title: Peripheral blood mononuclear cells (PBMC)-Patient HD10

source_name: PBMC HD10


title: Chipchip BW25113/pBAD-Myc-His C-mqsA in LB for 24 h 37oC with 0.5% L-arabinose suspension cell

status: Public on Nov 27 2009

type: genomic

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

description: His-tagged DNA extracted from planktonic cells of E. coli K-12 wild type BW25113/pBAD-Myc-His C-mqsA after 24 hours of growth in LB at 37oC with induction of 0.5% L-arabinose suspension cell

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45oC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

label: biotin

molecule: genomic DNA

organism: Escherichia coli

source_name: E. coli K-12 BW25113/pBAD-Myc-His C-mqsA in LB for 24 h 37oC with 0.5% L-arabinose suspension cell

label_protocol:
Following affymetrix protocol.
After removing RNA and protein, DNA fragmentation was checked to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.8 at 37oC with shaking (250 rpm), adding 0.5% L-arabinose and incubated for 24 h


title: ahg2-1sid2-2 rep1

type: RNA

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

country: Japan

institute: Okayama University

description: Gene expression data of ahg2-1 and sid2-2 double mutant geminating seedlings under normal conditions.

hyb_protocol: 30 ug cRNA was used. ATH1 GeneChip was used.

scan_protocol: Scanned using a GSC3000 scanner according to the manufacturer’s recommendations.

data_processing: RMA normalized using Cel file with affllmGUI.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: three week old plants

label_protocol: First-strand cDNA was synthesized using 15 µg of total RNA and SuperScript Double-stranded cDNA Synthesis kit (Invitrogen). The labeled cRNA was synthesized using BioArray RNA Transcripts Labeling Kit (T7) (ENZO Life Sciences inc.). After labeling, the cRNA was digested partially by incubating in 40 mM Tris-acetate, pH8.0, 100 mM KOAc, 30 mM MgOAc, at 94°C for 35 min. Then 30 µg cRNA was used for microarrary hybridization.

growth_protocol: The plates were kept in a growth chamber under the following conditions: 23°C, 16 hr light and 8 hr dark cycles.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent (Invitrogen) and purified using the RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Plants were grown on MS-2% sucrose plate for three weeks.

tag: strain

value: ahg2-1 and sid2-2 double mutant


title: ahg2-1abi1-1 rep2

description: Gene expression data of ahg2-1 and abi1-1 double mutant geminating seedlings under normal conditions.

value: ahg2-1 and abi1-1 double mutant


title: Peripheral blood mononuclear cells (PBMC)-Patient HD7

status: Public on Nov 30 2009

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

description: We used the default settings of GCOS software to scan the chips

hyb_protocol: Affymetrix GeneChips Human Genome U133 Array Set HG-U133A (Affymetrix) were hybridizated with 15 micrograms of fragmented cRNA, according to manufacturer’s instructions

data_processing: We used the default settings of Affymetrix Microarray Suite software version 5 (MAS 5.0; Affymetrix) to calculate scaled gene expression values.

label: Biotin

organism: Homo sapiens

source_name: PBMC HD7

label_protocol: The One-Cycle cDNA Synthesis Kit (Affymetrix) was used. Starting from 1.5 micrograms of total RNA we performed the in vitro transcription (IVT) reaction for complementary RNA (cRNA) amplification and biotin labeling, according to the manufacturer’s instructions. The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip brand expression arrays.

growth_protocol: Before RNA extraction, cells were thaw, counted and their viability determined by Trypan Blue exclusion (>90% PBMC were viable). A minimum of 5 milion cryopreserved PBMC were centrifuged, and immediately lysed for RNA extraction.

extract_protocol: Total RNA was extracted by RNeasy mini kit (QIAGEN Inc., Valencia, CA) according to the manufacturer’s instructions and resuspended in DEPC-treated Rnase-free distilled water. RNA concentration was determined by NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and its integrity was assessed by electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: The biological material was obtained at the beginning of the second hemodialysis session of the week. PBMC were immediately isolated from 20 ml of whole blood by Ficoll–Hypaque (Flow Laboratories, Irvine, UK) density gradient centrifugation. Isolated cells were stored at –80°C in FBS+10% DMSO until use.

tag: patient

tag: disease

value: chronic kidney disease

tag: treatment

value: undergoing hemodialysis

tag: group

value: Training


title: Chipchip BW25113/pBAD-Myc-His C in LB for 24 h 37oC with 0.5% L-arabinose suspension cell

description: His-tagged DNA extracted from planktonic cells of E. coli K-12 wild type BW25113//pBAD-Myc-His C (empty vector) after 24 hours of growth in LB at 37oC with induction of 0.5% L-arabinose suspension cell

source_name: E. coli K-12 BW25113/pBAD-Myc-His C in LB for 24 h 37oC with 0.5% L-arabinose suspension cell


description: RNA extracted from suspension cells of E. coli K-12 BW25113/pCA24N-mqsR after OD600=0.5 of growth with 2 mM IPTG in LB at 37oC

source_name: E. coli K-12 BW25113/pCA24N-mqsR at OD600=0.5 LB 37C 2 mM IPTG suspension cell

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.5 at 37oC under 2 mM IPTG with shaking (250 rpm), the planktonic cells were quickly removed and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: Chipchip BW25113/pCA24N in LB for 24 h 37oC with 2 mM IPTG biofilm cell

description: His-tagged DNA extracted from biofilm cells of E. coli K-12 wild type BW25113/pCA24N (empty vector) after 24 hours of growth in LB with glasswool at 37oC under 2 mM IPTG

source_name: E. coli K-12 BW25113/pCA24N in LB for 24 h 37oC with 2 mM IPTG biofilm cell


title: Chipchip BW25113/pCA24N-mqsR in LB for 24 h 37oC with 2 mM IPTG biofilm cell

description: His-tagged DNA extracted from biofilm cells of E. coli K-12 wild type BW25113/pCA24N-mqsR after 24 hours of growth in LB with glasswool at 37oC under 2 mM IPTG

source_name: E. coli K-12 BW25113/pCA24N-mqsR in LB for 24 h 37oC with 2 mM IPTG biofilm cell

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 24 h at 37oC with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0oC. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0oC. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


description: RNA extracted from suspension cells of E. coli K-12 BW25113/pCA24N (empty vector) after OD600=0.5 of growth with 2 mM IPTG in LB at 37oC

source_name: E. coli K-12 BW25113/pCA24N at OD600=0.5 LB 37C 2 mM IPTG suspension cell


description: RNA extracted from suspension cells of E. coli K-12 BW25113 wild type after OD600=0.5 of growth in LB at 37oC

source_name: E. coli K-12 BW25113 wt at OD600=0.5 LB 37C suspension cell

extract_protocol: The overnight culture was used to inoculate 25 ml of fresh LB medium. After incubation for OD600=0.5 at 37oC with shaking (250 rpm), the planktonic cells were quickly removed and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).


title: WT (Col) control rep1

description: Gene expression data of wild type geminating seedlings under normal conditions.

value: Columbia wild type


title: WT (Col) control rep2


title: ahg2-1 rep1

description: Gene expression data of ABA hypersensitive germination2-1 geminating seedlings under normal conditions.

value: ABA hypersensitive germination2-1


title: 252258910008_ATCC3502_CY5_A13S_CY3

status: Public on Nov 26 2009

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9407 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

description: None.

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Subtract the 95th percentile of the reserved spots.
      Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
4. Use TM4 suite software Ginkgo for CGH normalization:
    1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
    2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
    3). Perform Histogram Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
    4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

organism: Clostridium botulinum

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: Cells grown in TPGY medium (per litre: 50g trypticase peptone, 5g Bacto peptone, 4g D-glucose, 20g yeast extract, 1g cysteine.HCl, pH 7.4) for 2 days at 37 degrees Celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.


title: 252258910008_ATCC3502_CY5_CDCA3_CY3

description: None.


title: 252258910008_ATCC3502_CY5_7826A_CY3

description: None.


title: 252258910006_ATCC3502_CY5_KAP8_CY3

description: None.

treatment_protocol: None.

value: KAP


title: 252258910008_ATCC3502_CY5_HONEYA_CY3

description: None.

source_name: HONEYA

value: HONEYA


title: 252258910024_ATCC3502_CY5_F1_CY3


title: 252258910007_ATCC3502_CY5_CDCA13_CY3

description: None.


title: 252258910006_ATCC3502_CY5_QC_CY3

description: None.

source_name: QC

value: QC


title: 252258910007_ATCC3502_CY5_HAM_CY3

description: None.

source_name: HAM

value: HAM


title: 252258910007_ATCC3502_CY5_E9_CY3

description: None.


title: 252258910006_ATCC3502_CY5_MCA051_CY3

description: None.


title: 252258910005_ATCC3502_CY5_F13_CY3

description: None.


title: 252258910007_ATCC3502_CY5_14863_CY3

description: None.


title: 252258910024_ATCC3502_CY5_2B_CY3


title: 252258910023_ATCC3502_CY5_BP3_CY3


title: 252258910024_ATCC3502_CY5_4B_CY3


title: 252258910024_ATCC3502_CY5_F9_CY3


title: 252258910006_ATCC3502_CY5_AF84_CY3

description: None.


title: 252258910023_ATCC3502_CY5_213B_CY3


title: 252258910005_ATCC3502_CY5_14941_CY3

description: None.


title: 252258910022_ATCC3502_CY5_8718A_CY3


title: 252258910005_ATCC3502_CY5_67B_CY3

description: None.


title: 252258910023_ATCC3502_CY5_A207_CY3


title: 252258910005_ATCC3502_CY5_A661222_CY3

description: None.


title: 252258910004_ATCC3502_CY5_KAP2_CY3

description: None.


title: 252258910023_ATCC3502_CY5_14843_CY3


title: 252258910022_ATCC3502_CY5_TypeE2_CY3


title: 252258910022_ATCC3502_CY5_AF84sc2_CY3


title: 252258910016_ATCC3502_CY5_PHLS9_CY3

description: None.


title: 252258910004_ATCC3502_CY5_F10_CY3

description: None.


title: 252258910016_ATCC3502_CY5_NCTC_CY3

description: None.

source_name: NCTC

value: NCTC


title: 252258910021_ATCC3502_CY5_53B_CY3


title: 252258910021_ATCC3502_CY5_BF3_CY3


title: 252258910015_ATCC3502_CY5_BetE_CY3

description: None.

source_name: BetE

value: BetE


title: 252258910020_ATCC3502_CY5_E2_CY3

source_name: Strain is E2

source_name: Strain is ATCC3502


title: 252258910014_ATCC3502_CY5_PHLS7_CY3

description: None.


title: 252258910021_ATCC3502_CY5_A172_CY3


title: 252258910016_ATCC3502_CY5_LangelanF_CY3

description: None.

source_name: LangelanF

value: LangelanF


title: 252258910016_ATCC3502_CY5_E5_CY3

description: None.


title: 252258910004_ATCC3502_CY5_62A_CY3

description: None.


title: 252258910004_ATCC3502_CY5_E7811_CY3

description: None.


title: 252258910014_ATCC3502_CY5_KAP5_CY3

description: None.


title: 252258910003_ATCC3502_CY5_77A_CY3

description: None.


title: 252258910021_ATCC3502_CY5_14939_CY3


title: 252258910003_ATCC3502_CY5_F8_CY3

description: None.


title: 252258910015_ATCC3502_CY5_558_CY3

description: None.


title: 252258910015_ATCC3502_CY5_A69_CY3

description: None.


title: 252258910015_ATCC3502_CY5_A14_CY3

description: None.


title: 252258910014_ATCC3502_CY5_PHLS4_CY3

description: None.


title: 252258910003_ATCC3502_CY5_14931_CY3

description: None.


title: 252258910019_ATCC3502_CY5_G87_CY3


title: 252258910020_ATCC3502_CY5_buty1020_CY3


title: 252258910003_ATCC3502_CY5_PHLS6_CY3

description: None.


title: 252258910020_ATCC3502_CY5_1618_CY3


title: 252258910020_ATCC3502_CY5_4475_CY3


title: 252258910014_ATCC3502_CY5_E3_CY3

description: None.


title: 252258910022_ATCC3502_CY5_00032_CY3


title: 252258910019_ATCC3502_CY5_13983_CY3


title: 252258910013_ATCC3502_CY5_BSA_CY3

description: None.

source_name: BSA

value: BSA


title: 252258910019_ATCC3502_CY5_32B_CY3


title: 252258910002_ATCC3502_CY5_F5_CY3

description: None.


title: 252258910019_ATCC3502_CY5_6350_CY3


title: 252258910018_ATCC3502_CY5_10427_CY3


title: 252258910002_ATCC3502_CY5_ElPaso_CY3

description: None.

source_name: ElPaso

value: ElPaso


title: 252258910018_ATCC3502_CY5_8933E2_CY3


title: 252258910018_ATCC3502_CY5_4434_CY3


title: 252258910033_ATCC3502_CY5_G4_Cy3


title: 252258910017_ATCC3502_CY5_E3745_CY3


title: 252258910013_ATCC3502_CY5_PHLS11_CY3

description: None.


title: 252258910033_ATCC3502_CY5_BF2_Cy3


title: 252258910002_ATCC3502_CY5_14910_CY3

description: None.


title: 252258910012_ATCC3502_CY5_B7_CY3

description: None.


title: 252258910013_ATCC3502_CY5_A4_CY3

description: None.


title: 252258910033_ATCC3502_CY5_532_HALLAH_Cy3

source_name: HALLAH

value: HALLAH


title: 252258910002_ATCC3502_CY5_4206_CY3

description: None.


title: 252258910013_ATCC3502_CY5_A608_CY3

description: None.


title: 252258910017_ATCC3502_CY5_A15_CY3


title: 252258910032_ATCC3502_CY5_3281BF_Cy3


title: 252258910033_ATCC3502_CY5_14860_Cy3


title: 252258910017_ATCC3502_CY5_599a_CY3


title: 252258910018_ATCC3502_CY5_8411B_CY3


title: 252258910012_ATCC3502_CY5_10426_CY3

description: None.


title: 252258910017_ATCC3502_CY5_1158_CY3


title: 252258910032_ATCC3502_CY5_212B_Cy3


title: 252258910001_ATCC3502_CY5_PHLS8_CY3

description: None.


title: 252258910032_ATCC3502_CY5_19AITO_Cy3


title: 252258910032_ATCC3502_CY5_5311A_Cy3


title: 252258910012_ATCC3502_CY5_G3_CY3

description: None.


title: 252258910011_ATCC3502_CY5_LamannaB_CY3

description: None.

source_name: LamannaB

value: LamannaB


title: 252258910038_ATCC3502_CY5_A3758_CY3


title: 252258910031_ATCC3502_CY5_BF1_Cy3


title: 252258910031_ATCC3502_CY5_g89_Cy3


title: 252258910001_ATCC3502_CY5_F6_CY3

description: None.


title: 252258910031_ATCC3502_CY5_169B_Cy3


title: 252258910040_ATCC3502_CY5_Sporo59123_CY3


title: 252258910001_ATCC3502_CY5_PHLS5_CY3

description: None.


title: 252258910040_ATCC3502_CY5_D2_CY3


title: 252258910011_ATCC3502_CY5_14854_CY3

description: None.


title: 252258910012_ATCC3502_CY5_14868_CY3

description: None.


title: 252258910040_ATCC3502_CY5_S5_Strep_CY3


title: 252258910001_ATCC3502_CY5_13065_CY3

description: None.


title: 252258910011_ATCC3502_CY5_A33_CY3

description: None.


title: 252258910011_ATCC3502_CY5_12885_CY3

description: None.


title: 252258910040_ATCC3502_CY5_A172_CY3


title: 252258910039_ATCC3502_CY5_SporoC_CY3

source_name: SporoC

value: SporoC


title: 252258910029_ATCC3502_CY5_g1_Cy3


title: 252258910029_ATCC3502_CY5_SPORO4411_Cy3


title: 252258910029_ATCC3502_CY5_SPORO3679_Cy3


title: 252258910029_ATCC3502_CY5_14853


title: 252258910039_ATCC3502_CY5_SporoWR5_CY3


title: 252258910031_ATCC3502_CY5_4431_Cy3


title: 252258910039_ATCC3502_CY5_28_2_CY3


title: 252258910039_ATCC3502_CY5_C1_CY3


title: 252258910028_ATCC3502_CY5_OKRAB_Cy3

source_name: OKRAB

value: OKRAB


title: 252258910038_ATCC3502_CY5_Sporo3679_66_CY3


title: 252258910028_ATCC3502_CY5_5900b_Cy3


title: 252258910038_ATCC3502_CY5_A3759_CY3


title: 252258910028_ATCC3502_CY5_10329_Cy3


title: 252258910010_ATCC3502_CY5_E7_CY3

description: None.


title: 252258910027_ATCC3502_CY5_12412_Cy3


title: 252258910028_ATCC3502_CY5_C4_Cy3


title: 252258910027_ATCC3502_CY5_A4831_Cy3


title: 252258910010_ATCC3502_CY5_A336_CY3

description: None.


title: 252258910038_ATCC3502_CY5_a4831_CY3


title: 252258910010_ATCC3502_CY5_ChchA_CY3

description: None.

source_name: ChchA

value: ChchA


title: 252258910009_ATCC3502_CY5_PHLS12_CY3

description: None.


title: 252258910010_ATCC3502_CY5_CR1_CY3

description: None.


title: 252258910036_ATCC3502_CY5_SporoFOA_CY3

source_name: SporoFOA

value: SporoFOA


title: 252258910026_ATCC3502_CY5_SPORO4111_Cy3


title: 252258910009_ATCC3502_CY5_OSA_CY3

description: None.

source_name: OSA

value: OSA


title: 252258910036_ATCC3502_CY5_Sporo1026_CY3


title: 252258910009_ATCC3502_CY5_F2_CY3

description: None.


title: 252258910037_ATCC3502_CY5_S5_CY3


title: 252258910037_ATCC3502_CY5_Sporo4439_CY3


title: 252258910027_ATCC3502_CY5_B13_Cy3


title: 252258910026_ATCC3502_CY5_ALASKAE_Cy3

source_name: ALASKAE

value: ALASKAE


title: 252258910037_ATCC3502_CY5_E_PM_15_CY3


title: 252258910026_ATCC3502_CY5_4896A_Cy3


title: 252258910026_ATCC3502_CY5_E6_Cy3


title: 252258910037_ATCC3502_CY5_5328A_CY3


title: 252258910025_ATCC3502_CY5_D2_Cy3


title: 252258910025_ATCC3502_CY5_C1_Cy3


title: 252258910036_ATCC3502_CY5_Sporo6_CY3


title: 252258910035_ATCC3502_CY5_ATCC3502


title: 252258910035_ATCC3502_CY5_56A


title: 252258910035_ATCC3502_CY5_12412


title: 252258910035_ATCC3502_CY5_B13


title: 252258910009_ATCC3502_CY5_17B_CY3

description: None.


title: 252258910025_ATCC3502_CY5_2BNP_Cy3


title: 252258910034_ATCC3502_CY5_5328A_Cy3


title: Monocytes

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: miRNA expression data of monocytes

hyb_protocol: Biotin labeled samples were mixed with the eukaryotic hybridization controls (Affymetrix) and hybridized to Affymetrix miRNA arrays. Arrays were subsequently washed and stained in the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: To assess the raw probe signal intensities, chips were scanned using the GeneChip scanner 3000 (Affymetrix).

data_processing: RMA normalization and probe summarization was carried out on the human specific and control probe sets only.

source_name: FACS sorted monocytes

label_protocol: Samples were spiked with RNA spike control oligos (Genisphere) and labeled according to the GenisphereÒ solution using the Genisphere FlashTag™ Biotin RNA Labeling Kit.

extract_protocol: Total RNA was extracted using the miRNeasy mini kit (Qiagen) according to the manufacturer's protocol.

tag: cell type

value: Monocytes


title: Neutrophils

description: miRNA expression data of neutrophils

source_name: FACS sorted neutrophils

value: Neutrophils


title: 252258910034_ATCC3502_CY5_E8_Cy3


title: 252258910034_ATCC3502_CY5_WHOA_Cy3

source_name: WHOA

value: WHOA


title: CD4+ T-cells

description: miRNA expression data of CD4+ T-cells

source_name: FACS sorted CD4+ T-cells

value: CD4+ T-cells


title: B-cells

description: miRNA expression data of B-cells

source_name: FACS sorted B-cells

value: B-cells


title: CD8+ T-cells

description: miRNA expression data of CD8+ T-cells

source_name: FACS sorted CD8+ T-cells

value: CD8+ T-cells


title: Treated Sarcoma 4

city: HOUSTON

first: wei

last: zhang

state: TX

address: 1515 Holcombe Blvd, Unit 85

department: Pathology

institute: M. D. Anderson Cancer Center

hyb_protocol: Agilent FFPE version 5.0

data_processing: Agilent Feature Extraction Protocol 9.1.3.1

source_name: Treated Sarcoma4

label_protocol: Agilent FFPE version 5.0 - ULS

extract_protocol: standard Agilent protocol

tag: sample number

tag: gender

value: F

tag: age

tag: site

value: femur

tag: pathological diagnosis

value: Conventional

tag: untreated samples

tag: treated samples

value: 1 - treated

tag: tumor necrosis rate after chemotherapy

tag: recurrence

value: Yes

tag: metastasis

tag: outcome

value: alive

source_name: female DNA

tag: source

value: commecial female DNA (Promega, cat# G152A)


title: Treated Sarcoma 6

source_name: Treated Sarcoma6

value: M


title: After Treament Sarcoma Replicate 1

source_name: After Treament Sarcoma Replicate 1

value: fibula


title: Before Treament Sarcoma Replicate 1

source_name: Before Treament Sarcoma Replicate 1

value: 1 - untreated


title: Treated Sarcoma 5

source_name: Treated Sarcoma5


title: Untreated Sarcoma 1

source_name: Untreated Sarcoma1


title: PML-RARA_PR9_Zn_4H

city: Shanghai

first: Jiantao

last: Shi

state: Shanghai

address: 197 Ruijin Rd II

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (RJH-SJTU-SM)

description: RARa ChIP in ZnSO4 treated PR9 cells, three replicates

hyb_protocol: Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G.

data_processing:
Data was analyzed by a model-based algorithm MAT. MAT scores were reported in BAR files.
PML-RARA_PR9_Zn_4H_hg17.bar was generated by MAT (using hg17 based BPMAP file). PML-RARA_PR9_Zn_4H_hg17.bed contains all 2,979 high quality PML-RARa binding sites reported in the paper.

source_name: RARa ChIP DNA from ZnSO4 induced PR9 cells

label_protocol: 7.5μg of amplified DNA were fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). biotinylated compound were added to the ends of the fragments.

growth_protocol: PR9 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: ChIP and amplification were performed according to the Affymetrix protocol as described (Carroll et al., 2005). Three independent replicates were performed.

treatment_protocol: PR9 cells were treated with 100 μM of ZnSO4 for 4 hours.

tag: cell line

tag: time point

value: 4 hour

tag: antibody

value: RARa

source_name: Input DNA from ZnSO4 induced PR9 cells

value: PR9 cells

tag: timepoint


title: 252258910036_ATCC3502_CY5_Sporo9_CY3

tag: strain


title: Total leucocytes

description: miRNA expression data of total leukocytes

source_name: FACS sorted total leukocytes

tag: cell type

value: Total leucocytes


title: T-cells

description: miRNA expression data of T-cells

source_name: FACS sorted T-cells

value: T-cells


title: Treated Sarcoma 2

source_name: Treated Sarcoma2

tag: sample number

tag: gender

value: humerus


title: Treated Sarcoma 3

source_name: Treated Sarcoma3

tag: age

tag: site


title: WB-55

status: Public on Nov 25 2009

city: Essen

first: Lewin

last: Eisele

address: Hufelandstr. 55

department: Haematology

country: Germany

institute: University Hospital Essen

description: Immunomagnetically purified CD3+ cells from peripheral blood of B-CLL

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45°C on HG-U133A Arrays. The Arrays were washed and stained in a Affymetrix Fluidics Station 400

scan_protocol: Arrays were scanned using the GeneChip Scanner G3000

data_processing: MAS5 expression values and detection calls were computed with R version 2.8.1 and the Bioconductor package affy using default parameters

source_name: CD3+ T-cells, B-CLL

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6µg total RNA

extract_protocol: Isolation of total RNA was performed with QIAGEN Rneasy columns according to the manufacturer's instructions

tag: status

value: CLL

value: CD3+ T-cells


title: SG-62


title: WM-35


title: 252258910027_ATCC3502_CY5_56A_Cy3


title: WH-33


title: Treated Sarcoma 1

source_name: Treated Sarcoma1

value: tibia

tag: pathological diagnosis

tag: untreated samples

tag: treated samples


title: SE-56


title: MH-37


title: OG-30


title: PR-41


title: PH-19


title: MH-30


title: KE-29


title: LH-30


title: HM-17


title: GJ-28


title: RG-29


title: KH-45


title: Untreated Sarcoma 2

source_name: Untreated Sarcoma2

value: F

value: ilium

value: Conventional

tag: tumor necrosis rate after chemotherapy

tag: recurrence

tag: metastasis


title: GGG-37


title: 252258910025_ATCC3502_CY5_1138_Cy3


title: CO-59


title: FW-33


title: DR-29


title: BG-29


title: SM-43

description: Immunomagnetically purified CD3+ cells from peripheral blood of Normal Donor

source_name: CD3+ T-cells, Normal donor

value: ND


title: NM-47


title: BK-41


title: NW-40


title: ZR-42


title: VJ-47


title: OJ-28


title: KA-35


title: fry_NASH3(2)_PWR3(1)

city: West Vancouver

first: Wendy

last: Tymchuk

state: BC

address: 4160 Marine Drive

department: Science

country: Canada

institute: Fisheries & Oceans Canada

hyb_protocol: Hybridization followed the procedures at http://web.uvic.ca/grasp/microarray (Genisphere Array 50 Protocol).

scan_protocol: Fluorescence images were collected at 10μm resolution using a ScanArray microarray scanner (Perkin Elmer). The same laser power (95%) and photomultiplier tube (PMT) settings were used for all slides (Cy3 PMT 75, Cy5 PMT 65).  The otsu quantification method within TIGR Spotfinder was used to quantify the scanned microarray files.  Integrated intensities were corrected for background and any spots with expression levels < 2 standard deviations above background were removed.

data_processing: TIGR Microarray Data Analysis System (MIDAS) was used to average dye-swap technical replicates and Limma in R was used to apply a locally weighted linear regression (LOWESS) normalization module.  Missing values were imputed with the K-nearest neighbours method using K = 10.

organism: Salmo salar

source_name: whole fry prior to exogenous feeding

label_protocol: Reverse transcriptase of 20ug of total RNA was performed following the SuperScript II Reverse Transcriptase protocol (Invitrogen).  Indirect labeling was performed on individual cDNA following the Array 50 kit protocol (Genisphere).

growth_protocol: Eggs were fertilized and reared at a hatchery; samples were collected as fry prior to any exogenous feeding

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

value: NASH

tag: family

tag: population

value: PWR


title: SH-37NG


title: fry_USR3(2)_ECO3(2)

value: USR

value: ECO


title: fry_BSR3(2)_SERP3(1)

value: BSR

value: SERP


title: fry_STW3(1)_TOB3(1)

value: STW

value: TOB


title: fry_TOB3(2)_SJR3(1)

value: SJR


title: fry_PWR3(2)_USR3(1)


title: fry_SJR3(2)_GRV3(2)

value: GRV


title: fry_SERP3(2)_LAH1(4)

value: LAH


title: fry_ECO3(1)_NASH3(1)


title: fry_MED3(2)_BSR3(1)

value: MED


title: fry_GRV3(1)_STW3(1)


title: BK-20

value: CLL

value: CD3+ T-cells


title: fry_USR2(2)_ECO2(2)


title: fry_SJR2(1)_LAH2(2)


title: CI-56


title: AK-42


title: fry_SERP2(2)_USR2(1)


title: fry_TOB2(2)_SERP2(1)


title: fry_ECO2(1)_MED2(1)


title: fry_NASH2(2)_TOB2(1)


title: fry_STW2(2)_BSR2(1)


title: fry_BSR2(2)_PWR2(1)


title: fry_GRV2(2)_STW2(1)


title: fry_MED2(2)_NASH2(1)


title: fry_TOB1(2)_PWR1(1)


title: fry_BSR1(1)_TOB1(1)


title: fry_SERP1(2)_SJR1(1)


title: fry_SJR1(2)_USR1(1)


title: fry_LAH2(1)_GRV2(1)


title: fry_STW1(2)_NASH1(1)


title: fry_PWR1(2)_SERP1(1)


title: fry_MED1(2)_STW1(1)


title: fry_ECO1(2)_MED1(1)


title: fry_GRV1(2)_ECO1(1)


title: EC-TNF-LTBR-24h-1

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 450 Protocol: EukGe-WS2v4

hyb_protocol: 60rpm, 18h, 45°C in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

organism: Mus musculus

source_name: EC, endothelial cells

label_protocol: ENZO T7 High Yield Transcript Labelling Kit, 16h IVT

growth_protocol:
EC Medium: DMEM +20% FBS, 2mM L-Glutamin, 1x Non-essential amino acids,
1x Natriumpyruvat, 25mM HEPES (pH 7,0-7,6), 100µg/ml Heparin, 100µg/ml ECGS

extract_protocol: Qiagen RNEasy Lipid Tissue Mini Kit, Standard protocol

treatment_protocol:
Cells were feed 24h prior to stimulation, stimuli were
added in PBS, Cells were supplemented with PBS only

tag: genetic background

value: cultured aortic endothelial cell


title: Sinker replicate 3

city: Corvallis

first: Alan

middle: T

last: Bakalinsky

state: OR

address: Wiegand Hall

department: Food Science & Technology

institute: Alan Bakalinsky

description: Saccharomyces cerevisiae 3238-32 (MATa leu2∆1 lys2-801 ura3-52). This strain forms a liquid-air interfacial biofilm upon depletion of a glucose in a glucose-containing medium (e.g., YPD or YNB) (Zara et al., 2005). Planktonic cells ("sinkers") were harvested.

hyb_protocol: Hybridization to yeast YGS98 microarrays was performed according to the manufacturer’s instructions (GeneChip Expression Analysis Technical Manual 701021 rev. 1, Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was performed according to the manufacturer’s instructions (GeneChip Expression Analysis Technical Manual 701021 rev. 1, Affymetrix, Santa Clara, CA).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae 3238-32 (MATa leu2∆1 lys2-801 ura3-52), planktonic cells.

label_protocol: Synthesis of labelled aRNA was done according to the manufacturers protocol (Ambion MessageAmp[TM] aRNA kit, catalog #1750); purification and aRNA fragmentation were performed according to Affymetrix protocols (GeneChip Expression Analysis Technical Manual 701021 rev. 1, Affymetrix, Santa Clara, CA).

growth_protocol: See treatment protocol

extract_protocol: Yeast cells were processed for total RNA isolation immediately after they were collected essentially as described (Schmitt et al., 1990). The RNA was subsequently purified using a commercial kit (RNA Easy, Qiagen, Valencia, CA). A260/A280 ratios for the purified RNA preparations ranged from 1.96 to 2.07.

treatment_protocol: Cells were grown 24 h at 30°C in YEPD to a density of 5 x 108 cells/ml. At harvest, sugar was found to be depleted as measured by an enzymatic dip stick (Diastic, Bayer). Cells were pelleted and washed twice in sterile distilled water by centrifugation and then diluted 10-fold into 100 ml of Flor medium (YNB + 4% ethanol + leucine + histidine + uracil) in triplicate 250 ml beakers. Cultures were then grown statically in Flor medium at 27°C. Within a few hours following inoculation, the bulk liquid appeared to be clear, no biofilm was evident by visual observation, and a layer of settled cells was evident at the bottom of the beakers. After 48 h, a visible biofilm covered the entire surface while the thickness of the layer of settled cells appeared unchanged. After 48 h, biofilm cells (“floaters”) were collected by aseptic aspiration. Once the biofilm cells were removed, cells at the bottom of the beaker (“sinkers”) were collected similarly. Cells from both populations were washed once in sterile distilled water by centrifugation prior to RNA isolation. Significant cell clumping was evident in both populations of cells by microscopic observation. While cell viability was estimated by plating on YEPD, the resultant cfu/ml values could not be directly correlated with cell counts in a hemacytometer because clumps of cells containing at least one viable cell presumably produced only a single colony. Further, counting individual cells accurately in the numerous clumps containing large numbers of cells was not possible. Nonetheless, when cells were counted (clumps were counted as single cells) and compared to cfu/ml for the same suspension, the cfu/ml values were about 2-fold higher than the corresponding values for cell counts using the hemacytometer for both biofilm and bottom layer cells.

value: cells at the bottom of the beaker (sinkers)

tag: replicate


title: EC-Control-24h-3


title: Sinker replicate 2


title: EC-Control-24h-1


title: Sinker replicate 1


title: EC-TNF-LTBR-24h-2


title: Floater replicate 3

description: Saccharomyces cerevisiae 3238-32 (MATa leu2∆1 lys2-801 ura3-52). This strain forms a liquid-air interfacial biofilm upon depletion of a glucose in a glucose-containing medium (e.g., YPD or YNB) (Zara et al., 2005). Biofilm cells ("floaters") were harvested.

source_name: Saccharomyces cerevisiae 3238-32 (MATa leu2∆1 lys2-801 ura3-52), biofilm cells.

value: biofilm cells (floaters)


title: fry_USR1(2)_LAH1(2)

tag: strain


title: EC-Control-24h-2

tag: cell type


title: Floater replicate 2

growth_protocol: See Treatment protocol.


title: 252258910034_ATCC3502_CY5_BELUGAE_Cy3

source_name: BELUGAE

value: BELUGAE


title: Floater replicate 1

growth_protocol: See treatment protocol.

treatment_protocol: Cells were grown 24 h at 30°C in YEPD to a density of 500,000,000 cells/ml. At harvest, sugar was found to be depleted as measured by an enzymatic dip stick (Diastic, Bayer). Cells were pelleted and washed twice in sterile distilled water by centrifugation and then diluted 10-fold into 100 ml of Flor medium (YNB + 4% ethanol + leucine + histidine + uracil) in triplicate 250 ml beakers. Cultures were then grown statically in Flor medium at 27°C. Within a few hours following inoculation, the bulk liquid appeared to be clear, no biofilm was evident by visual observation, and a layer of settled cells was evident at the bottom of the beakers. After 48 h, a visible biofilm covered the entire surface while the thickness of the layer of settled cells appeared unchanged. After 48 h, biofilm cells (“floaters”) were collected by aseptic aspiration. Once the biofilm cells were removed, cells at the bottom of the beaker (“sinkers”) were collected similarly. Cells from both populations were washed once in sterile distilled water by centrifugation prior to RNA isolation. Significant cell clumping was evident in both populations of cells by microscopic observation. While cell viability was estimated by plating on YEPD, the resultant cfu/ml values could not be directly correlated with cell counts in a hemacytometer because clumps of cells containing at least one viable cell presumably produced only a single colony. Further, counting individual cells accurately in the numerous clumps containing large numbers of cells was not possible. Nonetheless, when cells were counted (clumps were counted as single cells) and compared to cfu/ml for the same suspension, the cfu/ml values were about 2-fold higher than the corresponding values for cell counts using the hemacytometer for both biofilm and bottom layer cells.


title: fry_PWR_G7(3)_SJR_S1(3)

data_processing: TIGR Microarray Data Analysis System (MIDAS) was used to average dye-swap technical replicates and Limma in R was used to apply a locally weighted linear regression (LOWESS) normalization module.  Missing values were imputed with the K-nearest neighbours method using K = 10. The normalized log 2 ratios from the merged dye swaps represent the ratio of the average of (ch1, slide 1 and ch2, slide2)/(ch2, slide1 and ch1, slide 2).

value: PWR


title: fry_EURO_R2(3)_PWR_G5(1)

value: EURO


title: fry_USR_Y2(2)_PWR_G5(2)

value: USR


title: fry_BSR_B8(2)_SJR_S3(2)

value: BSR


title: fry_EURO_R5(3)_USR_Y2(2)


title: fry_BSR_B8(3)_EURO_R3(2)


title: fry_LAH1(1)_GRV1(1)


title: fry_SJR_S2(3)_EURO_R3(1)


title: fry_USR_Y2(1)_SJR_S3(1)


title: T3BQBC07232008_H9312_CY3_STERNE_CY5_13846942_B

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: T3BQBC07232008_H9312_CY3_STERNE_CY5_13846942_anno_sub_95th_MDS.mev.refIsMEDB.out

hyb_protocol: Aminosaline coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 degree Celcius for 45 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry. Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in a solution of 35% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were denatured at 95 degree Celcius prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 degree Celcius. Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature.

scan_protocol: Scanned on Axon GenePix 4000 scanner. PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
(1). Species spot: oligos designed for the species under investigation.
(2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
(3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
|Xi - M|/MAD > Max
Xi = Each intensity value from the set of replicates.
M = Median intensity value from the set of replicates.
MAD = Median absolute deviation.
Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
3). Perform Log Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

organism: Bacillus cereus

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen). Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN). The purified labelled DNA was then dye coupled with the appropriate cyanine dye (Cy3/Cy5).

growth_protocol: Cells grown in Lysogeny broth (LB) at 37 degrees Celcius overnight.

extract_protocol: Epicentre MasterPure DNA Extraction Kit.

organism: Bacillus anthracis str. Sterne

source_name: Sterne reference

value: Sterne


title: fry_PWR_G6(2)_SJR_S2(2)


title: fry_USR_Y3(2)_PWR_G6(1)


title: T3BQBC07212008A_C1785_CY3_STERNE_CY5_13848760_B

description: T3BQBC07212008A_C1785_CY3_STERNE_CY5_13848760_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_H9310_CY3_STERNE_CY5_13846945_B

description: T3BQBC07232008_H9310_CY3_STERNE_CY5_13846945_anno_sub_95th_MDS.mev.refIsMEDB.out


title: fry_BSR_B7(2)_EURO_R2(2)


title: fry_BSR_B14(3)_USR_Y1(3)


title: T3BQBC07232008_03BB102_CY3_STERNE_CY5_13846938_B

description: T3BQBC07232008_03BB102_CY3_STERNE_CY5_13846938_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07212008A_C1784_CY3_STERNE_CY5_13848767_B

description: T3BQBC07212008A_C1784_CY3_STERNE_CY5_13848767_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_03BB108_CY3_STERNE_CY5_13846937_B

description: T3BQBC07232008_03BB108_CY3_STERNE_CY5_13846937_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_F3920_CY3_STERNE_CY5_13846941_B

description: T3BQBC07232008_F3920_CY3_STERNE_CY5_13846941_anno_sub_95th_MDS.mev.refIsMEDB.out


title: fry_SJR_S2(1)_EURO_R5(1)


title: T3BQBC07212008A_C1783_CY3_STERNE_CY5_13848768_B

description: T3BQBC07212008A_C1783_CY3_STERNE_CY5_13848768_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_2002734726_CY3_STERNE_CY5_13846936_B

description: T3BQBC07232008_2002734726_CY3_STERNE_CY5_13846936_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_H9311_CY3_STERNE_CY5_13846944_B

description: T3BQBC07232008_H9311_CY3_STERNE_CY5_13846944_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_H9312_CY5_STERNE_CY3_13846947_A

description: T3BQBC07232008_H9312_CY5_STERNE_CY3_13846947_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC07232008_H9310_CY5_STERNE_CY3_13846949_A

description: T3BQBC07232008_H9310_CY5_STERNE_CY3_13846949_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC07232008_03BB87_CY3_STERNE_CY5_13846939_B

description: T3BQBC07232008_03BB87_CY3_STERNE_CY5_13846939_anno_sub_95th_MDS.mev.refIsMEDB.out


title: fry_BSR_B14(2)_SJR_S1(2)


title: T3BQBC07232008_H9311_CY5_STERNE_CY3_13846948_A

description: T3BQBC07232008_H9311_CY5_STERNE_CY3_13846948_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3QBQBC01022008A_525_Cy3_STERNE_Cy5_13758781_B

description: T3QBQBC01022008A_525_Cy3_STERNE_Cy5_13758781_anno_sub_95th_MDS.mev.refIsMEDB.out


title: fry_BSR_B8(1)_PWR_G6(3)


title: T3QBQBC01022008A_80700019_Cy3_STERNE_Cy5_13758789_B.ou

description: T3QBQBC01022008A_80700019_Cy3_STERNE_Cy5_13758789_anno_sub_95th_MDS.mev.refIsMEDB.ou


title: fry_USR_Y3(1)_SJR_S1(1)


title: fry_EURO_R2(1)_PWR_G7(2)


title: fry_BSR_B14(1)_USR_Y1(1)


title: fry_BSR_B7(1)_PWR_G7(1)


title: fry_EURO_R5(2)_USR_Y1(2)


title: fry_LAH1(3)_MED3(1)


title: D3 ES cells on MEFmedium replicate 2

city: Singapore

first: Henry

last: Yang

address: 8A Biomedical Grove

department: Bioinformatics Group

country: Singapore

institute: SIgN

description: Replicate 2

hyb_protocol: 750ng of each labelled cRNA sample was hybridized to MouseRef-8 v2 Expression BeadChip microarrays (Illumina) according to manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing:
The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006).
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: D3 ES cells on MEFmedium replicate 2

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).

extract_protocol: Cells from repective clones or cell cultures were harvested and then washed with PBS, trypsinised, resuspended in RNAlater and stored at -20°C. Total RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

value: D3 ES


title: R1 ES cells on mESC medium replicate 4

description: Replicate 4

source_name: R1 ES cells on mESC medium replicate 4

value: R1 ES


title: D3 ES cells on MEFmedium replicate 1

description: Replicate 1

source_name: D3 ES cells on MEFmedium replicate 1


title: R1 ES cells on mESC medium replicate 1

description: Replicate 1

source_name: R1 ES cells on mESC medium replicate 1


title: T3BQBC07232008_03BB108_CY5_STERNE_CY3_13846989_A

description: T3BQBC07232008_03BB108_CY5_STERNE_CY3_13846989_anno_sub_95th_MDS.mev.refIsMEDA.out


title: R1 ES cells on mESC medium replicate 3

description: Replicate 3

source_name: R1 ES cells on mESC medium replicate 3


title: T3QBQBC01022008A_264_Cy3_STERNE_Cy5_13758795_B

description: T3QBQBC01022008A_264_Cy3_STERNE_Cy5_13758795_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 11

description: Clone 11

value: iPS


title: T3BQBC07232008_F3920_CY5_STERNE_CY3_13846946_A

description: T3BQBC07232008_F3920_CY5_STERNE_CY3_13846946_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC07232008_2002734726_CY5_STERNE_CY3_13846988_A

description: T3BQBC07232008_2002734726_CY5_STERNE_CY3_13846988_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_H3074_97_Cy3_STERNE_Cy5_58328_B

description: T3BQBC12172007A_H3074_97_Cy3_STERNE_Cy5_58328_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_H3081_97_Cy3_STERNE_Cy5_13758324_B

description: T3BQBC12172007A_H3081_97_Cy3_STERNE_Cy5_13758324_anno_sub_95th_MDS.mev.refIsMEDB.out


title: R1 ES cells on mESC medium replicate 2

description: Replicate 2

source_name: R1 ES cells on mESC medium replicate 2


title: T3BQBC12172007A_H1448_CY3_STERNE_CY5_13758336_B

description: T3BQBC12172007A_H1448_CY3_STERNE_CY5_13758336_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07232008_03BB102_CY5_STERNE_CY3_13846990_A

description: T3BQBC07232008_03BB102_CY5_STERNE_CY3_13846990_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC07232008_03BB87_CY5_STERNE_CY3_13846932_A

description: T3BQBC07232008_03BB87_CY5_STERNE_CY3_13846932_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_H1449_Cy3_STERNE_Cy5_13758397_B

description: T3BQBC12172007A_H1449_Cy3_STERNE_Cy5_13758397_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 8

description: Clone 8


title: T3BQBC12172007A_H1548_Cy3_STERNE_Cy5_13758333_B

description: T3BQBC12172007A_H1548_Cy3_STERNE_Cy5_13758333_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 7

description: Clone 7


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 9

description: Clone 9


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 5

description: Clone 5


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 6

description: Clone 6


title: T3BQBC07212008A_C1785_CY5_STERNE_CY3_13848763_A

description: T3BQBC07212008A_C1785_CY5_STERNE_CY3_13848763_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC07212008A_C1784_CY5_STERNE_CY3_13848765_A

description: T3BQBC07212008A_C1784_CY5_STERNE_CY3_13848765_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_G9898_CY3_STERNE_CY5_13758339_B

description: T3BQBC12172007A_G9898_CY3_STERNE_CY5_13758339_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_G9843_CY3_STERNE_CY5_13758398_B

description: T3BQBC12172007A_G9843_CY3_STERNE_CY5_13758398_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC07212008A_C1783_CY5_STERNE_CY3_13848764_A

description: T3BQBC07212008A_C1783_CY5_STERNE_CY3_13848764_anno_sub_95th_MDS.mev.refIsMEDA.out


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 3

description: Clone 3


title: T3BQBC12172007A_C3276_CY3_STERNE_CY5_13758417_B

description: T3BQBC12172007A_C3276_CY3_STERNE_CY5_13758417_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 4

description: Clone 4


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 1

description: Clone 1


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 9

description: Clone 9


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 10

description: Clone 10


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 10

description: Clone 10


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 7

description: Clone 7


title: iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3  clone 2

description: Clone 2


title: T3BQBC12172007A_B1357_CY3_STERNE_CY5_13758411_B

description: T3BQBC12172007A_B1357_CY3_STERNE_CY5_13758411_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12092007A_410_CY3_STERNE_CY5_13758413_B

description: T3BQBC12092007A_410_CY3_STERNE_CY5_13758413_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_B4266_CY3_STERNE_CY5_13758409_B

description: T3BQBC12172007A_B4266_CY3_STERNE_CY5_13758409_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_C1617_CY3_STERNE_CY5_13758415_B

description: T3BQBC12172007A_C1617_CY3_STERNE_CY5_13758415_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08212007_F7720_Cy3_STERNE_Cy5_104335_B

description: T3BQBC08212007_F7720_Cy3_STERNE_Cy5_104335_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 11

description: Clone 11


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 3

description: Clone 3


title: T3BQBC12092007_G2055_Cy3_STERNE_Cy5_13758689_B

description: T3BQBC12092007_G2055_Cy3_STERNE_Cy5_13758689_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 4

description: Clone 4


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 8

description: Clone 8


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 6

description: Clone 6


title: T3BQBC08212007_E3911_Cy3_STERNE_Cy5_103791_B

description: T3BQBC08212007_E3911_Cy3_STERNE_Cy5_103791_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08212007_F666_Cy3_STERNE_Cy5_104349_B

description: T3BQBC08212007_F666_Cy3_STERNE_Cy5_104349_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08212007_F5157_Cy3_STERNE_Cy5_104347_B

description: T3BQBC08212007_F5157_Cy3_STERNE_Cy5_104347_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 5

description: Clone 5


title: T3BQBC08212007_F6722_Cy3_STERNE_Cy5_104330_B

description: T3BQBC08212007_F6722_Cy3_STERNE_Cy5_104330_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08212007_E1149_Cy3_STERNE_Cy5_103756_B

description: T3BQBC08212007_E1149_Cy3_STERNE_Cy5_103756_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 1

description: Clone 1


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 7

description: Clone 7


title: T3BQBC08162007_2002734893_Cy3_STERNE_Cy5_100250_B

description: T3BQBC08162007_2002734893_Cy3_STERNE_Cy5_100250_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 8

description: Clone 8


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 6

description: Clone 6


title: T3BQBC08162007_2002734418_Cy3_STERNE_Cy5_100279_B

description: T3BQBC08162007_2002734418_Cy3_STERNE_Cy5_100279_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Klf4 clone 2

description: Clone 2


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 3

description: Clone 3


title: T3BQBC08162007_264_Cy3_STERNE_Cy5_100317_B

description: T3BQBC08162007_264_Cy3_STERNE_Cy5_100317_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08162007_1952_Cy3_STERNE_Cy5_100493_B

description: T3BQBC08162007_1952_Cy3_STERNE_Cy5_100493_anno_sub_95th_MDS.mev.refIsMEDB.out


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 1

description: Clone 1


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 4

description: Clone 4


title: T3BQBC08162007_04S00334_Cy3_STERNE_Cy5_100309_B

description: T3BQBC08162007_04S00334_Cy3_STERNE_Cy5_100309_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC03102008_Tsiankoffski_CY3_STERNE_CY5_13792503_B

description: T3BQBC03102008_Tsiankoffski_CY3_STERNE_CY5_13792503_anno_sub_95th_MDS.mev.refIsMEDB.out

organism: Bacillus anthracis

source_name: Tsiankoffski

value: Tsiankoffski


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 5

description: Clone 5


title: T3BQBC03102008_Pasteur_CY3_STERNE_CY5_13792510_B

description: T3BQBC03102008_Pasteur_CY3_STERNE_CY5_13792510_anno_sub_95th_MDS.mev.refIsMEDB.out

source_name: Pasteur

value: Pasteur


title: T3BQBC08162007_262_Cy3_STERNE_Cy5_100276_B

description: T3BQBC08162007_262_Cy3_STERNE_Cy5_100276_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC03102008_Vollum_CY3_STERNE_CY5_13792508_B

description: T3BQBC03102008_Vollum_CY3_STERNE_CY5_13792508_anno_sub_95th_MDS.mev.refIsMEDB.out

source_name: Vollum

value: Vollum


title: T3BQBC08212007_410_Cy3_STERNE_Cy5_103798_B

description: T3BQBC08212007_410_Cy3_STERNE_Cy5_103798_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_F666_CY3_STERNE_CY5_13759356_B

description: T3BQBC01142008A_F666_CY3_STERNE_CY5_13759356_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_F667_CY3_STERNE_CY5_13759361_B

description: T3BQBC01142008A_F667_CY3_STERNE_CY5_13759361_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_F5190_CY3_STERNE_CY5_13759257_B

description: T3BQBC01142008A_F5190_CY3_STERNE_CY5_13759257_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Estradiol minus_replicate 2_hybridization 2

city: Madison

first: Emery

middle: H.

last: Bresnick

state: WI

address: 1300 University Avenue 383 MSC

department: Pharmacology

institute: University of Wisconsin-Madison

description:
SAMPLE 7
Replicate 2, hyb 2

hyb_protocol: Hybridization to the Illumina Sentrix Expression BeadChip, staining and washing were carried out according to the manufacturer's protocol.

scan_protocol: Scanning procedures were carried out as described by Illumina.

data_processing: Data were normalized by rank invariant normalization using the Illumina Bead Studio software suite.

source_name: G1E-ER-GATA-1 uninduced

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

growth_protocol: G1E-ER-GATA-1 cells (Gregory et al., 1999; Johnson et al., 2002) were maintained in Iscove’s Modified Dulbecco’s Medium (IMDM) (GIBCO) supplemented with 15% FBS (Gemini), 1% penicillin-streptomycin (GIBCO), 2 u/ml erythropoietin, 120 nM monothioglycerol (MTG) (Sigma), 0.6% conditioned medium from a Kit-ligand-producing Chinese hamster ovary (CHO) cell line and 1 µg/ml puromycin (Sigma).

extract_protocol: Total RNA was isolated using TRIzol (GIBCO/BRL) according to the manufacturer's protocol.

treatment_protocol: ER-GATA-1 expression was induced with 1 µM β-estradiol and RNA was collected after 24 hours.


title: T3BQBC03102008_Aussie_CY3_STERNE_CY5_13792505_B

description: T3BQBC03102008_Aussie_CY3_STERNE_CY5_13792505_anno_sub_95th_MDS.mev.refIsMEDB.out

source_name: Aussie

value: Aussie


title: iPS from MEFs with overexpression of Oct4, Sox2 and Esrrb clone 2

description: Clone 2


title: Estradiol minus_replicate 1_hybridization 2

description:
SAMPLE 5
Replicate 1, hyb 2


title: Estradiol plus_replicate 1_hybridization 2

description:
SAMPLE 6
Replicate 1, hyb 2

source_name: G1E-ER-GATA-1 induced


title: Estradiol plus_replicate 2_hybridization 2

description:
SAMPLE 8
Replicate 2, hyb 2


title: Estradiol plus_replicate 2_hybridization 1

description:
SAMPLE 4
Replicate 2, hyb 1


title: Estradiol minus_replicate 2_hybridization 1

description:
SAMPLE 3
Replicate 2, hyb 1


title: T3BQBC01142008A_B5780_CY3_STERNE_CY5_13759323_B

description: T3BQBC01142008A_B5780_CY3_STERNE_CY5_13759323_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Anti-IgM Treated replicate 3

city: Umeå

last: Grundström

address: Analysvägen 1

department: Department of Molecular Biology

country: Sweden

institute: Umeå University

description: Anti-IgM Treated

hyb_protocol: Labeled cRNA (1.5 ug) were hybridized to the Sentrix MouseRef-6 Expression Beadchip for 16-18 h at 58 °C, according to the manufacturer's instructions (Illumina).

scan_protocol: Following attachment of Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences), arrays were scanned with an Illumina bead array reader.

data_processing: Signal intensities of genes were normalized by cubic spline method.

source_name: Spleen - Anti-IgM Treated

label_protocol: Total RNA was amplified and purified to yield biotinylated cRNA using an Ambion Illumina RNA amplification kit (Ambion).

growth_protocol: Mice were maintained for 8 weeks in a controlled environment with a 12 h dark/light cycle.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) and further purified using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Spleen of 8 weeks old mice was isolated and B cells were purified and stimulated with IL-4 (Pepro-Tech) and CD40L (R&D Systems) as indicated at 5 ng/ml and 200 ng/ml, respectively. The BCR of stimulated cells was activated by incubation with goat F(ab’)2 anti-mouse IgM (Southern Biotechnologies) at 2.5 μg/ml for 3 hour.

value: 8 weeks

tag: tissue

value: Spleen


title: Anti-IgM Treated replicate 1

description: Anti-IgM Treated


title: Estradiol plus_replicate 1_hybridization 1

description:
SAMPLE 2
Replicate 1, hyb 1


title: Estradiol minus_replicate 1_hybridization 1

description:
SAMPLE 1
Replicate 1, hyb 1


title: Anti-IgM Treated replicate 2

description: Anti-IgM Treated


title: T3BQBC03102008_Amesdelta_Cy3_STERNE_Cy5_13792457_B

description: T3BQBC03102008_Amesdelta_Cy3_STERNE_Cy5_13792457_anno_sub_95th_MDS.mev.refIsMEDB.out

source_name: Amesdelta

value: Amesdelta


title: T3BQBC01142008A_03BR1283_CY3_STERNE_CY5_13759286_B

description: T3BQBC01142008A_03BR1283_CY3_STERNE_CY5_13759286_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_04S00334_CY3_STERNE_CY5_13759358_B

description: T3BQBC01142008A_04S00334_CY3_STERNE_CY5_13759358_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_F665_CY3_STERNE_CY5_13759353_B

description: T3BQBC01142008A_F665_CY3_STERNE_CY5_13759353_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Untreated replicate 3

description: control

source_name: Spleen - Untreated


title: Untreated replicate 1

description: control


title: T3BQBC01022008A_H2576_97_CY3_STERNE_CY5_13758778_B

description: T3BQBC01022008A_H2576_97_CY3_STERNE_CY5_13758778_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_2002734893_CY3_STERNE_CY5_13759261_B

description: T3BQBC01142008A_2002734893_CY3_STERNE_CY5_13759261_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_H2573_97_CY3_STERNE_CY5_13756791_B

description: T3BQBC01022008A_H2573_97_CY3_STERNE_CY5_13756791_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.5 t30_t0

city: Wageningen

first: Maarten

last: Mols

address: Bomenweg 2

department: ATV

country: Netherlands

institute: Wageningen University

description: No extra description.

hyb_protocol: The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.

scan_protocol: Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.

data_processing: Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.

label_protocol: Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.5 for 30 min

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.5 for 0 min


title: T3BQBC01022008A_H2573_97_CY3_STERNE_CY5_13756789_B

description: T3BQBC01022008A_H2573_97_CY3_STERNE_CY5_13756789_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008_579_CY3_STERNE_CY5_13759349_B

description: T3BQBC01142008_579_CY3_STERNE_CY5_13759349_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_G1440_CY3_STERNE_CY5_13758547_B

description: T3BQBC01022008A_G1440_CY3_STERNE_CY5_13758547_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_1952_CY3_STERNE_CY5_13759331_B

description: T3BQBC01142008A_1952_CY3_STERNE_CY5_13759331_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_G9842_CY3_STERNE_CY5_13758549_B

description: T3BQBC01022008A_G9842_CY3_STERNE_CY5_13758549_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.5 t60_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.5 for 60 min


title: T3BQBC01022008A_G2008_CY3_STERNE_CY5_13758785_B

description: T3BQBC01022008A_G2008_CY3_STERNE_CY5_13758785_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_F65185_CY3_STERNE_CY5_13756790_B

description: T3BQBC01022008A_F65185_CY3_STERNE_CY5_13756790_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Untreated replicate 2

description: control

tag: age


title: Bc14579 pH4.5 t10_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.5 for 10 min


title: T3BQBC01022008A_F5191_CY3_STERNE_CY5_13758804_B

description: T3BQBC01022008A_F5191_CY3_STERNE_CY5_13758804_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.5 t0_t10

description: No extra description.


title: Bc14579 pH4.5 t0_t30

description: No extra description.


title: T3BQBC01022008A_F5157_CY3_STERNE_CY5_13758798_B

description: T3BQBC01022008A_F5157_CY3_STERNE_CY5_13758798_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_F6722_CY3_STERNE_CY5_13758802_B

description: T3BQBC01022008A_F6722_CY3_STERNE_CY5_13758802_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.5 t0_t60

description: No extra description.


title: T3BQBC01022008A_2002734418_CY3_STERNE_CY5_13758805_B

description: T3BQBC01022008A_2002734418_CY3_STERNE_CY5_13758805_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_F9930_CY3_STERNE_CY5_13758788_B

description: T3BQBC01022008A_F9930_CY3_STERNE_CY5_13758788_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.8 t10_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.8 for 10 min

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.8 for 0 min


title: T3BQBC01022008A_F439_CY3_STERNE_CY5_13756787_B

description: T3BQBC01022008A_F439_CY3_STERNE_CY5_13756787_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.8 t0_t60

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.8 for 60 min


title: Bc14579 pH4.8 t30_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH4.8 for 30 min


title: T3BQBC01022008A_2003_I_1253_CY3_STERNE_CY5_13758796_B

description: T3BQBC01022008A_2003_I_1253_CY3_STERNE_CY5_13758796_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008_F4976_CY3_STERNE_CY5_13759265_B

description: T3BQBC01022008_F4976_CY3_STERNE_CY5_13759265_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.0 t60_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.0 for 60 min

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.0 for 0 min


title: Bc14579 pH4.8 t0_t10

description: No extra description.


title: T3BQBC01022008_6047_Cy3_STERNE_Cy5_13765739_B

description: T3BQBC01022008_6047_Cy3_STERNE_Cy5_13765739_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH4.8 t0_t30

description: No extra description.


title: T3BQBC01022008_F438_CY3_STERNE_CY5_13756793_B

description: T3BQBC01022008_F438_CY3_STERNE_CY5_13756793_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.0 t0_t30

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.0 for 30 min


title: T3BQBC01022008_F65185_CY3_STERNE_CY5_13759274_B

description: T3BQBC01022008_F65185_CY3_STERNE_CY5_13759274_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.0 t10_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.0 for 10 min


title: T3BQBC0142008A_F439_CY3_STERNE_CY5_13759342_B

description: T3BQBC0142008A_F439_CY3_STERNE_CY5_13759342_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.0 t30_t0

description: No extra description.


title: Bc14579 pH5.0 t0_t10

description: No extra description.


title: Bc14579 pH5.0 t0_t60

description: No extra description.


title: T3BQBC0142008A_3297_CY3_STERNE_CY5_13759343_B

description: T3BQBC0142008A_3297_CY3_STERNE_CY5_13759343_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.4 t60_t0

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.4 for 60 min

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.4 for 0 min


title: T3BQBC0122008A_G3317_CY3_STERNE_CY5_13765685_B

description: T3BQBC0122008A_G3317_CY3_STERNE_CY5_13765685_anno_sub_95th_MDS.mev.refIsMEDB.out

tag: strain


title: T3BQBC0122008A_G9842_CY3_STERNE_CY5_13765675_B

description: T3BQBC0122008A_G9842_CY3_STERNE_CY5_13765675_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0122008A_D4214_CY3_STERNE_CY5_13765676_B

description: T3BQBC0122008A_D4214_CY3_STERNE_CY5_13765676_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0122008_F663_CY3_STERNE_CY5_13765680_B

description: T3BQBC0122008_F663_CY3_STERNE_CY5_13765680_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.4 t0_t30

description: No extra description.

extract_protocol: RNA was extracted as described by van Schaik et al., 2007.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.4 for 30 min


title: T3BBC12222007A_G9241_CY3_STERNE_CY5_13765673_B

description: T3BBC12222007A_G9241_CY3_STERNE_CY5_13765673_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0142008A_262_CY3_STERNE_CY5_13759285_B

description: T3BQBC0142008A_262_CY3_STERNE_CY5_13759285_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.4 t30_t0

description: No extra description.


title: T3BQBC0122008_E6345_CY3_STERNE_CY5_13765678_B

description: T3BQBC0122008_E6345_CY3_STERNE_CY5_13765678_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.4 t0_t60

description: No extra description.


title: Bc14579 pH5.4 t0_t10

description: No extra description.

tag: Bc ATCC 14579 OD600 0.5 exposed to pH5.4 for 10 min


title: T3BQBC0122008_G4200_CY3_STERNE_CY5_13765690_B

description: T3BQBC0122008_G4200_CY3_STERNE_CY5_13765690_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0102008A_G9844_CY3_STERNE_CY5_13765748_B

description: T3BQBC0102008A_G9844_CY3_STERNE_CY5_13765748_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3QBQBC01022008A_525_Cy5_STERNE_Cy3_13758782_A

description: T3QBQBC01022008A_525_Cy5_STERNE_Cy3_13758782_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BBC0122008A_E3911_CY3_STERNE_CY5_13765742_B

description: T3BBC0122008A_E3911_CY3_STERNE_CY5_13765742_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0102008A_C1617_Cy3_STERNE_Cy5_13765731_B

description: T3BQBC0102008A_C1617_Cy3_STERNE_Cy5_13765731_anno_sub_95th_MDS.mev.refIsMEDB.out


title: Bc14579 pH5.4 t10_t0

description: No extra description.


title: T3BBC0122008A_C3276_CY3_STERNE_CY5_13765669_B

description: T3BBC0122008A_C3276_CY3_STERNE_CY5_13765669_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0102008A_D8096_CY3_STERNE_CY5_13765747_B

description: T3BQBC0102008A_D8096_CY3_STERNE_CY5_13765747_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0122008_F7720_CY3_STERNE_CY5_13765679_B

description: T3BQBC0122008_F7720_CY3_STERNE_CY5_13765679_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3QBQBC01022008A_80700019_Cy5_STERNE_Cy3_13758790_A

description: T3QBQBC01022008A_80700019_Cy5_STERNE_Cy3_13758790_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3QBQBC01022008A_H2576_97_Cy5_STERNE_Cy3_13758779_A

description: T3QBQBC01022008A_H2576_97_Cy5_STERNE_Cy3_13758779_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_H3081_97_Cy5_STERNE_CY3_58323_A

description: T3BQBC12172007A_H3081_97_Cy5_STERNE_CY3_58323_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_H1548_Cy5_STERNE_CY3_13758334_A

description: T3BQBC12172007A_H1548_Cy5_STERNE_CY3_13758334_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_H3074_97_Cy5_STERNE_CY3_58327_A

description: T3BQBC12172007A_H3074_97_Cy5_STERNE_CY3_58327_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BBC0122008A_E1149_CY3_STERNE_CY5_13765733_B

description: T3BBC0122008A_E1149_CY3_STERNE_CY5_13765733_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_H1449_CY5_STERNE_CY3_13758337_A

description: T3BQBC12172007A_H1449_CY5_STERNE_CY3_13758337_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC12092007A_G2055_CY3_STERNE_CY5_13746863_B

description: T3ABC12092007A_G2055_CY3_STERNE_CY5_13746863_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC12092007A_410_CY3_STERNE_CY5_13746860_B

description: T3ABC12092007A_410_CY3_STERNE_CY5_13746860_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_G9842_CY5_STERNE_CY3_13758416_A

description: T3BQBC12172007A_G9842_CY5_STERNE_CY3_13758416_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_H1448_CY5_STERNE_CY3_13758400_A

description: T3BQBC12172007A_H1448_CY5_STERNE_CY3_13758400_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_G9843_CY5_STERNE_CY3_13758399_A

description: T3BQBC12172007A_G9843_CY5_STERNE_CY3_13758399_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_G1440_CY5_STERNE_CY3_13758381_A

description: T3BQBC12172007A_G1440_CY5_STERNE_CY3_13758381_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007A_410_CY5_STERNE_CY3_13746858_A

description: T3AQBC12092007A_410_CY5_STERNE_CY3_13746858_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_G9898_CY5_STERNE_CY3_13758401_A

description: T3BQBC12172007A_G9898_CY5_STERNE_CY3_13758401_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC01222008A_F7720_CY3_STERNE_CY5_13734712_B

description: T3ABC01222008A_F7720_CY3_STERNE_CY5_13734712_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_G9844_CY3_STERNE_CY5_13762193_B

description: T3ABC01162008A_G9844_CY3_STERNE_CY5_13762193_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_G1440_CY3_STERNE_CY5_13759051_B

description: T3ABC01162008A_G1440_CY3_STERNE_CY5_13759051_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_H2576_97_CY3_STERNE_CY5_13765226_B

description: T3ABC01162008A_H2576_97_CY3_STERNE_CY5_13765226_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_B4266_CY5_STERNE_CY3_13758412_A

description: T3BQBC12172007A_B4266_CY5_STERNE_CY3_13758412_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC01162008A_G4200_CY3_STERNE_CY5_13762137_B

description: T3ABC01162008A_G4200_CY3_STERNE_CY5_13762137_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12172007A_D4214_CY5_STERNE_CY3_13758321_A

description: T3BQBC12172007A_D4214_CY5_STERNE_CY3_13758321_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC01222008A_F5190_CY3_STERNE_CY5_13734765_B

description: T3ABC01222008A_F5190_CY3_STERNE_CY5_13734765_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC12092007A_410_CY5_STERNE_CY3_13758414_A

description: T3BQBC12092007A_410_CY5_STERNE_CY3_13758414_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_B1357_CY5_STERNE_CY3_13758408_A

description: T3BQBC12172007A_B1357_CY5_STERNE_CY3_13758408_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC08162007_525_Cy5_STERNE_CY3_100307_A

description: T3BQBC08162007_525_Cy5_STERNE_CY3_100307_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC12172007A_C1617_CY5_STERNE_CY3_13758410_A

description: T3BQBC12172007A_C1617_CY5_STERNE_CY3_13758410_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC01162008A_F6722_CY3_STERNE_CY5_13759049_B

description: T3ABC01162008A_F6722_CY3_STERNE_CY5_13759049_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_F663_CY3_STERNE_CY5_13762128_B

description: T3ABC01162008A_F663_CY3_STERNE_CY5_13762128_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08162007_2002734418_Cy5_STERNE_CY3_100318_A

description: T3BQBC08162007_2002734418_Cy5_STERNE_CY3_100318_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC01162008A_E3911_CY3_STERNE_CY5_13762177_B

description: T3ABC01162008A_E3911_CY3_STERNE_CY5_13762177_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_G2008_CY3_STERNE_CY5_13765232_B

description: T3ABC01162008A_G2008_CY3_STERNE_CY5_13765232_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_E1149_CY3_STERNE_CY5_13762191_B

description: T3ABC01162008A_E1149_CY3_STERNE_CY5_13762191_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC08162007_04S00334_Cy5_STERNE_CY3_100313_A

description: T3BQBC08162007_04S00334_Cy5_STERNE_CY3_100313_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3ABC01162008A_D4214_CY3_STERNE_CY5_13762123_B

description: T3ABC01162008A_D4214_CY3_STERNE_CY5_13762123_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_D8096_CY3_STERNE_CY5_13762184_B

description: T3ABC01162008A_D8096_CY3_STERNE_CY5_13762184_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC03102008_Pasteur_Cy5_STERNE_Cy3_13792511_A

description: T3BQBC03102008_Pasteur_Cy5_STERNE_Cy3_13792511_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008A_2002734893_CY5_STERNE_CY3_13759322_A

description: T3BQBC01142008A_2002734893_CY5_STERNE_CY3_13759322_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008A_1952_CY5_STERNE_CY3_13759262_A

description: T3BQBC01142008A_1952_CY5_STERNE_CY3_13759262_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC03102008_Aussie_Cy5_STERNE_Cy3_13792507_A

description: T3BQBC03102008_Aussie_Cy5_STERNE_Cy3_13792507_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC03102008_Tsiankoffski_CY5_STERNE_CY3_13792504_A

description: T3BQBC03102008_Tsiankoffski_CY5_STERNE_CY3_13792504_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008A_F665_CY5_STERNE_CY3_13759360_A

description: T3BQBC01142008A_F665_CY5_STERNE_CY3_13759360_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008A_F5190_CY5_STERNE_CY3_13759325_A

description: T3BQBC01142008A_F5190_CY5_STERNE_CY3_13759325_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC08152007_262_CY3_STERNE_CY5_108053_B

description: T3AQBC08152007_262_CY3_STERNE_CY5_108053_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3ABC01162008A_C3276_CY3_STERNE_CY5_13762142_B

description: T3ABC01162008A_C3276_CY3_STERNE_CY5_13762142_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_F667_CY5_STERNE_CY3_13759364_A

description: T3BQBC01142008A_F667_CY5_STERNE_CY3_13759364_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008A_03BR1283_CY5_STERNE_CY3_13759289_A

description: T3BQBC01142008A_03BR1283_CY5_STERNE_CY3_13759289_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007A_H3081_97_Cy3_STERNE_CY5_56711_B

description: T3AQBC12092007A_H3081_97_Cy3_STERNE_CY5_56711_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC03102008_Amesdelta_Cy5_STERNE_Cy3_13792458_A

description: T3BQBC03102008_Amesdelta_Cy5_STERNE_Cy3_13792458_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007A_H1548_Cy3_STERNE_CY5_13756709_B

description: T3AQBC12092007A_H1548_Cy3_STERNE_CY5_13756709_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008A_04S00334_CY5_STERNE_CY3_13759363_A

description: T3BQBC01142008A_04S00334_CY5_STERNE_CY3_13759363_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12172007A_E6345_CY3_STERNE_CY5_13762124_B

description: T3AQBC12172007A_E6345_CY3_STERNE_CY5_13762124_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01142008_F65185_CY5_STERNE_CY3_13759295_A

description: T3BQBC01142008_F65185_CY5_STERNE_CY3_13759295_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008_F4794_CY5_STERNE_CY3_13759344_A

description: T3BQBC01142008_F4794_CY5_STERNE_CY3_13759344_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01142008_262_CY5_STERNE_CY3_13759280_A

description: T3BQBC01142008_262_CY5_STERNE_CY3_13759280_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC03102008_Vollum_CY5_STERNE_CY3_13792509_A

description: T3BQBC03102008_Vollum_CY5_STERNE_CY3_13792509_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T1QBC_AH602_Cy3_AMES_Cy5_43094

hyb_protocol: Aminosaline coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 degree Celcius for 45 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry.  Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in a solution of 50% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were denatured at 95 degree Celcius prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 degree Celcius.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
      (1). Species spot: oligos designed for the species under investigation.
      (2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
      (3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
      Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
      Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
      |Xi - M|/MAD > Max
      Xi = Each intensity value from the set of replicates.
      M = Median intensity value from the set of replicates.
      MAD = Median absolute deviation.
      Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
      Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
      Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
      After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
    1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
    2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
    3). Perform Log Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
    4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
    1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

source_name: Ames

extract_protocol: Epicentre MasterPure DNA Extraction Kit

value: Ames

growth_protocol: Cells grown in Lysogeny broth (LB) at 37 degrees Celcius overnight


title: T3BQBC01022008A_G9842_CY5_STERNE_CY3_13758786_A

description: T3BQBC01022008A_G9842_CY5_STERNE_CY3_13758786_anno_sub_95th_MDS.mev.refIsMEDA.out

source_name: Sterne reference


title: T3BQBC01022008A_G9844_CY5_STERENE_CY3_13765737_A

description: T3BQBC01022008A_G9844_CY5_STERENE_CY3_13765737_anno_sub_95th_MDS.mev.refIsMEDA.out


title: IFNgR Chimera Lung 97 Days Infection

city: New York

first: Ludovic

last: Desvignes

state: NY

address: 522 First Avenue

institute: New York University School of Medicine

description: Both groups (control and experimental) were simultaneously infected via aerosol route with 100 colony forming units of M. tuberculosis strain H37Rv, euthanized after 97 days and their lung removed for total RNA isolation.

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 835 ng of the corresponding Cy3- or Cy5-labeled fragmented cRNA were combined and hybridized  overnight (17 hours, 65º C) to Agilent Whole Mouse Genome Oligo Microarray 4x44K using Agilent's recommended hydridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37º C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent's DNA microarray scanner (Agilent Technologies).

data_processing: The data were read out and processed using the Agilent Feature Extraction Software followed by the Rosetta Resolver Software. The VALUE column represent the normalized log2 ratio between the fluorescence intensity of the Cy3-labeled cRNA W→W samples (control) and the Cy5-labeled W→K samples (experimental).

source_name: W→W

label_protocol: To produce Cy3 labeled cRNA, 1 microgram of each total RNA was amplified using a linear T7-based amplification step and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer's protocol.

extract_protocol: Total RNA was extracted from the left lung using TriZol reagent (Invitrogen) and was processed as previously described for removal of contaminating genomic DNA and reverse transcription (Banaiee et al., 2006). RNA integrity of individual samples was confirmed by ribosomal RNA profiles at the Genomics Facility of the Cancer Institute of NYU Langone Medical Center. RNA samples of each group of mice were pooled.

tag: tissue

value: Lung

tag: sample

value: pool (5 mice)

tag: description

value: Ifngr+/+ mice gamma-irradiated and reconstituted i.v. with Ifngr+/+ bone marrow cells.

source_name: W→K

label_protocol: To produce Cy5 labeled cRNA, 1 microgram of each total RNA was amplified using a linear T7-based amplification step and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following the manufacturer's protocol.

value: Ifngr-/- mice gamma-irradiated and reconstituted i.v. with Ifngr+/+ bone marrow cells.


title: IFNgR Chimera Lung 63 Days Infection

description: Both groups (control and experimental) were simultaneously infected via aerosol route with 100 colony forming units of M. tuberculosis strain H37Rv, euthanized after 63 days and their lung removed for total RNA isolation.

value: pool (4 mice)

value: Ifngr+/+ mice gamma-irradiated and reconstituted with i.v. transfer of Ifngr+/+ bone marrow cells.

value: Ifngr-/- mice gamma-irradiated and reconstituted with i.v. transfer of Ifngr+/+ bone marrow cells.


title: T3AQBC12092007A_H1448_CY3_STERNE_CY5_13756730_B

description: T3AQBC12092007A_H1448_CY3_STERNE_CY5_13756730_anno_sub_95th_MDS.mev.refIsMEDB.out

value: Sterne


title: T3AQBC07302008A_C1785_CY3_STERNE_CY5_13849026_B

description: T3AQBC07302008A_C1785_CY3_STERNE_CY5_13849026_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC12092007A_H1449_CY3_STERNE_CY5_13756724_B

description: T3AQBC12092007A_H1449_CY3_STERNE_CY5_13756724_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T1QBC_AH599_Cy3_AMES_Cy5_43092


title: T3BQBC01022008A_F9930_CY5_STERNE_CY3_13758783_A

description: T3BQBC01022008A_F9930_CY5_STERNE_CY3_13758783_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC08152007_04S00334_Cy3_STERNE_CY5_108134_B

description: T3AQBC08152007_04S00334_Cy3_STERNE_CY5_108134_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_F6722_CY5_STERNE_CY3_13758801_A

description: T3BQBC01022008A_F6722_CY5_STERNE_CY3_13758801_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01022008A_G4200_CY5_STERNE_CY3_13765682_A

description: T3BQBC01022008A_G4200_CY5_STERNE_CY3_13765682_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC07302008A_C1784_CY3_STERNE_CY5_13849023_B

description: T3AQBC07302008A_C1784_CY3_STERNE_CY5_13849023_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC01022008A_F5157_CY5_STERNE_CY3_13758797_A

description: T3BQBC01022008A_F5157_CY5_STERNE_CY3_13758797_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01022008A_F5191_CY5_STERNE_CY3_13758803_A

description: T3BQBC01022008A_F5191_CY5_STERNE_CY3_13758803_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01022008A_2003_I_1253_CY5_STERNE_CY3_13758800_A

description: T3BQBC01022008A_2003_I_1253_CY5_STERNE_CY3_13758800_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01022008A_2002734418_CY5_STERNE_CY3_13758799_2_A

description: T3BQBC01022008A_2002734418_CY5_STERNE_CY3_13758799_2_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01022008A_264_CY5_STERNE_CY3_13758780_A

description: T3BQBC01022008A_264_CY5_STERNE_CY3_13758780_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC0142008A_B5780_CY5_STERNE_CY3_13759339_A

description: T3BQBC0142008A_B5780_CY5_STERNE_CY3_13759339_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T1QBC_AH568_Cy3_AMES_Cy5_124532


title: T3AQBC12092007A_G9898_CY3_STERNE_CY5_13756734_B

description: T3AQBC12092007A_G9898_CY3_STERNE_CY5_13756734_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T1QBC_AH564_Cy3_AMES_Cy5_124528


title: T1QBC_AH598_Cy3_AMES_Cy5_43091


title: T3BQBC0142008A_579_CY5_STERNE_CY3_13759348_A

description: T3BQBC0142008A_579_CY5_STERNE_CY3_13759348_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC01022008A_G2008_CY5_STERNE_CY3_13758784_A

description: T3BQBC01022008A_G2008_CY5_STERNE_CY3_13758784_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007A_G9843_CY3_STERNE_CY5_13756735_B

description: T3AQBC12092007A_G9843_CY3_STERNE_CY5_13756735_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0122008A_E6345_CY5_STERNE_CY3_13765681_A

description: T3BQBC0122008A_E6345_CY5_STERNE_CY3_13765681_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC0122008A_G2055_CY5_STERNE_CY3_13765688_A

description: T3BQBC0122008A_G2055_CY5_STERNE_CY3_13765688_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T1QBC_AH557_Cy3_AMES_Cy5_124397


title: T3AQBC12092007A_G9241_CY3_STERNE_CY5_13762130_B

description: T3AQBC12092007A_G9241_CY3_STERNE_CY5_13762130_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0102008A_E3911_CY5_STERNE_CY3_13765668_A

description: T3BQBC0102008A_E3911_CY5_STERNE_CY3_13765668_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007A_C1617_CY3_STERNE_CY5_13746855_B

description: T3AQBC12092007A_C1617_CY3_STERNE_CY5_13746855_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3AQBC12092007A_B4266_CY3_STERNE_CY5_13756736_B

description: T3AQBC12092007A_B4266_CY3_STERNE_CY5_13756736_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC0102008A_C1617_CY5_STERNE_CY3_13765730_A

description: T3BQBC0102008A_C1617_CY5_STERNE_CY3_13765730_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC0102008A_D8096_CY5_STERNE_CY3_13765751_A

description: T3BQBC0102008A_D8096_CY5_STERNE_CY3_13765751_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T1QBC_AH540_Cy3_AMES_Cy5_124042


title: T3BQBC0122008A_F7720_CY5_STERNE_CY3_13765677_A

description: T3BQBC0122008A_F7720_CY5_STERNE_CY3_13765677_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC0102008A_6047_cY5_STERNE_CY3_13765738_A

description: T3BQBC0102008A_6047_cY5_STERNE_CY3_13765738_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BQBC0102008A_E1149_CY5_STERNE_CY3_13765734_A

description: T3BQBC0102008A_E1149_CY5_STERNE_CY3_13765734_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T1QBC_AH533_Cy3_AMES_Cy5_124530


title: T3BBC12222007A_G3317_CY5_STERNE_CY3_13765686_A

description: T3BBC12222007A_G3317_CY5_STERNE_CY3_13765686_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007A_B1357_CY3_STERNE_CY5_13746862_B

description: T3AQBC12092007A_B1357_CY3_STERNE_CY5_13746862_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BBC12222007A_G9241_CY5_STERNE_CY3_13765687_A

description: T3BBC12222007A_G9241_CY5_STERNE_CY3_13765687_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3BBC0122008A_C3276_CY5_STERNE_CY3_13765674_A

description: T3BBC0122008A_C3276_CY5_STERNE_CY3_13765674_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC07302008A_C1783_CY3_STERNE_CY5_13849021_B

description: T3AQBC07302008A_C1783_CY3_STERNE_CY5_13849021_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T1QBC_AH407_Cy3_AMES_Cy5_124041


title: T3BBC0122008A_C3276_CY5_STERNE_CY3_13765663_A

description: T3BBC0122008A_C3276_CY5_STERNE_CY3_13765663_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T1QBC_AH405_Cy3_AMES_Cy5_124029


title: T3BBC12222007A_F663_CY5_STERNE_CY3_13765683_A

description: T3BBC12222007A_F663_CY5_STERNE_CY3_13765683_anno_sub_95th_MDS.mev.refIsMEDA.out


title: T3AQBC12092007_H3074_97_Cy3_STERNE_CY5_56713_B

description: T3AQBC12092007_H3074_97_Cy3_STERNE_CY5_56713_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T1QBC_AH818_Cy3_AMES_Cy5_84948


title: T3AQBC07302008_H9312_CY3_STERNE_CY5_13849009_B

description: T3AQBC07302008_H9312_CY3_STERNE_CY5_13849009_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC06182008A_3634_CY3_STERNE_CY5_13823982_B

description: T3BQBC06182008A_3634_CY3_STERNE_CY5_13823982_anno_sub_95th_MDS.mev.refIsMEDB.out

data_processing:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
(1). Species spot: oligos designed for the species under investigation.
(2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
(3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
|Xi - M|/MAD > Max
Xi = Each intensity value from the set of replicates.
M = Median intensity value from the set of replicates.
MAD = Median absolute deviation.
Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
3). Perform Log Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen). Labeled DNA was purified with the Qiaquick PCR purification kit (QIAGEN). The purified labelled DNA was then dye coupled with the appropriate cyanine dye (Cy3/Cy5).


title: T3BQBC06182008A_3615_CY3_STERNE_CY5_13824012_B

description: T3BQBC06182008A_3615_CY3_STERNE_CY5_13824012_anno_sub_95th_MDS.mev.refIsMEDB.out


title: T3BQBC06182008A_3646_CY3_STERNE_CY5_13824074_B

description: T3BQBC06182008A_3646_CY3_STERNE_CY5_13824074_anno_sub_95th_MDS.mev.refIsMEDB.out