.8,N2 over F29 : 0M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide6-1_1.txt


title: F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2 over F21 : 0.3M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide5-3_1.txt


title: F27 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F26 : 0.3M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide5-3_2.txt


title: 050-003_Peripheral_L_SFA_25APR2007_BWR


title: 050-001_Peripheral_R_SFA_09APR2007_BWR


title: 039-001_Peripheral_R_SFA_13APR2007_BWR


title: Cystine-repetition1


title: F26 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 over F29 : 0M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide5-2_2.txt


title: F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2 over F23 : 0.3M NaCl,1.1*AA, 37C,pH5.8,O2

description: Raw data file: slide5-4_1.txt


title: Methionine-repetition3-dye swap

source_name: growth on 10mM methionine

value: 10mM methionine

source_name: growth on 10µM methionine

value: 10µM methionine


title: 034-003_Peripheral_R_POP_03MAY2007_BWR


title: Methionine-repetition3


title: F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2 over F19 : 0.3M NaCl,1.1*AA, 28C,pH6.4,O2

description: Raw data file: slide5-2_1.txt


title: F25 : 0M NaCl,2*AA, 28C,pH5.8,O2 over F26 : 0.3M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide5-1_2.txt


title: 039-003_Peripheral_L_SFA_18APR2007_BWR


title: F27 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F28 : 0.3M NaCl,1.1*AA, 28C,pH5.8,N2

description: Raw data file: slide5-4_2.txt


title: Cystine-repetition1-dye swap


title: F22 : 0M NaCl,1.1*AA, 37C,pH5.8,O2 over F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2

description: Raw data file: slide4-4_2.txt


title: 119-016_Peripheral_R_SFA_06FEB2007_BWR


title: 034-003_Peripheral_R_SFA_03MAY2007_BWR


title: Methionine-repetition2-dye swap


title: Methionine-repetition2


title: F23 : 0.3M NaCl,1.1*AA, 37C,pH5.8,O2 over F22 : 0M NaCl,1.1*AA, 37C,pH5.8,O2

description: Raw data file: slide5-1_1.txt


title: Pre-injected fish held at 10C - rep 6

description: Biological replicate 6 of 6. Control fish that were held at 10C for the duration of the experiment.

source_name: Pre-injected fish held at 10C - replicate 6

value: Held at 10°C

source_name: Common Reference


title: Methionine-repetition1-dye swap


title: F21 : 0.3M NaCl,2*AA, 37C,pH5.8,N2 over F22 : 0M NaCl,1.1*AA, 37C,pH5.8,O2

description: Raw data file: slide4-3_2.txt


title: 013-001_Peripheral_L_SFA_15FEB2007_BWR


title: 119-051_Peripheral_R_SFA_entire_17APR2007_BWR-0335


title: F18 : 0M NaCl,2*AA, 37C,pH5.8,N2 over F15 : 0M NaCl,2*AA, 28C,pH6.4,N2

description: Raw data file: slide4-2_1.txt


title: F17 : 0M NaCl,1.1*AA, 28C,pH6.4,O2 over F16 : 0.3M NaCl,2*AA, 28C,pH6.4,N2

description: Raw data file: slide3-4_2.txt


title: F20 : 0M NaCl,2*AA, 37C,pH5.8,N2 over F24 : 0M NaCl,1.1*AA, 28C,pH5.2,N2

description: Raw data file: slide4-1_2.txt


title: F18 : 0M NaCl,2*AA, 37C,pH5.8,N2 over F13 : 0M NaCl,1.1*AA, 37C,pH6.4,N2

description: Raw data file: slide4-1_1.txt


title: 034-001_Peripheral_R_SFA_15JAN2007_P0R


title: Methionine-repetition1


title: F21 : 0.3M NaCl,2*AA, 37C,pH5.8,N2 over F20 : 0M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide4-2_2.txt


title: F14 : 0.3M NaCl,1.1*AA, 37C,pH6.4,N2 over F18 : 0M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide3-4_1.txt


title: F16 : 0.3M NaCl,2*AA, 28C,pH6.4,N2 over F18 : 0M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide3-3_2.txt


title: F18 : 0M NaCl,2*AA, 37C,pH5.8,N2 over F17 : 0M NaCl,1.1*AA, 28C,pH6.4,O2

description: Raw data file: slide4-3_1.txt


title: 945-001_Peripheral_R_SFA_prox_27MAR2007_BWR-0234


title: 114-021_Peripheral_L_SFA_mid_21MAR2007_BWR-0246


title: F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F11 : 0.3M NaCl,2*AA, 37C,pH6.4,O2

description: Raw data file: slide3-2_1.txt


title: 119-035_Peripheral_L_SFA_mid_13MAR2007_BWR-0224


title: 114-014_Peripheral_R_SFA_dist_08MAR2007_BWR-0202


title: F15 : 0M NaCl,2*AA, 28C,pH6.4,N2 over F16 : 0.3M NaCl,2*AA, 28C,pH6.4,N2

description: Raw data file: slide3-2_2.txt


title: strain 840 vs SC5314

type: genomic

city: Shanghai

first: Feng

last: Yang

address: Guohe Road

country: China

institute: Second Military Medical University

description: analysis used genomic contents of SC5314 as control samples for comparison to experimental samples

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, one hybridization strategy was perfomed, the geometric mean of lowess normalized log2 ratio (test/control) was calculated.

molecule: genomic DNA

organism: Candida albicans

source_name: clinical strain cells as test samples

label_protocol: the genomic DNA was sonicated to generate fragments 50–2000 bp in size,then the DNA fragment was labeled by fluorescent dye (Cy5 and Cy3-dCTP) with random primer and Klenow enzyme.

growth_protocol: C.albicans strains were cultivated overnight in 5 ml YEPD medium, at 30℃, with 200 rpm agitation, until cell density reached 108-109 cells/ml, harvested and washed three times with distilled water by centrifugation for 5 minutes at 3000 g, resuspended in 200μl lysis buffer (2% Triton Ⅹ-100, 1% SDS, 100 mM NaCl, 1 mM EDTA, 10 mM Tris,pH 8.0), and stored at -80℃ until used for DNA extraction.

extract_protocol: For DNA extraction, 200μl of 25:24:1 phenol/chloroform/isoamyl alcohol were added to the cells resuspended in lysis buffer, together with 300 mg of acid-washed glass beads. The mixture was vortexed for 3 minutes before the addition of 200μl of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH8.0). Following a 5 minutes centrifugation at 9300 g and 4℃ for phase separation (Eppendorf centrifuge 5415D), the DNA in the aqueous phase was precipitated with 1 ml ethanol (96%, v/v) at room temperature, resuspended in 400μl of TE containing 60 mg RNaseA (GE healthcare), and incubated at 37℃ for 6 hours, the DNA was precipitated with 40μl of 3 M ammonium acetate and 1 ml of cold absolute ethanol at -20℃ for 15 minutes, followed by a 5 minutes centrifugation at 9300 g at 4℃. The DNA pellet was carefully washed with 1 ml ethanol (70%, v/v), left to dry at room temperature, and resuspended in 50μl of TE buffer.   DNA was purified using the PCR Clean-up NucleoSpin Extract Ⅱ Kit (Macherey-Nagel, Germany) according to manufacturer’s directions.

source_name: normal cells as control sample


title: strain 928 vs SC5314


title: 900-008_Peripheral_R_PT_mid_28FEB2007_BWR-0162


title: F13 : 0M NaCl,1.1*AA, 37C,pH6.4,N2 over F14 : 0.3M NaCl,1.1*AA, 37C,pH6.4,N2

description: Raw data file: slide3-3_1.txt


title: 119-033_Peripheral_R_SFA_prox_06MAR2007_BWR-0183


title: strain 958 vs SC5314


title: F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F09 : 0.3M NaCl,1.1*AA, 28C,pH5.2,N2

description: Raw data file: slide3-1_1.txt


title: F15 : 0M NaCl,2*AA, 28C,pH6.4,N2 over F14 : 0.3M NaCl,1.1*AA, 37C,pH6.4,N2 (slide3-1_2.txt)

description: Raw data file: slide3-1_2.txt


title: F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2 over F07 : 0.3M NaCl,2*AA, 28C,pH5.2,O2

description: Raw data file: slide2-4_2.txt


title: F09 : 0.3M NaCl,1.1*AA, 28C,pH5.2,N2 over F08 : 0M NaCl,1.1*AA, 28C,pH5.2,N2

description: Raw data file: slide2-4_1.txt


title: F08 : 0M NaCl,1.1*AA, 28C,pH5.2,N2 over F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2

description: Raw data file: slide2-3_1.txt


title: F09 : 0.3M NaCl,1.1*AA, 28C,pH5.2,N2 over F10 : 0M NaCl,2*AA, 37C,pH6.4,O2 (slide2-1_2.txt)

description: Raw data file: slide2-1_2.txt


title: F11 : 0.3M NaCl,2*AA, 37C,pH6.4,O2 over F10 : 0M NaCl,2*AA, 37C,pH6.4,O2

description: Raw data file: slide2-3_2.txt


title: F07 : 0.3M NaCl,2*AA, 28C,pH5.2,O2 over F08 : 0M NaCl,1.1*AA, 28C,pH5.2,N2

description: Raw data file: slide2-2_1.txt


title: strain 379 vs SC5314


title: strain 530 vs SC5314


title: F10 : 0M NaCl,2*AA, 37C,pH6.4,O2 over F12 : 0M NaCl,1.1*AA, 28C,pH5.8,N2

description: Raw data file: slide2-2_2.txt


title: 119-023_Peripheral_L_SFA_entire_20FEB2007_BWR-0126


title: F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 over F05 : 0M NaCl,2*AA, 28C,pH5.2,O2

description: Raw data file: slide2-1_1.txt


title: strain 308 vs SC5314


title: strain 687 vs SC5314


title: 988-002_Peripheral_L_PRO_prox_08FEB2007_BWR-0095


title: strain 4 vs SC5314


title: strain 187 vs SC5314


title: F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 over F03 : 0M NaCl,1.1*AA, 37C,pH5.2,O2

description: Raw data file: slide1-4_2.txt


title: F03 : 0M NaCl,1.1*AA, 37C,pH5.2,O2 over F04 : 0.3M NaCl,1.1*AA, 37C,pH5.2,O2

description: Raw data file: slide1-4_1.txt


title: 114-001_Peripheral_R_PRO_ost_02FEB2007_BWR-0066


title: strain 25 vs SC5314


title: 988-005_Peripheral_R_POP_28FEB2007_BWR


title: F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 over F01 : 0M NaCl,2*AA, 37C,pH5.2,N2

description: Raw data file: slide1-3_2.txt


title: D. virilis whole body 6d +5C rep2

city: Jyväskylä

first: Laura

last: Vesala

address: Survontie 9

department: Department of Biological and Environmental Science

country: Finland

institute: University of Jyväskylä

hyb_protocol: 600 ng of each cRNA sample was hybridized to Agilent’s 8x15K D. montana / D. virilis custom arrays at 65˚C. Hybridization was performed overnight using Agilent’s Gene Expression Hybridization Kit and the plates were washed with Agilent’s Gene Expression Wash Pack and Stabilization and Drying solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner (model G2565CA) and numerical results were extracted with Feature Extraction software version 10.7.1 using 026691_D_F_20091221grid, GE1_107_Sep09 protocol and GE1_QCMT_Sep09 metric set.

data_processing: The downstream analysis of the microarray data was carried out using R (R Foundation for Statistical Computing) and Bioconductor software (Gentleman et al., 2004). Probe level quantile normalization method was used for between sample normalization, after which the signals were summarized for each probe type by taking a median value. The data was found to be of high quality and the Pearson's correlations between the samples were between 0.86 and 0.99 in the different sample groups indicating high reproducibility. The statistical analyses were carried out using Bioconductor's Limma package. For filtering out differentially expressed genes, the minimum fold change limit was set at 2 and false discovery rate (FDR) adjusted significance level at 0.05.

organism: Drosophila virilis

source_name: Whole body pool of ten flies cold acclimation rep2

label_protocol: 600 ng of total RNA from each replicate was amplified and Cy3-labeled with Agilent’s Quick Amp Labeling (One Color) Kit and processed together with Agilent’s One-Colour RNA Spike-in Kit.

extract_protocol: Three pools of ten flies per sample were grounded and transferred into 1.5 ml tubes and mixed with 600 µl of lysis buffer. The total RNA was extracted using Qiagen RNA extraction kit with RNase-Free DNase treatment according to manufacturer's protocols (QIAGEN, Hilden, Germany). The purity of each RNA sample was measured with NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and the integrity of the samples was studied with Agilent’s Bioanalyzer (Agilent, Santa Clara, CA, USA).

tag: gender

value: female

value: mature

tag: age

tag: treatment

value: Whole body 6d +5C


title: D. virilis whole body 6d +5C rep3

source_name: Whole body pool of ten flies cold acclimation rep3


title: F03 : 0M NaCl,1.1*AA, 37C,pH5.2,O2 over F02 : 0.3M NaCl,2*AA, 37C,pH5.2,N2

description: Raw data file: slide1-3_1.txt


title: 986-001_Peripheral_L_SFA_02MAY2007_BWR

tag: tissue

value: Peripheral plaque


title: F05 : 0M NaCl,2*AA, 28C,pH5.2,O2 over F04 : 0.3M NaCl,1.1*AA, 37C,pH5.2,O2

description: Raw data file: slide1-2_2.txt


title: D. virilis whole body 1h 0C rep3

source_name: Whole body pool of the flies cold hardening rep3

value: Whole body 1h 0C


title: D. virilis whole body 6d +5C rep1

source_name: Whole body pool of ten flies cold acclimation rep1


title: F02 : 0.3M NaCl,2*AA, 37C,pH5.2,N2 over F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2 (slide1-2_1.txt)

description: Raw data file: slide1-2_1.txt


title: 920-004_Peripheral_L_CFA_25JAN2007_BWR

source_name: Peripheral plaque

tag: sample id


title: F04 : 0.3M NaCl,1.1*AA, 37C,pH5.2,O2 over F06 : 0.3M NaCl,2*AA, 28C,pH5.8,O2

description: Raw data file: slide1-1_2.txt


title: D. virilis whole body 1h 0C rep2

source_name: Whole body pool of the flies cold hardening rep2

tag: developmental stage


title: D. virilis whole body 1h 0C rep1

source_name: Whole body pool of the flies cold hardening rep1


title: 951-005_Peripheral_L_SFA_05JAN2007_BWR


title: D. virilis whole body 19C control rep3

source_name: Whole body pool of then flies control rep3

value: Whole body 19C control


title: 900-003_Peripheral_R_POP_12FEB2007_BWR


title: F01 : 0M NaCl,2*AA, 37C,pH5.2,N2 over F02 : 0.3M NaCl,2*AA, 37C,pH5.2,N2

description: Raw data file: slide1-1_1.txt


title: D. virilis whole body 19C control rep2

source_name: Whole body pool of then flies control rep2


title: 119-002_Peripheral_L_CFA_12JAN2007_BWR


title: D. virilis whole body 19C control rep1

source_name: Whole body pool of then flies control rep1


title: 013-006_Peripheral_L_POP_20APR2007_BWR


title: PindicaFromDeadBarleyRoots_5d_rep1

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

country: Germany

institute: Fraunhofer ITEM

description: P.indica on dead barley roots, 5d after infection, replicate 1

hyb_protocol: Cye-3-labeled probes were afterwards hybridised to 2x105k custom-designed Agilent microarrays according to Agilent's One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol (version 5.7).

scan_protocol: Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner (G2565CA) using one color scan setting for 2x105k array slides (Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Microarray image files were analyzed using Agilent’s Feature Extraction software v. 10.5. For each spot, signal and background intensities were obtained. To allow for comparison of expression levels across experiments, the raw data were standardized by quantile normalization. To assess the quality of the slides diagnostic plots were generated. Intensities from same-nucleotide probes were averaged. In each group-comparison the log2-ratio between corresponding intensities was calculated and averaged over all probes of an EST. The Student´s t-statistic was applied to test EST averages for significant differences between groups. Probes with low reproducibility in the two experiments were discarded from further analysis. The selection of differentially expressed genes is based on a fold change of 2 and an absolute t-statistic of 1.96. Preliminary analysis of the microarrays data indicated that P. indica grown on 1/10 PNM was under conditions of severe starvation, therefore the data from this control were not further used in our study.

organism: Serendipita indica

source_name: Dead barley roots, P.indica inoculated, 5d

label_protocol: Two independent biological replicates for each treatment were labelled for microarrays analysis. RNA from the time points 36 and 48 hpi of P. indica colonizing roots were pooled together and referred to as the pre-penetration sample. Two more time points were selected for the hybridization, 72 hpi (early colonization) and 120 hpi (late colonization). Further RNA from 36, 48, 72 and 120 hpi of P. indica grown on CM or PNM were pooled together and used as controls, giving a total of 16 samples. The labelling preparation was performed according to Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) with Tecan HS Pro Hybridization protocol (version 6.0). For each reaction 500 ng of total RNA from each experiment was used.

growth_protocol: P. indica (DSM 11827, DSMZ) was cultivated on complex medium agar plates or liquid medium as described before (Zuccaro et al., 2009). Barley seeds (Hordeum vulgare L. cv. Golden Promise) were surface sterilized with 3 % sodium hypochlorite, rinsed in water and pregerminated for 3 days.

extract_protocol: Root and fungal material was harvested in liquid nitrogen after 24, 36, 48, 72, 120 and 168 hpi. For each time point roots from 15 to 20 living plants or 21 to 36 autoclaved plants were pooled. Total RNA was extracted with TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturer’s instructions. RNA quality was analysed with a 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: For inoculation of barley roots with P. indica, the roots were dipped in a chlamydospore suspension (500,000/ml in 0.05 % Tween water) or mock inoculated and grown in sterile culture on a minimal medium (1/10 PNM) and under same growth chamber conditions as described in Schäfer et al (2009).

value: autoclaved barley roots

tag: medium


title: D. montana whole body 1-hour recovery from chill coma rep3

organism: Drosophila montana

source_name: Whole body pool of then flies 1hourrecovery rep6

value: Whole body 1-hour recovery from chill coma


title: PindicaFromDeadBarleyRoots_36h48hpool_rep2

description: P.indica on dead barley roots, pool of material from 36h & 48h after infection, replicate 2

source_name: Dead barley roots, P.indica inoculated, 36h&48h pool


title: 962-002_Peripheral_L_POP_12APR2007_BWR


title: 988-006_Peripheral_R_POP_01MAR2007_BWR


title: PindicaFromDeadBarleyRoots_3d_rep2

description: P.indica on dead barley roots, 3d after infection, replicate 2

source_name: Dead barley roots, P.indica inoculated, 3d


title: PindicaFromDeadBarleyRoots_3d_rep1

description: P.indica on dead barley roots, 3d after infection, replicate 1


title: PindicaFromLivingBarleyRoots_3d_rep2

description: P.indica on living barley roots, 3d after infection, replicate 2

source_name: Living barley roots, P.indica inoculated, 3d

value: living barley roots


title: D. montana whole body 1-hour recovery from chill coma rep2

source_name: Whole body pool of then flies 1hourrecovery rep5


title: PindicaFromLivingBarleyRoots_5d_rep2

description: P.indica on living barley roots, 5d after infection, replicate 2

source_name: Living barley roots, P.indica inoculated, 5d


title: PindicaFromDeadBarleyRoots_5d_rep2

description: P.indica on dead barley roots, 5d after infection, replicate 2


title: PindicaFromDeadBarleyRoots_36h48hpool_rep1

description: P.indica on dead barley roots, pool of material from 36h & 48h after infection, replicate 1


title: PindicaFromLivingBarleyRoots_36h48hpool_rep2

description: P.indica on living barley roots, pool of material from 36h & 48h after infection, replicate 2

source_name: Living barley roots, P.indica inoculated, 36h&48h pool


title: PindicaOnCM_36hto5dpool_rep2

description: P.indica on CM medium, pool of material from 36h, 48h, 3d & 5d extractions, replicate 2

source_name: P.indica on CM, 36h,48h,3d&5d pool

value: CM (liquid culture)


title: 951-004_Peripheral_R_POP_04MAY2007_BWR


title: D. montana whole body 1-hour recovery from chill coma rep1

source_name: Whole body pool of then flies 1hourrecovery rep4


title: 920-008_Peripheral_R_TPT_23MAR2007_BWR


title: PindicaFromLivingBarleyRoots_5d_rep1

description: P.indica on living barley roots, 5d after infection, replicate 1


title: 920-009_Peripheral_R_AT_23APR2007_BWR


title: PindicaFromLivingBarleyRoots_3d_rep1

description: P.indica on living barley roots, 3d after infection, replicate 1


title: 48 hpf 300 mM ethanol rep 1 [miRNA]

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description:
This sample is comprised of 75 pooled embryos exposed to 300 mM ethanol from  4-24 hpf and harvested at 48 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 25_Z12.0_090091-0128.txt

hyb_protocol: cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications. Labeled cDNA samples were hybridized to miRZebrafish arrays (probe content reflects miRBase release 12.0) and images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were background-subtracted, normalized by LOWESS (Locally-weighted Regression), and analyzed for differential expression by t-test (p<0.05). Data processing was performed by LC Sciences using proprietary software (Bolstad, BM et al. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193).

source_name: whole embryo 48 hpf

growth_protocol: Adult Tropical 5D strain zebrafish (Danio rerio) were raised according to Institutional Animal Care and Use Committee protocols in the Sinnhuber Aquatic Research Laboratory at Oregon State University. Adults were maintained on a 14 h light/10 h dark schedule on a recirculating system in which water was maintained at 28±1 °C with a pH of 7.0±0.2. Following adult spawns, embryos were collected, rinsed, and housed at 28±1 °C in pools of 75 embryos until the start of the experiment.

extract_protocol: miRNA was isolated using a miRNeasy kit (Qiagen) from pooled tissue (75 embryos) harvested at 12-48 hpf (n=2).

treatment_protocol: Groups of embryos were waterborne exposed to 300 mM ethanol (absolute ethyl alcohol USP, 200 proof) in buffered embryo medium or embryo medium alone in 20-ml glass vials sealed with Teflon-lined lids to prevent volatilization. Each exposure group was considered a single replicate. Based on previous studies, embryos were exposed to ethanol from 4-24 hpf, rinsed and embryo homogenate was collected at 12, 24, 36, or 48 hpf.

value: Tropical 5D

tag: agent

value: ethanol

tag: dose

tag: locomotion phenotype

value: Abnormal

tag: collection time

value: 48 hpf


title: D. montana whole body 15-min recovery from chill coma rep3

source_name: Whole body pool of then flies 15minrecovery rep3

value: Whole body 15-min recovery from chill coma


title: 36 hpf control  [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to embryo medium control from  4-24 hpf and harvested at 36 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.
Raw data file: 21_Z12.0_090087-0127.txt

scan_protocol: cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications. Labeled cDNA samples were hybridized to miRZebrafish arrays (probe content reflects miRBase release 12.0) and images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

source_name: whole embryo 36 hpf

value: control

value: Normal

value: 36 hpf


title: 48 hpf 300 mM ethanol rep 2 [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf and harvested at 48 hpf. It is the second of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 26_Z12.0_090092-0128.txt

label_protocol: cDNA synthesis, labeling and hybridization were performed by LC Sciences as per the manufacturer’s specifications.


title: 48 hpf control  [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to embryo medium control from 4-24 hpf and harvested at 48 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.
Raw data file: 27_Z12.0_090093-0128.txt


title: PindicaFromLivingBarleyRoots_36h48hpool_rep1

description: P.indica on living barley roots, pool of material from 36h & 48h after infection, replicate 1


title: 36 hpf 300 mM ethanol rep 2 [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to 300 mM ethanol from  4-24 hpf and harvested at 36 hpf. It is the second of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 20_Z12.0_090086-0127.txt


title: D. montana whole body 15-min recovery from chill coma rep2

source_name: Whole body pool of then flies 15minrecovery rep2

value: female

value: mature


title: 36 hpf 300 mM ethanol rep 1 [miRNA]

description:
This sample is comprised of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf and harvested at 36 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 19_Z12.0_090085-0127.txt


title: 24 hpf control  [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to embryo medium control from 4-24 hpf and harvested at 24 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.
Raw data file: 14_Z12.0_090081-0127.txt

source_name: whole embryo 24 hpf

value: 24 hpf


title: F19 : 0.3M NaCl,1.1*AA, 28C,pH6.4,O2 over F20 : 0M NaCl,2*AA, 37C,pH5.8,N2

description: Raw data file: slide4-4_1.txt


title: D. montana whole body 6d +5C rep3

source_name: Whole body pool of ten flies cold acclimation rep3

value: Whole body 6d +5C


title: 12 hpf 300 mM ethanol rep 2 [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to 300 mM ethanol from 4-12 hpf and harvested at 12 hpf. It is the second of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 06_Z12.0_090072-0126.txt

source_name: whole embryo 12 hpf

value: 12 hpf


title: D. montana whole body 6d +5C rep2

source_name: Whole body pool of ten flies cold acclimation rep2


title: 24 hpf 300 mM ethanol rep 2 [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf and harvested at 24 hpf. It is the second of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 13_Z12.0_090079-0127.txt


title: PindicaOnCM_36hto5dpool_rep1

description: P.indica on CM medium, pool of material from 36h, 48h, 3d & 5d extractions, replicate 1


title: 900-009_Peripheral_L_POP_23MAR2007_BWR

description: Gene expression profiling of peripheral plaque. 290 subjects from CISTER study

source_name: Peripheral plaque

value: Peripheral plaque


title: 901-016_Peripheral_L_POP_20APR2007_BWR


title: 820-031_Peripheral_L_CFA_30NOV2006_BWR


title: D. montana whole body 15-min recovery from chill coma rep1

source_name: Whole body pool of then flies 15minrecovery rep1


title: D. montana whole body 6d +5C rep1

source_name: Whole body pool of ten flies cold acclimation rep1


title: D. montana whole body 1h 0C rep3

source_name: Whole body pool of the flies cold hardening rep3

value: Whole body 1h 0C


title: 24 hpf 300 mM ethanol rep 1 [miRNA]

description:
This sample is comprised of 75 pooled embryos exposed to 300 mM ethanol from 4-24 hpf and harvested at 24 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 12_Z12.0_090078-0127.txt


title: Cy5: Se-Low-5206

city: CASTANET TOLOSAN CEDEX

first: Cécile

last: Bonnefont

address: Auzeville B.P. 52627

hyb_protocol: Three ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol.

scan_protocol: Intensity values were collected with a 4000B Axon scanner. Two channel images were imported into the Agilent's Feature Extraction software for feature (spot) finding and alignment. Features were flagged as present/absent, saturated/unsaturated, uniform/non-uniform and pixel intensities for feature and background were recorded.

data_processing: Output Feature Extraction results (.txt) files were transferred into GeneSpring GX 11. LOESS-normalized data were imported as a single channel data to perform probe by probe analysis and a percentile shift to the median was performed for normalization across arrays.  Data were filtered to remove spots with very low intensity, saturated or not uniform. Only genes for which all data were flagged as present in 100% of one out of the six conditions (resistant line at T0, T3, and T8, and susceptible line at T0, T3, and T8) were conserved for the analysis to focus the analysis on genes that are representative of a condition.

organism: Ovis aries

source_name: Milk somatic cells (MSC)

label_protocol: They were labelled with Cy3 and Cy5 for hybridisation in a two-colour dye-swap experimental design.

extract_protocol: Total RNA was extracted using classical extraction method with Phenol/chloroform with (Trizol, Invitrogen). Extracted RNAs were further purified on RNeasy column (Qiagen). Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 9 was measured for all samples.Two hundred ng of RNA were converted to double-stranded cDNA and amplified with the Amino Allyl Message Amp II aRNA amplification procedure (Ambion kit).

tag: line

value: resistant

tag: challenge

value: S. epidermidis

tag: cell type

value: Milk somatics cells (MSC) 12h after challenge


title: 12 hpf control  [miRNA]

description:
This sample is  comprised of 75 pooled embryos exposed to embryo medium control from 4-12 hpf and harvested at 12 hpf. It is a pooled sample comprised of two biological replicates, each from separate pools of 75 embryos.
Raw data file: 07_Z12.0_090073-0126.txt

value: Tropical 5D


title: Cy5: Sa-High-5067

value: susceptible

value: S. aureus


title: 119-017_Peripheral_UNK1_SFA_06FEB2007_BWR


title: 840-009_Peripheral_L_POP_30JAN2007_BWR


title: Cy5: Se-High-5006


title: 12 hpf 300 mM ethanol rep 1 [miRNA]

description:
This sample is comprised of 75 pooled embryos exposed to 300 mM ethanol from 4-12 hpf and harvested at 12 hpf. It is the first of two biological replicates used in this experiment, each from seperate pools of embryos.
Raw data file: 05_Z12.0_090095-0130.txt

value: ethanol

value: Abnormal


title: D. montana whole body 1h 0C rep1

source_name: Whole body pool of the flies cold hardening rep1


title: D. montana whole body 1h 0C rep2

source_name: Whole body pool of the flies cold hardening rep2


title: D. montana whole body 19C control rep3

source_name: Whole body pool of the flies control rep3

value: Whole body 19C control


title: 050-003_Peripheral_L_POP_25APR2007_BWR


title: Cy5: Sa-High-5019  ##2


title: 800-001_Peripheral_R_POP_30MAR2007_BWR


title: 057-003_Peripheral_L_SFA_01MAY2007_BWR


title: 760-002_Peripheral_R_POP_27APR2007_BWR


title: 820-045_Peripheral_R_POP_25APR2007_BWR


title: MCF7.Dox.si38.1

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: RBM38 siRNA + doxorubicin, replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: RBM38 siRNA + doxorubicin

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

growth_protocol: MCF-7 cells were seeded at 80% confluency, transfected with siRNA and grown 72h in DMEM containing 10% FBS, penicillin and streptomycin at 37ºC and 5% CO2.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Before harvesting, MCF-7 cells were incubated 24h with or without 0.4μg/ml of doxorubicin

tag: cell line


title: MCF7.Dox.si38.2

description: RBM38 siRNA + doxorubicin, replicate 2


title: D. montana whole body 19C control rep2

source_name: Whole body pool of the flies control rep2


title: MCF7.Dox.scrl.2

description: scrambled siRNA + doxorubicin, replicate 2

source_name: scrambled siRNA + doxorubicin


title: Cy5: Se-Low-5009


title: MCF7.si38.1

description: RBM38 siRNA, replicate 1

source_name: RBM38 siRNA


title: D. montana whole body 19C control rep1

source_name: Whole body pool of the flies control rep1


title: Cy5: Se-Low-5073


title: Cy5: Sa-High-5006


title: Cy5: Se-Low-5136


title: MCF7.Dox.scrbl.1

description: scrambled siRNA + doxorubicin, replicate 1


title: MCF7.scrl1

description: scrambled siRNA, replicate 1

source_name: scrambled siRNA


title: Cy5: Se-Low-5179


title: FH 05003-11803-OCT-Carotid-Section-30

description: Gene expression profiling of carotid plaque. 6 subjects from OCT6 study. Plaques were sectioned in 1 mm slices. Half of the slices were profiled, and the other half, adjacent slices, were processed by IHC

source_name: carotid plaque

value: carotid plaque

tag: patient

value: FH 05003-11803-OCT-Carotid-Section-30


title: 820-040_Peripheral_L_POP_18JAN2007_BWR


title: MCF7 si38.2

description: RBM38 siRNA, replicate 2


title: FH 05003-11803-OCT-Carotid-Section-32

value: FH 05003-11803-OCT-Carotid-Section-32


title: Cy5: Se-High-5067


title: FH 05003-11803-OCT-Carotid-Section-28

value: FH 05003-11803-OCT-Carotid-Section-28


title: MCF7.scrl2

description: scrambled siRNA, replicate 2


title: Embryo PBS injected rep3

description:
The CR (common reference) was composed by combining RNA of excess embryos from the caudal vein injection experiment
Biological replicate 3 of 3: Zebrafish embryos injected in the caudal vein with phosphate buffered saline (PBS)

hyb_protocol: 825 ng for each channel were combined and made to 55 μl with 10x Blocking Agent and 25x Fragmentation Buffer. 55 μl of 2x Hi-RPM Hybridization Buffer was added (Gene Expression Hybridization Kit, Agilent Technologies). 100 μl of hybridization mixture was loaded onto each array and allowed to hybridize at 65°C (10 RPM) for 17h. The slides were washed with Gene Expression Wash Buffers I and II (Gene Expression Wash Buffer Kit, Agilent Technologies).

scan_protocol: Slides were scanned on an Agilent G2505B scanner at 5 μm resolution and data was extracted with Feature Extraction version 9.3.1.1. (Protocol GE2-v5_95).

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 500 ng of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

extract_protocol: Embryos were individually snap-frozen in liquid nitrogen and subsequently stored at -80°C. A frozen embryo was crushed with a chilled pestle and homogenized in 300 µl of TRI reagent (Ambion). 60 µl chloroform was added and the mixture was transferred to a 1.5 ml reaction tube containing 50 mg phase lock gel (Eppendorf) and incubated at room temperature for 5 minutes. The mixture was centrifuged at 12000 g at 4°C for 15 minutes, after which the aqueous phase was transferred to a fresh tube. 1 volume of 70 % ethanol was added and the mixture transferred to a RNeasy MinElute Cleanup kit (Qiagen) column which was centrifuged 15 seconds at 8000 g. 500 µl RPE buffer from the kit was applied to the column and centrifuged 15 seconds at 8000 g. 500 µl 80 % ethanol was applied to the column and centrifuged 2 minutes at 8000 g. The collection tube was replaced and the column centrifuged 5 minutes at 14000 g. 14 µl H2O was applied to the column and centrifuged 1 minute at 14000 g. The average amount of RNA isolated from a single embryo was 500 ng.

treatment_protocol: Zebrafish were dechorionated manually at 24 hpf. After onset of bloodflow embryos were injected with 200 CFUs of E. tarda or with sterile PBS (phosphate buffered saline). At 8 hpi the embryos were quenched in liquid nitrogen and stored at -80°C.

tag: comment

value: 24 hpf embryos were manually dechorionated and directly after onset of bloodflow injected in the caudal vein with 200 CFUs of E. tarda or with PBS. At 8 hpi the embryos were quenched in liquid nitrogen and stored at -80˚C. This sample is a mixture of embryos from the same experiment but not used as a sample on the microarray.

tag: sample type

value: pooled common reference

value: embryo

tag: time point

value: 36 hpi

tag: infection


title: FH 05003-11803-OCT-Carotid-Section-26

tag: tissue

value: FH 05003-11803-OCT-Carotid-Section-26