title: Clostridium beijerinckii NCIMB 8052 time course (27hr fermentation)

description: Clostridium beijerinckii NCIMB 8052 wild-type fermentation culture at individual time points during the transistion from the acidogenic phase to the solventogenic phase.

hyb_protocol: The printed array slides were re-hydrated and UV cross-linked.  The slides were then washed in 0.2% SDS (w/v) followed by a H2O rinse.  Washed slides were pre-hybridized in 75 mM sodium citrate and 750 mM NaCl pH 7.0 (5X SSC), 0.1% SDS and 1% (w/v) bovine serum albumin (BSA) in a 42 oC water bath for 45 min.  After pre-hybridization the slides were washed in H2O five times followed by a last wash in isopropanol.  The slides were spun dry immediately in 50 ml conical tubes at 700 x g for 1 min and kept until hybridization.  A set of oppositely labeled cDNA probes were mixed in 30 ul SlideHyb Glass Array Hybridization Buffer (Ambion) and heated at 95 oC for 2-3 min.  The probe set solution was applied to an array slide placed in a Corning hybridization chamber.  The slides were hybridized in a 42 oC water bath for 16-20 hr.  After hybridization the slides were washed with 1X SSC and 0.2% SDS at 42 oC for 5 min, followed by a second wash in 0.1X SSC and 0.2% SDS at room temperature for 5 min and two washes in 0.1X SSC at room temperature for 5 min.  The washed slides were spun dry immediately at 200 x g for 5 min.

label_protocol: 3ug total RNA was spiked with 6 ug random hexamer primers (GE Healthcare) in a 20 ul reaction, incubated at 70 oC for 10 min and then cooled on ice.  The spiked reaction was incubated with 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, 0.2 mM aminoallyl-dUTP and 400 units Superscript III reverse transcriptase (Invitrogen) in 1X First Strand Buffer (Invitrogen) in a total of 40 ul at 46 oC for 3-8 hr.  Aminoallyl-labelled cDNA in the mixture was purified on a QIAquick PCR purification column (QIAGEN) and dried in a speedvac.  Cy3 or Cy5 dye ester (Molecular Probes) was dissolved in 10 ul 100 mM Na2CO3 and mixed with dried cDNA sample.  The dye-coupling reaction was incubated in the dark at room temperature for 1 hr.  The reaction was neutralized with 395 ul of a 300 mM sodium acetate solution (pH 5.2).  The mixture was loaded onto a QIAquick PCR purification column (QIAGEN) to purifiy dye-labelled cDNA.  The quantity, quality and dye incorporation ratio of purified cDNA probes were determined by measuring A260, A280, A550 (for Cy3 probe) and A650 (for Cy5 probe) on a UV/vis-spectrophotometer.  Probes with dye incorporation of at least 20 dyes per 1,000 nucleotides were used for array hybridization.  Purified cDNAs were dried on a speedvac and used for hybridization within the same day.

growth_protocol: Clostridium beijerinckii NCIMB 8052 spore stock was stored at 4 oC in sterile H2O.  Solid culture was prepared in agar-solidified TGY plates (TGY containing 30 g/L tryptone, 20 g/L glucose, 10 g/L yeast extract, 1 g/L L-cysteine and 4.5 g/L agar).  Liquid cultures were inoculated with single colonies from plates.  Cultures were grown in Cooked Meat Medium (CMM containing 100 g/L cooked meat medium and 10 g/L glucose) to late exponential phase at 35 °C in an anaerobic chamber.  CMM culture was then inoculated into fresh TGY medium and grown at 35 °C for a few hours.  TGY pre-culture was inoculated into Complete P2 Medium containing P2 stock solutions supplemented with 60 g/L glucose and 1 g/L yeast extract (P2 Medium, Qureshi, N. and Blaschek, H. P. 1999. Biomass Bioenergy 17:175-184) and grown at 35 °C into late stationary phase. Samples were taken at selected time points during the course of fermentation.

extract_protocol: 10 ml sample was collected at a specific time point from a batch fermentation culture. Cells were pelleted by centrifuging at 4,000 x g at 4 oC for 10 min.  Total RNA was extracted from cell pellets using RNeasy Mini Kits (Qiagen) according to the manufacturer’s protocol.  RNA quality was determined using nanochip on an Agilent 2100 Bioanalyzer (Agilent Technologies).  RNA concentration was quantified by A260 using a UV/vis spectrophotometer (Biotek Instruments). A RNA pool was generated by mixing equal amounts of RNA preparations obtained from samples taken at different time points during fermentation.

source_name: Clostridium beijerinckii NCIMB 8052 27hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 27hr fermentation culture.

treatment_protocol: A Sample was taken at 27hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.


title: UT03 0538 #7_02 (SNP)

status: Public on Jun 02 2009

type: genomic

city: Boston

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Ave

country: USA

institute: Dana-Farber Cancer Institute

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Genotyping was performed using Affymetrix Genotyping Tools Version 2.0.  dChip was used to normalize probe-level signal intensities to a baseline array with median intensity using invariant set normalization and obtain SNP-level signal intensities using a model-based (PM/MM) method,

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: clear cell renal cell carcinoma

label_protocol: biotin

extract_protocol: Genomic DNA was isolated from tissue or cell pellets using SDS/proteinase K followed by phenol/chloroform and isopropanol precipitation, and quantified using Picogreen.

tag: disease state

value: clear cell renal cell carcinoma

tag: genotype

value: VHL biallelically inactivated


title: UT04 142 #10_06 (SNP)


title: Clostridium beijerinckii NCIMB 8052 time course (24hr fermentation)

type: RNA

city: Urbana

first: Zhen

last: Shi

state: IL

address: 1206 West Gregory Drive

department: Institute for Genomic Biology

institute: University of Illinois

scan_protocol: Slides were scanned using an Axon 4000B Microarray Scanner (Molecular Devices).

data_processing: Feature intensity statistics were extracted using GenePix Pro 6.0 (Molecular Devices). Median spot intensity was obtained by substracting median intensity of non-specific background from median intensity of each feature. Spot intensities for all the features on an array were normalized using TIGR MIDAS. Expression ratios for duplicate spots representing the same probe sequence were averaged after normalization.

molecule: total RNA

organism: Clostridium beijerinckii NCIMB 8052

source_name: Clostridium beijerinckii NCIMB 8052 mixture of RNA samples collected at various time points

treatment_protocol: Samples were taken at different stages of fermentation from a batch culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium. Samples were combined to produce a pool for the generation of a reference probe for array hybridization.

tag: A pool of samples representating different stages of fermentation of Clostridium beijerinckii NCIMB 8052

source_name: Clostridium beijerinckii NCIMB 8052 24hr fermentaton sample

label_protocol: Same as Channel 1

growth_protocol: Same as Channel 1

extract_protocol: Same as Channel 1 except that total RNA was extracted from 24hr fermentation culture.

treatment_protocol: A Sample was taken at 24hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 24 hours after fermentor inoculation


title: UT03 0599 #6_03 (SNP)


title: Clostridium beijerinckii NCIMB 8052 time course (13hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 13hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 13hr fermentation culture.

treatment_protocol: A Sample was taken at 13hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 13 hours after fermentor inoculation


title: UT04 142 #9_05 (SNP)


title: UT03 0599 #4_02 (SNP)


title: Clostridium beijerinckii NCIMB 8052 time course (11hr fermentation)

tag: A pool of samples representating different stages of fermentation of Clostridium beijerinckii NCIMB 8052.

source_name: Clostridium beijerinckii NCIMB 8052 11hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 11hr fermentation culture.

treatment_protocol: A Sample was taken at 11hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 11 hours after fermentor inoculation


title: Clostridium beijerinckii NCIMB 8052 time course (8hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 8hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 8hr fermentation culture.

treatment_protocol: A Sample was taken at 8hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 8 hours after fermentor inoculation


title: E6m

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio, quantile normalization

label: Biotin

organism: Mus musculus

source_name: Skeletal muscle, KIKO E6

label_protocol: Illumina protocol

growth_protocol: 6-month old mice

extract_protocol: Trizol

value: KIKO

tag: tissue

value: Skeletal Muscle


title: E3m

source_name: Skeletal muscle, KIKO E3


title: E7m

source_name: Skeletal muscle, KIKO E7


title: Clostridium beijerinckii NCIMB 8052 time course (9hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 9hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 9hr fermentation culture.

treatment_protocol: A Sample was taken at 9hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 9 hours after fermentor inoculation


title: C8h

source_name: Heart, control C8

value: WT

value: Heart


title: UT03 0538 #3 (expression)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

extract_protocol: For total RNA extraction, tumor regions containing at least 70% of tumor cells were isolated from the frozen blocks utilizing a 2mm punch.   Frozen tissue fragments were pulverized with a chilled mortar and pestle and homogenized in 1 ml of Triazol reagent (Gibco/BRL).


title: C4h

source_name: Heart, control C4


title: UT03 0599 #4_02 (expression)


title: UT03 0538 #3 (SNP)


title: RCC 64T (SNP)

value: sporadic tumor


title: Clostridium beijerinckii NCIMB 8052 time course (5hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 5hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 5hr fermentation culture.

treatment_protocol: A Sample was taken at 5hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 5 hours after fermentor inoculation


title: Clostridium beijerinckii NCIMB 8052 time course (7hr fermentation)

growth_protocol: C. beijerinckii NCIMB 8052 spore stock was stored at 4 oC in sterile H2O.  Solid culture was prepared in agar-solidified TGY plates (TGY containing 30 g/L tryptone, 20 g/L glucose, 10 g/L yeast extract, 1 g/L L-cysteine and 4.5 g/L agar).  Liquid cultures were inoculated with single colonies from plates.  Cultures were grown in Cooked Meat Medium (CMM containing 100 g/L cooked meat medium and 10 g/L glucose) to late exponential phase at 35 °C in an anaerobic chamber.  CMM culture was then inoculated into fresh TGY medium and grown at 35 °C for a few hours.  TGY pre-culture was inoculated into Complete P2 Medium containing P2 stock solutions supplemented with 60 g/L glucose and 1 g/L yeast extract (P2 Medium, Qureshi, N. and Blaschek, H. P. 1999. Biomass Bioenergy 17:175-184) and grown at 35 °C into late stationary phase. Samples were taken at selected time points during the course of fermentation.

source_name: Clostridium beijerinckii NCIMB 8052 7hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 7hr fermentation culture.

treatment_protocol: A Sample was taken at 7hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 7 hours after fermentor inoculation


title: RCC 117T (SNP)


title: C3h

source_name: Heart, control C3


title: RCC 51T (SNP)

value: VHL not biallelicall inactivated


title: CC 129T (SNP)


title: E7h

source_name: Heart, KIKO E7


title: Clostridium beijerinckii NCIMB 8052 time course (3hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 3hr fermentaton sample

extract_protocol: Same as Channel 1 except that total RNA was extracted from 3hr fermentation culture.

treatment_protocol: A Sample was taken at 3hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 3 hours after fermentor inoculation


title: Clostridium beijerinckii NCIMB 8052 time course (1hr fermentation)

source_name: Clostridium beijerinckii NCIMB 8052 1hr fermentaton sample

label_protocol: Same as Channel 1.

growth_protocol: Same as Channel 1.

extract_protocol: Same as Channel 1 except that total RNA was extracted from 1 hr fermentation culture.

treatment_protocol: A Sample was taken at 1hr after initiation of a batch fermentation culture of Clostridium beijerinckii NCIMB 8052 in Complete P2 Medium.

tag: Sample collected 1 hour after fermentor inoculation.


title: E6h

source_name: Heart, KIKO E6


title: E3h

source_name: Heart, KIKO E3


title: RCC 25T (SNP)

source_name: clear cell renal cell carcinoma


title: udder_healthy_24h_rep1_2

status: Public on Jun 01 2009

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

description: udder tissue, healthy untreated animal

hyb_protocol: fragmented cRNA was hybridized to Affymetrix GeneChip Bovine Genome Arrays and washed and stained with Affymetrix Wash&Stain Kit on an Affymetrix Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: RMA Normalization

organism: Bos taurus

source_name: mammary gland tissue, udder quarter neighboring to one treated with E. coli 1303, 24h

label_protocol: total RNA was transcribed and labeled with Ambion Kit MessageAmp II Biotin Enhanced according to the manufacturers protocol

growth_protocol: 10 healthy, primiparous, midlactating German Holstein Frisian cows; no history of clinical mastitis; quarter milk samples less than 50,000 somatic cells/ml and free of mastitis pathogens; oestrus synchronized with Cloprostenol (Prostaglandin-F2alpha-analogue, Selectavet,Weyarn), before trial cows were entirely milked out with 20 I.U. Oxytocin i.v. (Veyx-Pharma, Schwarzenborn).

extract_protocol: Total RNA was extracted from bovine mammary gland tissue with the Trizol method according to the manufacturers protocol

treatment_protocol: E. coli 1303 was isolated from clinical cases; Inoculum Dose: Bovine mastitis isolate E. coli 1303 belongs to the major E. coli phylogenetic group A (E. coli collection of reference strains, ECOR-A). According to a multiplex PCR-based screening for virulence-associated genes of pathogenic E. coli, this strain does not represent an extraintestinal or intestinal pathogenic E. coli isolate. Only the genes coding for type 1 fimbriae, F17 fimbriae, antigen 43, the ferric citrate siderophore system and the EAST1 toxin could be detected. Bacteria were kept cryo-conserved (Mikrobank-system CryobankTM, Mast Diagnostika, Reinfeld, Germany) for subsequent infections. Bacteria were plated on Columbia sheep blood agar and incubated (37°C) for 24h. A few colonies were transferred to a tube of brain-heart infusion broth (Oxoid, Wesel, Germany) and incubated for 6h (37°C); then a 100-μl sample was transferred to a tube of trypticase soy broth (9.9ml, Oxoid, Wesel, Germany). Serial dilutions were made after 18h to prepare the desired inoculum dose of 500CFU/2ml 0.9% sterile, pyrogen free saline. The inoculum dose was plated for control and ranged from 421-613CFU/2ml. Inoculum was administered intracisternally in one quarter through the teat canal. Cows were slaughtered after 24h. Mammary gland tissue was isolated from quarters neighboring to infected quarters. Samples from untreated quarters from healthy animals served as controls.

value: udder

tag: infection

value: uninfected

tag: time


title: udder_healthy_24h_rep4_2

description: udder tissue, healthy untreated animal


title: udder_neigboring_24h_rep5

description: udder tissue, neighboring to infection with E.coli 1303

value: udder (neighbor of E.coli 1303-infected quarter)


title: udder_neigboring_24h_rep3


title: udder_healthy_24h_rep2_2

description: udder tissue, healthy untreated animal


title: udder_healthy_24h_rep5_2

description: udder tissue, healthy untreated animal


title: udder_neigboring_24h_rep2


title: udder_healthy_24h_rep3_2

description: udder tissue, healthy untreated animal


title: RCC 56T (SNP)


title: udder_neigboring_24h_rep4


title: RCC 53T (SNP)


title: udder_neigboring_24h_rep1


title: RCC 50T (SNP)


title: Liver_E3

source_name: Liver, KIKO E3

value: liver


title: udder_healthy_24h_REP3_1

description: Udder tissue; healthy untreated animal

source_name: mammary gland tissue, healthy, external control

treatment_protocol: E. coli 1303 was isolated from clinical cases; Inoculum Dose: Bovine mastitis isolate E. coli 1303 belongs to the major E. coli phylogenetic group A (E. coli collection of reference strains, ECOR-A). According to a multiplex PCR-based screening for virulence-associated genes of pathogenic E. coli, this strain does not represent an extraintestinal or intestinal pathogenic E. coli isolate. Only the genes coding for type 1 fimbriae, F17 fimbriae, antigen 43, the ferric citrate siderophore system and the EAST1 toxin could be detected. Bacteria were kept cryo-conserved (Mikrobank-system CryobankTM, Mast Diagnostika, Reinfeld, Germany) for subsequent infections. Bacteria were plated on Columbia sheep blood agar and incubated (37°C) for 24h. A few colonies were transferred to a tube of brain-heart infusion broth (Oxoid, Wesel, Germany) and incubated for 6h (37°C); then a 100-μl sample was transferred to a tube of trypticase soy broth (9.9ml, Oxoid, Wesel, Germany). Serial dilutions were made after 18h to prepare the desired inoculum dose of 500CFU/2ml 0.9% sterile, pyrogen free saline. The inoculum dose was plated for control and ranged from 421-613CFU/2ml. Inoculum was administered intracisternally in one quarter through the teat canal. Cows were slaughtered after 24h. Samples from untreated quarters from healthy cows served as controls.


title: udder_healthy_24h_REP1_1

description: Udder tissue; healthy untreated animal


title: udder_healthy_24h_REP5_1

description: Udder tissue; healthy untreated animal


title: udder_healthy_24h_REP2_1

description: Udder tissue; healthy untreated animal


title: udder_healthy_24h_rep5_3

description: udder tissue, healthy untreated animal

label_protocol: total RNA was transcribed and labeled with Affymetrix Kits (One-Cycle cDNA Synthesis and IVT Labeling Kit) according to the manufacturers protocol

treatment_protocol: E. coli 1303 was isolated from clinical cases; Inoculum Dose: Bovine mastitis isolate E. coli 1303 belongs to the major E. coli phylogenetic group A (E. coli collection of reference strains, ECOR-A). According to a multiplex PCR-based screening for virulence-associated genes of pathogenic E. coli, this strain does not represent an extraintestinal or intestinal pathogenic E. coli isolate. Only the genes coding for type 1 fimbriae, F17 fimbriae, antigen 43, the ferric citrate siderophore system and the EAST1 toxin could be detected. Bacteria were kept cryo-conserved (Mikrobank-system CryobankTM, Mast Diagnostika, Reinfeld, Germany) for subsequent infections. Bacteria were plated on Columbia sheep blood agar and incubated (37°C) for 24h. A few colonies were transferred to a tube of brain-heart infusion broth (Oxoid, Wesel, Germany) and incubated for 6h (37°C); then a 100_l sample was transferred to a tube of trypticase soy broth (9.9ml, Oxoid, Wesel, Germany). Serial dilutions were made after 18h to prepare the desired inoculum dose of 500CFU/2ml 0.9% sterile, pyrogen free saline. The inoculum dose was plated for control and ranged from 421-613CFU/2ml. Inoculum was administered intracisternally in one quarter through the teat canal. Cows were slaughtered after 6h. Samples from untreated quarters from healthy animals served as controls.


title: udder_infected_24h_rep2

description: Udder tissue; late stage of infection with E.coli 1303

source_name: mammary gland tissue, treated with E. coli 1303, 24h

value: E.coli 1303


title: udder_infected_24h_rep4


title: udder_healthy_24h_REP4_1

description: Udder tissue; healthy untreated animal


title: udder_infected_24h_rep3


title: udder_healthy_24h_rep4_3

description: udder tissue, healthy untreated animal


title: udder_healthy_24h_rep2_3

description: udder tissue, healthy untreated animal


title: udder_infected_24h_rep1


title: udder_healthy_24h_rep1_3

description: udder tissue, healthy untreated animal


title: udder_healthy_24h_rep3_3

description: udder tissue, healthy untreated animal


title: udder_infected_24h_rep5


title: udder_infected_6h_rep3

description: udder tissue, early stage of infection with E.coli 1303

source_name: mammary gland tissue, treated with E. coli 1303, 6h


title: udder_infected_6h_rep4


title: Mtb response to uncoated SP-A (4 replicates)

city: Ithaca

first: Ute

middle: Elisabeth

last: Schwab

state: NY

department: Microbiology-Immunology

institute: Cornell University Veterinary School

hyb_protocol: 5-10 ug of Cy-labeled cDNA or Alexa-labeled aRNA from paired samples was dried using a Speedvac and resuspended in 50 ul of hybridization buffer (5X SSC, 25% formamide, 0.1% SDS, and 25 g salmon sperm DNA). Samples were denatured at 95oC for 5 min and briefly cooled to 60oC before being applied to arrays under a glass LifterSlip (Erie Scientific). Slides were prehybridized for 1 hr in 25% formamide, 5X SSC, 0.1% SDS, 1% BSA and washed with H2O and isopropanol. Labeled targets were hybridized to microarrays in humidified slide chambers (Corning) at 45oC for 16-18 hr. Arrays were washed sequentially with buffer 1 (2X SSC, 0.1% SDS) pre-warmed to 45oC, buffer 2 (0.2X SSC, 0.1% SDS), buffer 3 (0.2X SSC), and buffer 4 (0.05X SSC). Slides were briefly dipped in de-ionized ultrafiltered water before being dried by centrifugation (700 X g, 10 min).

scan_protocol: Microarrays were scanned with a GenePix 4000B instrument (Axon Instruments, Inc.) with preliminary image analysis, spot intensity determination, background measurements, spot quality assessment and flagging conducted using Imagene software (version 6.0, Biodiscovery). PMT levels for scanning were set to equalize signal intensity of positive control spots and minimize saturated spots.

data_processing: Preliminary image analysis, spot intensity determination, background measurements, spot quality assessment and flagging conducted using Imagene software (version 6.0, Biodiscovery). Poor quality spots with signal intensities less than three standard deviations above background were excluded from further analysis. Subsequent normalization, statistical analysis, and visualization of array data were performed with Genespring 7.3 (Agilent). Lowess normalization was used, Genespring Cross-Gene error model was activated. Genes with significant changes in expression levels relative to controls were identified based on fold change (1.5-fold) and reproducibility between replicates (p-value <0.05).

label: Alexa 647

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis exposed to PBS 2h (control)

label_protocol: Using the MessageAmpTM-II Bacteria RNA Amplification system (Ambion), we amplified 100-250 ng total RNA to generate sufficient RNA from mycobacteria isolated from infected MØ for microarray hybrization. Briefly, total bacterial RNA was first polyadenylated by E. coli poly(A) polymerase. Using an oligo(dT) primer that incorporated a T7 promoter, poly(A) tailed RNA was reverse transcribed to yield double-stranded cDNA. The resulting cDNA served as the template for in vitro transcription (IVT) by T7 RNA polymerase which generates multiple antisense RNA (aRNA) copies of each transcript in the sample. Amino-allyl UTP was incorporated into aRNA during the IVT reaction to permit fluorophore post-labeling. amino-allyl modified aRNA were labeled with Alexa Fluor 647 (Invitrogen) and purified using a MegaClear kit (Ambion).

growth_protocol: Mtb was grown in Middlebrook 7H9 broth (Difco, Detroit, Mich.) supplemented with OADC enrichment (Difco),  Tween 80 (Sigma, St. Louis, Mo.), and glycerol at 37oC to an A600 ~0.7 under static conditions.  Bacteria were harvested by centrifugation (10 min, 3,000 rpm) at room temperature, resuspended in DMEM with 2% fetal calf serum (FCS) and 5 mM HEPES and syringed to break clumps of Mtb.

extract_protocol: For isolation of RNA GTC lysis/stabilization buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M mercaptoethanol) was added, and pelleted Mtb were washed and then digested with lysozyme (Rohde et al. 2008). TRIzol (Invitrogen) was added, and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK). After extraction of Mtb lysates with chloroform, ethanol was added to the aqueous phase before loading samples onto Qiagen RNeasy mini columns. Subsequent steps were then performed according to the instructions of the manufacturer. Following elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA), and stored at -70oC until analysis.

treatment_protocol: As a control 650 ul PBS were left on the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to PBS control for 2h at 37oC. Two independent biological replicates were studied.

tag: Strain CDC1551 was exposed to PBS for 2h (control)

label: Alexa 555

source_name: Mycobacterium tuberculosis exposed to uncoated SP-A 2h

label_protocol: Using the MessageAmpTM-II Bacteria RNA Amplification system (Ambion), we amplified 100-250 ng total RNA to generate sufficient RNA from mycobacteria isolated from infected MØ for microarray hybrization. Briefly, total bacterial RNA was first polyadenylated by E. coli poly(A) polymerase. Using an oligo(dT) primer that incorporated a T7 promoter, poly(A) tailed RNA was reverse transcribed to yield double-stranded cDNA. The resulting cDNA served as the template for in vitro transcription (IVT) by T7 RNA polymerase which generates multiple antisense RNA (aRNA) copies of each transcript in the sample. Amino-allyl UTP was incorporated into aRNA during the IVT reaction to permit fluorophore post-labeling. amino-allyl modified aRNA were labeled with Alexa Fluor 555 (Invitrogen) and purified using a MegaClear kit (Ambion).

treatment_protocol: Purified human SP-A was examined for its effects on Mtb transcription, and phosphate buffered saline (PBS) was used as a “no treatment” control. Human SP-A was a gift from Dr. J. R. Wright at Duke University, and was isolated from bronchoalveolar lavage from patients with alveolar proteinosis as described previously (Wright et al. 1987). SP-A (in 650 µl PBS) was directly added to the flask and incubated with Mtb (in 3.35 ml of DMEM; supplemented with 2% FCS and 5 mM HEPES) for 2h at 37oC.   SP-A was studied at a level of 0.165 mg in a total volume of 4 ml based on its putative concentration of approximately 5% in endogenous surfactant.  Two independent biological replicates were studied

tag: Strain CDC1551 was exposed to uncoated SP-A for 2h


title: Mtb response to SP-A 2h (2 replicates)

tag: Strain CDC1551 exposed to PBS for 2h (control)

source_name: Mycobacterium tuberculosis exposed to SP-A 2h

treatment_protocol: Purified human SP-A was also examined for its effects on Mtb transcription, and phosphate buffered saline (PBS) was used as a “no treatment” control. Human SP-A was a gift from Dr. J. R. Wright at Duke University, and was isolated from bronchoalveolar lavage from patients with alveolar proteinosis as described previously (Wright et al. 1987).  In experiments with SP-A (in 650 µl PBS), the pure apoprotein was pre-coated on the flask as done with the surfactant preparations. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated SP-A for 2h at 37oC.   SP-A was studied at a level of 0.165 mg in a total volume of 4 ml based on its putative concentration of approximately 5% in endogenous surfactant.  Two independent biological replicates were studied.

tag: Strain CDC1551 exposed to SP-A for 2h


title: Mtb response to PPL 30 min (2 replicates)

source_name: Mycobacterium tuberculosis exposed to PBS 30 min (control)

treatment_protocol: As a control 650 ul PBS were left on the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to PBS control for 30 min at 37oC. Two independent biological replicates were studied.

tag: Strain CDC1551 exposed to PBS for 30 min

source_name: Mycobacterium tuberculosis exposed to PPL 30 min

treatment_protocol:
Mixed lung surfactant phospholipids (PPL) were isolated from CLSE by column chromatography with an elution solvent of 1:1 (v/v) chloroform-methanol plus 5% 0.1 N HCl [57]. Two passes through a Sephadex LH-20 column (Pharmacia-LKB Biotechnology, Piscataway, NJ) separated phospholipids away from hydrophobic surfactant apoproteins and neutral lipids (Notter et al. 2002). Acid remaining in PPL fractions was removed by a second chloroform-methanol extraction. Final PPL had a protein content below the limits of detection of both the Folin-phenol assay of Lowry et al.(1951) and the amido black assay of Kaplin and Pedersen (1989), modified by the addition of 15% sodium dodecyl sulfate (SDS) to allow accurate quantitation in the presence of lipid.
To determine the effects of PPL on the transcriptional response of Mtb, PPL in 650 µl PBS was initially coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated surfactant for 30 min at 37oC.  Amounts of PPL used per experiment were 3.3 mg in a total volume of 4 ml.  Two independent biological replicates were studied

tag: Strain CDC1551 exposed to PPL for 30 min


title: Mtb response to CLSE 30 min (4 replicates)

extract_protocol: For isolation of RNA GTC lysis/stabilization buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M mercaptoethanol) was added, and pelleted Mtb were washed and then digested with lysozyme as described by Rohde et al. (2008). TRIzol (Invitrogen) was added, and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK). After extraction of Mtb lysates with chloroform, ethanol was added to the aqueous phase before loading samples onto Qiagen RNeasy mini columns. Subsequent steps were then performed according to the instructions of the manufacturer. Following elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA), and stored at -70oC until analysis.

treatment_protocol: As a control 650 ul PBS were left on the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to PBS control for 30 min at 37oC. Four independent biological replicates were studied.

tag: Strain CDC1551 exposed to PBS for 30 min (control)

source_name: Mycobacterium tuberculosis exposed to CLSE 30 min

treatment_protocol:
Calf lung surfactant extract (CLSE) was prepared by extraction of WLS into chloroform-methanol by the method of Bligh and Dyer (1959), as described in our prior work (Hall SB et al. 1994). CLSE is conceptually identical to the substance of the clinical surfactant Infasurf® (Hudak ML et al. 1997). The composition of CLSE by weight was approximately 94% phospholipid, 4.5% cholesterol, and 1.5% protein (a mixture of SP-B and SP-C) as defined previously (Notter RH et al. 2002).
To determine the effects of CLSE on the transcriptional response of Mtb, CLSE in 650 µl PBS was initially coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated surfactant for 30 min at 37oC.  Four independent biological replicates were studied.

tag: Strain CDC1551 exposed to CLSE for 30 min


title: Mtb response to PPL 2h (2 replicates)

treatment_protocol: As a control 650 ul PBS were left on the bottom surface of a 25 cm2 cell culture flask for 2h at 37oC. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to PBS control for 2h at 37oC. Two independent biological replicates were studied.

source_name: Myobacterium tuberculosis exposed to PPL 2h

treatment_protocol:
Mixed lung surfactant phospholipids (PPL) were isolated from CLSE by column chromatography with an elution solvent of 1:1 (v/v) chloroform-methanol plus 5% 0.1 N HCl [57]. Two passes through a Sephadex LH-20 column (Pharmacia-LKB Biotechnology, Piscataway, NJ) separated phospholipids away from hydrophobic surfactant apoproteins and neutral lipids (Notter et al. 2002). Acid remaining in PPL fractions was removed by a second chloroform-methanol extraction. Final PPL had a protein content below the limits of detection of both the Folin-phenol assay of Lowry et al.(1951) and the amido black assay of Kaplin and Pedersen (1989), modified by the addition of 15% sodium dodecyl sulfate (SDS) to allow accurate quantitation in the presence of lipid.
To determine the effects of PPL on the transcriptional response of Mtb, PPL in 650 µl PBS was initially coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated surfactant for 2h at 37oC.  Amounts of PPL used per experiment were 3.3 mg in a total volume of 4 ml.  Two independent biological replicates were studied

tag: Strain CDC1551 exposed to PPL for 2h


title: udder_infected_6h_rep1

tag: tissue


title: udder_infected_6h_rep2


title: udder_infected_6h_rep5


title: Mtb response to WLS 30 min (5 replicates)

source_name: Mycobacterium tuberculosis exposed to PBS for 30 min (control)

extract_protocol: For islation of RNA GTC lysis/stabilization buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M mercaptoethanol) was addd, and pelleted Mtb were washd and then digested with lysozyme.  Trizol (Invirogen) was added and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK).  After extraction of Mtb lysates with chloroform, ethanol was added to the aqueous phase before loading samples onto Qiagen RNeasy mini columns. Subsequent steps were then performed according to the instructions of the manufacturer.  Fllowing elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA) and stored at -70oC until analysis.

treatment_protocol: As a control 650 µl PBS were left on the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to  PBS control for 30 min at 37oC.  Five independent biological replicates were studied.

tag: Strain CD1551 exposed to PBS for 30 min (control)

source_name: Mycobacterium tuberculosis exposed to WLS for 30 min

extract_protocol: For islation of RNA GTC lysis/stabilization buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M beta-mercaptoethanol) was addd, and pelleted Mtb were washd and then digested with lysozyme.  Trizol (Invirogen) was added and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK).  After extraction of Mtb lysates with chlorofom, ethanol was added to the aqueous phase before loading samples onto Qiagen RNeasy mini columns. Subsequent steps were then performed according to the instructions of the manufacturer.  Fllowing elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA) and stored at -70oC until analysis.

treatment_protocol: Whole lung surfactant (WLS) was obtained by centrifugation of lavage fluid (0.15M NaCl) from the intact lungs of freshly killed calves (ONY, Inc, Amherst, NY). Centrifugation was done at 12,000 x g at room temperature to pellet the active large aggregate surfactant fraction. To determine the effects of WLS on the transcriptonal response of Mtb, WLS in 650 ul PBS was coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated WLS for 30 min at 37oC.  Five independent biological replicates were studied.

tag: Strain CD1551 exposed to WLS for 30 min


title: Peripheral blood cells in healthy individual-6

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

country: Japan

institute: Wakayama Medical University

description: Genes expressed in peripheral blood cells from patients with SLE.

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42℃. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: The median background intensities were subtracted from median intensities of Channel 1 (Cy3) or Channel 2 (Cy5). Log2 ratios of Cy3 to Cy5 were calculated. The VALUE shown were log2 Cy3/Cy5 ratios of all spots on the DNA microarray which were normalized by the method of global ratio median normalization.

source_name: Peripheral blood cells from healthy individual-6

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3.

extract_protocol: Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA kit with the optimal on-column DNase digestion according to the manufacturer's instructions.

tag: Gender

value: female

source_name: Peripheral blood cells from 12 healthy women

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy5.

tag: Healthy women without any identified diseases.


title: Peripheral blood cells in healthy individual-5

source_name: Peripheral blood cells from healthy individual-5


title: Mtb response to WLS 2h (3 replicates)

hyb_protocol: 5-10 ug of Alexa-labeled aRNA from paired samples was dried using a Speedvac and resuspended in 50 ul of hybridization buffer (5X SSC, 25% formamide, 0.1% SDS, and 25 g salmon sperm DNA). Samples were denatured at 95oC for 5 min and briefly cooled to 60oC before being applied to arrays under a glass LifterSlip (Erie Scientific). Slides were prehybridized for 1 hr in 25% formamide, 5X SSC, 0.1% SDS, 1% BSA and washed with H2O and isopropanol. Labeled targets were hybridized to microarrays in humidified slide chambers (Corning) at 45oC for 16-18 hr. Arrays were washed sequentially with buffer 1 (2X SSC, 0.1% SDS) pre-warmed to 45oC, buffer 2 (0.2X SSC, 0.1% SDS), buffer 3 (0.2X SSC), and buffer 4 (0.05X SSC). Slides were briefly dipped in de-ionized ultrafiltered water before being dried by centrifugation (700 X g, 10 min).

source_name: Mycobacterium tuberculosis exposed to PBS for 2h (control)

label_protocol: Using the MessageAmpTM-II Bacteria RNA Amplification system (Ambion), we amplified 100-250 ng total RNA to generate sufficient RNA from mycobacteria for microarray hybrization. Briefly, total bacterial RNA was first polyadenylated by E. coli poly(A) polymerase. Using an oligo(dT) primer that incorporated a T7 promoter, poly(A) tailed RNA was reverse transcribed to yield double-stranded cDNA. The resulting cDNA served as the template for in vitro transcription (IVT) by T7 RNA polymerase which generates multiple antisense RNA (aRNA) copies of each transcript in the sample. Amino-allyl UTP was incorporated into aRNA during the IVT reaction to permit fluorophore post-labeling. amino-allyl modified aRNA were labeled with Alexa Fluor 555 and Alexa Fluor 647 (Invitrogen) and purified using a MegaClear kit (Ambion).

growth_protocol: Strain CDC1551 was grown in Middlebrook 7H9 broth (Difco, Detroit, Mich.) supplemented with OADC enrichment (Difco),  Tween 80 (Sigma, St. Louis, Mo.), and glycerol at 37oC to an A600 ~0.7 under static conditions.  Bacteria were harvested by centrifugation (10 min, 3,000 rpm) at room temperature, resuspended in DMEM with 2% fetal calf serum (FCS) and 5 mM HEPES and syringed to break clumps of Mtb.

extract_protocol: For isolation of RNA GTC lysis/stabilization buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M beta-mercaptoethanol) was added, and pelleted Mtb were washed and then digested with lysozyme. TRIzol (Invitrogen) was added, and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK). After extraction of Mtb lysates with chloroform, ethanol was added to the aqueous phase before loading samples onto RNeasy mini columns (Qiagen, Valencia, CA). Subsequent steps were then performed according to the manufacturer’s instructions. Following elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA), and stored at -70oC until analysis.

treatment_protocol: As a control 650 µl PBS were left on the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to PBS control for 2h at 37oC.   Three independent biological replicates were studied.

source_name: Mycobacterium tuberculosis exposed to coated WLS for 2h

treatment_protocol: Whole lung surfactant (WLS) was obtained by centrifugation of lavage fluid (0.15M NaCl) from the intact lungs of freshly killed calves (ONY, Inc, Amherst, NY). Centrifugation was done at 12,000 x g at room temperature to pellet the active large aggregate surfactant fraction. To determine the effects of WLS on the transcriptional response of Mtb, WLS in 650 µl PBS was coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated surfactant for 2h at 37oC.  Three independent biological replicates were studied.

tag: Strain CDC1551 exposed to WLS for 2h


title: Peripheral blood cells in healthy individual-4

source_name: Peripheral blood cells from healthy individual-4


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-10

source_name: Peripheral blood cells from SLE patient 10

value: female,  Age :54,  Disease :Systemic Lupus Erythematosus


title: Peripheral blood cells in healthy individual-1

source_name: Peripheral blood cells from healthy individual-1


title: Mtb response to CLSE 2h (2 replicates)

source_name: Mycobacterium tuberculosis exposed to PBS 2h (control)

source_name: Mycobacterium tuberculosis exposed to CLSE 2h

extract_protocol: For isolation of RNA GTC lysis/stabilization buffer (4 M guanidine thiocyanate, 0.5% Na N-lauryl sarcosine, 25 mM sodium citrate, and 0.1M mercaptoethanol) was added, and pelleted Mtb were washed and then digested with lysozyme. TRIzol (Invitrogen) was added, and organisms were disrupted using glass beads in a Mini-Bead Beater (BioSpec Products, Inc. Bartlesville, OK). After extraction of Mtb lysates with chloroform, ethanol was added to the aqueous phase before loading samples onto Qiagen RNeasy mini columns. Subsequent steps were then performed according to the instructions of the manufacturer. Following elution with RNase-free water, the RNA samples were treated with DNase (Turbo DNAfree, Applied Biosystems, Foster City, CA), and stored at -70oC until analysis.

treatment_protocol:
Calf lung surfactant extract (CLSE) was prepared by extraction of WLS into chloroform-methanol by the method of Bligh and Dyer (1959), as described in our prior work (Hall SB et al. 1994). CLSE is conceptually identical to the substance of the clinical surfactant Infasurf® (Hudak ML et al. 1997). The composition of CLSE by weight was approximately 94% phospholipid, 4.5% cholesterol, and 1.5% protein (a mixture of SP-B and SP-C) as defined previously (Notter RH et al. 2002).
To determine the effects ofCLSE on the transcriptional response of Mtb, CLSE in 650 µl PBS was initially coated onto the bottom surface of a 25 cm2 cell culture flask for 30 min at 37oC to mimic a surfactant layer. Mtb was added to the flask in 3.35 ml of DMEM (supplemented with 2% FCS and 5 mM HEPES) and exposed to coated surfactant for 2h at 37oC.  Two independent biological replicates were studied

tag: Strain CDC1551 exposed to CLSE for 2h


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-6

source_name: Peripheral blood cells from SLE patient 6

value: female,  Age :35,  Disease :Systemic Lupus Erythematosus


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-8

source_name: Peripheral blood cells from SLE patient 8

value: female,  Age :44,  Disease :Systemic Lupus Erythematosus


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-11

source_name: Peripheral blood cells from SLE patient 11

value: female,  Age :30,  Disease :Systemic Lupus Erythematosus


title: Peripheral blood cells in healthy individual-2

source_name: Peripheral blood cells from healthy individual-2


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-7

source_name: Peripheral blood cells from SLE patient 7

value: female,  Age :72,  Disease :Systemic Lupus Erythematosus


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-4

source_name: Peripheral blood cells from SLE patient 4

value: female,  Age :27,  Disease :Systemic Lupus Erythematosus


title: Vps75 whole genome sample 2

status: Public on Apr 11 2009

city: South Mimms

first: Luke

last: Selth

state: Herts.

address: Blanch Lane

country: United Kingdom

institute: Cancer Research UK

description:
Genome-wide analysis of the binding pattern of Vps75 along S. cerevisiae chromosomes (Second repeat)
Selth L, and Svejstrup JQ. (2007) Vps75, a new yeast member of the NAP histone chaperone family. J Biol Chem 282:12358-62.

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes and then hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Probe-level signals were converted to a log base 2 scale.  Each array was normalized to its median signal. Log ratios of IP-SUP were calculated for each probe.

organism: Saccharomyces cerevisiae W303

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells

label_protocol: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells were grown at 30C in YPD medium and cross-linked at a density of 1 x 107 cells/mL.

extract_protocol: ChIP analyses were performed essentially as previously described (Selth et al, 2007). Cells were grown under the conditions described above, cross-linked with formaldehyde, disrupted by bead-beating in a FastPrep 24 instrument (MP Biomedicals), and whole cell extracts sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with 9E11 antibody (monoclonal antibody against Myc tag of Vps75) coupled to protein A-sepharose beads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse cross-links. Then, as previously described (Katou et al 2003), the immunoprecipitated genomic DNA was incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming. 10ug of the amplified DNA was digested with DNase I and end-labelled using TdT Terminal Transferase and Biotin-N6-ddATP.

treatment_protocol: ChIP and hybridization protocols were performed as previously described (Selth et al. 2007; Katou et al. 2003)

tag: genotype

tag: cell description

value: Cells expressing a C-terminally tagged version of Vps75 expressed from its own promoter (Selth et al., 2007)

tag: strain

value: Vps75-HTM (Selth et al., 2007)

tag: antibody

value: 9E11 anti-Myc

source_name: Input DNA from Saccharomyces cerevisiae cells from unbound fraction

treatment_protocol: ChIP and hybridization protocols were performed as previously described (Selth et al. 2005; Katou et al. 2003)


title: day 5-6 post-secondary infection

status: Public on May 27 2009

city: Beltsville

first: Hyun

last: Lillehoj

state: MD

address: USDA-ARS, Bldg. 1040, BARC-East

department: Animal Research Service

institute: US Department of Agriculture

description: Secondary day 3-4 vs day 5-6 post infection.

hyb_protocol: For hybridization, a circular loop design was employed with technical replication without dye-swap (day 0 vs. days 1-2, days 1-2 vs. 3-4, days 3-4 vs. 5-6, and days 5-6 vs. 7-8) for primary and secondary infections. Two-color microarray hybridizations were performed using HybIt hybridization buffer in a hybridization cassette (Telechem) at 50°C overnight, and the slides were washed 3 times in 0.5X SSC, 0.01% SDS for 5 min, 3 times in 0.06X SSC, 0.01% SDS at 50°C for 5 min,  and 3 times for 5 min in 0.06X SSC at room temperature.

scan_protocol: Microarray images were acquired by using a ScanArray Lite system at a resolution of 10 µm, and analyzed using ScanArray Express 3.0 (Perkin-Elmer).

data_processing: The MIDAS 2.19 of the TM4 package (http://www.tigr.org) was used to qualify and normalize the array data. The poor-quality channel tolerance policy was stringent and the signal-to-noise threshold was 2.0.  Two-step normalization, total intensity and global LOWESS (locally-weighted regression and smoothing scatter plots) methods were applied followed by standard deviation (SD) regularization between blocks and slides.

organism: Gallus gallus

source_name: intestinal duodenal tissues, 3-4 day post-secondary infection

label_protocol: DNase-treated total RNA (3.0 μg) from 2 consecutive days were pooled (days 1-2, 3-4, 5-6, and 7-8) and used for synthesis of aRNA using the Amino Allyl Message Amp II aRNA Amplification Kit according to the manufacturer’s protocol (Ambion, Austin, TX).  Two 15 μg aliquots of each aRNA were fluorescently labeled with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen).

growth_protocol: Fertilized eggs of White Leghorn SPAFAS chickens (Charles River Laboratories, Storrs, CT) were hatched at the Animal and Natural Resources Institute.

extract_protocol: Intestinal duodenal tissues were removed from 12 chickens/group at daily intervals between days 0 and 8 post-primary or post-secondary infections, cut longitudinally, and washed three times with ice-cold HBSS containing 100 units/ml of penicillin and 100 mg/ml of streptomycin (Sigma, St. Louis, MO).  The tissues were carefully scraped with a rounded surgical scalpel and washed 3 times with HBSS.  The scrapings of mucosal layers from 12 chickens of each group were pooled and total RNA was prepared using TRIzol (Invitrogen) and the RNeasy Mini RNA Purification Kit (Qiagen).

treatment_protocol: Chickens were orally inoculated with 1.0 X 10e4 sporulated oocysts of E. acervulina at 3 weeks of age.  Secondary infection with 2.0 X 10e4 oocysts was performed at day 21 post-primary infection (i.e., 6 weeks of age).

tag: breed

value: White Leghorn SPAFAS

value: duodenal intestinal epithelia

tag: treatment

value: Eimeria acervulina infection

source_name: Intestinal duodenal tissues, 5-6 day post-secondary infection


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-9

source_name: Peripheral blood cells from SLE patient 9

value: female,  Age :32,  Disease :Systemic Lupus Erythematosus

source_name: Peripheral blood cells from 12 healthy women


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-5

source_name: Peripheral blood cells from SLE patient 5


title: day 7-8 post-primary infection

description: Primary day 5-6 vs day 7-8 post infection.

source_name: intestinal duodenal tissues, 5-6 day post-primary infection

source_name: intestinal duodenal tissues, 7-8 day post-primary infection


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)

source_name: Peripheral blood cells from SLE patient 1

value: female,  Age :38,  Disease :Systemic Lupus Erythematosus


title: day 1-2 post-secondary infection

description: Secondary control vs day 1-2 post infection.

source_name: intestinal duodenal tissues, 0 day secondary infection

value: uninfected

source_name: Intestinal duodenal tissues, 1-2 day post-secondary infection


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-2

source_name: Peripheral blood cells from SLE patient 2

value: female,  Age :39,  Disease :Systemic Lupus Erythematosus


title: day 5-6 post-primary infection

description: Primary day 3-4 vs day 5-6 post infection.

source_name: intestinal duodenal tissues, 3-4 day post-primary infection


title: Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-3

source_name: Peripheral blood cells from SLE patient 3

value: female,  Age :33,  Disease :Systemic Lupus Erythematosus


title: day 3-4 post-secondary infection

description: Secondary day 1-2 vs day 3-4 post infection.

source_name: intestinal duodenal tissues, 1-2 day post-secondary infection

source_name: Intestinal duodenal tissues, 3-4 day post-secondary infection


title: day 7-8 post-secondary infection

description: Secondary day 5-6 vs day 7-8 post infection.

source_name: intestinal duodenal tissues, 5-6 day post-secondary infection

source_name: Intestinal duodenal tissues, 7-8 day post-secondary infection


title: day 3-4 post-primary infection

description: Primary day 1-2 vs day 3-4 post infection.

source_name: intestinal duodenal tissues, 1-2 day post-primary infection


title: day 1-2 post-primary infection

description: Primary control vs day 1-2 post infection.

source_name: intestinal duodenal tissues, 0 day primary infection


title: Vps75 whole genome sample 1

description:
Genome-wide analysis of the binding pattern of Vps75 along S. cerevisiae chromosomes (First repeat)
Selth L, and Svejstrup JQ. (2007) Vps75, a new yeast member of the NAP histone chaperone family. J Biol Chem 282:12358-62.

label: DNA was labeled with biotin-N6-ddATP using terminal transferase TdT (Roche, 400U/µl)

source_name: ChIP DNA from yeast Saccharomyces cerevisiae cells

source_name: Input DNA from Saccharomyces cerevisiae cells from unbound fraction


title: modified_chr6+TUB1_galactose_sample9

status: Public on Jan 13 2009

city: Spokane

first: Kirk

last: Anders

state: WA

address: 502 E. Boone Ave, AD 5

department: Biology

institute: Gonzaga University

description: 48 sector array, 13 rows, 16 columns

hyb_protocol: Cy3- and Cy5-labeled DNAs were combined and hybridized to the microarray at 65 deg C for 18 hours in a solution of 3X SSC, 730 ug/ml PolyA RNA, 240 ug/ml tRNA, 24 mM HEPES buffer (pH 7), and 0.24% SDS. Arrays were washed in a final solution of 0.05X SSC at room temperature and placed in a vacuum chamber until scanning.

scan_protocol: Scanned with a GenePix 4000B scanner.

data_processing: Array images were analyzed with ScanAlyze [M Eisen, http://rana.lbl.gov/EisenSoftware.htm]. RAT2 is the red/green ratio (ch2I-ch2B)/(ch1I-ch1B). This was log(2) transformed. Spots with intensity less than 2-fold over background (I/B < 2) in either channel were filtered out as low-quality spots. Data was examined using the Karyoscope viewer of Java Treeview (Saldanha, 2004). Data was normalized such that the average log(2) ratio of the unaffected chromosomes was set to zero by adding a constant to each log(2)ratio.

organism: Saccharomyces cerevisiae

source_name: euploid KAY600

label_protocol: 2 ug DNA was digested with HaeIII, purified, then resuspended in water. The DNA was boiled in the presence of 15 ug random nonamer nucleotide primers, then cooled on ice. The hybridized primers were extended with the use of 20 units of exo- Klenow polymerase (New England Biolabs) in a 50 ul reaction containing 180 uM each of dATP, dGTP, dCTP, 72 uM dTTP, 10^8 uM 5-(3-aminoallyl)-dUTP, 50 mM NaCl, 10 mM Tris (pH 7.9), 10 mM MgCl2, and 1 mM dithiothreitol. After 2 hours at 37 deg C, EDTA (pH 8.0) was added to 45 mM. The primer-extension products were purified through a DNA Clean and Concentrator-5 spin column (Zymo Research) and resuspended in 50 mM sodium bicarbonate (pH 9). Reactive Cy3 (or Cy5) mono NHS ester dyes (GE Healthcare, Cat. No. PN5661) were coupled to the aminoallyl groups in the DNA as directed by the supplier. The labeled DNA was purified through another spin column and resuspended in 20 ul 10 mM Tris (pH 8.5).

growth_protocol: Batch culture was grown in YPD rich medium overnight at 30 deg C.

extract_protocol: Hoffman-Winston DNA preparation, modified by Maitreya Dunham and Cheryl Christianson (November 2005). Cells were grown overnight, and 10^8 to 10^9 cells were pelleted, then resuspended in 0.5 ml water. Cells were pelleted again, supernatant poured off, and pellet resuspended in residual liquid. 200 ul lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) was added, 200 ul phenol/chloroform/isoamyl alcohol (25:24:1) was added, and 300 mg acid-washed glass beads (~500 micron size) was added. Tube was vortexed 8 minutes. 200 ul TE was added and mixed. After spinning tube 5 minutes, aqueous layer was transferred to new tube, and 1 ml 100% ethanol was added and mixed. Tube was spun 2 minutes. The pellet was resuspended in 400 ul+30 ug RNaseA and incubated 37 deg C for 30 minutes. 10 ul 4 M ammonium acetate and 1 ml 100% ethanol was added and mixed, and DNA was pelleted in a 2 minute spin. Pellet was air dried, then resuspended in 50 ul TE.

treatment_protocol: Haploid parent strain carrying PGAL1-CEN3 ura3::HIS3 at the centromere of the target chromosome.

value: KAY600, MATa his3-del200 leu2del0 ura3del0 cen6::PGAL1-CEN3 ura3::HIS3(at CEN6)

source_name: Ura+His+ derivative

growth_protocol: Batch culture was grown in supplemented YNB minimal medium lacking uracil and histidine overnight at 30 deg C.

treatment_protocol: Haploid parent strain carrying PGAL1-CEN3 ura3::HIS3 at the centromere of the target chromosome was grown to saturation in supplemented minimal medium that contained raffinose as its carbon source, diluted at least 2000-fold into fresh medium and grown overnight to obtain log-phase cultures. The cultures were split when the density was 0.5-1 x 10^7 cells/ml. To one half, galactose was added to a final concentration of 1.5%. Cell density was monitored until cultures had grown approximately 1.3 doublings (2.5-fold increase in density). The cells were pelleted, resuspended in water, diluted and plated to selective medium lacking both histidine and uracil. Ura+His+ colonies were scored to determine frequency of duplication and excision, and were picked as candidate disomes.

tag: strain kay683. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6

value: :PGAL1-CEN3 ura3::HIS3(at CEN6) [pRB327:TUB1, 2micron]


title: modified_chr6+TUB1_galactose_sample7

description: 48 sector array, 13 rows, 16 columns

tag: strain kay681. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr6+TUB1_galactose_sample6

description: 48 sector array, 13 rows, 16 columns

tag: strain kay680. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr4_raffinose_sample3

description: 48 sector array, 13 rows, 16 columns

source_name: euploid KAY614

value: KAY614, MATa his3-del200 ura3del0 cen4::PGAL1-CEN3 ura3::HIS3(at CEN4)

tag: strain kay643. ura+his+ derivative from strain kay619. mata his3-del200 ura3-del0 cen4

value: :PGAL1-CEN3 ura3::HIS3(at CEN4)


title: modified_chr6+TUB1_galactose_sample1

description: 48 sector array, 13 rows, 16 columns

tag: strain kay604. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr6+TUB1_galactose_sample2

description: 48 sector array, 13 rows, 16 columns

tag: strain kay605. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: Peripheral blood cells in healthy individual-3

source_name: Peripheral blood cells from healthy individual-3

value: female

source_name: Peripheral blood cells from 12 healthy women


title: modified_chr6+TUB1_galactose_sample3

description: 48 sector array, 13 rows, 16 columns

tag: strain kay606. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr4_raffinose_sample5

description: 48 sector array, 13 rows, 16 columns

tag: strain kay645. ura+his+ derivative from strain kay619. mata his3-del200 ura3-del0 cen4


title: modified_chr6+TUB1_galactose_sample4

description: 48 sector array, 13 rows, 16 columns

tag: strain kay678. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr4_raffinose_sample1

description: 48 sector array, 13 rows, 16 columns

tag: strain kay640. ura+his+ derivative from strain kay614. mata his3-del200 ura3-del0 cen4


title: modified_chr4_galactose_sample6

description: 48 sector array, 13 rows, 16 columns

tag: strain kay639. ura+his+ derivative from strain kay614. mata his3-del200 ura3-del0 cen4


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2 miR-106b, 25nM, 10hr

status: Public on Feb 19 2009

city: Seattle

first: Irena

last: Ivanovska

address: 401 Terry Ave N

institute: Merck

description: microRNAs in the miR-106b family are overexpressed in multiple tumor types and are correlated with the expression of genes that regulate the cell cycle. Consistent with these observations, miR-106b family gain of function promotes cell cycle progression, whereas loss of function reverses this phenotype. Microarray profiling uncovers multiple targets of the family, including the cyclin-dependent kinase inhibitor p21/CDKN1A. We show that p21 is a direct target of miR-106b and that its silencing plays a key role in miR-106b-induced cell cycle phenotypes. We also show that miR-106b overrides a doxorubicin-induced DNA damage checkpoint. Thus, miR-106b family members contribute to tumor cell proliferation in part by regulating cell cycle progression and by modulating checkpoint functions.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: HCT116 Dicer -/-

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

treatment_protocol: mock

tag: cell line

value: HCT116 Dicer-/- #2


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2 miR-20, 25nM, 10hr


title: modified_chr4_raffinose_sample2

description: 48 sector array, 13 rows, 16 columns

tag: strain kay642. ura+his+ derivative from strain kay619. mata his3-del200 ura3-del0 cen4


title: modified_chr6+TUB1_galactose_sample5

description: 48 sector array, 13 rows, 16 columns

tag: strain

tag: strain kay679. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr4_raffinose_sample6

description: 48 sector array, 13 rows, 16 columns

tag: strain kay646. ura+his+ derivative from strain kay614. mata his3-del200 ura3-del0 cen4


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2, luc, 25nM, 10hr

treatment_protocol: luc, 25nM, 10hr


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2 miR-106a, 25nM, 10hr


title: HCT116 Dicer-/- #2, mock vs. HCT116 Dicer-/- #2 miR-17-5p, 25nM, 10hr


title: modified_chr4_raffinose_sample4

description: 48 sector array, 13 rows, 16 columns

tag: strain kay644. ura+his+ derivative from strain kay619. mata his3-del200 ura3-del0 cen4


title: modified_chr6+TUB1_galactose_sample8

description: 48 sector array, 13 rows, 16 columns

tag: strain kay682. ura+his+ derivative from strain kay600. mata his3-del200 leu2-del0 ura3-del0 cen6


title: modified_chr4_galactose_sample4

description: 48 sector array, 13 rows, 16 columns

tag: strain kay637. ura+his+ derivative from strain kay619. mata his3-del200 ura3-del0 cen4


title: modified_chr3_galactose_sample3

description: 48 sector array, 13 rows, 16 columns

source_name: euploid KAY400

value: KAY400, MATa his3-del200 ura3-52 cen3::PGAL1-CEN3 ura3::HIS3(at CEN3)

tag: strain kay496. ura+his+ derivative from strain kay400. mata his3-del200 leu2-del1 ura3-52 cen3

value: :PGAL1-CEN3 ura3::HIS3(at CEN3)


title: modified_chr4_galactose_sample2

description: 48 sector array, 13 rows, 16 columns

source_name: euploid KAY619

value: KAY619, MATa his3-del200 ura3del0 cen4::PGAL1-CEN3 ura3::HIS3(at CEN4)

tag: strain kay564. ura+his+ derivative from strain kay464. mata his3-del200 ura3-52 cen4


title: modified_chr4_galactose_sample3

description: 48 sector array, 13 rows, 16 columns

tag: strain kay641. ura+his+ derivative from strain kay619. mata his3-del200 ura3-del0 cen4


title: modified_chr4_galactose_sample1

description: 48 sector array, 13 rows, 16 columns

tag: strain kay563. ura+his+ derivative from strain kay458. mata his3-del200 ura3-52 cen4


title: modified_chr4_galactose_sample5

description: 48 sector array, 13 rows, 16 columns

tag: strain kay638. ura+his+ derivative from strain kay614. mata his3-del200 ura3-del0 cen4


title: modified_chr3_galactose_sample1

description: 48 sector array, 13 rows, 16 columns

tag: strain kay494. ura+his+ derivative from strain kay400. mata his3-del200 leu2-del1 ura3-52 cen3


title: modified_chr3_galactose_sample2

description: 48 sector array, 13 rows, 16 columns

tag: strain kay495. ura+his+ derivative from strain kay400. mata his3-del200 leu2-del1 ura3-52 cen3


title: NT208_N_Mapping250K_Nsp

status: Public on Mar 13 2009

city: Tokyo

first: Yuyan

last: Chen

address: Hongo7-3-1, Bunkyo-ku

department: Pediatrics

institute: University of Tokyo

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Copy number analyzer CNAG and allele specific copy number analysis algorithm AsCNAR 3.0

label: biotin phytoerythrin

source_name: neuroblastoma primary tumor

label_protocol: Affymetrix standard

extract_protocol: standard DNA extraction

value: neuroblastoma


title: SK-N-SHNB_X_Mapping50K_Xba240

status: Public on Oct 16 2008

description: cell line

source_name: neuroblastoma derived cell line


title: SJNB8_X_Mapping50K_Xba240

description: cell line


title: UTP-N1NB_X_Mapping50K_Xba240

description: cell line


title: SJNB7_X_Mapping50K_Xba240

description: cell line


title: NH-12NB_X_Mapping50K_Xba240

description: cell line


title: SJNB4_X_Mapping50K_Xba240

description: cell line


title: SJNB3_X_Mapping50K_Xba240

description: cell line


title: SJNB6_X_Mapping50K_Xba240

description: cell line


title: LAN5NB_H_Mapping50K_Xba240

description: cell line


title: LAN2NB_X_Mapping50K_Xba240

description: cell line


title: SJNB2_X_Mapping50K_Xba240

description: cell line


title: NB16NB_X_Mapping50K_Xba240

description: cell line


title: SJNB5_X_Mapping50K_Xba240

description: cell line


title: SCMC-N5NB_X_Mapping50K_Xba240

description: cell line


title: NB19_X_Mapping50K_Xba240

description: cell line


title: SJNB1_X_Mapping50K_Xba240

description: cell line


title: NB-1_2_N_Mapping250K_Nsp

description: cell line


title: UTP-N-1_2_N_Mapping250K_Nsp

description: cell line


title: NB-1_H_Mapping50K_Hind240

description: cell line


title: SCMC-N4NB_X_Mapping50K_Xba240

description: cell line


title: CHP134NB_X_Mapping50K_Xba240

description: cell line


title: NT213_N_Mapping250K_Nsp

description: stage 4

source_name: neuroblastoma derived fresh tumor


title: SCMC-N2_H_Mapping50K_Hind240

description: cell line


title: TGW_H_Mapping50K_Hind240

description: cell line


title: LAN-1_H_Mapping50K_Hind240

description: cell line


title: NT211_N_Mapping250K_Nsp

description: stage 4


title: NT199_N_Mapping250K_Nsp

description: stage 4


title: NT209_N_Mapping250K_Nsp

description: stage 4


title: GOTO_H_Mapping50K_Hind240

description: cell line


title: NT200_N_Mapping250K_Nsp

description: stage 4


title: NT212_N_Mapping250K_Nsp

description: stage 4


title: NT210_N_Mapping250K_Nsp

description: stage 4


title: SK-N-SH_250K_NSP

status: Public on Oct 10 2008

description: stage NA

source_name: neuroblastoma-derived cell line


title: SJNB6_250K_NSP

description: stage NA


title: SCMC-N5_250K_NSP

description: stage NA


title: SJNB3_250K_NSP

description: stage NA


title: SJNB7_250K_NSP

description: stage NA


title: SJNB4_250K_NSP

description: stage NA


title: SJNB2_250K_NSP

description: stage NA


title: InputSpermD4 and MeDIPSpermD4, Replica 1, Slide 2

status: Public on Jun 15 2009

city: Salt Lake City

first: Bradley

middle: R.

last: Cairns

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: HHMI and Huntsman Cancer Institute

description: chIP-chip, Eurogentec 5-Methylcytidine antibody BI-MECY-0500, relica 1

hyb_protocol: Fluorescently labeled DNA samples were heat denatured after being combined with cot-1 DNA, Agilent aCGH blocking agent and Agilent Hi-RPM hybridization solution.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization Oven and were incubated at 65ºC for 40 hours with a rotational speed of 20 rpm.  Following incubation, the microarray slide was washed for 5 minute in aCGH/ChIP-on-chip Wash Buffer 1 (0.5X SSPE, 0.005% N-lauroylsarcosine; room temperature) and 5 minute in aCGH/ChIP-on-chip Wash Buffer 2 (0.1X SSPE, 0.005% N-lauroylsarcosine; 31ºC).  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing:
The Tiling Microarray Analysis Tools 2 package (http://timat2.sourceforge.net) was used to quantile normalize both treatment and control samples, median scale, and window scan (150bp) the tiled gene promoters.  Rank lists (best to worst) of enriched regions/ intervals were generated by setting log2 ratio thresholds that generated the top 100, 200, 400, 800, 1600, 3200, and 6400 regions.

The enriched regions are listed in the '*EnrichedRegions.xls' files, available from the GSE15701 record.

The files containing oligo ratio data (log2(AveTreatment/AveControl)) are in the '*OligoRatioData.zip' folders, also available from the GSE15701 record.

All coordinates are relative to Hg18/ NCBI 36.1/ H_sapiens_Mar_2006.

source_name: Sperm Patient D4

label_protocol: PCR-amplified DNA samples (2-3 µg) derived from chromatin immunoprecipitation reactions were labeled using the Agilent Genomic DNA Labeling Kit PLUS.  The labeling kit uses random primers and the exo-Klenow fragment to label DNA through incorporation of fluorescently labeled nucleotides (Cy3-dUTP or Cy5-dUTP).  Following termination of the labeling reaction, fluorescently labeled DNA molecules were purified by isopropanol precipitation.  Precipitated pellets were dried and then rehydrated in distilled water.  The concentration of purified samples was determined using a NanoDrop ND-1000 spectrophotometer.  A fraction of the labeled DNA (100 ng) was run on an Agilent BioAnalyzer to validate the size distribution of the labeled DNA molecules.

growth_protocol: Sperm samples were obtained from three known fertile donors attending the University of Utah Andrology laboratory, consented for research. Primary human fibroblast cells were obtained from Lonza (CC2511) and were cultured in DMEM containing 10% FBS and supplemented with penicillin and streptomyocin (37°C and 5% CO2).

extract_protocol: Sperm samples were collected after 2-5 days abstinence and subjected to an ISolate density gradient (to purify viable, motile, mature sperm) and treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 20 min on ice to eliminate white blood cell contamination. Samples were centrifuged at 10,000 G for 3 min and the sperm pellet was resuspended in 1X PBS and used immediately for chromatin preparation. Chromatin was prepared as previously described by Zalenskaya et al Biochem Biophys Res Commun 279, 213-8 (2000) in the absence of crosslinking reagent. Sperm was treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were used for chromatin immunopreciptation (below), or the DNA extracted and gel purified (~140-155bp) for  array analysis. All Chromatin IPs (ChIPs) were performed as previously described by Gordon et al Mol Cell Biol 27, 4058-69 (2007). All Data for CHIP modifications and histone variants were normalized to the three Histone replicates as input. Fibroblast chromatin was processed according to Zalenskaya et al 2000 and ChIPed according to Gordon et al 2007.

tag: tissue

value: sperm

tag: chip antibody


title: SJNB5_250K_NSP

description: stage NA

tag: cell line


title: NT204_250K_NSP

description: stage 1

source_name: samples from primary neuroblastoma cases


title: SCMC-N4_250K_NSP

description: stage NA


title: NT207_250K_NSP

description: stage 4


title: NT206_250K_NSP

description: stage 4


title: NT218_250K_NSP

description: stage 1


title: SJNB8_250K_NSP

description: stage NA


title: NT214_250K_NSP

description: stage 4


title: SCMC-N2_250K_NSP

description: stage NA


title: NT215_250K_NSP

description: stage 4


title: NT217_250K_NSP

description: stage 4


title: NT201_250K_NSP

description: stage 4


title: NT202_250K_NSP

description: stage 4


title: SJNB1_250K_NSP

description: stage NA


title: NT205_250K_NSP

description: stage 4


title: NT203_250K_NSP

description: stage 4


title: NT216_250K_NSP

description: stage 4


title: NT198_250K_NSP

description: stage 3


title: TGW_250K_NSP

description: stage NA


title: NT190_250K_NSP

description: stage 4


title: NT195_250K_NSP

description: stage 4


title: NT193_250K_NSP

description: stage 3


title: NT196_250K_NSP

description: stage 4


title: NT191_250K_NSP

description: stage 3


title: NT186_250K_NSP

description: stage 4s


title: NT192_250K_NSP

description: stage 4


title: NT188_250K_NSP

description: stage 4s


title: NT183_250K_NSP

description: stage 4s


title: NT181_250K_NSP

description: stage 4s


title: NT185_250K_NSP

description: stage 4s


title: NT009_250K_NSP

description: stage 1


title: NT189_250K_NSP

description: stage 4


title: NT180_250K_NSP

description: stage 4s


title: NT177_250K_NSP

description: stage 4s


title: NT182_250K_NSP

description: stage 4s


title: NT176_250K_NSP

description: stage 4s


title: NT173_250K_NSP

description: stage 4s


title: NT187_250K_NSP

description: stage 4s


title: NT174_250K_NSP

description: stage 4s


title: NT175_250K_NSP

description: stage 4s


title: NT179_250K_NSP

description: stage 4s


title: NT197_250K_NSP

description: stage 4


title: NT172_250K_NSP

description: stage 4s


title: NT170_250K_NSP

description: stage 4


title: NT194_250K_NSP

description: stage 4


title: Nor-F4567-0|04

status: Public on Jul 31 2009

city: Mukilteo

first: Michael

middle: Joseph

last: Lodes

address: 6500 Harbour Heights Pkwy, Suite 303

department: Assay Development

institute: CombiMatrix Corp

hyb_protocol: Sectored array chambers (4 chambers per array) (CombiMatrix 4×2K arrays™) were each filled with 30 μl of Pre-Hybridization Solution (CombiMatrix Corp) and incubated for 10 min at 45°C.  MicroRNA was mixed with 9 μl 20× SSPE (Ambion), 4.8 μl BSA at 50 mg/ml (Ambion), 3.6 μl deionized formamide (Sigma) and 7.5 μl of 10% SDS (Ambion) and heated to 95°C for 3 min.  30 μl of each sample were added to sectored hybridization chambers, sealed with aluminum tape, and incubated at 45°C for 16 hr with rotation.  After hybridization, arrays were washed 2 × with 2 × SSC with 0.1% SDS at room temperature (RT) for 10 sec (CombiMatrix Corp), 2 × with 2× SSC at RT for 10 sec and then washed 1 × with 0.2 × SSC at RT for 10 sec each.  Arrays were blocked with 5× PBS/Casein Blocking Buffer at RT for 10 min and then labeled with streptavidin-Cy5 labeling solution for fluorescence scanning and incubated for 30 min at RT.  Arrays were then washed 2 × with Biotin Wash Solution (2× PBST) for 30 sec each at room temp and again washed 2 × with 2 × PBS followed by scanning with an Axon instrument.

scan_protocol: Arrays were scanned with an Axon Instruments GenePix 4000B scanner

data_processing: Data were extracted from scanned images with the CombiMatrix software Microarray Imager.  For each miRNA mature region, two controls were written on the chip: a sense wild-type probe (s), an anti-sense wild-type (PM) form and a double mutant control (MM). This probe set was used to evaluate significance as well as intensity of each miRNA mature form. For each hybridization, the raw signal was extracted and probes were grouped by the miRNA that they were designed for. PM signal was log2 transformed, and Z-normalized. For the classifier and for the focused cancer versus normal hierarchical clustering, we used a simple heuristic to determine if a probe was indeed present. For each miRNA that was evaluated, we counted a signal significant if the signal for PM/MM >1.0. If so, then the Z-normalized log2 (signal) was used for that miRNA, otherwise the probe data for that particular probe was not used. Normalization was thus performed over anti-sense wild-type probes across the chip; however, only data from significant probes were used for clustering and classification.   Data Mining was performed using the WEKA package. Normalized probe intensity data was converted into ARFF format and input into the WEKA program. Hybridizations were grouped into two classes, ‘cancer’ and ‘normal’. We used the CfsSubsetEval routine to choose miRNA’s (attributes). This method gave the best classification of the data into the two classes. This routine assesses the predictive ability of each attribute as well as the degree of redundancy among each miRNA. It prefers attributes that are highly correlated within each class, but that have low inter-correlation. The choice of attributes was performed using 10-fold cross-validation, and selection of the 28 best attributes was based upon their being selected at least 30% of the time.    We next extracted signal from each hybridization for just this selected set of miRNA’s. Two different classifiers were used to distinguish cancer vs. normal samples. A Bayesian network and an instance-based method called K* were able to clearly differentiate the two classes within 36 samples. Clustering was next performed using the Cluster program from Eisen et al. Average linkage was used as the tree-building criteria and Spearman rank correlation was used as the distance function.

source_name: Serum,RNA

label_protocol: Approximately one μg of isolated RNA was labeled with a Mirus miRNA Biotin labeling kit (MIR8450) following manufacturers directions.  Briefly, 1 μg RNA was diluted to 86 μl with water and 10 μl of 10 × buffer was added followed by 4 μl LabelIT biotin labeling reagent and incubation at 37°C for 1 hr.  The reaction was stopped with 10 μl stop reagent and the sample precipitated as described above.  The dried pellet was resuspended in 5.1 μl water.

extract_protocol: An aliquot of 400 μl of each serum sample was mixed with 500 μl lysis buffer (RLT, Qiagen, Valencia, CA) and 800 μl acid phenol: Chloroform (Ambion, Foster City, CA), vortexed for 30 seconds and centrifuged at 16000 rcf for 10 min at 25°C.  The aqueous phase was extracted 2 × with an equal volume of acid phenol:chloroform and centrifuged at 16000 rcf for 10 min at 25°C.  The resulting aqueous phase was then precipitated with 0.1 vol 5 M NaCl, 2 μl precipitation enhancer (Mirus, Madison, WI), 2 μl GlycoBlue (Ambion) and 2.5 vol 100% ethanol at –20ºC for at least 1 hr.  After centrifugation at 4ºC for 30 min, the pellets were washed 2 × with 75% ethanol and then air-dried.  Precipitated RNA was resuspended in 50 μl molecular grade water (Ambion) and quantified with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE).

treatment_protocol: Human serum samples were purchased from Bioreclamation, Inc, Hicksville, NY and include: stages 2 to 4 prostate, stages 1 to 4 colon, stage 4 ovarian, stage 4 breast, and stages 3 and 4 lung cancer sera; and sera from normal male and female donors. Samples were stored at minus 80ºC until use.

tag: gender

tag: tumor stage

tag: tumor site

value: Normal


title: NT163_250K_NSP

description: stage 4


title: NT168_250K_NSP

description: stage 4


title: NT157_250K_NSP

description: stage 4


title: NT154_250K_NSP

description: stage 4


title: NT160_250K_NSP

description: stage 4


title: NT166_250K_NSP

description: stage 4


title: NT164_250K_NSP

description: stage 4


title: NT159_250K_NSP

description: stage 4


title: NT165_250K_NSP

description: stage 4


title: NT155_250K_NSP

description: stage 4


title: NT162_250K_NSP

description: stage 4


title: NT167_250K_NSP

description: stage 4


title: NT147_250K_NSP

description: stage 4


title: NT169_250K_NSP

description: stage 4


title: NT146_250K_NSP

description: stage 4


title: NT151_250K_NSP

description: stage 4


title: NT156_250K_NSP

description: stage 4


title: NT149_250K_NSP

description: stage 4


title: NT153_250K_NSP

description: stage 4


title: NT148_250K_NSP

description: stage 4


title: NT144_250K_NSP

description: stage 4


title: NT152_250K_NSP

description: stage 4


title: NT150_250K_NSP

description: stage 4


title: NT145_250K_NSP

description: stage 4


title: NT143_250K_NSP

description: stage 4


title: NT142_250K_NSP

description: stage 4


title: NT141_250K_NSP

description: stage 4


title: NT139_250K_NSP

description: stage 4


title: NT135_250K_NSP

description: stage 4


title: NT130_250K_NSP

description: stage 4


title: NT133_250K_NSP

description: stage 4


title: NT138_250K_NSP

description: stage 4


title: NT134_250K_NSP

description: stage 4


title: NT132_250K_NSP

description: stage 4


title: NT127_250K_NSP

description: stage 4


title: NT129_250K_NSP

description: stage 4


title: NT137_250K_NSP

description: stage 4


title: NT136_250K_NSP

description: stage 4


title: NT123_250K_NSP

description: stage 4


title: NT119_250K_NSP

description: stage 4


title: NT124_250K_NSP

description: stage 4


title: NT128_250K_NSP

description: stage 4


title: NT158_250K_NSP

description: stage 4


title: NT125_250K_NSP

description: stage 4


title: NT131_250K_NSP

description: stage 4


title: NT120_250K_NSP

description: stage 4


title: NT161_250K_NSP

description: stage 4


title: NT117_250K_NSP

description: stage 4


title: NT122_250K_NSP

description: stage 4


title: NT121_250K_NSP

description: stage 4


title: NT118_250K_NSP

description: stage 4


title: NT115_250K_NSP

description: stage 4


title: NT116_250K_NSP

description: stage 4


title: NT111_250K_NSP

description: stage 4


title: NT113_250K_NSP

description: stage 4


title: NT126_250K_NSP

description: stage 4


title: NT110_250K_NSP

description: stage 4


title: NT114_250K_NSP

description: stage 4


title: NT103_250K_NSP

description: stage 4


title: NT112_250K_NSP

description: stage 4


title: NT109_250K_NSP

description: stage 4


title: NT108_250K_NSP

description: stage 4


title: NT106_250K_NSP

description: stage 4


title: NT104_250K_NSP

description: stage 4


title: NT101_250K_NSP

description: stage 4


title: NT094_250K_NSP

description: stage 4


title: NT095_250K_NSP

description: stage 4


title: NT107_250K_NSP

description: stage 4


title: NT096_250K_NSP

description: stage 4


title: NT140_250K_NSP

description: stage 4


title: NT100_250K_NSP

description: stage 4


title: NT102_250K_NSP

description: stage 4


title: NT098_250K_NSP

description: stage 4


title: NT092_250K_NSP

description: stage 4


title: NT093_250K_NSP

description: stage 4


title: NT099_250K_NSP

description: stage 4


title: NT084_250K_NSP

description: stage 4


title: NT097_250K_NSP

description: stage 4


title: NT089_250K_NSP

description: stage 4


title: NT090_250K_NSP

description: stage 4


title: NT086_250K_NSP

description: stage 4


title: NT088_250K_NSP

description: stage 4


title: NT087_250K_NSP

description: stage 4


title: NT083_250K_NSP

description: stage 4


title: NT085_250K_NSP

description: stage 4


title: NT091_250K_NSP

description: stage 4


title: NT079_250K_NSP

description: stage 4


title: NT078_250K_NSP

description: stage 4


title: NT077_250K_NSP

description: stage 4


title: NT081_250K_NSP

description: stage 4


title: NT082_250K_NSP

description: stage 4


title: NT080_250K_NSP

description: stage 4


title: NT074_250K_NSP

description: stage 3


title: NT076_250K_NSP

description: stage 4


title: NT105_250K_NSP

description: stage 4


title: NT075_250K_NSP

description: stage 3


title: NT068_250K_NSP

description: stage 3


title: NT073_250K_NSP

description: stage 3


title: NT072_250K_NSP

description: stage 3


title: NT070_250K_NSP

description: stage 3


title: NT066_250K_NSP

description: stage 3


title: NT065_250K_NSP

description: stage 3


title: NT071_250K_NSP

description: stage 3


title: NT061_250K_NSP

description: stage 3


title: NT064_250K_NSP

description: stage 3


title: NT063_250K_NSP

description: stage 3


title: NT059_250K_NSP

description: stage 3


title: NT062_250K_NSP

description: stage 3


title: NT058_250K_NSP

description: stage 3


title: NT069_250K_NSP

description: stage 3


title: NT057_250K_NSP

description: stage 3


title: NT056_250K_NSP

description: stage 3


title: NT060_250K_NSP

description: stage 3


title: NT067_250K_NSP

description: stage 3


title: NT047_250K_NSP

description: stage 2


title: NT050_250K_NSP

description: stage 3


title: NT049_250K_NSP

description: stage 3


title: NT048_250K_NSP

description: stage 3


title: NT045_250K_NSP

description: stage 2


title: NT055_250K_NSP

description: stage 3


title: NT037_250K_NSP

description: stage 2


title: NT043_250K_NSP

description: stage 2


title: NT051_250K_NSP

description: stage 3


title: NT036_250K_NSP

description: stage 2


title: NT054_250K_NSP

description: stage 3


title: NT053_250K_NSP

description: stage 3


title: NT041_250K_NSP

description: stage 2


title: NT044_250K_NSP

description: stage 2


title: NT042_250K_NSP

description: stage 2


title: 13484379 - RIL 210 vs RIL 220

status: Public on Jun 05 2009

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: WP3 : Biodiversity of seed traits : state of the art

hyb_protocol: RIL 220 Cy5 / RIL 210 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: RIL 220

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: silique and seed - Media : soil (growth chamber) Hygrometry : 65% Temperature : 25degreeC Light : long day (5h-21h, harvest at 13h)

treatment_protocol: no treatment

tag: ecotype

value: arabidopsis thaliana (ril bay-0 x shahdara)

tag: age

value: 10 days after pollinisation

source_name: RIL 210

value: 10 days after pollination


title: NT035_250K_NSP

description: stage 2


title: NT038_250K_NSP

description: stage 2


title: NT039_250K_NSP

description: stage 2


title: NT052_250K_NSP

description: stage 3


title: NT046_250K_NSP

description: stage 2


title: NT034_250K_NSP

description: stage 2


title: NT033_250K_NSP

description: stage 1


title: NT040_250K_NSP

description: stage 2


title: NT032_250K_NSP

description: stage 1


title: NT028_250K_NSP

description: stage 1


title: NT030_250K_NSP

description: stage 1


title: NT031_250K_NSP

description: stage 1


title: NT027_250K_NSP

description: stage 1


title: NT029_250K_NSP

description: stage 1


title: NT025_250K_NSP

description: stage 1


title: NT024_250K_NSP

description: stage 1


title: NT026_250K_NSP

description: stage 1


title: NT021_250K_NSP

description: stage 1


title: NT012_250K_NSP

description: stage 1


title: NT023_250K_NSP

description: stage 1


title: NT007_250K_NSP

description: stage 1


title: NT010_250K_NSP

description: stage 1


title: NT019_250K_NSP

description: stage 1


title: NT022_250K_NSP

description: stage 1


title: NT008_250K_NSP

description: stage 1


title: NT017_250K_NSP

description: stage 1


title: NT016_250K_NSP

description: stage 1


title: NT018_250K_NSP

description: stage 1


title: NT015_250K_NSP

description: stage 1


title: NT006_250K_NSP

description: stage 1


title: NT013_250K_NSP

description: stage 1


title: NT020_250K_NSP

description: stage 1


title: NT014_250K_NSP

description: stage 1


title: NT001_250K_NSP

description: stage 1


title: NT002_250K_NSP

description: stage 1


title: NT004_250K_NSP

description: stage 1


title: NT003_250K_NSP

description: stage 1


title: Skin vs pool

status: Public on Aug 15 2008

first: Amit

middle: V

last: Kulkarni

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Skin vs pool

molecule: polyA RNA

source_name: Skin

extract_protocol: Total RNA isolated using Qiagen RNeasy spin columns with DNAse treatment; polyA+ RNA isolated from total RNA via magnetic bead-based mRNA extraction (Ambion, Poly(A) Purist)

tag: 48 diverse human tissues and cell lines were hybridized to a 17-array set.  Samples were purchased as pools from multiple donors, typically over 10 (Clontech, Mountainview, CA).

source_name: pool

tag: Pooled RNA from 20 diverse disease-free adult tissue pools comprised the reference pool.


title: Stomach vs pool

description: Stomach vs pool

source_name: Stomach


title: NT011_250K_NSP

description: stage 1


title: NT005_250K_NSP

description: stage 1


title: Thyroid vs pool

description: Thyroid vs pool

source_name: Thyroid


title: Spinal Cord vs pool

description: Spinal Cord vs pool

source_name: Spinal Cord


title: Skeletal Muscle vs pool

description: Skeletal Muscle vs pool

source_name: Skeletal Muscle


title: NB69_250K_NSP

description: stage NA


title: NH12_250K_NSP

description: stage NA


title: Retina vs pool

description: Retina vs pool

source_name: Retina


title: Mammary gland vs pool

description: Mammary gland vs pool

source_name: Mammary gland


title: Testis vs pool

description: Testis vs pool

source_name: Testis


title: Ileum vs pool

description: Ileum vs pool

source_name: Ileum


title: NB19_250K_NSP

description: stage NA


title: Jejunum vs pool

description: Jejunum vs pool

source_name: Jejunum


title: Fetal Brain vs pool

description: Fetal Brain vs pool

source_name: Fetal Brain


title: Kidney vs pool

description: Kidney vs pool

source_name: Kidney


title: Fetal Lung vs pool

description: Fetal Lung vs pool

source_name: Fetal Lung


title: LAN5_250K_NSP

description: stage NA

source_name: neuroblastoma-derived cell line


title: NB16_250K_NSP

description: stage NA


title: Prostate vs pool

description: Prostate vs pool

source_name: Prostate


title: Fetal Kidney vs pool

description: Fetal Kidney vs pool

source_name: Fetal Kidney


title: Lung vs pool

description: Lung vs pool

source_name: Lung


title: Thyroid vs pool

description: Thyroid vs pool

source_name: pool


title: Fetal Liver vs pool

description: Fetal Liver vs pool

source_name: Fetal Liver


title: Ovary vs pool

description: Ovary vs pool

source_name: Ovary


title: Stomach vs pool

description: Stomach vs pool

source_name: Stomach


title: GOTO_250K_NSP

description: stage NA


title: LAN2_250K_NSP

description: stage NA


title: CHP134_250K_NSP

description: stage NA


title: LAN1_250K_NSP

description: stage NA


title: Skeletal Muscle vs pool

description: Skeletal Muscle vs pool

source_name: Skeletal Muscle


title: Spinal Cord vs pool

description: Spinal Cord vs pool

source_name: Spinal Cord


title: Heart vs pool

description: Heart vs pool

source_name: Heart