title: BWH_Comstock_B_fragilis_ddungD_dPSH_study_mutant_rep3

first: Michael

middle: J

last: Coyne

address: 181 Longwood Avenue

department: Medicine

institute: Brigham & Women's Hospital

description: This sample is of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Bacteroides fragilis NCTC 9343

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

growth_protocol: Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH was grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: This triple deletion mutant was prepared by serially deleting 1,805 bp of the ungD1 gene (BF1706, deletion corresponds to bases 1,987,566 through 1,989,375 of NC_003228), 1,816 bp of the ungD2 gene (BF2848, deletion corresponds to bases 3,308,565 through 3,310,380 of NC_003228), and 4,929 bp of the PSH capsular polysaccharide locus (impacting BF3454 through BF3459, deletion corresponds to bases 4,079,324 through 4,084,252 of NC_003228) by allelic replacement procedures.

tag: Accession

tag: GI

tag: Taxname

value: Bacteroides fragilis NCTC 9343

tag: Taxid

tag: This sample is of a triple deletion mutant in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely.


title: BWH_Comstock_B_fragilis_ddungD_dPSH_study_mutant_rep2

status: Public on Sep 02 2008

type: RNA

city: Boston

state: MA

country: USA

description: This sample is of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

molecule: total RNA


title: Upper part of hair follicle_1

city: Vancouver

first: Kevin

last: McElwee

state: BC

department: Dermatology and Skin Science

country: Canada

institute: University of British Columbia

description: All treated biologicaly replicated samples were hybridized with the same universal human reference RNA (reference).

scan_protocol: The two fluorescent images (Cy3 and Cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA).

data_processing: Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software, (ImaGene 7.0 software: BioDiscovery Inc., El Segundo, CA, USA). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA).

organism: Homo sapiens

source_name: upper part of hair follicle

label_protocol: 1 ug RNA were amplified using the SenseAmp plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. sense RNA from amplification was labeled with Cy5, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays

growth_protocol: sample was stored in an RNA stabilization reagent

extract_protocol: Total RNA was isolated with an RNeasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's protocols.The quantity and quality of the RNAs was measured by electrophoresis using the Agilent 2100 bioanalyzer and RNA 6000 nano kit (Agilent Technologies, Palo Alto, CA)

treatment_protocol: samples of human hair follicles were collected from scalp biopsies of normal individuals undergoing cosmetic procedures.Hair follicles were microdissected to remove the lower one third, including the hair bulb, leaving the root sheaths including the bulge region.

tag: Upper part of hair follicle

label_protocol: Total 10ug RNA universal human reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3 , with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

extract_protocol: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: BWH_Comstock_B_fragilis_ddungD_dPSH_study_wild-type_rep2

description: This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Bacteroides fragilis NCTC 9343

growth_protocol: Bacteroides fragilis NCTC 9343 was grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075).

treatment_protocol: None (wild-type sample)

tag: wild-type sample


title: Normal, synovial membrane patient EB 125 (U133A)

city: Hannover

first: René

last: Huber

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute for Clinical Chemistry

country: Germany

institute: Hannover Medical School

description: see publication for details

hyb_protocol: according to supplier´s instructions, Affymetrix

scan_protocol: by laser scanning (Hewlett Packard gene scanner)

data_processing: background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix)

label: biotin

source_name: synovial membrane patient EB 125 (normal controls)

extract_protocol: according RNeasy Kit, Qiagen

tag: sex

value: m

tag: age

tag: normal control


title: Post-irradiated at 2.0Gy 2hrs Rep1

city: Montreal

first: Olivier

middle: Charles

last: Maes

state: Quebec

address: 3999 Cote Ste Catherine

department: Bloomfield Centre for Research in Aging

institute: Lady Davis Institute for Medical Research

description: A broad coverage of the human genome (approximately 6424 unique genes) was analyzed using the NIA Human MGC cDNA microarray, which consist of full-length cDNA clones generated by the National Cancer Institute’s Mammalian Gene Collection (http://mgc.nci.nih.gov/).

hyb_protocol: Nadon NL, Mohr D, Becker KG. National Institute on Aging microarray facility--resources for gerontology research. Journals of Gerontology Series A-Biological Sciences & Medical Sciences 2005;60(4):413-5 (PMID: 15933377)

scan_protocol: Hybridization intensities were measured using a Storm PhosphorImager (Amersham BioSciences, USA).

data_processing:
Data acquisition and global background correction were obtained using the Array-Pro Analyzer 4.5 software (Media Cybernetics, MD, USA).  There has been no data processing or normalization of the background-corrected raw data prior to their analysis.
Net intensity was derived from whole cell area measurement and corrected with mean intensity from background cells, calculated using a biquadratic polynomial.

source_name: Foreskin fibroblasts (AG1522)

label_protocol: Three µg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and M-MLV reverse transcribed (Invitrogen) in the presence of 100 mCi of [32P]dCTP (Amersham Bioscience, Piscataway, NJ) according to Maes et al. 2007 (Neurobiol Aging. 28:1795-809).

growth_protocol: Cells and culture conditions were previously described by Wu et al. (2002)  Journal of radiation research 43 Suppl:S181-5.

extract_protocol: Total RNA was extracted by Trizol reagent.

treatment_protocol: Confluent cell cultures were irradiated with 250 kV X-rays at two dose levels, either 0.1 or 2 Gy, at NASA’s Johnson Space Center (JSC, Houston, TX, USA). The exposure at 2 Gy took 3.2 minutes; that at 0.1 Gy took 42 seconds.

tag: Low-LET irradiation of  2.0 Gy

tag: Expression after 2hrs


title: Non-irradiated control  Rep2

tag: Non-irradiated

tag: Control expression


title: BWH_Comstock_B_fragilis_ddungD_dPSH_study_wild-type_rep3

description: This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Normal, synovial membrane patient EB 184 (U133A)

description: see publication for details

source_name: synovial membrane patient EB 184 (normal control)

label_protocol: according to supplier´s instructions, Affymetrix

tag: normal controls


title: Post-irradiated at 2.0Gy 2hrs Rep2


title: Upper part of hair follicle_6

hyb_protocol: 3DNA array detection 350 kit (Genisphere)

source_name: universal human reference RNA (Stratagene, Cedar Creek, TX)

tag: The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: BWH_Comstock_B_fragilis_ddungD_dPSH_study_wild-type_rep1

description: This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.


title: Upper part of hair follicle_5

treatment_protocol: universal human reference RNA (Stratagene, Cedar Creek, TX)


title: Upper part of hair follicle_7


title: BWH_Comstock_B_fragilis_ddungD_dPSH_study_mutant_rep1

description: This sample is of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Normal, synovial membrane patient EB228 (U133A)

description: see publication for details

source_name: synovial membrane patient EB228 (normal control)


title: Non-irradiated control  Rep3


title: Normal, synovial membrane patient EB188 (U133A)

description: see publication for details

source_name: synovial membrane patient EB188 (normal control)

value: f


title: Upper part of hair follicle_3


title: Upper part of hair follicle_4


title: Non-irradiated control  Rep1


title: Rheumatoid arthritis, synovial membrane patient EB40 (U133A)

description: see publication for details

source_name: synovial membrane patient EB40 (rheumatoid arthritis)

treatment_protocol:
NSARD,
prednisolone,
MTX

tag: disease

value: rheumatoid arthritis


title: Upper part of hair follicle_2


title: relA_tp9_hyb1: 945 min post-inoculation

status: Public on Aug 27 2008

city: Norman

first: Joe

last: Grissom

state: OK

address: 101 David L. Boren Blvd

department: Advanced Center for Genome Technology

institute: University of Oklahoma

hyb_protocol: Equal amounts of the Cy-3- and Cy-5-labeled samples were hybridized in triplicate to microarrays by using a Discovery system and ChipMap reagents (Ventana Medical Systems). For all microarrays, the experimental sample was labeled with Cy-5, and the control, from early logarithmic growth of E. coli MG1655 wild type on minimal glucose medium, was labeled with Cy-3.

scan_protocol: For all microarrays, the experimental sample was labeled with Cy-5, and the control, from early logarithmic growth of E. coli MG1655 wild type on minimal glucose medium, was labeled with Cy-3. Hybridized slides were scanned on a GenePix 4000 scanner (Axon Instruments), and the data were collected by using GENEPIX 5.0 software.

data_processing: The data were normalized by using a local Loess algorithm

organism: Escherichia coli

source_name: E. coli relA tp9: 945 min post-inoculation

label_protocol: RNA was labeled by first-strand cDNA synthesis using reverse transcriptase, random primers, and aminoallyl-dUTP incorporation; Cy-3 or Cy-5 dyes were chemically coupled in vitro to the aminoallyl-derivatized cDNA

growth_protocol: E. coli MG1655 wild-type and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 degrees C and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow. Growth was monitored as absorbance at 600nm.

extract_protocol: Total RNA was extracted from cells that had been diluted into ice-cold RNA-Later (Ambion) immediately upon culture sampling and purified using RN-Easy columns with  DNase treatment (Qiagen).

tag: Escherichia coli MG1655

tag: 945 min post-inoculation

source_name: E. coli wild-type tp1: 780 min post-inoculation

tag: wild-type

tag: 780 min post-inoculation


title: relA_tp10_hyb1: 955 min post-inoculation

source_name: E. coli relA tp10: 955 min post-inoculation

tag: 955 min post-inoculation


title: relA_tp11_hyb2: 966 min post-inoculation

source_name: E. coli relA tp11: 966 min post-inoculation

tag: 966 min post-inoculation


title: relA_tp8_hyb2: 935 min post-inoculation

source_name: E. coli relA tp8: 935 min post-inoculation

tag: 935 min post-inoculation


title: relA_tp7_hyb3: 925 min post-inoculation

source_name: E. coli relA tp7: 925 min post-inoculation

tag: 925 min post-inoculation


title: relA_tp7_hyb2: 925 min post-inoculation


title: relA_tp8_hyb3: 935 min post-inoculation


title: relA_tp9_hyb3: 945 min post-inoculation


title: relA_tp9_hyb2: 945 min post-inoculation


title: relA_tp11_hyb1: 966 min post-inoculation


title: relA_tp7_hyb1: 925 min post-inoculation


title: relA_tp10_hyb3: 955 min post-inoculation


title: relA_tp10_hyb2: 955 min post-inoculation


title: relA_tp6_hyb3: 916 min post-inoculation

source_name: E. coli relA tp6: 916 min post-inoculation

tag: 916 min post-inoculation


title: relA_tp11_hyb3: 966 min post-inoculation


title: relA_tp8_hyb1: 935 min post-inoculation


title: relA_tp6_hyb2: 916 min post-inoculation


title: relA_tp6_hyb1: 916 min post-inoculation


title: relA_tp5_hyb2: 909 min post-inoculation

source_name: E. coli relA tp5: 909 min post-inoculation

tag: 909 min post-inoculation


title: relA_tp5_hyb3: 909 min post-inoculation


title: relA_tp4_hyb3: 896 min post-inoculation

source_name: E. coli relA tp4: 896 min post-inoculation

tag: 896 min post-inoculation


title: relA_tp4_hyb2: 896 min post-inoculation


title: crp_tp7_hyb2: 450 min post-inoculation

source_name: E. coli crp tp7: 450 min post-inoculation

tag: 450 min post-inoculation


title: crp_tp7_hyb3: 450 min post-inoculation


title: relA_tp1_hyb1: 832 min post-inoculation

source_name: E. coli relA tp1: 832 min post-inoculation

tag: 832 min post-inoculation


title: crp_tp6_hyb4: 420 min post-inoculation

source_name: E. coli crp tp6: 420 min post-inoculation

tag: 420 min post-inoculation


title: relA_tp1_hyb3: 832 min post-inoculation


title: crp_tp6_hyb2: 420 min post-inoculation


title: relA_tp1_hyb2: 832 min post-inoculation


title: crp_tp6_hyb3: 420 min post-inoculation


title: crp_tp7_hyb1: 450 min post-inoculation


title: relA_tp4_hyb1: 896 min post-inoculation


title: relA_tp2_hyb1: 865 min post-inoculation

source_name: E. coli relA tp2: 865 min post-inoculation

tag: 865 min post-inoculation


title: relA_tp2_hyb2: 865 min post-inoculation


title: crp_tp6_hyb1: 420 min post-inoculation


title: crp_tp5_hyb4: 405 min post-inoculation

source_name: E. coli crp tp5: 405 min post-inoculation

tag: 405 min post-inoculation


title: relA_tp5_hyb1: 909 min post-inoculation


title: crp_tp2_hyb4: 250 min post-inoculation

source_name: E. coli crp tp2: 250 min post-inoculation

tag: 250 min post-inoculation


title: crp_tp5_hyb2: 405 min post-inoculation

tag: Escherichia coli MG1655


title: crp_tp7_hyb4: 450 min post-inoculation


title: crp_tp5_hyb3: 405 min post-inoculation


title: relA_tp2_hyb3: 865 min post-inoculation


title: crp_tp5_hyb1: 405 min post-inoculation


title: rpoS_tp13_hyb3: 330 min post-inoculation

source_name: E. coli rpoS tp13: 330 min post-inoculation

tag: 330 min post-inoculation


title: rpoS_tp13_hyb2: 330 min post-inoculation

tag: wild-type


title: crp_tp2_hyb2: 250 min post-inoculation

tag: 780 min post-inoculation


title: crp_tp2_hyb3: 250 min post-inoculation


title: rpoS_tp13_hyb1: 330 min post-inoculation


title: crp_tp2_hyb1: 250 min post-inoculation


title: rpoS_tp12_hyb3: 315 min post-inoculation

source_name: E. coli rpoS tp12: 315 min post-inoculation

tag: 315 min post-inoculation


title: GFP integrated Human Umbilical Cord lining Epithelial cells 2

status: Public on Sep 01 2008

type: genomic

city: Singapore

first: Jaichandran

last: Sivalingam

address: 11 Hospital Drive

department: Division of Medical Sciences

country: Singapore

institute: National Cancer Center

description: Copy number data for GFP integrated Human Umbilical Cord lining Epithelial cells

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA, for 17 hours.

scan_protocol: Scanning was performed according to the standard Affymetrix protocol from 250 ng genomic DNA using Genechip scanner 3000 7G.

data_processing: CHP files were generated by Affymetrix GTYPE using the BRLMM algorithm with default settings. Copy number was derived by CNAT4.0 (Affymetrix) using the microdeletion parameter settings as suggested by Affymetrix.

label: Biotin

molecule: genomic DNA

source_name: Human Umbilical Cord lining Epithelial cells ID #33 Integrated with EGFP cDNA using Phage Integrase

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA

growth_protocol: Establised primary cultures were cultured in pTTE1 (provided by CellResearch Corporation) medium.

extract_protocol: Genomic DNA was extracted from cultured cells using Qiagen Blood and Cell Culture Maxi kit according to manufactures protocol.

treatment_protocol: EGFP cDNA integrated into genomic DNA using phage integrase.

tag: Gender

value: Female

tag: Karyotype

value: 46 XX, Normal

tag: In vitro Passage Number


title: rpoS_tp11_hyb2: 290 min post-inoculation

source_name: E. coli rpoS tp11: 290 min post-inoculation

tag: 290 min post-inoculation

source_name: E. coli wild-type tp1: 780 min post-inoculation


title: rpoS_tp11_hyb1: 290 min post-inoculation


title: rpoS_tp12_hyb2: 315 min post-inoculation


title: rpoS_tp10_hyb3: 250 min post-inoculation

source_name: E. coli rpoS tp10: 250 min post-inoculation


title: rpoS_tp10_hyb1: 250 min post-inoculation


title: rpoS_tp10_hyb2: 250 min post-inoculation


title: Human Umbilical Cord lining Epithelial cells 2

description: Copy number data for Human Umbilical Cord lining Epithelial cells

treatment_protocol: No Treatment

tag: Human Umbilical Cord lining Epithelial cells ID #33


title: rpoS_tp8_hyb3: 210 min post-inoculation

source_name: E. coli rpoS tp8: 210 min post-inoculation

tag: 210 min post-inoculation


title: rpoS_tp11_hyb3: 290 min post-inoculation


title: rpoS_tp9_hyb2: 220 min post-inoculation

source_name: E. coli rpoS tp9: 220 min post-inoculation

tag: 220 min post-inoculation


title: rpoS_tp9_hyb3: 220 min post-inoculation


title: rpoS_tp9_hyb1: 220 min post-inoculation


title: rpoS_tp8_hyb2: 210 min post-inoculation


title: rpoS_tp12_hyb1: 315 min post-inoculation


title: rpoS_tp8_hyb1: 210 min post-inoculation


title: rpoS_tp7_hyb2: 200 min post-inoculation

source_name: E. coli rpoS tp7: 200 min post-inoculation

tag: 200 min post-inoculation


title: rpoS_tp7_hyb3: 200 min post-inoculation


title: Human Umbilical Cord lining Epithelial cells 1


title: rpoS_tp6_hyb3: 190 min post-inoculation

source_name: E. coli rpoS tp6: 190 min post-inoculation

tag: 190 min post-inoculation


title: rpoS_tp6_hyb2: 190 min post-inoculation


title: rpoS_tp7_hyb1: 200 min post-inoculation


title: rpoS_tp5_hyb3: 180 min post-inoculation

source_name: E. coli rpoS tp5: 180 min post-inoculation

tag: 180 min post-inoculation


title: rpoS_tp5_hyb1: 180 min post-inoculation


title: rpoS_tp4_hyb4: 170 min post-inoculation

source_name: E. coli rpoS tp4: 170 min post-inoculation

tag: 170 min post-inoculation


title: dXRN1, biological replicate 4

status: Public on Aug 21 2008

city: Los Angeles

first: Guillaume

middle: Francois

last: Chanfreau

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

description: Genomic region identification from tiling arrays for dXRN1 S.c.

hyb_protocol: Hybridizatio followed the standard Affymetrix tiling array manufacturer instructions

scan_protocol: Scanning was done according to the Affymetrix tiling array manufacturer instructions

data_processing: The data was intensity analyzed using Affymetrix TAS software (1.0) with a target scaling factor of 500 and a bandwidth of 30.

organism: Saccharomyces cerevisiae

source_name: xrn1 delete

label_protocol: Labelling was done according to the Affymetrix tiling array manufacturer instructions

growth_protocol: Strains were grown in synthetic complete media and harvested during log phase (O.D.600nm between 0.4-0.8).

extract_protocol: Extraction followed the standard Affymetrix tiling array manufacturer instructions

treatment_protocol: Chemical transfection - the upf1 or xrn1 locus was knocked out using standard yeast genetics methods

tag: xrn1 delete


title: GFP integrated Human Umbilical Cord lining Epithelial cells 1


title: dXRN1, biological replicate 2


title: rpoS_tp6_hyb1: 190 min post-inoculation

tag: Escherichia coli MG1655


title: rpoS_tp5_hyb2: 180 min post-inoculation


title: dXRN1, biological replicate 3


title: rpoS_tp3_hyb3: 160 min post-inoculation

source_name: E. coli rpoS tp3: 160 min post-inoculation

tag: 160 min post-inoculation


title: rpoS_tp3_hyb4: 160 min post-inoculation

tag: wild-type


title: rpoS_tp4_hyb3: 170 min post-inoculation

tag: 780 min post-inoculation


title: dUPF1, biological replicate 2

description: Genomic region identification from tiling arrays for dUPF1 S.c.

source_name: upf1 delete

tag: upf1 delete


title: dUPF1, biological replicate 1


title: dUPF1, biological replicate 4


title: dUPF1, biological replicate 3


title: rpoS_tp2_hyb1: 150 min post-inoculation

source_name: E. coli rpoS tp2: 150 min post-inoculation

tag: 150 min post-inoculation


title: rpoS_tp2_hyb3: 150 min post-inoculation


title: rpoS_tp2_hyb2: 150 min post-inoculation


title: rpoS_tp1_hyb4: 120 min post-inoculation

source_name: E. coli rpoS tp1: 120 min post-inoculation

tag: 120 min post-inoculation


title: rpoS_tp1_hyb2: 120 min post-inoculation


title: rpoS_tp4_hyb2: 170 min post-inoculation


title: WT, biological replicate 4

description: Genomic region identification from tiling arrays for wt S.c.

source_name: wildtype for Upf1 and Xrn1

tag: wildtype for Upf1 and Xrn1


title: WT, biological replicate 3


title: rpoS_tp1_hybA: 120 min post-inoculation


title: rpoS_tp3_hyb2: 160 min post-inoculation


title: WT, biological replicate 1


title: dXRN1, biological replicate 1


title: WT, biological replicate 2


title: Human Skeletal Muscle Total RNA, Replicate 5

status: Public on Aug 19 2008

city: Santa Clara

first: Robert

last: Ach

address: 5301 Stevens Creek Boulevard

department: Agilent Laboratories

institute: Agilent Technologies

description: For a complete description of the columns in the supplemental array data files, see Agilent's Reference Guide for Feature Extraction Software v9.5, http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50416

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

scan_protocol: Scanned on an Agilent G2505A Scanner

data_processing:
Agilent Feature Extraction v9.5.3, default miRNA parameters

The data table below represents all replicate probes per miRNA. The VALUE column reports the combined results from all replicate probes for a given miRNA (i.e., the same VALUE is reported multiple times for each replicate probe of a given miRNA).

source_name: Human Skeletal Muscle Total RNA

label_protocol: Direct labeling with Cy3-pCp. See Agilent Technologies website for miRNA labeling protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

extract_protocol: Total RNA prepared by Ambion (ABI). According to the manufacturer, RNA was prepared using a modified version of Ambion's ToTALLY RNA Kit for RNA isolation. Tissues were stored in RNAlater stabilization solution or frozen until processed. RNA was DNase-treated to minimize DNA contamination.

tag: Human skeletal muscle total RNA, purchased from Ambion. Catalog # AM7982. Lot #035P020602115B. Male donor, caucasian, age 71.


title: Human Testes Total RNA, Replicate 1

source_name: Human Testes Total RNA

tag: Human testes total RNA, purchased from Ambion. Catalog # AM7972. Lot #105P010702031I. Male donor, caucasian, age 39.


title: Human Skeletal Muscle Total RNA, Replicate 2


title: Human Ovary Total RNA, Replicate 5

source_name: Human Ovary Total RNA

tag: Human ovary total RNA, purchased from Ambion. Catalog # AM7974. Lot #105P010705006A. Female donor, caucasian, age 48.


title: Human Ovary Total RNA, Replicate 1


title: Human Ovary Total RNA, Replicate 2


title: Human Skeletal Muscle Total RNA, Replicate 3


title: Human Testes Total RNA, Replicate 4


title: Human Testes Total RNA, Replicate 2


title: Human Liver Total RNA, Replicate 3

source_name: Human Liver Total RNA

tag: Human liver total RNA, purchased from Ambion. Catalog # AM7960. Lot #055P030400001F. Male donor, caucasian, age 37.


title: Human Ovary Total RNA, Replicate 4


title: Human Ovary Total RNA, Replicate 3


title: Human Thymus Total RNA, Replicate 4

source_name: Human Thymus Total RNA

tag: Human thymus total RNA, purchased from Ambion. Catalog # AM7964. Lot #02030914. Male donor, caucasian, age 40.


title: Human Thymus Total RNA, Replicate 3


title: Human Liver Total RNA, Replicate 5


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, QIAGEN miRNeasy Prep #1, Label/Hyb Replicate #1

source_name: ZR-75-1 human breast cancer tissue culture cell line

extract_protocol: QIAGEN miRNeasy extraction from 10,000,000 cells. Preps were performed according to the manufacturer’s protocol: http://www1.qiagen.com/literature/handbooks/literature.aspx?id=1000642.pdf

tag: ZR-75-1 cells, purchased as a frozen cell pellet


title: Human Skeletal Muscle Total RNA, Replicate 1


title: Human Testes Total RNA, Replicate 3


title: Human Liver Total RNA, Replicate 1


title: Human Skeletal Muscle Total RNA, Replicate 4


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, QIAGEN miRNeasy Prep #1, Label/Hyb Replicate #2


title: Human Liver Total RNA, Replicate 4


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, QIAGEN miRNeasy Prep #2


title: Human Thymus Total RNA, Replicate 1


title: Human Thymus Total RNA, Replicate 2


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, miRVana Prep #5, Label/Hyb Replicate 2

extract_protocol: miRVana extraction from 10,000,000 cells. Preps were performed according to the manufacturer’s protocol (Ambion/ABI): http://www.ambion.com/techlib/prot/fm_1560.pdf


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, miRVana Prep #4, Label/Hyb Replicate 2


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, QIAGEN miRNeasy Prep #3


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, miRVana Prep #6


title: Human Liver Total RNA, Replicate 2


title: Human Heart Total RNA, Replicate 3

source_name: Human Heart Total RNA

tag: Human heart total RNA, purchased from Ambion. Catalog # AM7966. Lot #055P010501002C. Male donor, caucasian, age 56.


title: Human Breast Total RNA, Replicate 2

source_name: Human Breast Total RNA

tag: Human breast total RNA, purchased from Ambion. Catalog # AM7952. Lot #025P030704007E. Female donor, caucasian, age 56.


title: Human Heart Total RNA, Replicate 4


title: Human Brain Total RNA, Replicate 5

source_name: Human Brain Total RNA

tag: Human brain total RNA, purchased from Ambion. Catalog # AM7962. Lot #09040042. Male donor, age 61.


title: HeLa Cell Total RNA, miRVana Prep #1, Label/Hyb Replicate 2

source_name: HeLa cells

extract_protocol: miRVana extraction from 5,000,000 cells. Preps were performed according to the manufacturer’s protocol (Ambion/ABI): http://www.ambion.com/techlib/prot/fm_1560.pdf

tag: HeLa cells, purchased as a frozen cell pellet


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, miRVana Prep #5, Label/Hyb Replicate 1


title: Human Heart Total RNA, Replicate 5


title: Human Heart Total RNA, Replicate 2


title: HeLa Cell Total RNA, miRVana Prep #1, Label/Hyb Replicate 1


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 6


title: Human Brain Total RNA, Replicate 4


title: Human Breast Total RNA, Replicate 5


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 7


title: Human Breast Total RNA, Replicate 1


title: Human Breast Total RNA, Replicate 4


title: Human Brain Total RNA, Replicate 3


title: Human Heart Total RNA, Replicate 1


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 5


title: Human Brain Total RNA, Replicate 2


title: HeLa Cell Total RNA, miRVana Prep #8, Label/Hyb Replicate 4

extract_protocol: miRVana extraction from 5,000,000 cells. Preps were performed according to the manufacturer’s protocol (Ambion/ABI):  http://www.ambion.com/techlib/prot/fm_1560.pdf


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 2


title: Human Placenta Total RNA, Replicate 4

source_name: Human Placenta Total RNA

tag: Human placenta total RNA, purchased from Ambion. Catalog # AM7950. Lot #030301510J. Female donor, caucasian, age 35.


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 4


title: Human Placenta Total RNA, Replicate 2

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol:  http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

label_protocol: Direct labeling with Cy3-pCp.  See Agilent Technologies website for miRNA labeling protocol:  http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

extract_protocol: Total RNA prepared by Ambion (ABI).  According to the manufacturer, RNA was prepared using a modified version of Ambion's ToTALLY RNA Kit for RNA isolation.  Tissues were stored in RNAlater stabilization solution or frozen until processed.  RNA was DNase-treated to minimize DNA contamination.


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 3


title: Human Breast Total RNA, Replicate 3


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #4, Label/Hyb Replicate 2

extract_protocol: QIAGEN miRNeasy extraction from 5,000,000 cells. Preps were performed according to the manufacturer’s protocol:  http://www1.qiagen.com/literature/handbooks/literature.aspx?id=1000642


title: Human Brain Total RNA, Replicate 1


title: HeLa Cell Total RNA, miRVana Prep #8, Label/Hyb Replicate 1


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #9, Label/Hyb Replicate 3


title: HeLa Cell Total RNA, miRVana Prep #6, Label/Hyb Replicate 1


title: Human Placenta Total RNA, Replicate 3


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #2, Label/Hyb Replicate 1


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #4, Label/Hyb Replicate 1


title: Human Placenta Total RNA, Replicate 1

tag: Human placenta total RNA, purchased from Ambion.  Catalog # AM7950.  Lot #030301510J.  Female donor, caucasian, age 35.


title: HeLa Cell Total RNA, miRVana Prep #8, Label/Hyb Replicate 2


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #2, Label/Hyb Replicate 2


title: HeLa Cell Total RNA, miRVana Prep #8, Label/Hyb Replicate 3


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #9, Label/Hyb Replicate 2


title: HeLa Cell Total RNA, QIAGEN miRNeasy Prep #9, Label/Hyb Replicate 1


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, TRIzol Prep #3, Label/Hyb Replicate 1

extract_protocol: TRIzol extraction from 10,000,000 cells.  TRIzol preps were performed according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA) using an isopropanol precipitation.  Briefly, 1 ml of TRIzol reagent was added to the cell pellet and cells were lysed by repetitive pipetting, and then incubated at room temperature for 5 minutes.  200 ul of chloroform were added, followed by vigorous shaking and incubation for 2-3 minutes at room temperature.  Samples were centrifuged 15 minutes at 12000xg at 4°C.  The aqueous layer was transferred to a new tube, and the RNA was precipitated by adding 0.5ml isopropanol, incubating 10 minutes at room temperature, and spinning for 10 minutes (12000xg at 4°C).  Pellets were washed with 80% ethanol and resuspended in nuclease-free dH2O (Ambion).


title: HeLa Cell Total RNA, TRIzol Prep #3, Label/Hyb Replicate 1

extract_protocol: Trizol extraction from 5,000,000 cells.  TRIzol preps were performed according to the manufacturer’s protocol (Invitrogen, Carlsbad, CA) using an isopropanol precipitation.  Briefly, 1 ml of TRIzol reagent was added to the cell pellet and cells were lysed by repetitive pipetting, and then incubated at room temperature for 5 minutes.  200 ul of chloroform were added, followed by vigorous shaking and incubation for 2-3 minutes at room temperature.  Samples were centrifuged 15 minutes at 12000xg at 4°C.  The aqueous layer was transferred to a new tube, and the RNA was precipitated by adding 0.5ml isopropanol, incubating 10 minutes at room temperature, and spinning for 10 minutes (12000xg at 4°C).  Pellets were washed with 80% ethanol and resuspended in nuclease-free dH2O (Ambion).


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, TRIzol Prep #6, Label/Hyb Replicate 2


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, TRIzol Prep #5, Label/Hyb Replicate 2


title: HeLa Cell Total RNA, TRIzol Prep #3, Label/Hyb Replicate 2


title: C33_IP_TF3Cmyc_NOC

status: Public on Jul 21 2008

city: London

first: claudio

last: d'ambrosio

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Cancer Research UK

description:
C33_IP_TF3Cmyc_NOC.CEL
Note: The header of C33_IP_TF3Cmyc_NOC.CEL incorrectly identifies the array as S_cerevisiaeR_4x. The correct array assignment is S_cerevisiaeF_4x.

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized for 16 hours at 42ºC in a hybridization oven (GeneChip Hybridization Oven 640, Affymetrix)

scan_protocol: The washing and scanning protocol, provided by Affymetrix, was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix)

data_processing: Data were processed following the protocol provided by Affymetrix (GCOS ver 1.4)

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 in YP + 2% glucose were synchronized in metaphase with the spindle depolymerising drug nocodazole

extract_protocol: Extraction was performed as previously described (Katou et al. 2003).

tag: Saccharomyces cerevisiae (W303 background)

tag: Genotype

value: MATa Brn1-9PK  Tfc3-myc18 delta tRNA tE(UUC)J chr X 116 kb

tag: 2 hours nocodazole arrested cells

tag: Strain

tag: Antibody

value: anti-myc


title: Human Placenta Total RNA, Replicate 5


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, TRIzol Prep #5, Label/Hyb Replicate 1


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, TRIzol Prep #6, Label/Hyb Replicate 1


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, TRIzol Prep #3, Label/Hyb Replicate 2


title: HeLa Cell Total RNA, TRIzol Prep #6, Label/Hyb Replicate 2


title: C26_IP_3475_NOC

description:
C26_IP_3475_NOC.CEL
Note: The header of C26_IP_3475_NOC.CEL incorrectly identifies the array as S_cerevisiaeR_4x. The correct array assignment is S_cerevisiaeF_4x.

treatment_protocol: Extraction was performed as previously described (Katou et al. 2003)

value: MATa Brn1-9PK B box (386,600 chr V)

value: anti-PK


title: HeLa Cell Total RNA, TRIzol Prep #9, Label/Hyb Replicate 3


title: espR mutant complemented with R8A espR gene (R- R8A)

status: Public on Aug 08 2008

city: San Francisco

first: Paolo

last: Manzanillo

department: Microbiology and Immunology

institute: University of California at San Francisco

description:
Biological replicate 1
espR mutant (R-) complemented with an espR gene containing an R8A amino acid subsitution (R- R8A)

hyb_protocol: Cy5 and Cy3 labelled probes were mixed and hybridized to oligonucleotide MTB arrays (Operon Biosystems) at 63 C for 18h. After hybridization, slides were washed in batch.

scan_protocol: Slides were scanned using an Axon 4000B scanner and GenePix software. Data was acquired using Spotreader 1.3.1.0 and Acuity 4.0 software.

data_processing: Ratio-based normalization using Acuity 4.0.

organism: Mycobacterium tuberculosis

source_name: Complemented espR mutant M.tb strain R8A

label_protocol: 5 ug total RNA was reverse transcribed into cDNA using random hexamer primers in the presence of aa-dUTP. cDNA was labelled with Cy dyes (Amersham) and purified over Zymo DNA binding columns.

growth_protocol: M. tuberculosis growing in 7H9 with 0.05% Tween 80 in early log phase.

extract_protocol: RNA was extracted from 50 ml of culture by beadbeating in Trizol and RNA was purified with Qiagen Rneasy columns per manufacturers instructions.

tag: M. tuberculosis Erdman strain

source_name: Reference Pool

tag: Pooled from all samples used


title: C18 NOC IP 3096

value: MATa TFC3-9Pk BRN1-HA6


title: C29_IP_tRNAd_NOC

description:
C29_IP_tRNAd_NOC.CEL
Note: The header of C29_IP_tRNAd_NOC.CEL incorrectly identifies the array as S_cerevisiaeR_4x. The correct array assignment is S_cerevisiaeF_4x.

value: MATa Brn1-9PK  delta tRNA tE(UUC)J chr X 116 kb


title: C16_SUP_2200_NOC

source_name: Input DNA from Saccharomyces cerevisiae cells from unbound fraction

value: MATa Brn1-9PK


title: espR mutant complemented with espR gene containing 5-aa C-terminal truncation (R- delta5)

description:
Biological replicate 1
espR mutant (R-) complemented with an espR gene containing a C-terminal 5 amino acid truncation (R- delta5)

source_name: Complemented espR mutant M.tb strain delta5


title: espR mutant complemented with espR gene containing 10-aa C-terminal truncation (R- delta10)

description:
Biological replicate 1
espR mutant (R-) complemented with an espR gene containing a C-terminal 10 amino acid truncation (R- delta10)

source_name: Complemented espR mutant M.tb strain delta10


title: HeLa Cell Total RNA, TRIzol Prep #6, Label/Hyb Replicate 1


title: C28_IP_3485_NOC

description:
C28_IP_3485_NOC.CEL
Note: The header of C28_IP_3485_NOC.CEL incorrectly identifies the array as S_cerevisiaeR_4x. The correct array assignment is S_cerevisiaeF_4x.


title: HeLa Cell Total RNA, TRIzol Prep #9, Label/Hyb Replicate 2

tag: HeLa cells, purchased as a frozen cell pellet.


title: ZR-75-1 Cells, Human Breast Cancer Cell Line, miRVana Prep #4, Label/Hyb Replicate 1


title: C15_IP_2200_NOC_tiling


title: Histone H3 A111G mutant 1

status: Public on Jul 19 2008

type: other

city: Albany

first: Randall

middle: Heywood

last: Morse

state: NY

institute: Wadsworth Center

hyb_protocol: Per Affymetrix recommendation

scan_protocol: Scanned using Affymetrix 7G scanner

data_processing: CEL  and GRD files created from Affymetrix GCOS software; Affymetrix Tiling Array Software used to create .bar files

molecule: other

source_name: Nucleosomal DNA from histone H3(A111G) mutant yeast

label_protocol: biotinylated with Biotin-N6-ddATP using terminal deoxynucleotidyl transferase

growth_protocol: Grown in YPD to mid-log phase at 30 C

extract_protocol: Chromatin was digested with micrococcal nuclease to yield predominantly mononucleosomal DNA

tag: Strain RMY306


title: Wild type 1

source_name: Wild type yeast nucleosomal DNA

tag: Strain RMY301


title: Histone H3 A111G mutant 3


title: Histone H3 A111G mutant 2


title: espR mutant complemented with R21A espR gene (R- R21A)

description:
Biological replicate 1
espR mutant (R-) complemented with an espR gene containing an R21A amino acid subsitution (R- R21A)

source_name: Complemented espR mutant M.tb strain R21A


title: C34_IP_3528_NOC

description:
C34_IP_3528_NOC.CEL
Note: The header of C34_IP_3528_NOC.CEL incorrectly identifies the array as S_cerevisiaeR_4x. The correct array assignment is S_cerevisiaeF_4x.

value: MATa Brn1-9PK 2tRNA tH(GUG)E1 (386,500 chr V)


title: C16 IP 2200 NOC


title: ESPR- mutant (R-) rep3

status: Public on Jul 04 2008

description:
Biological replicate 3
ESPR- mutant (R-) rep3

hyb_protocol: Cy5 and Cy3 labelled probes were mixed and hybridized to oligonucleotide MTB arrays (Operon Biosystems) at 63 C for 18h.After hybridization, slides were washed in batch.

scan_protocol: Slides were scanned using an Axon 4000B scanner and GenePix software. Data was acquired using Spotreader 1.3.1.0 and Acuity 4.0 software

data_processing: Ratio-based normalization using Acuity 4.0

source_name: espR mutant M.tb

growth_protocol: M. tuberculosis growing in 7H9 with 0.05% Tween 80 in early log phase

extract_protocol: RNA was extracted from 50 ml of culture by beadbeating in Trizol and RNA purified with Qiagen Rneasy columns per manufacturers instructions.


title: WT TB rep3

description:
Biological replicate 3
WT TB rep3

source_name: Wt M.tb


title: HeLa Cell Total RNA, TRIzol Prep #9, Label/Hyb Replicate 1


title: Human Saliva Male 6

status: Public on May 20 2008

first: David

last: Wong

email: dtww@ucla.edu, mikehu@ucla.edu

address: 10833 Le Conte Ave, CHS 73-017

department: Dental Research Institute

institute: University of California, Los Angeles

description:
Library files included in primary analysis:
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.clf
HuEx-1_0-st-v2.r2.antigenomic.bgp
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

source_name: Healthy male

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Whole saliva was collected by direct spitting into 50ml Falcon tubes placed on ice. Supernatant was obtained following centrifugation of whole saliva for 15 minutes at 2600 g.

extract_protocol: RNA was isolated from 560 µL of saliva supernatant with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

tag: saliva supernatant

tag: male


title: Human Saliva Male 4


title: Human Saliva Female 9

source_name: Healthy female

tag: female


title: Human Saliva Male 7


title: Human Saliva Male 2


title: Human Saliva Female 5


title: Human Saliva Female 10


title: Human Saliva Female 7


title: Human Saliva Female 3


title: Human Saliva Female 6


title: Human Saliva Male 3


title: Human Saliva Female 8


title: Human Saliva Female 2


title: Human Saliva Female 4


title: WT_tp17_hyb3: 1089 min post-inoculation

status: Public on Mar 17 2007

source_name: E. coli wild-type tp17: 1089 min post-inoculation

extract_protocol: Total RNA was extracted from cells that had been diluted into ice-cold RNA-Later (Ambion) immediately upon culture sampling and purified using RN-Easy columns with  DNase treatment (Qiagen).

tag: Escherichia coli MG1655

tag: wild-type

tag: 1089 min post-inoculation

source_name: E. coli wild-type tp1: 780 min post-inoculation

tag: 780 min post-inoculation


title: WT_tp16_hyb2: 1070 min post-inoculation

source_name: E. coli wild-type tp16: 1070 min post-inoculation

tag: 1070 min post-inoculation


title: WT_tp15_hyb3: 1049 min post-inoculation

source_name: E. coli wild-type tp15: 1049 min post-inoculation

tag: 1049 min post-inoculation


title: Human Saliva Female 11


title: WT_tp16_hyb1: 1070 min post-inoculation


title: WT_tp16_hyb3: 1070 min post-inoculation


title: WT_tp17_hyb2: 1089 min post-inoculation


title: Human Saliva Male 5


title: WT_tp17_hyb1: 1089 min post-inoculation


title: WT_tp15_hyb2: 1049 min post-inoculation


title: Human Saliva Male 1


title: WT_tp13_hyb3: 999 min post-inoculation

source_name: E. coli wild-type tp13: 999 min post-inoculation

tag: 999 min post-inoculation


title: WT_tp14_hyb3: 1035 min post-inoculation

source_name: E. coli wild-type tp14: 1035 min post-inoculation

tag: 1035 min post-inoculation


title: WT_tp13_hyb2: 999 min post-inoculation


title: WT_tp13_hyb1: 999 min post-inoculation


title: Human Saliva Female 1


title: WT_tp12_hyb2: 969 min post-inoculation

source_name: E. coli wild-type tp12: 969 min post-inoculation

tag: 969 min post-inoculation


title: WT_tp9_hyb3: 919 min post-inoculation

source_name: E. coli wild-type tp9: 919 min post-inoculation

tag: 919 min post-inoculation


title: WT_tp15_hyb1: 1049 min post-inoculation


title: WT_tp12_hyb3: 969 min post-inoculation


title: WT_tp14_hyb2: 1035 min post-inoculation


title: WT_tp8_hyb3: 908 min post-inoculation

source_name: E. coli wild-type tp8: 908 min post-inoculation

tag: 908 min post-inoculation


title: WT_tp10_hyb1: 929 min post-inoculation

source_name: E. coli wild-type tp10: 929 min post-inoculation

tag: 929 min post-inoculation


title: WT_tp11_hyb3: 939 min post-inoculation

source_name: E. coli wild-type tp11: 939 min post-inoculation

tag: 939 min post-inoculation


title: WT_tp11_hyb1: 939 min post-inoculation


title: Complemented espR mutant (R+) rep3

description:
Biological replicate 3
Complemented espR mutant (R+) rep3

source_name: Complemented espR mutant M.tb

tag: M. tuberculosis Erdman strain

source_name: Reference Pool

tag: Pooled from all samples used


title: WT_tp11_hyb2: 939 min post-inoculation


title: WT_tp10_hyb3: 929 min post-inoculation


title: WT_tp12_hyb1: 969 min post-inoculation


title: WT_tp10_hyb2: 929 min post-inoculation


title: WT_tp8_hyb1: 908 min post-inoculation


title: WT_tp9_hyb2: 919 min post-inoculation


title: WT_tp9_hyb1: 919 min post-inoculation


title: WT_tp8_hyb2: 908 min post-inoculation


title: WT_tp7_hyb3: 898 min post-inoculation

source_name: E. coli wild-type tp7: 898 min post-inoculation

tag: 898 min post-inoculation


title: WT_tp7_hyb1: 898 min post-inoculation


title: WT_tp14_hyb1: 1035 min post-inoculation


title: WT_tp7_hyb2: 898 min post-inoculation


title: WT_tp6_hyb2: 888 min post-inoculation

source_name: E. coli wild-type tp6: 888 min post-inoculation

tag: 888 min post-inoculation


title: WT_tp4_hyb3: 869 min post-inoculation

source_name: E. coli wild-type tp4: 869 min post-inoculation

tag: Escherichia coli MG1655

tag: 869 min post-inoculation


title: WT_tp3_hyb2: 861 min post-inoculation

source_name: E. coli wild-type tp3: 861 min post-inoculation

tag: wild-type

tag: 861 min post-inoculation


title: WT_tp1_hyb3: 780 min post-inoculation

tag: 780 min post-inoculation


title: WT_tp5_hyb2: 878 min post-inoculation

source_name: E. coli wild-type tp5: 878 min post-inoculation

tag: 878 min post-inoculation


title: WT_tp5_hyb1: 878 min post-inoculation

source_name: E. coli wild-type tp1: 780 min post-inoculation


title: WT_tp1_hyb2: 780 min post-inoculation


title: WT_tp4_hyb2: 869 min post-inoculation


title: WT_tp3_hyb1: 861 min post-inoculation


title: WT_tp1_hyb1: 780 min post-inoculation


title: WT_tp2_hyb2: 830 min post-inoculation

source_name: E. coli wild-type tp2: 830 min post-inoculation

tag: 830 min post-inoculation


title: WT_tp5_hyb3: 878 min post-inoculation


title: WT_tp2_hyb1: 830 min post-inoculation


title: WT_tp4_hyb1: 869 min post-inoculation


title: WT_tp2_hyb3: 830 min post-inoculation


title: WT_tp6_hyb1: 888 min post-inoculation


title: WT_tp6_hyb3: 888 min post-inoculation


title: Wild type 2

source_name: Wild type yeast nucleosomal DNA

tag: Strain RMY301


title: WT_tp3_hyb3: 861 min post-inoculation


title: p63_ChIP-chip_B1, (+)ActD, chip 10 of 14

status: Public on Dec 01 2006

last: Struhl

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

description:
Input and ChIP DNA was amplified by two rounds of primer extension (Round A) with random primers, followed by purification and two successive rounds of PCR (Round B and C).
The samples were then purified using column purification and ready for array hybridization protocols.

hyb_protocol: Biotinylated DNA was hybridized to the Affymetrix tiled, human whole genome arrays, washed, and stained according to manufacturer's instructions.

scan_protocol: The microarrays were scanned using a custom-built Affymetrix scanner with a laser spot size of 3.5 um and a resolution (pixel size) of 1.0 um. Thus each feature on the array with the size of 5x5 um was represented by 25 data points (pixels). To estimate the intensity of each feature, the outer rim of pixels was discarded and the 75th-percentile of the remaining 9 pixels was used as the estimate of the intensity.

data_processing: A binding P-value for each genomic position was determined by the Wilcoxon rank sum test.

source_name: Cervical carcinoma

label_protocol: Amplified ChIP (or matching input) DNA was fragmented with DNase I, and then biotin-labeled using terminal transferase (TdT).

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum

extract_protocol:
1. Trypsinized cells were placed into fresh media and cross-linked by the addition of formaldehyde.
2. Cells were then spun down and the cell pellet was then resuspended in micrococcal nuclease (MNase) reaction buffer.
3. The chromatin was then sonicated, spun down and the supernatant was diluted with IP-dilution buffer.
4. Diluted chromatin was precleared with protein A/G sepharose beads, and a portion reserved for control, or 'input', DNA (i.e. omitting immunoprecipitation).
5. The remaining chromatin was incubated with 4A4 anti-p63 antibody-coupled protein A/G sepharose beads.
6. Input and eluted material was de-crosslinked and purified.

treatment_protocol: Cells were treated with 5nM Actinomycin D or ethanol (vehicle control) for 24-26 hrs before harvesting by trypsinization

tag: Age

value: 66 yrs Gender:Female  Ethnicity:Caucasian


title: p63_ChIP-chip_B1, (+)ActD, chip 08 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 10 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 10 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 08 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 08 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 10 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 08 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 10 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 01 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 03 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 03 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 03 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 03 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 08 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 08 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 01 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 01 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 01 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 01 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 03 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 07 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 03 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 10 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 07 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 07 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 01 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 07 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 07 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 07 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 11 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 14 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 14 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 06 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 06 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 11 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 06 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 14 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 14 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 11 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 06 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 05 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 11 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 06 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 14 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 11 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 06 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 09 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 13 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 11 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 09 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 14 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 13 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 05 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 09 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 05 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 13 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 09 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 13 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 13 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 05 of 14


title: MAQC_TAQ_1_D4

status: Public on Sep 08 2006

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

data_processing: POLR2A was chosen as the reference gene and each replicate CT was subtracted from the average POLR2A CT to give the log2 difference (delta CT), the normalized value. For delta CT calculations, a CT value of 35 was used for any replicate that had CT > 35.

label: FAM

source_name: MAQC sample D, i.e., MAQC samples A and B mixed at 25%:75% ratio (A:B).

label_protocol: Each TaqMan(R) Assay was run in four replicates for each RNA sample using 10 ng total cDNA (measured as total input RNA) in a 10 ul final volume. Assays were run with 2X Universal Master Mix (without UNG) on Applied Biosystems 7900 Fast Real-Time PCR System using universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

tag: MAQC sample


title: MAQC_TAQ_1_D3


title: MAQC_TAQ_1_D2


title: MAQC_TAQ_1_C3

source_name: MAQC sample C, i.e., MAQC samples A and B mixed at 75%:25% ratio (A:B).


title: p63_ChIP-chip_B1, (-)ActD, chip 05 of 14


title: MAQC_TAQ_1_C2


title: p63_ChIP-chip_B2, (-)ActD, chip 09 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 05 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 02 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 02 of 14


title: p63_ChIP-chip_B2, (+)ActD, chip 04 of 14


title: MAQC_TAQ_1_C1


title: p63_ChIP-chip_B3, (-)ActD, chip 12 of 14


title: MAQC_TAQ_1_B3

source_name: MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)


title: MAQC_TAQ_1_B4


title: p63_ChIP-chip_B2, (+)ActD, chip 12 of 14


title: MAQC_TAQ_1_B1


title: MAQC_TAQ_1_A4

source_name: MAQC sample A, i.e., Stratagene Universal Human Reference RNA (UHRR, Catalog #740000)


title: p63_ChIP-chip_B1, (+)ActD, chip 12 of 14


title: p63_ChIP-chip_B3, (-)ActD, chip 04 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 02 of 14


title: p63_ChIP-chip_B1, (+)ActD, chip 04 of 14


title: MAQC_TAQ_1_C4


title: p63_ChIP-chip_B3, (+)ActD, chip 12 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 12 of 14


title: MAQC_TAQ_1_A3


title: p63_ChIP-chip_B2, (-)ActD, chip 02 of 14


title: p63_ChIP-chip_B3, (+)ActD, chip 04 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 13 of 14


title: MAQC_TAQ_1_A2


title: p63_ChIP-chip_B3, (-)ActD, chip 09 of 14


title: n5t0n

status: Public on Feb 15 2006

city: Bethesda

middle: L

last: Danner

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: Clinical Center

description: Naïve cells (RPMI 1640 for 48 h).  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.

source_name: U937 cells; Human monoblastoid line devoid of guanylate cyclase


title: ADH3

status: Public on Apr 07 2005

city: Washington

first: Indira

last: Poola

state: DC

address: 520 W Street, NW

department: Biochemistry and MOlecular Biology

institute: Howard University College of Medicine

description:
Fresh Atypical ductal hyperplasia tissue collected from breast of a women who had no prior history of breast cancer and had not developed breast cancer in five years after diagnosis
Keywords = Homo sapiens, Atypical Ductal Hyperplasia

source_name: breast precancerous tissue


title: ADHC3

description:
Fresh Atypical ductal hyperplasia (ADH) tissue collected from breast of a women who had cancer before ADH, or had cancer at the time as ADH or developed cancer after ADH diagnosis
Keywords = Homo sapiens, Atypical Ductal Hyperplasia


title: ADHC1


title: ADH2


title: p63_ChIP-chip_B1, (-)ActD, chip 02 of 14


title: p63_ChIP-chip_B1, (-)ActD, chip 12 of 14


title: ADHC2


title: ADH1


title: p63_ChIP-chip_B3, (-)ActD, chip 02 of 14


title: p63_ChIP-chip_B2, (-)ActD, chip 04 of 14


title: MAQC_TAQ_1_D1


title: MAQC_TAQ_1_B2


title: p63_ChIP-chip_B1, (-)ActD, chip 04 of 14


title: Human Ntera2 cells, EED1 ENCODE

status: Public on Jun 06 2006

city: Davis

first: Sharon

last: Squazzo

address: 4617 GBSF, 451 E. Health Sci. Dr.

department: Pharmacology

institute: UC Davis Genome Center

description: Human Ntera2 cells

data_processing: log base 2 ratios

source_name: Ntera2 cells

tag: EED1 antibody

tag: control total input


title: MAQC_TAQ_1_A1


title: Human Ntera2 cells, Suz12 ENCODE

description: Human Ntera2 cells

tag: Suz12 antibody


title: Human Ntera2 cells, H3meK27 ENCODE

description: Human Ntera2 cells

tag: H3meK27 antibody


title: Human Ntera2 cells, EZH2 ENCODE

description: Human Ntera2 cells

tag: EZH2 antibody


title: effects of MN1 expression_12

status: Public on Sep 09 2008

city: Rotterdam

first: Magda

last: Meester

address: Dr. Molewaterplein 40

department: Pathology

country: Netherlands

institute: Erasmus Medical Center

description: Dye swap and/or biological duplicate of H6, A8, B1

hyb_protocol: labeled aRNA was fragmented (Ambion RNA Fragmentation Reagents) and mixed with blocking solution containing Poly d(A), Cot-1 DNA and yeast t-RNA. Hybridization was overnight at 42C on a Tecan HS4800 hybridization station. Protocol: M016 (http://erasmusmc.nl/biomics). It includes a 15 min prehybridization with a solution containing 4% (w/v) BSA.

scan_protocol: Perkin Elmer ScanArray Express HT instrument Imagene software version 6.0

data_processing: Imagene data was uploaded into the CMF database (NKI, The Netherlands) and normalized using lowess subarray method. No background correction.

source_name: number 29, exp B

label_protocol: 3 ug of RNA was used for linear amplification using the Superscript III RNA amplification kit (Invitrogen). 1 ug of amplified RNA was labeled using the ULS-Cy3/5 aRNA fluorescent labeling kit (Kreatech)

growth_protocol: cell were cultured in RPMI 1640 with 10% FCS, pen/strep, 0.5 ug/ml puromycin, 100 ug/ml hygromycin and 1ug/ml tetracyclin.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified using RNeasy columns

treatment_protocol: tetracyclin-controlled gene expression was induced by resuspending the cells in fresh medium without tetracyclin. If desired, ATRA was added to a final concentration of 1 uM.

tag: see experimental_design.jpg

tag: MN1 is a derivative of U937 and MN1 is under control of TET system

source_name: number 41, exp B


title: UF22_Xylem-Rep1

status: Public on Sep 06 2008

city: Gainesville

first: Matias

last: Kirst

state: FL

institute: University of Florida

hyb_protocol: 1.5ug labeled ds-cDNA was denatured at 95░C for 5min and hybridized to custom in situ synthesized oligonucleotide microarrays (produced by NimbleGen, Madison, WI) at 42░C overnight (16-20h).  Hybridization and wash buffers are described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf)

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf).

data_processing: Raw intensity data was background corrected (Irizarry et al. 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data.  Biostatistics 4: 249-264) and normalized using the Quantile normalization method (Bolstad et al. 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193).

organism: Populus trichocarpa x Populus deltoides

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, secondary xylem tissue

label_protocol: RNA extracted from each progeny was converted to double-stranded (ds-) cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturerÆs protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37░C.

growth_protocol: A pseudo-backcross population (Family 52-124) derived from the cross of a female P. trichocarpa X P. deltoides hybrid (genotype æ52-225Æ) and a male P. deltoides (genotype æD124Æ) was obtained from the Department of Forestry at the University of Minnesota-Duluth as hardwood cuttings. After rooting, bud break and shoot elongation, fresh softwood terminal cuttings were harvested and placed in rooting media pellets (Jiffy Forestry Products, Lorain, OH) for two weeks. Rooted cuttings were planted in two gallon pots and grown for six weeks in ebb-and-flow benches in a greenhouse under long day conditions (16h light:8hr dark) and standard nutrient regime (HockingÆs Modified Complete Fertilizer, Cooke et al. 2003, Plant Cell and Environment 26: 757-770) supplemented with 25mM nitrogen (NH4NO3). Plants were distributed in the greenhouse in a partially balanced incomplete block design with three biological replications per genotype.

extract_protocol: At harvest, the main plant organs (stems, roots, leaves and sylleptic branches) were collected separately. Stems were further dissected into secondary xylem tissue and phloem/bark/immature xylem. Leaf, secondary xylem, and root tissue from two biological replicates of each genotype were selected for gene expression analysis. All tissue was flash-frozen in liquid nitrogen immediately after harvest and stored at -80░ Celsius (C) prior to lyophilization and subsequent RNA isolation.  RNA was isolated by a standard protocol described previously (Chang S, J. Puryear, J. Cairney 1993, A simple and efficent method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116).

tag: 25mM supplemental N, long day conditions


title: UF396_Xylem-Rep1