title: MEF cultured in iCD1

source_name: mouse embryonic fibroblast cells isolated from 13.5dpc 129/OG2 mice

treatment_protocol: Cells are cultured in indicated medium

tag: growth conditions

value: cultured in iCD1


title: MM_4_HSC

status: Public on Oct 27 2010

type: RNA

city: Düsseldorf

first: Ingmar

last: Bruns

state: NRW

address: Moorenstr. 5

department: Hematology, Oncology and Clinical Immunology

country: Germany

institute: University of Düsseldorf

description: (MM) Multiple Myeloma / Hematopoietic Stem Cells

hyb_protocol: According to manufacturer's instructions

data_processing: MAS 5.0, Scaling Factor 500

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

label_protocol:
GeneChip Expression 3’-Amplification One-Cycle-Target Labeling & Control Reagents
(Affymetrix; 900493)

extract_protocol: Qiagen RNeasy micro kit (Qiagen; 74004)

tag: cell type

value: hematopoietic stem cells

tag: disease state

value: Multiple Myeloma Patient


title: MM_7_GMP

scan_protocol: According to manufacturer's instructions

value: granulocyte/monocyte progenitors


title: OG2 ES cultured in N2B27(2i)

city: Guangzhou

first: liu

last: jing

state: guangdong

address: 190 Kai Yuan Avenue

country: China

institute: GIBH

description: expression data from iPS cells at D3 post-retroviral infection

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

label: biotin

organism: Mus musculus

source_name: mouse embryonic fibroblast cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Cultured in 37℃ with 5% CO2 in the media descripted in sample source name.

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

value: mouse embryonic stem cell

tag: genetic background

value: cultured in N2B27(2i)


title: iPS cell line O4-4 cultured in KSR

source_name: iPS cell line indcued by Oct4 cultured in iCD1

value: mouse embryonic fibroblast cells infected by Oct4

tag: cell line

value: cultured in KSR


title: MM_7_MEP

value: megakaryocyte/erythroid progenitors


title: MM_5_CMP

value: common myeloid progenitors


title: D3 OK+S(TetOn)  MEF in iCD1 +dox

source_name: MEFs infected by OK retrivirals and TetOn Sox2 virus  cultured in iCD1  supplemented with Dox at D3 post-infection

treatment_protocol: MEFs were infected with  Oct4/Klf4/TetOn-Sox2 or Oct4/Sox2/TetOn-Klf4  virus and then cultured in indicated media.

tag: sample type

value: mouse embryonic fibroblast cells infected by Oct4/Klf4/TetOn-Sox2

value: mouse embryonic fibroblast

tag: transfection

tag: treatment

value: plus doxycycline

tag: time

value: 3 d


title: MM_5_MEP


title: iPS cell line O4-1 cultured in KSR


title: iPS cell line O4-2 cultured in KSR


title: MEF cultured in FBS

value: cultured in FBS


title: iPS cell line O4-1 cultured in N2B27(2i)


title: MM_6_HSC


title: Congenital ectopic thyroid HC-22

type: genomic

city: Montreal

first: Johnny

middle: Yvan

last: Deladoëy

state: QC

address: 3175 Côte Sainte-Catherine

department: Pediatrics; U of Montreal

country: Canada

institute: Research Center CHU Sainte-Justine

description: MeDIP-chip DNA of congenital ectopic thyroid

hyb_protocol: Nimblegen kit, hybridized at Nimblegen facilities in Iceland.

scan_protocol: Nimblegen protocol, scanned at Nimblegen facilities in Iceland.

data_processing: Arrays were processed at Nimblegen facilities in Iceland using Nimblegen's standard protocol (using Roche NimbleGen NimbleScanTM software v2.5) for ChIP-chip analysis.

molecule: genomic DNA

source_name: MeDIP DNA from thyroid

label_protocol: DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: DNA was isolated from ectopic thyroids and peripheral blood leucocytes by using the phenol/chloroform protocol (John et al.; Nucleic Acids Research, 1991)

tag: tissue

value: congenital ectopic thyroid

source_name: Input DNA from thyroid


title: Orthotopic thyroid SP

description: MeDIP-chip DNA of orthotopic thyroid

value: orthotopic thyroid


title: MM_3_MEP


title: MM_5_GMP


title: Orthotopic thyroid HC-16

description: MeDIP-chip DNA of orthotopic thyroid


title: Congenital ectopic thyroid HC-23


title: Congenital ectopic thyroid HC-6


title: MM_2_GMP


title: MM_2_HSC


title: MM_1_MEP


title: MM_2_CMP


title: MM_1_HSC


title: MM_3_HSC


title: MM_3_CMP


title: Control_5_MEP

description: (Control) Healthy donor / Hematopoietic Stem Cells

value: Healthy Donor


title: 4QMT08242009A_WT3-Cu.Cy5_WT3+Cu.Cy3_14017991.LOW_MDS.mev.refIsIB.out

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

country: USA

institute: The J. Craig Venter Institute

description: Aminosilane-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 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95ºC prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   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, then dried in air, and scanned with an Axon GenePix 4000 scanner (http://intranet.jtc.jcvsf.org/sops/M008.pdf).  All wash buffers were supplemented with 1-ml of 0.1M DTT per liter of wash buffer.

hyb_protocol: Aminosilane-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 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   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, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing in the supplemented with Cu

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: The wildtype cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours.

extract_protocol: RNA was extracted from Mtb as follows: an equal volume of 4 M guanidinium isothiocyanate (GTC), 0.5% sodium N-lauryl sarcosine, 25 mM trisodium citrate) was added to cultures to arrest transcription, and cells were collected by centrifugation at 2,885 x g. Bacterial were resuspended in 1 ml TRIzol reagent (Invitrogen) and bead beat with zirconia silica beads (BioSpec Products) in a BioSpec Mini Bead Beater two times for 30 s, with 1 min cooling on ice in between. Samples were either stored at -80 C degree or used immediately. Samples were centrifuged for 5 min at 16,100 5 g at 4 C degree to pellet cellular debris. 300 ml of chloroform was added to PhaseLock tubes (Heavy 2 ml, 5Prime) after which the TRIzol samples were added. Tubes were vigorously inverted for 15 s and allowed to rest at RT for 5 min. Tubes were centrifuged for 10 min at 10,500 g at 4 C degree. The aqueous phases were added to microfuge tubes containing 270 ml isopropanol and 270 ml high salt solution (0.8 M trisodium citrate, 1.2 M NaCl) and vortexed for 5 s. After a 10 min incubation at RT, tubes were microcentrifuged at 16,100 g for 10 min at 4 C degree to pellet RNA. RNA pellets were washed with 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4 C degree. Pellets were allowed to dry by air and resuspended in 50 µl of RNA storage buffer (Ambion). 2 µl were used for quantification and another 2 µl were added to 80% formamide/ 20% loading dye to check RNA integrity on an (1.6%) agarose gel. The purification process was repeated two times to obtain DNA-free RNA. RNA aliquots were stored at -80 C degree.

treatment_protocol: Exposed to 500uM copper sulfate

tag: strain

tag: genotype/variation

value: wildtype

source_name: M. tuberculosis CDC1551 strain Cy5 cell culture growing in the absence of Cu

growth_protocol: The wildtype cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5).

treatment_protocol: No copper sulfate treatment


title: MM_3_GMP

value: Multiple Myeloma Patient


title: 4QMT08242009A_WT3-Cu.Cy3_WT3+Cu.Cy5_14017990.LOW_MDS.mev.refIsIA.out

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing in the absence of Cu

treatment_protocol: No copper sulfate treatment.

source_name: M. tuberculosis CDC1551 strain Cy5 cell culture growing in the suplemented with Cu


title: MM_1_GMP

value: granulocyte/monocyte progenitors


title: Control_5_HSC

value: hematopoietic stem cells


title: Control_5_GMP


title: MM_1_CMP


title: Control_5_CMP


title: Orthotopic thyroid HC-15

description: MeDIP-chip DNA of orthotopic thyroid


title: JBH364 (MicMa132) Replicate 2

city: Cold Spring Harbor

first: Jude

last: Kendall

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: These samples were hybridized to two color-reversal arrays

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

label_protocol: Complexity-reduced representations, consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrimelabeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: Control_4_MEP


title: 4QMT08242009A_WT3-Cu.Cy5_Rv0190.2-Cu.Cy3_14017989_MDS.mev.refIsIB.out

source_name: M. tuberculosis Rv0190 strain Cy3 cell culture growing to mid log

growth_protocol: The mutant cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5).

value: Rv0190 mutation

source_name: M. tuberculosis CDC1551 strain Cy5 cell culture growing to mid log


title: 4QMT08242009A_WT1-Cu.Cy5_Rv0190.1-Cu.Cy3_14018005_MDS.mev.refIsIB.out


title: PYS R3

city: Salamanca

last: Martin

address: Avd/Universidad de Coimbra s/n

department: CSC Biology

country: Spain

institute: OSP

description:
Total RNA was reverse transcribed, preamplified and loaded on TLDA Taqman real time assay card A and B.
Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

data_processing:
TLDA were run in the 7900 HT Sequence Detection system.
The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values.
To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.
Automatic baseline and manual CT were calculated by new algorithm of RQ Manager Software for all samples.
Statistical analysis of TLDA: The global data set of miRs from card A and B was used for analysis.
Data were normalized using Real Time STatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].
Input data for analysis consisted of the all samples miR expression CT values normalized to most stable endogenous housekeeping (MummU6, snoRNA135, snoRNA202 for A and B Card) calculated as Minimun Variance Median.
Value: [delta] CT = CT,sample - CT,reference.

label: FAM

source_name: Cancer Cell Line

growth_protocol:
Morphology: adherent epithelial-like cells growing as monolayers
Medium: 90% Dulbecco's MEM + 10% FBS
Subculture: split confluent culture 1:5 to 1:10 every 2-3 days using trypsin/EDTA; seed out at ca. 2-3 x 10 cells/80 cm2
Incubation: at 37C with 5-10% CO2
Doubling time: ca. 24 hours
Harvest: cell harvest of ca. 15 x 106 cells/80 cm2
http://www.dsmz.de/human_and_animal_cell_lines/

extract_protocol: mirVana miRNA Isolation Kit, see http://www.ambion.com/catalog/CatNum.php?1560

value: Teratocarcinoma Cell Line


title: 4QMT08242009A_WT1-Cu.Cy3_Rv0190.1-Cu.Cy5_14017952_MDS.mev.refIsIA.out

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing to mid log

source_name: M. tuberculosis Rv0190 strain Cy5 cell cell culture growing to mid log


title: 4QMT08242009A_WT2+Cu.Cy5_Rv0190.1+Cu.Cy3_14018001_MDS.mev.refIsIB.out

source_name: M. tuberculosis Rv0190 strain Cy3 cell culture growing in the suplemented with Cu

growth_protocol: The mutant cells were grown in Sauton's minimal media to early stationary phase (OD580 = 1.5) and treated with 500 mM copper sulfate (CuSO4) for four hours.


title: 4QMT08242009A_WT2-Cu.Cy3_Rv0190.2-Cu.Cy5_14017984_MDS.mev.refIsIA.out


title: JBH363 (MicMa132) Replicate 1


title: JBH362 (MicMa263) Replicate 2


title: JBH361 (MicMa263) Replicate 1


title: PYS R1


title: PYS R2


title: MR294 (WZ137) Replicate 2


title: 4QMT08242009A_WT1+Cu.Cy5_Rv0190.2+Cu.Cy3_14017985_MDS.mev.refIsIB.out


title: Control_4_GMP


title: Control_3_GMP


title: Control_3_MEP

value: megakaryocyte/erythroid progenitors


title: 4QMT08242009A_WT1+Cu.Cy3_Rv0190.2+Cu.Cy5_14017955_MDS.mev.refIsIA.out

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu

source_name: M. tuberculosis Rv0190 strain Cy5 cell culture growing in the suplemented with Cu


title: Control_4_HSC

source_name: Bone Marrow


title: HC-23

description: CGH ectopic thyroid vs. matched leucocytes

data_processing: Arrays were processed at Nimblegen facilities in Iceland using Nimblegen's standard protocol (using Roche NimbleGen NimbleScanTM software). Arrays 12766002 (HC-22) and 1311102 (HC-23) were analyzed in the reversed dye orientation (635/532).  Array 12753002 was analyzed in the standard dye orientation (532/635). Qspline normalization (Bioconductor).

source_name: DNA from ectopic thyroid

extract_protocol: DNA was isolated from ectopic thyroids and peripheral blood leucocytes by using the phenol/chloroform technique (John et al.; Nucleic Acids Research, 1991)

source_name: DNA from leucocytes

value: leucocyte


title: Control_4_CMP

value: common myeloid progenitors


title: 4QMT08242009A_WT2+Cu.Cy3_Rv0190.1+Cu.Cy5_14017977_MDS.mev.refIsIA.out


title: MR293 (WZ137) Replicate 1


title: HC-6


title: M1 R2

growth_protocol:
Morphology: round cells growing singly in suspension
Medium: 80-90% mixture of MEM with Earle's salts + Dulbecco's MEM (at 1:1) + 10-20% FBS + 2x non-essential amino acids + 2x vitamins
Subculture: maintain at 0.5-1.0 x 106 cells/ml; optimal split ratio of 1:2 to 1:4 every 3-5 days; seed out at 0.5-0.7 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 25-50 hours
Harvest: saturation density at ca. 2.5 x 106 cells/ml
http://www.dsmz.de/human_and_animal_cell_lines/

value: Myeloid leukemia Cell line


title: M1 R3


title: M1 R1


title: HC-22


title: JBH543 (MicMa318) Replicate 1


title: Control_3_CMP


title: MR426 (MicMa406) Replicate 2


title: 4QMT08242009A_Wt1-Cu.Cy5_CsoR1-Cu.Cy3_14017963_MDS.mev.refIsIB.out

source_name: M. tuberculosis csoR strain Cy3 cell culture growing to mid log

value: csoR mutation

source_name: M. tuberculosis CDC1551 strain Cy5 cell cell culture growing to mid log


title: JBH544 (MicMa318) Replicate 2


title: L-1210 R1

growth_protocol:
Morphology: single round, lymphoblast-like cells in suspension
Medium: 90% Dulbecco's MEM + 10% horse serum
Subculture: maintain at 0.5-1.0 x 106 cells/ml; split 1:2 to 1:4 every 1-2 days; seed out at ca. 0.5-1.0 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 50 hours
Harvest: maximum density at about 2.0 x 106 cells/ml
http://www.dsmz.de/human_and_animal_cell_lines/

value: Lymphocitic leukemia Cell Line


title: 4QMT08242009A_Wt2-Cu.Cy5_CsoR2-Cu.Cy3_14017974_MDS.mev.refIsIB.out


title: L-1210 R2


title: L-1210 R3


title: EL662 (MicMa031) Replicate 2


title: 4QMT08242009A_Wt2+Cu.Cy5_CsoR2+Cu.Cy3_14017969_MDS.mev.refIsIB.out

source_name: M. tuberculosis csoR strain Cy3 cell culture growing in the suplemented with Cu


title: MR425 (MicMa406) Replicate 1


title: 4QMT08242009A_Wt1+Cu.Cy5_CsoR1+Cu.Cy3_14017966_MDS.mev.refIsIB.out


title: 4QMT08242009A_Wt1-Cu.Cy3_CsoR1-Cu.Cy5_14017968_MDS.mev.refIsIA.out

treatment_protocol: Was not exposed.

source_name: M. tuberculosis csoR strain Cy5 cell cell culture growing to mid log

growth_protocol: The mutant cells were grown in Sauton minimal media to early stationary phase (OD580 = 1.5).

treatment_protocol: The mutant cells were grown in 7H9 minimal media to early stationary phase (OD580 = 1.5).


title: Control_3_HSC


title: 4QMT08242009A_Wt2-Cu.Cy3_CsoR2-Cu.Cy5_14017973_MDS.mev.refIsIA.out

source_name: M. tuberculosis csoR strain Cy5 cell culture growing to mid log


title: Control_2_CMP


title: Control_2_GMP


title: 4QMT08242009A_Wt2+Cu.Cy3_CsoR2+Cu.Cy5_14017972._MDS.mev.refIsIA.out

source_name: M. tuberculosis csoR strain Cy5 cell culture growing in the suplemented with Cu


title: Control_2_HSC


title: EL684 (MicMa234) Replicate 2


title: CT-BM R3

source_name: Primary Cells

growth_protocol:
Morphology: single round, cells in suspension
Medium: 90% Dulbecco's MEM + 10-20% FBS + 2x non-essential aminoacids + 2x vitamins
Subculture: maintain at 0.5-1.0 x 106 cells/ml; split 1:2 to 1:4 every 1-2 days; seed out at ca. 0.5-1.0 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 25-50 hours
Harvest: maximum density at about 1.0 x 106 cells/ml

value: Mouse-Bone Marrow Cells


title: EL661 (MicMa031) Replicate 1


title: CT-BM R2


title: CT-BM R1


title: Control_1_MEP


title: EL683 (MicMa234) Replicate 1


title: EL165 (MicMa201) Replicate 1


title: EL166 (MicMa201) Replicate 2


title: Time course in HU mec1-1 60 min

status: Public on Oct 26 2010

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

description:
ChIP_supplementary_file_name: LC109_IP4.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

hyb_protocol: DNA was hybridized to Affymetrix Genechip S. cerevisiae Tiling 1.0R Array (5 bp resolution, Affymetrix PN 900645) using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, PN 900720).

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G.

data_processing: Signals from two to four biological replicates were normalized with TAS 1.1.02 (Affymetrix) using quantile normalisation. Analysis results were stored in Log2 scale for signal intensity and in -10Log10 for p-values. Probe signals were analysed using perfect matches only with a bandwidth of 300. P-value intervals were generated using the following parameters: cutoff: 10-5, max gap: 80 and min run: 40. Significant intervals were scored as active origins when signal intensity was above a threshold arbitrarily determined as 50% of the signal range and when BrdU tracks were larger than 1 kb. Replication profiles (signal log ratio) were displayed with IGB 6.1. BrdU peaks overlapping with replication origins referenced in OriDB were scored with Galaxy. BrdU peaks that overlap with repetitive sequences such as transposons and subtelomeric repeats were not used in this study.

organism: Saccharomyces cerevisiae

source_name: BrdU-IP from mec1-1 cells in HU, 60 min

label_protocol: 7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer’s recommendations.

growth_protocol: The origin of each biological sample is Saccharomyces cerevisiae (W303 background). G1-synchronised cells were released into S phase in the presence of Hydroxyurea (200mM) and BrdU (400µg/ml) for the indicated time.

extract_protocol: For immunoprecipitation of BrdU-labelled DNA, 1.5x109 cells were lysed for 5 x 2 minutes in NIB buffer (17 % glycerol, 50 mM MOPS buffer, 150mM potassium acetate, 2 mM magnesium chloride, 500 µM spermidine and 150 µM spermine, pH7.2) with Zirconium beads on a Vibrax (VXR basic, Ika) at 4°C. DNA was isolated using Qiagen Genomic DNA extraction kit and sonicated to reach an average DNA size of 300-600 bp. For each immunoprecipitation, 10 µl of mouse anti-BrdU IgG1 (BDBioscience 555627) was prebound to Dynabeads M-280 Sheep anti-mouse IgG (Invitrogen 112.02) and added to the denatured purified DNA.

tag: antibody

value: BrdU

tag: genotype

tag: time point

value: 60 min

source_name: Input genomic DNA from S.cerevisiae

tag: fraction

value: input


title: Thal5.10_Post_C

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using Beadstudio software gene expression module version. Data was quantile normalized using preprocessCore package of Bioconductor.

source_name: undifferentiated iPS cell line (thal 5.10), post excision of programming vector

label_protocol: According to Illumina protocol.

extract_protocol: Total RNA from thal-iPS cell lines was isolated with Trizol (Invitrogen).

tag: gender

value: Female

value: undifferentiated iPS cells, post excision of programming vector


title: GD_skin_Replicate 2

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

source_name: Skin and the underlying muscle_GD-affected

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

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

value: Broiler

tag: age

value: day 34

value: Skin and the underlying muscle

source_name: Skin and the underlying muscle_Healthy


title: Control_1_GMP

tag: cell type

value: granulocyte/monocyte progenitors

value: Healthy Donor


title: MN1 transduced

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

description: Gene expression data from human CD34+ cells transduced with MN1 retrovirus vector

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Human Genome U133 Plus2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: MN1 transduced CD34+ cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Purified human CD34+ cells (Stemcell Technologies, Vancouver, BC, Canada) were cultured (37C, 5% CO2) in total 5 days in serum free X-VIVO medium (BioWhittaker, Walkerville, MD) supplemented with RPMI medium supplemented with 2mM glutamax, 100U/ml penicillin, 100ug/ml streptomycin (Life Technologies), SCF (50ng/ml), Flt3-L (50ng/ml), and TPO (50ng/ml) (Peprotech, Rocky Hill, NJ).

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

treatment_protocol: Cells were transduced with retroviral vectors and harvested 1 day later for RNA isolation.


title: Control_1_CMP

tag: disease state


title: mec1-1 BrdU HU 90 min

description:
ChIP_supplementary_file_name: LC109_IP5.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from mec1-1 cells in HU, 90 min

value: 90 min


title: mec1-1 BrdU HU 120 min

description:
ChIP_supplementary_file_name: LC109_IP6.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from mec1-1 cells in HU, 120 min

value: 120 min


title: Thal5.10_Post_A


title: rad53-11 BrdU HU 120 min

description:
ChIP_supplementary_file_name: LC109_IP3.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: LC039_WCEA.CEL

source_name: BrdU-IP from rad53-11 cells in HU, 120 min


title: GD_skin_Replicate 1

description: Biological replicate 1 of 2


title: 4QMT08242009A_Wt1+Cu.Cy3_CsoR1+Cu.Cy5_14017967_MDS.mev.refIsIA.out

description: Aminosilane-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 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95篊 prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   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, then dried in air, and scanned with an Axon GenePix 4000 scanner (http://intranet.jtc.jcvsf.org/sops/M008.pdf).  All wash buffers were supplemented with 1-ml of 0.1M DTT per liter of wash buffer.

hyb_protocol: Aminosilane-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 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   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, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner.

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

source_name: M. tuberculosis CDC1551 strain Cy3 cell culture growing in the suplemented with Cu

label_protocol: DNA probes for microarray experiments were generated by adding 2 ng of total RNA in a mixture containing 6 ng of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

extract_protocol: RNA was extracted from Mtb as follows: an equal volume of 4 M guanidinium isothiocyanate (GTC), 0.5% sodium N-lauryl sarcosine, 25 mM trisodium citrate) was added to cultures to arrest transcription, and cells were collected by centrifugation at 2,885 x g. Bacterial were resuspended in 1 ml TRIzol reagent (Invitrogen) and bead beat with zirconia silica beads (BioSpec Products) in a BioSpec Mini Bead Beater two times for 30 s, with 1 min cooling on ice in between. Samples were either stored at -80 C degree or used immediately. Samples were centrifuged for 5 min at 16,100 5 g at 4 C degree to pellet cellular debris. 300 ml of chloroform was added to PhaseLock tubes (Heavy 2 ml, 5Prime) after which the TRIzol samples were added. Tubes were vigorously inverted for 15 s and allowed to rest at RT for 5 min. Tubes were centrifuged for 10 min at 10,500 g at 4 C degree. The aqueous phases were added to microfuge tubes containing 270 ml isopropanol and 270 ml high salt solution (0.8 M trisodium citrate, 1.2 M NaCl) and vortexed for 5 s. After a 10 min incubation at RT, tubes were microcentrifuged at 16,100 g for 10 min at 4 C degree to pellet RNA. RNA pellets were washed with 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4 C degree. Pellets were allowed to dry by air and resuspended in 50 ul of RNA storage buffer (Ambion). 2 ul were used for quantification and another 2 ul were added to 80% formamide/ 20% loading dye to check RNA integrity on an (1.6%) agarose gel. The purification process was repeated two times to obtain DNA-free RNA. RNA aliquots were stored at -80 C degree.

treatment_protocol: Exposed to 500uM copper sulfate.

value: wildtype


title: EL680 (MicMa148) Replicate 2

value: Ductal Breast Carcinoma

value: EBV Immortalized Fibroblast Reference


title: rad53-11 BrdU HU 90 min

description:
ChIP_supplementary_file_name: JP012_IPG.CEL
ChIP_supplementary_file_name: LC109-IP2.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from rad53-11 cells in HU, 90 min


title: vector transduced

description: Gene expression data from human CD34+ cells transduced with vector only

source_name: vector transduced CD34+ cells


title: Thal5.10_Pre_B

source_name: undifferentiated iPS cell line (thal 5.10), pre excision of programming vector

value: undifferentiated iPS cells, pre excision of programming vector


title: Control_1_HSC

source_name: Bone Marrow

value: hematopoietic stem cells


title: Time course in HU rad53-11 60 min

description:
ChIP_supplementary_file_name: LC109-IP1.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: LC039_WCEA.CEL

source_name: BrdU-IP from rad53-11 cells in HU, 60 min

value: BrdU


title: EL679 (MicMa148) Replicate 1


title: MR386 (MicMa106) Replicate 2


title: wt BrdU HU 120 min

description:
ChIP_supplementary_file_name: LC105_IP3.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from wt cells in HU, 120 min


title: wt BrdU HU 90 min

description:
ChIP_supplementary_file_name: LC105_IP2.CEL
ChIP_supplementary_file_name: JP012_IPE.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from wt cells in HU, 90 min


title: Time course in HU wt 60 min

description:
ChIP_supplementary_file_name: LC105_IP1.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from wt cells in HU, 60 min

value: 60 min


title: Thal5.10_Post_B


title: MR385 (MicMa106) Replicate 1


title: Thal5.10_Pre_A


title: rev3 rad30 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC076_IPA.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from rev3D rad30delta cells in HU, 60 min

value: rev3D rad30D

source_name: Input genomic DNA from S.cerevisiae

value: input


title: rad24 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL088_IPB.CEL
ChIP_supplementary_file_name: LC104_IPB.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from rad24delta cells in HU, 60 min


title: ctf4 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC037_IPC.CEL
ChIP_supplementary_file_name: LC029_IPd.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from ctf4delta cells in HU, 60 min


title: rpd3 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL088_IPA.CEL
ChIP_supplementary_file_name: LC104_IPA.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from rpd3delta cells in HU, 60 min


title: Cdc45p in mrc1 HU 60 min

description:
ChIP_supplementary_file_name: LC081_IPB.CEL
input_supplementary_file_name: AL070_WCEA.CEL
input_supplementary_file_name: LC081_WCEA.CEL

source_name: Cdc45p ChIP from mrc1delta cells in HU, 60 min

extract_protocol: Cdc45p immunoprecipitation was performed as previously described (Katou et al, Nature 2003) with 5ul of Mouse Anti-V5 tag antibody (Serotec, MCA1360) prebound to 60ul of Dynabeads Protein A (Invitrogen 100.02).


title: elg1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL088_IPC.CEL
ChIP_supplementary_file_name: LC104_IPC.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from elg1delta cells in HU, 60 min


title: pol2-12 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC084_IP8.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from pol2-12 cells in HU, 60 min


title: ctf8 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC029_IPC.CEL
ChIP_supplementary_file_name: LC037_IPB.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from ctf8delta cells in HU, 60 min


title: Thal2.1-67_Ery_A

source_name: Erythroid derivates of iPS cell lines (thal 2.1-67)

value: Female

value: Erythroid derivates of iPS cells


title: Thal5.10_Pre_C


title: PBMC of pigs infected with Streptcoccus suis 2 strain SC19.rep2

city: Wuhan

first: Liu

middle: Man

last: li

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

description: Gene expression data from porcine tissus after incubated with Streptcoccus suis 2 strain SC19

hyb_protocol: Labeled cRNA was fractionated and hybridized with the GeneChip Porcine Genome Array according to the standard procedures provided by the manufacturer.

scan_protocol: GeneChips were scanned using the GeneArrayTM scanner 3000.

data_processing:
The data were analyzed by GCOS1.4 (Affymetrix) and GeneSpring 7.31 (Agilent) for normalization. P-value was analyzed by Welch T-test and cutoff for differential expression genes was set at 0.05.
Fold change≥2 and the p≤0.05 belonged to the up-regulated, and fold change≤-2 and the p≤0.05 belonged to the down-regulated.

organism: Sus scrofa

source_name: PBMC of porcine with Streptcoccus suis 2 strain SC19

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

growth_protocol: 40 days age pigs with Streptcoccus suis 2 free.

extract_protocol: Tissues were grinded to powder with liquid nitrogen. And trizol was used for total RNA extraction according to the manufacturer’s instructions.

treatment_protocol: The infected group was intravenous injection with Streptococcus suis 2 strain SC19 at a dose of 3×105 colony-forming units (CFU). The noninfected group used PBS instead.

value: Porcine PBMC

tag: bacteria strain

value: Streptcoccus suis 2 strain SC19

tag: infection status

value: infected


title: Thal2.1-67_Ery_B


title: Thal2.1-67_A

source_name: undifferentiated iPS cell line (thal 2.1-67) derived from thalassemia patients

value: undifferentiated iPS cells derived from thalassemia patients


title: Thal1.52-38_C

source_name: undifferentiated iPS cell line (thal 1.52-38) derived from thalassemia patients

value: Male


title: Thal2.1-67_B


title: ddc1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL088_IPD.CEL
ChIP_supplementary_file_name: LC104_IPD.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from ddc1delta cells in HU, 60 min


title: PBMC of pigs infected with Streptcoccus suis 2 strain SC19.rep3


title: Cdc45p in ctf18 HU 60 min

description:
ChIP_supplementary_file_name: AL070_IPA.CEL
ChIP_supplementary_file_name: LC081_IPA.CEL
input_supplementary_file_name: AL070_WCEA.CEL
input_supplementary_file_name: LC081_WCEA.CEL

source_name: Cdc45p ChIP from ctf18delta cells in HU, 60 min


title: ctf18 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC029_IPB.CEL
ChIP_supplementary_file_name: AL063_IPB.CEL
ChIP_supplementary_file_name: LC037_IPA.CEL
input_supplementary_file_name: AL063_WCEA.CEL
input_supplementary_file_name: LC029_WCEB.CEL

source_name: BrdU-IP from ctf18delta cells in HU, 60 min


title: dcc1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC037_IPD.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from dcc1delta cells in HU, 60 min


title: eco1-1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC041_IPB.CEL
input_supplementary_file_name: LC041_WCEA.CEL

source_name: BrdU-IP from eco1-1 cells in HU, 60 min


title: Control_2_MEP

description: (Control) Healthy donor / Hematopoietic Stem Cells

source_name: Bone Marrow

value: megakaryocyte/erythroid progenitors

value: Healthy Donor


title: mec1-100 BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC084_IP2.CEL
ChIP_supplementary_file_name: CA99_IPC.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: CA99_WCEC.CEL

source_name: BrdU-IP from mec1-100 cells in HU, 60 min

source_name: Input genomic DNA from S.cerevisiae


title: Thal1.52-38_Ery_A2

description: Technical Replicate

source_name: Erythroid derivates of iPS cell lines (thal 1.52-38)


title: mec1-1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL058_IPC.CEL
ChIP_supplementary_file_name: LC039_IPB.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from mec1-1 cells in HU, 60 min


title: mrc1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: JP012_IPD.CEL
ChIP_supplementary_file_name: LC034_IPD.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from mrc1delta cells in HU, 60 min


title: PBMC of pigs uninfected.rep3

description: Gene expression data from porcine tissus after incubated with PBS

source_name: PBMC of porcine with PBS

value: uninfected


title: PBMC of pigs infected with Streptcoccus suis 2 strain SC19.rep1


title: PBMC of pigs uninfected.rep2


title: mrc1aq BrdU HU 60 min

description:
ChIP_supplementary_file_name: JP012_IPB.CEL
ChIP_supplementary_file_name: CA99_IPB.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from mrc1aq cells in HU, 60 min


title: Lung of pigs infected with Streptcoccus suis 2 strain SC19.rep2

source_name: Lungs of porcine with Streptcoccus suis 2 strain SC19

value: Porcine Lung


title: PBMC of pigs uninfected.rep1


title: Thal1.52-17_Ery_B

source_name: Erythroid derivates of iPS cell lines (thal 1.52-17)


title: Thal1.52-38_B


title: Lung of pigs uninfected.rep2

source_name: Lungs of porcine with PBS


title: Lung of pigs uninfected.rep3


title: Lung of pigs infected with Streptcoccus suis 2 strain SC19.rep1


title: rad9 ctf18 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL063_IPD.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from rad9D ctf18delta cells in HU, 60 min

value: rad9D ctf18D


title: Thal1.52-38_A

source_name: undifferentiated iPS cell line (thal 1.52-38) derived from thalassemia patients


title: Thal1.52-17_A

source_name: undifferentiated iPS cell line (thal 1.52-17) derived from thalassemia patients


title: Thal1.52-17_Ery_A


title: Brain of pigs infected with Streptcoccus suis 2 strain SC19.rep2

source_name: Brains of porcine with Streptcoccus suis 2 strain SC19

value: Porcine Brain


title: Brain of pigs infected with Streptcoccus suis 2 strain SC19.rep3


title: Thal1.52-17_C


title: tof1 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL058_IPE.CEL
ChIP_supplementary_file_name: LC039_IPC.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC029_WCEA.CEL

source_name: BrdU-IP from tof1delta cells in HU, 60 min

value: BrdU


title: Lung of pigs uninfected.rep1


title: rad9 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL063_IPC.CEL
ChIP_supplementary_file_name: LC084_IP1.CEL
input_supplementary_file_name: AL032_SUA.CEL
input_supplementary_file_name: LC084_WCE1.CEL

source_name: BrdU-IP from rad9delta cells in HU, 60 min

value: 60 min


title: rad53-11 BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL058_IPB.CEL
ChIP_supplementary_file_name: LC039_IPA.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: LC039_WCEA.CEL

source_name: BrdU-IP from rad53-11 cells in HU, 60 min


title: rad9 mrc1aq BrdU HU 60 min

description:
ChIP_supplementary_file_name: LC084_IP5.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from rad9D mrc1aq cells in HU, 60 min

value: rad9D mrc1aq


title: Brain of pigs infected with Streptcoccus suis 2 strain SC19.rep1

description: Gene expression data from porcine tissus after incubated with Streptcoccus suis 2 strain SC19


title: Thal1.52-17_B


title: Thal1.52-10_Ery_B

source_name: Erythroid derivates of iPS cell lines (thal 1.52-10)


title: Thal1.52-10_Ery_A


title: Brain of pigs uninfected.rep3

source_name: Brains of porcine with PBS


title: wt BrdU HU 60 min

description:
ChIP_supplementary_file_name: AL058_IPA.CEL
ChIP_supplementary_file_name: LC029_IPA.CEL
ChIP_supplementary_file_name: LC034_IPC.CEL
input_supplementary_file_name: LC029_WCEA.CEL
input_supplementary_file_name: JP012_WCEA.CEL

source_name: BrdU-IP from wt cells in HU, 60 min

value: wildtype

source_name: Input genomic DNA from S.cerevisiae

value: input


title: Brain of pigs uninfected.rep2


title: Thal1.52-10_B

source_name: undifferentiated iPS cell line (thal 1.52-10) derived from thalassemia patients


title: Thal1.52-10_A2

description: Technical Replicate


title: Thal1.52-10_A


title: Thal1.52_Ery

source_name: Erythroid derivates of iPS cell lines (thal 1.52), without beta-globin gene insertion

value: Erythroid derivates of iPS cells, without beta-globin gene insertion


title: KD_vs_NRX E11.5, dye-swap

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: KD(Cy3) vs. NRX(Cy5) E11.5, dyeswap

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: The arrays were scanned at 5µm resolution using an Agilent G2565AA DNA microarray laser scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction, LOWESS normalization, and dye-normalization.

source_name: E11.5 embryos derived from NRXNRX+/+ C57BL/6J mice

label_protocol: 500 ng of total RNA was labeled using the low RNA Input Linear Amp kit (Agilent Technologies, Palo Alto, CA, USA). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and  at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from E9.5 and E11.5 embryos derived from NRX+/+ and NRX-/- mice using the RNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: No teatment.

tag: developmental stage

value: NRX +/+

source_name: E11.5 embryos derived from NRXNRX-/- C57BL/6J mice

value: NRX -/-


title: Thal1.52_C

source_name: undifferentiated iPS cell line (thal 1.52) derived from thalassemia patients, without beta-globin gene insertion

value: undifferentiated iPS cells derived from thalassemia patients, without beta-globin gene insertion


title: NRX_vs_KD E11.5

description: NRX(Cy3) vs. KD(Cy5) E11.5


title: Brain of pigs uninfected.rep1

value: Streptcoccus suis 2 strain SC19


title: Thal1.52_D

value: Male


title: KD_vs_NRX E9.5, dye-swap

description: KD(Cy3) vs. NRX(Cy5) E9.5, dyeswap

source_name: E9.5 embryos derived from NRXNRX+/+ C57BL/6J mice

source_name: E9.5 embryos derived from NRXNRX-/- C57BL/6J mice


title: Thal1.52_A


title: Thal1.52_B


title: NRX_vs_KD E9.5

description: NRX(Cy3) vs. KD(Cy5) E9.5


title: Susceptible phenotype, DG, technical replicate 3

status: Public on Oct 25 2010

city: München-Neuherberg

first: Dietrich

last: Trümbach

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

institute: Helmholtz Zentrum München, German Research Center for Environmental Health

description:
Frozen brains were sectioned at the level of the dorsal hippocampus, and the subregions CA1 as well as dentate gyrus were laser-microdissected
Illumina Protocol DOC#11176829 Rev. D

hyb_protocol: Standard Protocol Illumina Sentrix 8 BeadChip microarrays omitting blocking and detection reaction

scan_protocol: StandardWithBackground; ColorChannel = Green; automatic Illumina outlier removal; PMT Factor = 4.56487465

data_processing: The raw data were processed using cubic spline normalization of the BeadStudio software (Version 1.5.1.3)

label: aminoallyl

source_name: Animals with very high basal corticosterone levels, subregion dentate gyrus

label_protocol: Two rounds of linear amplification with standard protocol Amino Allyl MessageAmp RNA Amplification Kit (Ambion Inc. Austin, Texas, USA); Dye coupling with Cy3

extract_protocol: Tissue dissection was performed according to Datson et al., 2004 with some minor modifications. In short, brain slices of the hippocampal region were cut at 20 μm and thaw-mounted on membrane-coated slides (P.A.L.M. Microlaser Technologies, Bernried, Germany). Laser dissection of CA1 and dentate gyrus material was performed using a laser capture microscope (P.A.L.M. Microlaser Technologies, Bernried, Germany). Extracted samples were immediately dissolved in 100μl TRIZOL (Invitrogen Life Technologies, Carlsbad, USA) and RNA was extracted according the the manufacturer's instructions. RNA quality and quantity was checked by analysing 1μl of RNA on the Agilent 2100 Bioanalyser using the RNA 6000 Pico LabChip Kit (Agilent Technologies, Palo Alto, CA, USA) according to the manufacturer’s instructions.

tag: 5 weeks after stress procedure

tag: pooled together from five mice


title: Resistant phenotype, DG, technical replicate 4

source_name: Animals with very low basal corticosterone secretion, subregion dentate gyrus


title: Susceptible phenotype, DG, technical replicate 1


title: Susceptible phenotype, CA1, technical replicate 4

description:
Frozen brains were sectioned at the level of the dorsal hippocampus, and the subregions CA1 as well as dentate gyrus were laser-microdissected
Illumina Protocol DOC#11176829 Rev. C

source_name: Animals with very high basal corticosterone levels, subregion CA1


title: Susceptible phenotype, DG, technical replicate 4


title: Thal1.52-38_Ery_A

source_name: Erythroid derivates of iPS cell lines (thal 1.52-38)

value: Erythroid derivates of iPS cells


title: Resistant phenotype, CA1, technical replicate 4

source_name: Animals with very low basal corticosterone secretion, subregion CA1


title: Resistant phenotype, DG, technical replicate 2


title: Resistant phenotype, DG, technical replicate 1


title: Resistant phenotype, CA1, technical replicate 2


title: Resistant phenotype, CA1, technical replicate 1


title: Resistant phenotype, CA1, technical replicate 3


title: Susceptible phenotype, DG, technical replicate 2


title: Susceptible phenotype, CA1, technical replicate 3


title: Resistant phenotype, DG, technical replicate 3


title: Six fish injected with 5 mg/kg body weight/injection tBHP, 1 replicate slide/fish.

city: Haifa

first: Moshe

last: Tom

department: Marine Biology and Biotechnology

country: Israel

institute: Israel Oceanographic and Limnological Research

description:
One year old fish exhibited no reproductive activity were sampled.
The sample is part of a broader dose response experimental setup which included two experiments. Experiment 1 contained three tBHP dose treatments. Two tBHP doses were applied om Experiment 2. This sample belong to Experiment 2. The two labeling channels were symmetrical. Each channel was used to label polyA RNA of treated or control fish. Alternate labeling of specific fish was aimed at partially compensating potential dye effect. Two aliquots of the poly RNA of each treated or control fish were labeled by Cy3 and Cy5, respectively. In experiment 1 four replicate slides/fish were used to hybridize randomly selected treated fish versus randomly selected control and dye swap design was applied. The same design was used for the second experiment, using only one replicate/fish pair.

hyb_protocol: Microarray slides were incubated with pre-hybridization solution (1% BSA; 5x SSC; 0.1% SDS, 25% formamide) for 2h at 42ºC to block non-specific DNA interactions, reducing background fluorescence, followed by two short rinses in water, one in ethanol and drying by mild centrifugation of vertical slides. Dual-labeled solutions, aimed at binary comparisons between two experimental conditions, were prepared by mixing the two compared labeled cDNA populations, followed by 1:1 dilution with hybridization solution containing 200 µg/ml salmon sperm DNA, 10x SSC, 0.2% SDS, 50% formamide. The heat denatured hybridization mixture (3' at 95ºC) was layered onto the microarray, covered (Lifterslip, Erie Scientific; #25x60-2-4789) and incubated over night at 42°C in humidified hybridization chamber (Corning). Following incubation, slides were washed as follows: 5’ at 42°C in x2 SSC - 0.1% SDS, mild shaking for 10’ at room temperature in x0.1 SSC - 0.1% SDS; mild shaking 4x for 5’ at room temperature in x0.1 SSC, ending by two quick dips, one in water and one in ethanol. The slides were dried by centrifugation.

scan_protocol: The slides were scanned by Axon 4000B laser scanner in two wavelengths, corresponding to the Cy3 and Cy5 emissions. The TIF imaged dual fluorescence was quantified by the GENEPIX Pro 6.1 software (Axon), which provided also weight index of the quality for each hybridized spot.

data_processing: Data analysis was conducted separately for each of the two experiments, under the computational R environment. Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each spot across the binary comparisons between treated and control fish, was carried out using the LIMMA package (Linear Models for Microarray data Analysis; (Gentleman, R., Carey, V.J., Huber, W., Irizarry, R.A. and Dudoit, S. (eds) 2005. Bioinformatics and computational biology solutions using R and bioconductor. Statistics for biology and health. Springer, New York, NY). GENEPIX Pro 6.1 quantified image files were imported into LIMMA and eligible spots processed. Cy5 and Cy3 intensities within each slide were normalized using the print-tip LOWESS method. No background subtraction was applied by LIMMA, as the area under each spot was protected from none-specific fluorescent signal, revealing lower signal than the background when not specifically hybridized. LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. LIMMA calculated for each spot in the sample an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an average emission intensity A-value [A=(log2(Cy5)*Cy3))/2] across the analyzed experiment, designated meanA. Only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. Differential expression of each gene in the treated fish (M≠0) was tested by a T–test and the obtained P values were adjusted by multiple testing corrections.

label: Cy3 or Cy5

molecule: polyA RNA

organism: Lithognathus mormyrus

source_name: Five daily injections to fish of 5 mg/kg body weight tBHP

label_protocol: Poly A RNA was labeled by the fluorescent dye Cy3, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70ºC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42ºC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65ºC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the Cy3 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA23001) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 550 nm for Cy3 labeling intensity measurement. Please see 'hybridization_design.txt' file for sample label details.

growth_protocol: Fish were sampled alive by gillnetting in a clean habitat along the Mediterranean coast of Israel. Winter sampling was aimed at avoiding catching fish during their reproductive season. Fish were kept in the laboratory maintenance facilities two months prior to experiment conduction. Flow through seawater at 20-21°C fish food pellets were provided.

extract_protocol: EZ-RNA II Kit (Biological Industries, Israel) was used for total RNA extraction. PolyATtract kit (Promega) was used for mRNA extraction from total RNA solutions.

treatment_protocol: Fish were intra peritoneally injected for five consecutive days with doses of 5 mg/kg body weight/injection of tBHP dissolved in saline. A control group of six fish was similarly sham-injected daily with saline, the tBHP carrier. Both the control and the treated fish were sacrificed three days after the last injection.

tag: treatment group

value: Five daily injections to fish with 5 mg/kg body weight tBHP carrier

value: One year old

tag: reproductive activity

source_name: Five daily injections to fish of 5 mg/kg body weight the tBHP carrier

label_protocol: Poly A RNA was labeled by the fluorescent dye Cy5, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70ºC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42ºC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65ºC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the Cy5 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA25001) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 650 nm for Cy5 labeling intensity measurement. Please see 'hybridization_design.txt' file for sample label details.

value: Five daily injections to fish with the tBHP carrier


title: Susceptible phenotype, CA1, technical replicate 2


title: Five fish injected with 5 mg/kg body weight/injection tert butyl hydroperoxide (tBHP), 4 replicate slide/fish.

description:
One year old fish exhibited no reproductive activity were sampled.
The sample is part of a broader dose response experimental setup which included two experiments. Experiment 1 to which this sample belongs contained three tBHP dose treatments. Two tBHP doses were applied om Experiment 2. The two labeling channels were symmetrical. Each channel was used to label polyA RNA of treated or control fish. Alternate labeling of specific fish was aimed at partially compensating potential dye effect. Two aliquots of the poly RNA of each treated or control fish were labeled by Cy3 and Cy5, respectively. In experiment 1 four replicate slides/fish were used to hybridize randomly selected treated fish versus randomly selected control and dye swap design was applied. The same design was used for the second experiment, using only one replicate/fish pair.

scan_protocol: Microarray slides were incubated with pre-hybridization solution (1% BSA; 5x SSC; 0.1% SDS, 25% formamide) for 2h at 42ºC to block non-specific DNA interactions, reducing background fluorescence, followed by two short rinses in water, one in ethanol and drying by mild centrifugation of vertical slides. Dual-labeled solutions, aimed at binary comparisons between two experimental conditions, were prepared by mixing the two compared labeled cDNA populations, followed by 1:1 dilution with hybridization solution containing 200 µg/ml salmon sperm DNA, 10x SSC, 0.2% SDS, 50% formamide. The heat denatured hybridization mixture (3' at 95ºC) was layered onto the microarray, covered (Lifterslip, Erie Scientific; #25x60-2-4789) and incubated over night at 42°C in humidified hybridization chamber (Corning). Following incubation, slides were washed as follows: 5’ at 42°C in x2 SSC - 0.1% SDS, mild shaking for 10’ at room temperature in x0.1 SSC - 0.1% SDS; mild shaking 4x for 5’ at room temperature in x0.1 SSC, ending by two quick dips, one in water and one in ethanol. The slides were dried by centrifugation.

data_processing: Data analysis was conducted under the computational R environment. Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each spot across the binary comparison between treated and control fish, was carried out using the LIMMA package (Linear Models for Microarray data Analysis; (Gentleman, R., Carey, V.J., Huber, W., Irizarry, R.A. and Dudoit, S. (eds) 2005. Bioinformatics and computational biology solutions using R and bioconductor. Statistics for biology and health. Springer, New York, NY). GENEPIX Pro 6.1 quantified image files were imported into LIMMA and eligible spots processed. Cy5 and Cy3 intensities within each slide were normalized using the print-tip LOWESS method. No background subtraction was applied by LIMMA, as the area under each spot was protected from none-specific fluorescent signal, revealing lower signal than the background when not specifically hybridized. LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. LIMMA calculated for each spot in the sample an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an average emission intensity A-value [A=(log2(Cy5)*Cy3))/2] across the analyzed experiment, designated meanA. Only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. Differential expression of each gene in the treated fish (M≠0) was tested by a T–test and the obtained P values were adjusted by multiple testing corrections.

source_name: Fish injected with three consecutive 5 mg/kg body weight doses tBHP

growth_protocol: Fish were sampled alive by gillnetting in a clean habitat along the Mediterranean coast of Israel. Winter sampling was aimed at avoiding catching fish during their reproductive season. Fish were kept in the laboratory maintenance facilities a month prior to experiment conduction. Flow through seawater at 20-21°C fish food pellets were provided.

treatment_protocol: Five fish were injected with a dose of 5 mg/kg body weight/injection of tBHP dissolved in saline. Three intra peritoneal injections were applied to each fish with three day intervals between consecutive injections. A control group of five fish was sham-injected with saline, the tBHP carrier. Both the control and the treated fish were sacrificed three days after the last injection.

source_name: Fish injected with three consecutive 5 mg/kg body weight doses the tBHP carrier

value: Fish injected with three consecutive doses of the tBHP carrier


title: Five fish injected with 0.5 mg/kg body weight/injection tert butyl hydroperoxide (tBHP), 4 replicate slide/fish.

data_processing: Data analysis was conducted under the computational R environment. Calculation and statistical analysis of log2 expression ratios (VALUE column of the sample data table) of each spot across the binary comparison between treated and control fish, was carried out using the LIMMA package (Linear Models for Microarray data Analysis; (Gentleman, R., Carey, V.J., Huber, W., Irizarry, R.A. and Dudoit, S. (eds) 2005. Bioinformatics and computational biology solutions using R and bioconductor. Statistics for biology and health. Springer, New York, NY). GENEPIX Pro 6.1 quantified image files were imported into LIMMA and eligible spots processed. Cy5 and Cy3 intensities within each slide were normalized using the print-tip LOWESS method. No background subtraction was applied by LIMMA, as the area under each spot was protected from none-specific fluorescent signal, revealing lower signal than the background when not specifically hybridized.  LIMMA fitted a linear model to the expression data followed by Empirical Bayes smoothing. LIMMA calculated for each spot in the sample an M-value [M=log2(Cy5)/Cy3); Cy5 / Cy3 are the normalized emission intensities of the spot] and an average emission intensity A-value [A=(log2(Cy5)*Cy3))/2] across the analyzed experiment, designated meanA. Only spots with meanA > 8.5 were included in the analysis, avoiding faint emissions. Differential expression of each gene in the treated fish (M≠0) was tested by a T–test and the obtained P values were adjusted by multiple testing corrections.

source_name: Fish injected with three consecutive 0.5 mg/kg body weight doses tBHP

label_protocol: Poly A RNA was labeled by the fluorescent dye Cy3, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70ºC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42ºC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65ºC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the Cy3 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA23001) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 550 nm for Cy3  labeling intensity measurement. Please see 'hybridization_design.txt' file for sample label details.

source_name: Fish injected with three consecutive 0.5 mg/kg body weight doses the tBHP carrier

label_protocol: Poly A RNA was labeled by the fluorescent dye Cy5, using the amino allyl indirect cDNA labeling method, as follows: 200-400 ng mRNA of the transcript population was incubated for 10’ at 70ºC with 100 µg dT primer (T15VN) and was immediately chilled on ice. The resulting RNA-dT primer hybrid was reverse transcribed in a total volume of 30 µl for 1h at 42ºC, in a solution containing: reverse transcriptase (ImProm II, Promega #A3802; 1.5 µl/reaction), 32 units of RNase inhibitor, 3.5 mM of MgCl2 solution and 0.5 mM dNTP mix in which the dTTP was replaced by Amino Allyl-dUTP / dTTP mixture (4:1). The reverse transcription was followed by mRNA hydrolysis for 15’ at 65ºC in alkaline pH (0.2 M NaOH (fresh), and 0.1 M of EDTA). The alkaline solution was neutralized by 0.35 M HEPES (pH 7.0) followed by buffer replacement and cDNA concentration, accomplished by wash x3 of the solution by 450 µl of water through Microcon YM-30 filter (Amicon, #42410) ending with a volume of 50-100 µl. The cDNAs were coupled to an aliquot of the Cy5 mono-reactive succinimidyl ester-derivetized NHS-ester through the reactive Amino Allyl groups. Raw dye solution was prepared from a tube of dry dye (Amersham PA25001) dissolved in 72 µl DMSO, divided into 8 single labeling aliquots. The reaction was carried out for 1h at room temperature in 9 µl of 0.1M fresh Na-Bicarbonate Buffer pH 9.0. Hydroxylamine was added to the solution at a final concentration of 1.33M and was incubated for 15’ at room temperature. Finally the solution was neutralized by sodium acetate, pH=5.2 to a final concentration of 72 mM and purified by affinity column-based kit (Qiaquick, Qiagen). Labeling level was evaluated by spectrophotometry at both 260 nm for cDNA estimation and 650 nm for Cy5  labeling intensity measurement. Please see 'hybridization_design.txt' file for sample label details.

treatment_protocol: Five fish were injected with a dose of 0.5 mg/kg body weight/injection of tBHP dissolved in saline. Three intra peritoneal injections were applied to each fish with three day intervals between consecutive injections. A control group of five fish was sham-injected with saline, the tBHP carrier. Both the control and the treated fish were sacrificed three days after the last injection. The livers were dissected out and their polyA RNA was extracted.


title: S_coelicolor_M752_22hr_rep2

type: mixed

city: Minneapolis

first: Marlene

last: Castro-Melchor

state: MN

address: 421 Washington Ave SE

department: Department of Chemical Engineering and Materials Science

institute: University of Minnesota

hyb_protocol: The labeled cDNA and gDNA were then mixed and co-hybridized to microarray slides in the presence of 50% formamide. After 16 hours incubation at 50°C, slides were washed and scanned.

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) to obtain raw intensity data for each spot. The median fluorescence intensity from each spot was used for all subsequent analysis.

data_processing: A quantile normalization method was employed to normalize these log2 ratios from each hybridization (S Mehra, W Lian, KP Jayapal, SP Charaniya, DH Sherman, WS Hu: A framework to analyze multiple time series data: a case study with Streptomyces coelicolor. J Ind Microbiol Biotechnol 2006, 33:159-72). The resulting log2 ratios were not only used to compare transcript levels of the same mRNA species in different biological samples, but also used as an estimate of the relative abundance of each mRNA species.

organism: Streptomyces coelicolor

source_name: S. coelicolor RNA SMM medium 22hr

label_protocol: The cDNA was then incubated with Alexa 647 (Invitrogen, Carlsbad, CA) for labeling as per manufacturer's instructions.

growth_protocol: S. coelicolor A3(2) strain M752 was maintained on SMMS agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for spores. For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into SMM liquid medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) at a density of ~10exp7 spores/ml. Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures. Cultures were incubated at 30°C in an orbital shaker at 300 rpm. For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51). Absorbance of the resulting solution at 450 nm was then taken as a measure of growth. Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

extract_protocol: Immediately after culture samples were collected, one-fifth volume of an ice-cold stop solution (5% phenol in ethanol) (Bernstein, J. A., A. B. Khodursky, P. H. Lin, S. Lin-Chao, and S. N. Cohen. 2002. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc Natl Acad Sci U S A 99:9697-702) was added to the sample volume to prevent RNA degradation. The sample was quickly centrifuged at 4°C and the supernatant was discarded. The remaining sample was then stored at -80°C. To isolate RNA, the frozen pellets were transferred to a mortar and pestle and ground to fine powder in the presence of liquid nitrogen. RLT solution from RNeasy Mini Kit (Qiagen Inc., Valencia, CA) was added before the ground pellets thawed. The remaining steps for RNA isolation were carried out as per manufacturer’s instructions. RNA integrity was determined by gel electrophoresis while its quantity and purity were estimated by UV absorbance at OD260 and OD260/OD280, respectively. Total RNA was reverse transcribed to cDNA by SuperscriptII (Invitrogen, Carlsbad, CA) with random hexamers (IDT, Coralville, IA) incorporating aminoallyl-dUTP (Ambion, Austin, TX).

tag: strain

tag: replicate

source_name: S. coelicolor genomic DNA

label_protocol: The DNA was labeled with Label IT® Cy3 Labeling Kit (Mirus Bio Corp., Madison, WI) according to suppliers instructions.

growth_protocol: Spores for S. coelicolor M145 were generated on Mannitol-Soy flour or R5 agar Cultures for genomic DNA preparation were performed in YEME medium with 0.5% glycine supplement at 30°C until early stationary phase (refer to T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000).

extract_protocol: Genomic DNA (gDNA) extraction was carried out using Kirby mix procedure as described elsewhere (T Kieser, MJ Bibb, MJ Buttner, KF Chater, DA Hopwood: Practical Streptomyces Genetics: The John Innes Foundation, Norwich, UK; 2000). About 500 µl of 20 µg/µl gDNA was sonicated briefly for 30-40 sec for shearing them to ~500 bp average size (confirmed by gel electrophoresis).


title: S_coelicolor_M752_39hr

source_name: S. coelicolor RNA SMM medium 39hr


title: S_coelicolor_M752_20hr

source_name: S. coelicolor RNA SMM medium 20hr


title: S_coelicolor_M752_22hr_rep1


title: Five fish injected with 50 mg/kg body weight/injection tert butyl hydroperoxide (tBHP), 4 replicate slide/fish.

source_name: Fish injected with three consecutive 50 mg/kg body weight doses tBHP

treatment_protocol: Five fish were injected with a dose of 50 mg/kg body weight/injection of tBHP dissolved in saline. Three intra peritoneal injections were applied to each fish with three day intervals between consecutive injections. A control group of five fish was sham-injected with saline, the tBHP carrier. Both the control and the treated fish were sacrificed three days after the last injection.

source_name: Fish injected with three consecutive 50 mg/kg body weight doses the tBHP carrier


title: Six fish injected with 50 mg/kg body weight/injection tBHP, 1 replicate slide/fish.

description:
One year old fish exhibited no reproductive activity were sampled.
The sample is part of a broader dose response experimental setup which included two experiments. Experiment 1 contained three tBHP dose treatments. Two tBHP doses were applied om Experiment 2. This sample belongs to Experiment 2. The two labeling channels were symmetrical. Each channel was used to label polyA RNA of treated or control fish. Alternate labeling of specific fish was aimed at partially compensating potential dye effect. Two aliquots of the poly RNA of each treated or control fish were labeled by Cy3 and Cy5, respectively. In experiment 1 four replicate slides/fish were used to hybridize randomly selected treated fish versus randomly selected control and dye swap design was applied. The same design was used for the second experiment, using only one replicate/fish pair.

source_name: Five daily injections to fish of 50 mg/kg body weight tBHP

treatment_protocol: Fish were intra peritoneally injected for five consecutive days with doses of 50 mg/kg body weight/injection of tBHP dissolved in saline. A control group of six fish was similarly sham-injected daily with saline, the tBHP carrier. Both the control and the treated fish were sacrificed three days after the last injection.

value: Five daily injections to fish with 50 mg/kg body weight/injection tBHP

source_name: Five daily injections to fish of 50 mg/kg body weight the tBHP carrier


title: Susceptible phenotype, CA1, technical replicate 1

source_name: Animals with very high basal corticosterone levels, subregion CA1


title: Lung of pigs infected with Streptcoccus suis 2 strain SC19.rep3

source_name: Lungs of porcine with Streptcoccus suis 2 strain SC19

tag: tissue

value: Porcine Lung

value: infected


title: S_coelicolor_M752_14hr

scan_protocol: Images were analyzed using ImaGene (BioDiscovery, Inc, El Segundo, CA) to obtain raw intensity data for each spot. The median fluorescence intensity from each spot was used for all subsequent analysis.

source_name: S. coelicolor RNA SMM medium 14hr


title: S_coelicolor_M145_20hr_replicate1, culture #3

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using ImaGene (BioDiscovery, El Segundo, CA) to obtain raw intensity data for each spot. The median fluorescence intensity from each spot was used for all subsequent analysis.

growth_protocol: S. coelicolor A3(2) strain M145 was maintained on SMMS agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for spores. For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into SMM liquid medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) at a density of ~10exp7 spores/ml. Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures. Cultures were incubated at 30°C in an orbital shaker at 300 rpm. For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51). Absorbance of the resulting solution at 450 nm was then taken as a measure of growth. Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.


title: S_coelicolor_M752_19hr

source_name: S. coelicolor RNA SMM medium 19hr


title: S_coelicolor_M145_34hr, culture #3

source_name: S. coelicolor RNA SMM medium 34hr


title: S_coelicolor_M752_17hr

source_name: S. coelicolor RNA SMM medium 17hr


title: S_coelicolor_M145_20hr_replicate2, culture #3


title: S_coelicolor_M145_40hr, culture #3

source_name: S. coelicolor RNA SMM medium 40hr


title: S_coelicolor_M752_15hr

source_name: S. coelicolor RNA SMM medium 15hr


title: S_coelicolor_M752_16hr

source_name: S. coelicolor RNA SMM medium 16hr


title: S_coelicolor_M145_18.5hr, culture #3

source_name: S. coelicolor RNA SMM medium 18.5hr


title: S_coelicolor_M145_17.5hr, culture #3

source_name: S. coelicolor RNA SMM medium 17.5hr

source_name: S. coelicolor genomic DNA


title: AML#1, ins(21;8)

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

institute: Charité

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/66789.gif

hyb_protocol: not provided

scan_protocol: Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Common Reference

label_protocol: RNA  was labeled with Cy3-dUTP using an anchored poly(dT) primer during first strand reverse transcription (Superscript II).

extract_protocol: not provided

tag: reference

value: universal reference RNA (pooled from 11 cell lines)

label_protocol: RNA from AML specimens was labeled with Cy5-dUTP using an anchored poly(dT) primer during first strand reverse transcription (Superscript II).

extract_protocol: Normal karyotype acute myeloid leukemia (NK-AML) specimens comprise Ficoll gradient purified mononuclear cells (>80% blasts) from diagnostic peripheral blood or bone marrow.  Total RNA was isolated from stored, frozen mononuclear AML-cell pellets using Trizol reagent, and RNA quality assessed by gel electrophoresis

tag: source

value: Acute Myeloid Leukemia

tag: karyotype


title: S_coelicolor_M145_15.5hr, culture #3

source_name: S. coelicolor RNA SMM medium 15.5hr

tag: time point


title: S_coelicolor_M145_14.5_replicate3, culture #3

source_name: S. coelicolor RNA SMM medium 14.5hr


title: S_coelicolor_M145_14.5_replicate2, culture #3


title: AML#3, ins(8;21)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68435.gif


title: VCaP control

city: Stanford

first: Hongjuan

last: Zhao

state: CA

address: 300 Pasteur Dr

department: Urology

institute: Stanford

description:
Simple annotation: prostate cancer, therapy
Image: http://smd.stanford.edu/MicroArray/gifs/2008-09/81315.gif

scan_protocol: GenePix

source_name: stratagene universal reference RNA

label_protocol: not provided

value: stratagene universal reference RNA

source_name: VCaP clorgyline 24hr control

tag: cell line

value: VCaP

tag: treatment

value: untreated


title: S_coelicolor_M145_14.5_replicate1, culture #3


title: S_coelicolor_M145_14hr_replicate5, culture #3


title: S_coelicolor_M145_14hr_replicate3, culture #3


title: S_coelicolor_M145_14hr_replicate4, culture #3


title: S_coelicolor_M145_14hr_replicate1, culture #3


title: S_coelicolor_M145_14hr_replicate2, culture #3


title: S_coelicolor_M145_19hr, culture #2


title: S_coelicolor_M145_23.5hr, culture #2

source_name: S. coelicolor RNA SMM medium 23.5hr


title: S_coelicolor_M145_40hr_replicate2, culture #1

scan_protocol: Arrays were scanned using ScanArray5000 (Perkin Elmer, Wellesley, MA). Images were analyzed using GenePix (Axon Instruments, Union City, CA) or ImaGene (BioDiscovery, El Segundo, CA) to obtain raw intensity data for each spot. The median fluorescence intensity from each spot was used for all subsequent analysis.


title: S_coelicolor_M145_40hr_replicate1, culture #1


title: S_coelicolor_M145_25hr, culture #2

source_name: S. coelicolor RNA SMM medium 25hr


title: S_coelicolor_M145_17hr, culture #2


title: S_coelicolor_M145_42hr, culture #2

source_name: S. coelicolor RNA SMM medium 42hr


title: S_coelicolor_M145_22.5hr, culture #2

source_name: S. coelicolor RNA SMM medium 22.5hr


title: S_coelicolor_M145_20.5hr, culture #2

source_name: S. coelicolor RNA SMM medium 20.5hr


title: S_coelicolor_M145_21hr_replicate1, culture #1

source_name: S. coelicolor RNA SMM medium 21hr


title: S_coelicolor_M145_19hr_replicate3, culture #1

source_name: S. coelicolor RNA SMM medium 19hr


title: S_coelicolor_M145_15.5hr, culture #2


title: S_coelicolor_M145_21hr_replicate2, culture #1


title: S_coelicolor_M145_21hr_replicate3, culture #1


title: S_coelicolor_M145_20hr_replicate1, culture #1

source_name: S. coelicolor RNA SMM medium 20hr


title: S_coelicolor_M145_20hr_replicate2, culture #1


title: S_coelicolor_M145_18hr_replicate3, culture #1

source_name: S. coelicolor RNA SMM medium 18hr


title: S_coelicolor_M145_18hr_replicate2, culture #1


title: S_coelicolor_M145_18hr_replicate1, culture #1


title: S_coelicolor_M145_16hr, culture #1

source_name: S. coelicolor RNA SMM medium 16hr


title: S_coelicolor_M145_19hr_replicate2, culture #1


title: S_coelicolor_M145_17hr_replicate1, culture #1

source_name: S. coelicolor RNA SMM medium 17hr


title: S_coelicolor_M145_19hr_replicate1, culture #1

source_name: S. coelicolor genomic DNA


title: S_coelicolor_M145_14hr_replicate1, culture #1

source_name: S. coelicolor RNA SMM medium 14hr


title: S_coelicolor_M145_14hr_replicate2, culture #1


title: S_coelicolor_M145_17hr_replicate2, culture #1


title: S_coelicolor_M145_15hr_replicate1, culture #1

source_name: S. coelicolor RNA SMM medium 15hr


title: S_coelicolor_M145_15hr_replicate2, culture #1


title: S_coelicolor_LY2517_35hr_replicate_1

source_name: S. coelicolor RNA R5- medium 35hr

growth_protocol: S. coelicolor A3(2) strain LY2517 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores. For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml. Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures. Cultures were incubated at 30°C in an orbital shaker at 300 rpm. For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51). Absorbance of the resulting solution at 450 nm was then taken as a measure of growth. Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.

tag: time


title: S_coelicolor_LY2517_14hr

source_name: S. coelicolor RNA R5- medium 14hr


title: S_coelicolor_LY2517_30hr

source_name: S. coelicolor RNA R5- medium 30hr


title: S_coelicolor_LY2517_26hr

source_name: S. coelicolor RNA R5- medium 26hr


title: S_coelicolor_LY2517_37hr

source_name: S. coelicolor RNA R5- medium 37hr


title: S_coelicolor_LY2517_39hr

source_name: S. coelicolor RNA R5- medium 39hr


title: S_coelicolor_LY2517_34hr

source_name: S. coelicolor RNA R5- medium 34hr


title: S_coelicolor_LY2517_24hr

source_name: S. coelicolor RNA R5- medium 24hr


title: S_coelicolor_LY2517_22hr

source_name: S. coelicolor RNA R5- medium 22hr


title: S_coelicolor_LY2517_32hr

source_name: S. coelicolor RNA R5- medium 32hr


title: S_coelicolor_LY2517_20hr

source_name: S. coelicolor RNA R5- medium 20hr


title: S_coelicolor_LY2517_28hr

source_name: S. coelicolor RNA R5- medium 28hr


title: S_coelicolor_LY2517_16hr

source_name: S. coelicolor RNA R5- medium 16hr


title: S_coelicolor_LY2517_35hr_replicate_2


title: S_coelicolor_LY2517_43hr_replicate_1

source_name: S. coelicolor RNA R5- medium 43hr


title: S_coelicolor_LY2517_18hr

source_name: S. coelicolor RNA R5- medium 18hr

source_name: S. coelicolor genomic DNA


title: S_coelicolor_LY2517_24hr_replicate_1


title: S_coelicolor_LY2517_22hr_replicate_1


title: S_coelicolor_LY2517_24hr_replicate_2


title: S_coelicolor_LY2517_15hr_replicate_2

source_name: S. coelicolor RNA R5- medium 15hr


title: S_coelicolor_LY2517_26hr_replicate_1


title: S_coelicolor_LY2517_26hr_replicate_2


title: S_coelicolor_LY2517_22hr_replicate_2


title: S_coelicolor_LY2517_43hr_replicate_2


title: S_coelicolor_LY2517_15hr_replicate_1


title: S_coelicolor_WL6268_21hr_replicate_1

source_name: S. coelicolor RNA R5- medium 21hr

growth_protocol: S. coelicolor A3(2) strain WL6268 was maintained on R5 solid agar (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) for high density spores. For liquid culture, spores were pre-germinated in 2xYT medium (Kieser, T., M. J. Bibb, M. J. Buttner, K. F. Chater, and D. A. Hopwood. 2000. Practical Streptomyces Genetics. The John Innes Foundation, Norwich, UK) and inoculated into R5- liquid medium (Huang, J., C. J. Lih, K. H. Pan, and S. N. Cohen. 2001. Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15:3183-92) at a density of ~10exp7 spores/ml. Baffled 2L flasks containing stainless steel coils with 350 ml working volume were used for liquid cultures. Cultures were incubated at 30°C in an orbital shaker at 300 rpm. For measuring cell growth, samples were collected at regular intervals and mixed with one-eighth volume of 2.5 M HCl and then subjected to sonication to break mycelial pellets (Brana, A. F., S. Wolfe, and A. L. Demain. 1986. Relationship between nitrogen assimilation and cephalosporin synthesis in Streptomyces clavuligerus. Arch Microbiol 146:46-51). Absorbance of the resulting solution at 450 nm was then taken as a measure of growth. Proper dilution was made to ensure an OD450 measurement below 1, which is in the linear range of detection.


title: S_coelicolor_WL6268_25hr_replicate_2

source_name: S. coelicolor RNA R5- medium 25hr


title: S_coelicolor_WL6268_33hr_replicate_1

source_name: S. coelicolor RNA R5- medium 33hr


title: nos-GAL4 HS 1hr rec 3hr vs. NS rep2

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

institute: Canadian Drosophila Microarray Centre

hyb_protocol: differently labeled samples, heat shocked and non heat shocked of the same genotype, were pooled and cohybridized to the 14K long oligo array from the Canadian Drosophila Microarray Centre (www.flyarrays.com) according to previously described methods (Neal, 2002)

scan_protocol: Images of the hybridized microarrays were obtained using a ScanArray 4000 scanner (Perkin-Elmer) and were quantified using QuantArray 3.0 software (Perkin-Elmer)

data_processing: Data were normalized using lowest sub-grid normalization (Yang, 2002) and Genetraffic Duo (Stratagene /Agilent) analysis software.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster, nos-GAL4 Heat Shocked at 37 degrees C for 1hr, 3 hrs recovery

label_protocol: Total RNA samples were labeled using the ‘indirect’ method (Semotok 2008)

growth_protocol: Strains used in these studies were maintained on standard yeast-agar media in a 25°C incubator, and include Oregon-R, tubulin (tub)-GAL4 (Bloomington No. 5138), nanos (nos)-GAL4 (Bloomington No. 4442), mwh1 (Bloomington No. 549), Hsp70- (also referred to as Df(3R)Hsp70A, Df(3R)Hsp70B) (Bloomington No. 8841), Hsp70B- (also referred to as Df(3R)Hsp70B) (Bloomington No. 8843), and hsf4 (Bloomington No. 5489).

extract_protocol: total RNA was extracted with TRIzol reagent according to the manufacture's protocol. RNA quality was evaluated using spectrophotometry and integrity was confirmed using gel electrophoresis of glyoxal-denatured samples.  Samples were cleaned using MEGAclear kit (Ambion AM1908).

value: heat shocked at 37 degrees C for 1hr, 3 hrs recovery

source_name: Drosophila melanogaster, nos-GAL4 flies

value: non-shocked


title: S_coelicolor_WL6268_21hr_replicate_2


title: S_coelicolor_WL6268_16hr_replicate_3


title: S_coelicolor_WL6268_18