title: E.coli_stat_dynamic_1

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: ChIP-chip E.coli stationary phase, RNAP beta subunit without rifampicin treatment

hyb_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

data_processing: The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E.coli RNAP beta subunit ChIP DNA from stationary condition without rifampicin treatment

growth_protocol: E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation and harvested at stationary phase. (OD600nm ~ 1.5)

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. 6 uL of mouse antibody (NT63, Neoclone) was used to immunoprecipitate the chromatin complex of RNA polymerase subunit (rpoB) and DNA. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR.

treatment_protocol: Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by NT63 mouse antibody.

tag: test

value: ChIP DNA

tag: condition

tag: strain

tag: antibody

value: RNAP beta subunit (NT63)

source_name: Input DNA from stationary condition without rifampicin treatment

treatment_protocol: Cross-linked and sonicated chromatin complex of RNAP beta-subunit and DNA was immunoprecipitated by normal mouse IgG (Upstate) for the control (mock-IP).

tag: reference

value: Input DNA

value: IgG


title: E.coli_nitrogen_dynamic_1

status: Public on Nov 04 2009

type: genomic

state: CA

country: USA

description: ChIP-chip E.coli nitrogen limitation, RNAP beta subunit without rifampicin treatment

scan_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

molecule: genomic DNA

source_name: E.coli RNAP beta subunit ChIP DNA from nitrogen-limiting condition without rifampicin treatment

growth_protocol: E. coli MG1655 strain was cultured in W2 minimal medium (for nitrogen-limiting condition) at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6) (Powell, B. S. et al. J of Biol. Chem.270(9):4822)

source_name: Input DNA from nitrogen-limiting condition without rifampicin treatment


title: E.coli_stat_dynamic_2

label_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

value: stationary condition without rifampicin treatment


title: B806

type: RNA

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1870

hyb_protocol: Per manufacturer's recommendation

scan_protocol: Per manufacturer's recommendation

data_processing: RMA as implemented in Bioconductor package affy

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Osteosarcoma; B806

label_protocol: Per manufacturer's recommendation

extract_protocol: Per manufacturer's recommendation for trizol extraction

tag: alive-or-dead

value: A

tag: days-followup


title: B796

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1221

source_name: Human Osteosarcoma; B796


title: B802

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 386

source_name: Human Osteosarcoma; B802

value: D


title: B803

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1669

source_name: Human Osteosarcoma; B803


title: B799

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 352

source_name: Human Osteosarcoma; B799


title: pCMX_20% O2 vs. pCMX_2% O2, H1

city: Grenoble

first: Gaelle

last: Saint-Auret

address: 17 rue des martyrs

country: France

institute: CEA

description:
Simultaneous hybridization of Hep-1 and Hep-2 on H1 array.
Hep-1 is a technical replicate.

hyb_protocol: The Whole Human Genome Oligonucleotides Microarray 4x44K (G4112F) were purchased from Agilent technology. The hybridizations on these slides were performed using Gene expression Hybridization kit (Agilent technology).

scan_protocol: The hybridized microarrays were scanned with an Agilent G2505B scanner using PMT Cy3 XDR High 100% low 10% and PMT Cy5 XDR 100%, low 10% adjustments and 5µm resolution.

data_processing: Raw data were extracted using Agilent Feature Extraction 9.1.3 (Agilent technology) with GE2-v5_91_806 protocol and the grid 014850_D_20060807. The data are analyzed using the following parameters: correct background and signal biases (spatial detrend). The correction of dye biases was processed by Linear lowess.

source_name: HepG2 cells transfected by pCMX, 20% oxygen

label_protocol: Within each RNA preparation prepared as above, the target poly(A) mRNAs were labelled as follows : 500 nanogrammes of total RNAs were labelled using the Low RNA input linear amplification (Agilent Technologies). These RNAs were labelled by incorporation of cyanine 3- or cyanine 5- CTP. The reactions were purified using Rneasy Mini Kit from QIAgen. These labelled cRNA were quantified using Bioanalyzer 2100 (Agilent technology) and broken up into 50-200 mer nucleotides.

growth_protocol: HepG2 human hepatoma cells (American Type Culture Collection HB-8065) were cultured as monolayers at 37°C in a humidified 95% air/5% CO2 incubator. The culture medium used was a 1:1 mixture of DMEM and Ham-F12 media with Glutamax-I, supplemented with 10%(v/v) fetal bovine serum, 100µg/ml gentamycine and 2,5µg/ml fungizone (all from Invitrogen, San Diego, CA).

extract_protocol: Total RNA was isolated using TRIZOLTM LS reagent (Invitrogen).

tag: cell line

tag: transfection

value: pCMX (empty vector)

tag: culture oxygen

tag: culture time

tag: sample name

tag: sample type

value: control

source_name: HepG2 cells transfected by pCMX, 2% oxygen

treatment_protocol: Engineered HepG2 cells were 70-80% confluent before use. Hypoxic treatment was performed for 24h in sealed chambers, exactly as described in Chauvet et al BJ 2002, 364, 449-456. Final oxygen concentration of 2% was used.

value: 2% (hypoxic)


title: pCMX_20% O2 vs. pCMX_2% O2, H2

description:
Simultaneous hybridization of Hep-3 and Hep-4 on H2 array.
Hep-3 is a technical replicate.

treatment_protocol: Engineered HepG2 cells were 70-80% confluent before use. Hypoxic treatment was performed for 24h in sealed chambers, exactly as described in Chauvet et al BJ 2002, 364, 449-456.


title: E.coli_heat_dynamic_2

description: ChIP-chip E.coli heat-shock, RNAP beta subunit without rifampicin treatment

source_name: E.coli RNAP beta subunit ChIP DNA from heat-shocked condition without rifampicin treatment

growth_protocol: E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation. For heat-shock, culture was mix with pre-warmed medium (50 °C) and incubated at 45 °C for 10 min.

source_name: Input DNA from heat-shocked condition without rifampicin treatment


title: B795

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1024

source_name: Human Osteosarcoma; B795


title: E.coli_nitrogen_dynamic_2

value: nitrogen-limiting condition without rifampicin treatment


title: ELK1-siRNA transfected cells vs. mock transfected cells-siRNA2

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

description: ELK1 knock-down vs control

hyb_protocol: Samples were hybridized using Agilent's gene expression hybridization kit and wash buffers according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Agilent Feature Extraction Software (v 9.5) was used for data extraction.

source_name: MDA-MB-231 cell line

label_protocol: Samples labeled using Agilent Quick-Amp Labeling kit following manufacyurer's instructions

growth_protocol: MDA-MB-231 cells were growin in D10F medium and were transfected using LipofectamineTM 2000 (invitrogen)

extract_protocol: Total RNA extracted using mirVana™ miRNA Isolation Kit following manufacturer's instructions

value: 72hr post-transfection with ELK1-siRNA

value: 72hr after mock-transfection


title: NFYA-siRNA transfected cells vs. mock transfected cells-siRNA1

description: NFYA knock-down vs control

value: 72hr post-transfection with NFYA-siRNA


title: NFYA-siRNA transfected cells vs. mock transfected cells-siRNA2

description: NFYA knock-down vs control


title: E.coli_heat_dynamic_1

value: heat-shocked condition without rifampicin treatment


title: E.coli_log_rif_2

description: ChIP-chip E.coli logphase, RNAP beta subunit with rifampicin treatment

source_name: E.coli RNAP beta subunit ChIP DNA from mid-exponential condition with rifampicin treatment

growth_protocol: E. coli MG1655 strain was cultured in M9 complete medium at 37 °C with constant agitation and harvested at mid-exponential phase. (OD600nm ~ 0.6)

source_name: Input DNA from mid-exponential condition with rifampicin treatment


title: E.coli_log_rif_3

value: mid-exponential condition with rifampicin treatment


title: B794

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 1060

source_name: Human Osteosarcoma; B794


title: E.coli_log_rif_1


title: B792

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 1388

source_name: Human Osteosarcoma; B792


title: ELK1-siRNA transfected cells vs. mock transfected cells-siRNA1

description: ELK1 knock-down vs control


title: B790

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1758

source_name: Human Osteosarcoma; B790


title: B218

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 483

source_name: Human Osteosarcoma; B218


title: E.coli_log_dynamic_2

description: ChIP-chip E.coli logphase, RNAP beta subunit without rifampicin treatment

source_name: E.coli RNAP beta subunit ChIP DNA from mid-exponential condition without rifampicin treatment

source_name: Input DNA from mid-exponential condition without rifampicin treatment


title: MLN, PCV2 pig, 29 dpi, biological rep 4

city: Bellaterra

first: Anna

last: Tomas

state: Barcelona

address: campus UAB

department: Viral infections

country: Spain

institute: CReSA

description: Gene expression data of mediastinal lymph node of a pig inoculated with PCV2 at day 29

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using the Genechip Scanner 3000

data_processing: The data were analyzed with the Data Mining Tool (DMT) from Affymetrix. RMA was used as normalization method.

label: Biotin

organism: Sus scrofa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (One-Cycle Target Labeling kit, Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mediastinal lymph nodes were collected at necropsy, immediately frozen in liquid nitrogen and kept at -80ºC until usage

extract_protocol: Total RNA was extracted with the RiboPure kit (Ambion Cat #1924) according to the manufacturer's instructions.

treatment_protocol: 24 seven-day-old, CDCD piglets were used; a first group of pigs (n=8) was kept as un-inoculated controls and the rest of pigs (n=16) were oronasally inoculated with 105.2 TCID50 of the Burgos isolate of PCV2.

tag: cell type

value: mediastinal lymph node

tag: agent

value: Inoculated with PCV2

tag: age

value: 24 seven-day-old


title: Decoy-1 transfected vs. scrambled-1 transfected cells

description: Expression consequences of decoy vs scrambled oligos

tag: transfection time

value: 72hr post-transfection

tag: oligo

value: decoy caattGAAATTTTGagcaa

value: scrambled gtTtATAcAcTaaaGaTGa


title: Decoy-2 transfected vs. scrambled-2 transfected cells

value: decoy gctggAAAAAATTTaagac

value: scrambled aagATTgctAgAAgAaATc


title: B178

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 176

source_name: Human Osteosarcoma; B178

value: D


title: MLN, PCV2 pig, 29 dpi, biological rep 3

source_name: mediastinal lymph node of a pig inoculated with PCV2 at day 29


title: A816

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 3303

source_name: Human Osteosarcoma; A816

value: A


title: MLN, PCV2 pig, 29 dpi, biological rep 1


title: E.coli_log_dynamic_1

tag: test

value: ChIP DNA

tag: condition

value: mid-exponential condition without rifampicin treatment

value: RNAP beta subunit (NT63)

value: Input DNA

value: IgG


title: ec_nitrogen_2

description: This sample is of wild-type E. coli MG1655 under nitrogen-limiting condition. It is the second of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scan was performed with an Axon GenePix 4000B scanner by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to 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.).

source_name: E. coli K12 MG1655, W2 minimal medium, log phase

label_protocol: Labeling was performed with an amino-allyl indirect labeling protocol followed by a Dnase I fragmentation step.

extract_protocol: Total RNA was extracted using the RNeasy Plus 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 Thermo NanoDrop 1000.

tag: medium

value: W2 minimal medium

tag: growth phase

value: log phase

tag: genotype

value: Wild type


title: ec_nitrogen_3

description: This sample is of wild-type E. coli MG1655 under nitrogen-limiting condition. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: ec_nitrogen_1

description: This sample is of wild-type E. coli MG1655 under nitrogen-limiting condition. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: MLN, PCV2 pig, 29 dpi, biological rep 2

value: mediastinal lymph node

value: Inoculated with PCV2


title: Hs_OS-8

description: total RNA; biotin

tag: disease state

value: Tumor

tag: tissue

value: human osteosarcoma_OS-8


title: A504

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 2903

source_name: Human Osteosarcoma; A504

tag: alive-or-dead

tag: days-followup


title: Hs_OS-91

description: total RNA; biotin

value: human osteosarcoma_OS-91


title: MLN, PCV2 pig, 8 dpi, biological rep 2

description: Gene expression data of mediastinal lymph node of a pig inoculated with PCV2 at day 8

value: 24 seven-day-old


title: MLN, PCV2 pig, 8 dpi, biological rep 3

source_name: mediastinal lymph node of a pig inoculated with PCV2 at day 8


title: Hs_OS-84

description: total RNA; biotin

value: human osteosarcoma_OS-84


title: A509

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 625

source_name: Human Osteosarcoma; A509

value: D


title: MLN, PCV2 pig, 8 dpi, biological rep 1


title: A498

description: Human Osteosarcoma; AliveOrDead: D; DaysFollowUp: 2065

source_name: Human Osteosarcoma; A498


title: MLN, PCV2 pig, 5 dpi, biological rep 2

description: Gene expression data of mediastinal lymph node of a pig inoculated with PCV2 at day 5


title: MLN, PCV2 pig, 5 dpi, biological rep 3

source_name: mediastinal lymph node of a pig inoculated with PCV2 at day 5


title: ec_stat_2

description: This sample is of wild-type E. coli MG1655 under stationary condition. It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: E. coli K12 MG1655, M9 complete medium, stationary phase

value: M9 complete medium

value: stationary phase


title: E.coli_log_dynamic_3

value: ChIP DNA

value: mid-exponential condition without rifampicin treatment

tag: strain

tag: antibody

tag: reference


title: MLN, PCV2 pig, 5 dpi, biological rep 1

tag: cell type


title: stageIII colorectal cancer patient11 with no recurrence in validation phase

status: Public on Nov 05 2009

city: Suita

first: masakazu

last: miyake

state: Osaka

address: Yamadaoka 2-2

department: Gastroenterological Surgery

country: Japan

institute: Graduate School of Medicine, Osaka University

description: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -97°C until RNA extraction.

hyb_protocol: Hybridized for 16 h at 42 °C. Hybridization buffer and washing protocol was followed by the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

scan_protocol: ScanArray HT (PerkinElmer Japan Co., Ltd.) was used for scanning. Array images were analyzed with DNASIS Array V2.6(Hitachi Software Engineering Co., Ltd.).

data_processing: In each sample, the Cy5/Cy3 ratio values were log-transformed and global equalization to remove a deviation of the signal intensity between whole Cy3- and Cy5-fluorescence was performed by subtracting a median of all log (Cy5/Cy3) values from each log (Cy5/Cy3) value. Genes with missing values in more than 10% of samples were excluded from further analysis.

source_name: 40 Total RNAs mixture from normal colorectal mucosa labeled with Cyanine-3 (green).

label_protocol: Amino Allyl aRNA was synthesized by Amino Allyl MessageAmp aRNA Amplification Kit (Ambion).CyeDye coupling and fragmentation were performed using the protocol supplied by Hitachi Software Engineering Co., Ltd. (DNA Chip Research Inc. / AceGene website)

extract_protocol: Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

treatment_protocol: Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.

value: mixture of normal colorectal mucosa

source_name: Total RNA from primary colorectal cancer of stageIII patient with no recurrence labeled with Cyanine-5 (red).

value: stageIII colorectal cancer with no recurrence


title: Hs_OS-6

description: total RNA; biotin

value: human osteosarcoma_OS-6


title: ec_heat_2

description: This sample is of wild-type E. coli MG1655 under heat-shocked condition. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.

source_name: E. coli K12 MG1655, M9 complete medium, log phase, heat shock 45 °C, 10 min

value: log phase, heat shock 45 °C, 10 min


title: MLN, PCV2 pig, 2 dpi, biological rep 3

description: Gene expression data of mediastinal lymph node of a pig inoculated with PCV2 at day 2

tag: agent


title: Hs_OS-54

description: total RNA; biotin

value: human osteosarcoma_OS-54


title: ec_heat_3

description: This sample is of wild-type E. coli MG1655 under heat-shocked condition. It is the third of three biological replicates used in this experiment, each from separate cultures.

value: Wild type


title: ec_stat_1

description: This sample is of wild-type E. coli MG1655 under stationary condition. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: ec_logphase_3

description: This sample is of wild-type E. coli MG1655 under mid-exponential condition. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: E. coli K12 MG1655, M9 complete medium, log phase

value: log phase


title: ec_logphase_2

description: This sample is of wild-type E. coli MG1655 under mid-exponential condition. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Hs_OS-53

description: total RNA; biotin

value: Tumor

value: human osteosarcoma_OS-53


title: Hs_OS-4

description: total RNA; biotin

value: human osteosarcoma_OS-4


title: Hs_OS-44

description: total RNA; biotin

value: human osteosarcoma_OS-44


title: B793

description: Human Osteosarcoma; AliveOrDead: A; DaysFollowUp: 1686

source_name: Human Osteosarcoma; B793

value: A


title: Hs_OS-16A

description: total RNA; biotin

value: human osteosarcoma_OS-16A


title: Hs_OS-15

description: total RNA; biotin

value: human osteosarcoma_OS-15


title: MLN, PCV2 pig, 2 dpi, biological rep 1

source_name: mediastinal lymph node of a pig inoculated with PCV2 at day 2

value: mediastinal lymph node

value: Inoculated with PCV2

tag: age

value: 24 seven-day-old


title: MLN, PCV2 pig, 1 dpi, biological rep 2

description: Gene expression data of mediastinal lymph node of a pig inoculated with PCV2 at day 1


title: MLN, PCV2 pig, 2 dpi, biological rep 2


title: MLN, PCV2 pig, 1 dpi, biological rep 3

source_name: mediastinal lymph node of a pig inoculated with PCV2 at day 1


title: MLN, PCV2 pig, 1 dpi, biological rep 1


title: Hs_OS-1

description: total RNA; biotin

value: human osteosarcoma_OS-1


title: MLN, control pig, 29dpi, biological rep 4

description: Gene expression data of mediastinal lymph node of a control pig at day 29

value: Control


title: Wild type cortex 3

city: Cleveland

first: Donny

middle: D

last: Licatalosi

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

description: mouse wild type cortex

scan_protocol: Affymetrix GeneChip Operating Software (GCOS) v1.4; GeneChip Scanner 3000 7G.

data_processing: The average probe values used by ASPIRE version 2 were (RMA signal estimates from Expression Console 1.1). All exon (PSR) and junction (JUC) probe values were analysed by the second and third step of ASPIRE version 2. The median value of background probes with the same GC content was subtracted from each probe value. Probe values with high variability and weak signal were removed from analysis before calculating the median value of all probes within a probeset.

label: TdT (Affymetrix WT Sense Target Labeling Assay)

organism: Mus musculus

source_name: mouse wild type cortex

extract_protocol: Trizol Extraction

value: P10 cortex


title: Nova2 KO cortex 3

description: mouse Nova2 knockout cortex

hyb_protocol: Affymetrix WT Sense Target Labeling Assay

source_name: mouse Nova2 knockout cortex


title: Hs_OS-13

description: total RNA; biotin

value: human osteosarcoma_OS-13


title: Nova2 KO cortex 1

description: mouse Nova2 knockout cortex

label_protocol: Affymetrix WT Sense Target Labeling Assay


title: Nova2 KO cortex 2

description: mouse Nova2 knockout cortex


title: ec_logphase_1

description: This sample is of wild-type E. coli MG1655 under mid-exponential condition. It is the first of three biological replicates used in this experiment, each from separate cultures.

value: M9 complete medium


title: Wild type cortex 2

description: mouse wild type cortex


title: Hs_OS-10B

description: total RNA; biotin

value: human osteosarcoma_OS-10B


title: Hs_OS-12

description: total RNA; biotin

value: human osteosarcoma_OS-12


title: MLN, control pig, 29dpi, biological rep 3

source_name: mediastinal lymph node of a control pig at day 29


title: lymph node_2

description: total RNA; biotin

source_name: lymph node_2

value: Normal

value: lymph node_2


title: lymph node_1

description: total RNA; biotin

source_name: lymph node_1

value: lymph node_1


title: MSC-amplified

city: The Bronx

first: Eric

last: Bouhassira

address: 1300 Morris Park avenue

institute: Albert Einstein College of Medicine

description: genomic DNA was amplified about  200 fold (from 10ng to 2 ug ) using Qiagen repli-g kit

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
The S and G1 signals were normalized using a log2 transformation and 2 adjustable parameters per track: a and d
S = log 2 (signal + d) + a
d, a damping factor, was added to the signal to minimize large fluctuations of the log ratio when the signal is very weak. d=256 is usually a good value, but the damper was optimized for each channel by studying the histogram of the damped signal and normalizing the slope at the first inflexion point of the histogram. This reference point corresponds to the unreplicated regions of the genome for the S samples, and provides a good comparison relative to the G1 samples. We then adjusted a for every G1 track, so that the average value of Z across all probes is constant (=10). Finally, we fine-tuned the a of the S tracks, so that their lowest values in the genome (usually in the gene poor region on chromosome 16) matched the G1 tracks.

label_protocol: 1-4 µg genomic DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 or Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: DMEM_10% serum

extract_protocol: 1 million cells fixed with 70% ethanol and stained with propidium iodide were sorted acccording to cell cycle position and genomic DNA was extracted.

treatment_protocol: fixed with alcohol, stained with propidium iodide, sorted

value: mesenchymal stem cell

tag: cell cycle phase

value: S

growth_protocol: matrigel


title: MLN, control pig, 5dpi

description: Gene expression data of mediastinal lymph node of a control pig at day 5


title: MLN, control pig, 29dpi, biological rep 2


title: Wild type cortex 1

description: mouse wild type cortex


title: MLN, control pig, 29dpi, biological rep 1


title: MLN, control pig, 2dpi

description: Gene expression data of mediastinal lymph node of a control pig at day 2


title: MLN, control pig, 8dpi

description: Gene expression data of mediastinal lymph node of a control pig at day 8


title: liver_2

description: total RNA; biotin


title: MLN, control pig, 1dpi

description: Gene expression data of mediastinal lymph node of a control pig at day 1


title: liver_1

description: total RNA; biotin


title: MSC-rep1


title: Nova2 KO cortex 4

description: mouse Nova2 knockout cortex

scan_protocol: The scanning and image acquisition was done using Affymetrix GeneChip Operating Software (GCOS) v1.4. The scanner model is GeneChip Scanner 3000 7G.

data_processing: ArrayAssist (Stratagene); PLIER extended-antigenomic; DABG (p<0.05)


title: kidney_2

description: total RNA; biotin


title: H3-012706

description: total RNA; biotin

tag: cell line


title: kidney_1

description: total RNA; biotin


title: Nova2 KO cortex 3

description: mouse Nova2 knockout cortex


title: H2-012706

description: total RNA; biotin


title: Nova2 KO cortex 1

description: mouse Nova2 knockout cortex


title: H1-012706

description: total RNA; biotin


title: erythroblast-S3-rep1

description: no additional information

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

data_processing:
data was processed as decribed in text of article
The S and G1 signals were normalized using a log2 transformation and 2 adjustable parameters per track: a and d
S = log 2 (signal + d) + a
d, a damping factor, was added to the signal to minimize large fluctuations of the log ratio when the signal is very weak. d=256 is usually a good value, but the damper was optimized for each channel by studying the histogram of the damped signal and normalizing the slope at the first inflexion point of the histogram. This reference point corresponds to the unreplicated regions of the genome for the S samples, and provides a good comparison relative to the G1 samples. We then adjusted a for every G1 track, so that the average value of Z across all probes is constant (=10). Finally, we fine-tuned the a of the S tracks, so that their lowest values in the genome (usually in the gene poor region on chromosome 16) matched the G1 tracks.

growth_protocol: 35_days-FHB_14 days_liquid-culture

extract_protocol: 1 million cells fixedwith 70% ethanol, stained with propidium iodide were sorted acccording to cell cycle position and genomic DNA was extracted

value: erythroblast


title: erythroblast-S1-rep1

description: no additional information


title: erythroblast-S2-rep1

description: no additional information


title: hESC-G1control-rep1

description: no additional information

value: embryonic stem cells


title: Gene expression analysis of TT2-G9aflox/delta NPC/ASd9, +OHT, replicate 1

status: Public on Nov 03 2009

city: Tallahassee

first: Ichiro

last: Hiratani

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

description: submitted as of 9/6/09

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 labeled DNA samples (6 ug) were hybridized to a Nimblegen mouse expression microarray representing 42,586 transcripts (Roche NimbleGen Inc., 2006-08-03_MM8_60mer_expr).

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw data (i.e. from .pair files) were converted to gene-by-gene data of 42,586 transcripts using RMA algorithm in NimbleScan.

source_name: Total RNA extracted from TT2-G9aflox/delta NPC/ASd9, +OHT

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, RNA specimens were converted to double-stranded cDNA according to NimbleGen's instructions, and cDNA samples (1 ug each) were Cy3-labeled by Klenow reaction using end-labeled Cy3-random 9-mers.

extract_protocol: Total RNA was prepared using RNeasy Kit (QIAGEN), following the manufacturer's instructions.


title: Gene expression analysis of TT2-G9aflox/delta NPC/ASd9, +OHT, replicate 2

description: submitted as of 9/6/09


title: Wild type cortex 4

description: mouse wild type cortex


title: Wild type cortex 3

description: mouse wild type cortex


title: Gene expression analysis of TT2-G9aflox/delta NPC/ASd9, Mock, replicate 2

description: submitted as of 9/6/09

source_name: Total RNA extracted from TT2-G9aflox/delta NPC/ASd9, Mock


title: Wild type cortex 2

description: mouse wild type cortex


title: Gene expression analysis of TT2-G9aflox/delta NPC/ASd9, Mock, replicate 1

description: submitted as of 9/6/09


title: Gene expression analysis of TT2-G9aflox/delta ESC, +OHT, replicate 2

description: submitted as of 9/6/09

source_name: Total RNA extracted from TT2-G9aflox/delta ESC, +OHT


title: Wild type cortex 1

description: mouse wild type cortex


title: Nova2 KO cortex 2

description: mouse Nova2 knockout cortex


title: Gene expression analysis of TT2-G9aflox/delta ESC, Mock, replicate 2

description: submitted as of 9/6/09

source_name: Total RNA extracted from TT2-G9aflox/delta ESC, Mock


title: Gene expression analysis of TT2-G9aflox/delta ESC, Mock, replicate 1

description: submitted as of 9/6/09


title: MSC-wholeS-rep2

description: no additional information


title: hESC-wholeS-rep2

description: no additional information


title: erythroblast-wholeS-rep2

description: no additional information


title: erythroblast-wholeS-rep1

description: no additional information


title: hESC-wholeS-rep1

description: no additional information


title: E. coli 8624 WT

status: Public on Nov 02 2009

city: Baltimore

first: David

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
All protocols were done according to manufacturer's specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli

source_name: E. coli 8624

growth_protocol: Escherichia coli 8624 grown in DMEM

extract_protocol: Ambion RiboPure RNA Isolation

tag: Escherichia coli 8624 grown in DMEM


title: Arabidopsis plants treated with 1.6 mM Tween 20, collection time 2.5 h

city: Bochum

first: Gretel

middle: Mara

last: Hunzicker

state: NRW

address: Universitätstr. 150

department: Plant Physiology

country: Germany

institute: Ruhr-Universität

description: All the induction experiments in this study were performed at the same time of the day in the place were the plants were grown to avoid additional stresses and to eliminate any influence of circadian gene activity on results.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: leaf material from Arabidopsis thaliana plants

growth_protocol: For every experiment a total of three independent replicas (33 Arabidopsis thaliana Col-0 plants per experiment) were done. The plants used were growing under sterile conditions in 0.5 L glass jars containing MS medium (supplemented with vitamins and with 1% (w/v) sucrose and 0.8 % (w/v) agar). Growth occurred in a growth chamber with 8 h of light (150 ?E m-2 s-1 photosynthetically active radiation) and 16 h of darkness under controlled conditions (22?C to 24?C at day 18?C to 20?C at night and 70 to 90 % relative humidity).

extract_protocol: Total RNA from 1 g of leaf material was extracted with TRIzol? (Invitrogen, Karlsruhe, Germany). Three independently isolated RNA-samples were pooled for each experiment. RNA quality and quantity control, cRNA labeling, hybridizations, expression data normalization and analysis were performed in collaboration with Carsten M?and Thomas Altmann (Max-Planck-Institute for Molecular Plant Physiology, Golm) according to the Affymetrix manual and as described by M?et al. (2003).

treatment_protocol: The plants were sprayed with distilled water and the leave material was weighted and immediately frozen in liquid nitrogen. The harvesting time was 2.5 h after the treatment.

tag: Ecotype

tag: Age

value: 28 days


title: Arabidopsis plants treated with 1.6 mM Tween 20, collection time 1 h. Exp. IA


title: MSC-wholeS-rep1

description: no additional information


title: Arabidopsis plants treated distilled water, collection time 1 h. Exp. IA


title: Arabidopsis plants sprayed with distilled water, collection time 1 h. Exp. IB

description: All the experiments were conducted at the same day time in the morning (8.30 h). For every experiment a total of three independent replicas (33 Arabidopsis thaliana Col-0 plants per experiment) were done.

source_name: Leaf material from Arabidopsis thaliana plants

growth_protocol: The plants used were growing under sterile conditions in 0.5 L glass jars containing MS medium (supplemented with vitamins and with 1% (w/v) sucrose and 0.8 % (w/v) agar).

extract_protocol: The plant material was collected in a random way from the different glass jars, the samples were dried in tissue paper, weighted (1 g) and immediately frozen in liquid nitrogen. This complete procedure took place in less than 1 min. Total RNA extraction from every individual experiment was made with TRIzol® reagent (Invitrogen, Germany). Once the RNA quality of every independent induction experiment was satisfactory, the RNA samples were mixed. The samples were hybridized in collaboration with Dr. Carsten Müssig (MPI for Molecular Plant Physiology, Golm, Potsdam, Germany).

treatment_protocol: The samples were sprayed with distilled water


title: Arabidopsis treated with distilled water, collection time 2.5 h

growth_protocol: For every experiment a total of three independent replicas (33 Arabidopsis thaliana Col-0 plants per experiment) were done. The plants used were growing under sterile conditions in 0.5 L glass jars containing MS medium (supplemented with vitamins and with 1% (w/v) sucrose and 0.8 % (w/v) agar). Growth occurred in a growth chamber with 8 h of light (150 µE m-2 s-1 photosynthetically active radiation) and 16 h of darkness under controlled conditions (22°C to 24°C at day 18°C to 20°C at night and 70 to 90 % relative humidity).

extract_protocol: Total RNA from 1 g of leaf material was extracted with TRIzol® (Invitrogen, Karlsruhe, Germany). Three independently isolated RNA-samples were pooled for each experiment. RNA quality and quantity control, cRNA labeling, hybridizations, expression data normalization and analysis were performed in collaboration with Carsten Müssig and Thomas Altmann (Max-Planck-Institute for Molecular Plant Physiology, Golm) according to the Affymetrix manual and as described by Müssig et al. (2003).


title: Ecoli_ko_ubiE_1%_isobutanol_Sample2_TechRep2

city: Princeton

first: Mark

last: Brynildsen

state: NJ

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

description: Cells were grown in MOPS media/0.2% glucose and aerobic conditions.

hyb_protocol: Samples were hybridized as specified in the Corning UltraGAPS manual.  Slides were blocked and washed as specified in the Corning UltraGAPS manual.

scan_protocol: Slides were scanned immediately after washing with a Virtek/BioRad scanner.

data_processing: Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files.  The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

source_name: Ecoli ko-ubiE grown in MOPS

label_protocol: Indirect labeling with amino-allyl dUTP

extract_protocol: Qiagen RNeasy Midikit

source_name: Ecoli ko-ubiE grown in MOPS, 10 minutes after 1% isobutanol treatment

treatment_protocol: Treated with 1% vol/vol isobutanol 10 minutes prior to harvest


title: Ecoli_ko_ubiE_1%_isobutanol_Sample2_TechRep1


title: Arabidopsis plants sprayed with 1.6 mM Tween 20, collection time 1 h. Exp. IB

extract_protocol: The plant material was collected in a random way from the different glass jars, the samples were dried in tissue paper, weighted (1 g) and immediately frozen in liquid nitrogen. This complete procedure took place in less than 1 min. Total RNA extraction from every individual experiment was made with TRIzol? reagent (Invitrogen, Germany). Once the RNA quality of every independent induction experiment was satisfactory, the RNA samples were mixed. The samples were hybridized in collaboration with Dr. Carsten M?(MPI for Molecular Plant Physiology, Golm, Potsdam, Germany).


title: Ecoli_ko_ubiE_1%_isobutanol_Sample1_TechRep1


title: Ecoli_ko_ubiE_1%_isobutanol_Sample1_TechRep2


title: Cells transduced with vector expressing Mouse testis library (MCF10A LIB 2 Selected)

status: Public on Oct 21 2009

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Transduced with vector expressing Mouse testis library

hyb_protocol: 1500 ng of cRNA was hyb on mouse-6 for 16-20 hours. Array washing was performed using wash buffer; an high strincengy temp wash was performed at 55C for 30 minutes. Arrays were stained with SA-Cy3

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

data_processing: Data are summarized with beadstudio 1.5.1.3 and intentionally not normalized to preserve the asymmetry due to selection and enrichment of a limited number of transcripts.

label: biotin-SA Cy3

source_name: MCF20A LIB 2 Selected

label_protocol: cRNA synthesis was performed using the Illumina TotalPrep RNA amplification kit introducing  the following variations: 20 ug of total RNA using pFB specific primer starting from

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).


title: iwr1 mutant (replicate 2)

status: Public on Oct 13 2009

city: Burjassot

first: Paco

last: Estruch

state: Valencia

address: Dr. Moliner, 50

department: Dpt. Bioquimica i Biologia Molecular

institute: Universitat de Valencia

description: Hybridization on macrochip V4-L2.

hyb_protocol: Hybridization Solution was: 5X SSC, 5X Denhardt's, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 5X10exp6 dpm/mL of radioactive sample and hybridized for 42h. Washing conditions were: once at 65ºC for 20 min in 2X SSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2X SSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

data_processing: Raw image quantization/background subtracted provided as supplementary files. Data normalization described in PMID 15260981 (Molecular Cell, Volume 15, Issue 2, 303-313, 23 July 2004).

organism: Saccharomyces cerevisiae

source_name: iwr1 yeast mutant cells exponentially grown in YPD medium

label_protocol: About 40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP), oligo dT (500ng) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 42ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

extract_protocol: Cells were lysed with glass beads in LETS buffer, and total RNA was extracted with phenol and precipitated with 5M LiCl.

value: iwr1 mutant


title: iwr1 mutant (replicate 1)

description: Hybridization on macrochip V4-L2.


title: iwr1 mutant (replicate 3)

description: Hybridization on macrochip V4-L2.


title: Replication timing of TT2-G9aflox/delta NPC/ASd9, +OHT

description: submitted as of 9/6/09

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (6 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were labeled reciprocally were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of TT2-G9aflox/delta NPC/ASd9, +OHT

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: developmental stage

value: NPC, ASd9

source_name: Late-replicating DNA of TT2-G9aflox/delta NPC/ASd9, +OHT


title: Wild type (replicate 3)

description: Hybridization on macrochip V4-L2.

source_name: Wild type yeast cells exponentially grown in YPD medium

tag: genotype

value: Wild type


title: Wild type (replicate 2)

description: Hybridization on macrochip V4-L2.


title: Replication timing of TT2-G9aflox/delta NPC/ASd9, Mock

description: also used in Hiratani et al., PLoS Biology (2008) 6:e245 as TT2NPC

source_name: Early-replicating DNA of TT2-G9aflox/delta NPC/ASd9, Mock

source_name: Late-replicating DNA of TT2-G9aflox/delta NPC/ASd9, Mock


title: Wild type (replicate 1)

description: Hybridization on macrochip V4-L2.


title: heavy smoker 179

status: Public on Sep 15 2009

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

description: middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to cy-3 fluorescent dye.

scan_protocol: Arrays were scaned using BeadArray Reader (Illumina) and bead level data were extracted by BeadStudio Software (Illumina).

data_processing: Bead summary data were imported into R statistical environment (www.r-project.org) and normalized by quantile method in Lumi package. Only probes with detection p-value p<0.01 in more than 50% of arrays were included for further analyses (n=10,590). Differential gene expression between smokers and non-smokers was analysed in Limma package. Linear model was fitted for each gene given a series of arrays using lmFit fiction. Multiple testing correction was performed using Benjamini & Hochberg method.

source_name: term placenta

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: The middle parts of placenta sections were frozen in RNA Later solution (Ambion) and stored at –80°C until RNA isolation. Total RNA was extracted from the tissue using Rneasy Mini Kit (Qiagen) according to the manufacture instructions. Quality control was performed with Agilent 2100 Bioanalyser (Agilent) and only samples with the RIN above 7.0 were processed.

tag: age (years)

tag: status

value: smoker

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental volume (cm3)


title: light smoker 174

value: caesarean


title: non-smoker 168

value: non-smoker


title: Replication timing of TT2-G9aflox/delta ESC, +OHT

description: submitted as of 9/6/09

source_name: Early-replicating DNA of TT2-G9aflox/delta ESC, +OHT

value: ESC

source_name: Late-replicating DNA of TT2-G9aflox/delta ESC, +OHT


title: heavy smoker 170


title: non-smoker 167


title: non-smoker 173


title: non-smoker 175


title: non-smoker 171


title: non-smoker 177


title: non-smoker 176


title: non-smoker 178


title: non-smoker 166


title: non-smoker 164


title: non-smoker 163

value: not available

value: not avalaible


title: Replication timing of TT2-G9aflox/delta ESC, Mock

description: also used in Hiratani et al., PLoS Biology (2008) 6:e245 as TT2ESC

source_name: Early-replicating DNA of TT2-G9aflox/delta ESC, Mock

source_name: Late-replicating DNA of TT2-G9aflox/delta ESC, Mock


title: non-smoker 161


title: non-smoker 160


title: heavy smoker 162


title: non-smoker 159


title: non-smoker 154


title: non-smoker 153


title: non-smoker 155


title: light smoker 157


title: non-smoker 156


title: non-smoker 146


title: non-smoker 158


title: non-smoker 145


title: non-smoker 148


title: non-smoker 151


title: non-smoker 147


title: non-smoker 152


title: non-smoker 149


title: non-smoker 144


title: heavy smoker 150


title: non-smoker 141


title: non-smoker 143


title: non-smoker 142


title: non-smoker 140


title: light smoker 137


title: heavy smoker 139


title: non-smoker 138


title: ec_heat_1

description: This sample is of wild-type E. coli MG1655 under heat-shocked condition. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: E. coli K12 MG1655, M9 complete medium, log phase, heat shock 45 °C, 10 min

tag: medium

value: M9 complete medium

tag: growth phase

value: log phase, heat shock 45 °C, 10 min


title: non-smoker 136


title: non-smoker 135


title: non-smoker 134


title: non-smoker 130


title: non-smoker 132


title: heavy smoker 131


title: non-smoker 123


title: light smoker 133


title: non-smoker 124


title: non-smoker 129


title: non-smoker 122


title: non-smoker 127


title: non-smoker 128


title: non-smoker 121


title: non-smoker 126


title: non-smoker 120


title: non-smoker 118


title: non-smoker 117


title: non-smoker 125


title: non-smoker 119


title: non-smoker 116


title: heavy smoker 115


title: non-smoker 113


title: non-smoker 112


title: non-smoker 114


title: non-smoker 111


title: non-smoker 110


title: Brdu

status: Public on Sep 05 2009

city: Milano

first: Andrea

last: Cocito

state: MI

address: Via Adamello 16

department: Molecular Medicine Program

institute: IFOM Institute FIRC  of Molecular Oncology

description: Brdu wt SY2201 S

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]
TXT results were produced by GCOS using a custom CDF which summarizes probes into sets covering 50 basepairs ranges.
Submitter unable to obtain the CDF file.

label: Brdu-Brdu

source_name: IP fraction of Brdu wt SY2201 S

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YPD

extract_protocol: Extracton was performed as described in Katou et al., 2003.

treatment_protocol:
G1 synchronization was performed by α−factor treatment (2 μg/ml), S synchronization release from factor block in 200 mM HU, G1-G2 synchronization released from alpha factor block in nocodazole 15 μg/ml.
Glu: Strains were grown in YPD  (at 23 degree) containing 2% glucose as fermentable carbon source
Gal: Strains were grown in YP  plus 2% galactose as fermentable carbon source
HU: Strains were arrested in G1 and released in 0.2M HU in YPD.
HU-Rel: Strains were arrested in G1 and released in 0.2M HU for 90'.  Then cells HU was washed away and cells released in a new YPD medium.
37C: Strains were grown in YPD at 37 degree

tag: strain

tag: phase

source_name: SUP of Brdu wt SY2201 S


title: Rpb3-37C

description: Rpb3-PK wt CY8519 S 37C

source_name: IP fraction of Rpb3-PK wt CY8519 S 37C

tag: treatment

source_name: SUP of Rpb3-PK wt CY8519 S 37C


title: Hmo1-G2-37C

description: Hmo1-PK wt CY8516 G2 37C

source_name: IP fraction of Hmo1-PK wt CY8516 G2 37C

source_name: SUP of Hmo1-PK wt CY8516 G2 37C


title: Rpb3-CY8641-37C

description: Rpb3-PK mut top2-1 CY8641 S 37C

source_name: IP fraction of Rpb3-PK mut top2-1 CY8641 S 37C

source_name: SUP of Rpb3-PK mut top2-1 CY8641 S 37C


title: Hmo1-CY8599-37C

description: Hmo1-PK mut top2-1 CY8599 S 37C

source_name: IP fraction of Hmo1-PK mut top2-1 CY8599 S 37C

source_name: SUP of Hmo1-PK mut top2-1 CY8599 S 37C


title: Rpb3-CY8642-37C

description: Rpb3-PK mut top2-1hmo1D CY8642 S 37C

source_name: IP fraction of Rpb3-PK mut top2-1hmo1D CY8642 S 37C

source_name: SUP of Rpb3-PK mut top2-1hmo1D CY8642 S 37C


title: Rpb3-CY8640-37C

description: Rpb3-PK mut hmo1D CY8640 S 37C

source_name: IP fraction of Rpb3-PK mut hmo1D CY8640 S 37C

source_name: SUP of Rpb3-PK mut hmo1D CY8640 S 37C


title: Hmo1-CY8599-G2-37C

description: Hmo1-PK mut top2-1 CY8599 G2 37C

source_name: IP fraction of Hmo1-PK mut top2-1 CY8599 G2 37C

source_name: SUP of Hmo1-PK mut top2-1 CY8599 G2 37C


title: Hmo1-37C

description: Hmo1-PK wt CY8516 S 37C

source_name: IP fraction of Hmo1-PK wt CY8516 S 37C

source_name: SUP of Hmo1-PK wt CY8516 S 37C


title: non-smoker 102

source_name: term placenta


title: Top2-CY8478-37C

description: Top2-Flag mut hmo1D CY8478 S 37C

source_name: IP fraction of Top2-Flag mut hmo1D CY8478 S 37C

source_name: SUP of Top2-Flag mut hmo1D CY8478 S 37C


title: Top2-37C

description: Top2-Flag wt CY7315 S 37C

source_name: IP fraction of Top2-Flag wt CY7315 S 37C

source_name: SUP of Top2-Flag wt CY7315 S 37C


title: non-smoker 107


title: non-smoker 109


title: non-smoker 106


title: non-smoker 103


title: non-smoker 104


title: light smoker 105


title: non-smoker 101


title: Htz1

description: Htz1-Flag wt SY2512 S

data_processing:
BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]
TXT results were produced by GCOS using a custom CDF which summarizes probes into sets covering 50 basepairs ranges.
Submitter unable to obtain the raw data (.CEL) file for this Sample nor the CDF file.

source_name: IP fraction of Htz1-Flag wt SY2512 S

source_name: SUP of Htz1-Flag wt SY2512 S


title: non-smoker 108


title: Hmo1-3c2

description: Hmo1-PK wt CY8516 S (Fig. 3c2)

source_name: IP fraction of Hmo1-PK wt CY8516 S (Fig. 3c2)

source_name: SUP of Hmo1-PK wt CY8516 S (Fig. 3c2)


title: H2A-CY8423-37C

description: H2A mut top2-1 CY8423 37C

source_name: IP fraction of H2A mut top2-1 CY8423 37C

tag: chip antibody

value: anti-H2A (From A. Verreault's lab)

source_name: SUP of H2A mut top2-1 CY8423 37C


title: Hmo1-G2

description: Hmo1-PK wt CY8516 G2

source_name: IP fraction of Hmo1-PK wt CY8516 G2

source_name: SUP of Hmo1-PK wt CY8516 G2


title: Top2

description: Top2-Flag wt CY8592 S GLU

source_name: IP fraction of Top2-Flag wt CY8592 S GLU

value: Anti-Flag M2 (Sigma)

value: S

value: GLU

source_name: SUP of Top2-Flag wt CY8592 S GLU


title: Top2-GAL

description: Top2-Flag wt CY8592 S GAL

source_name: IP fraction of Top2-Flag wt CY8592 S GAL

value: GAL

source_name: SUP of Top2-Flag wt CY8592 S GAL


title: Rpb3-G1

description: Rpb3-PK wt CY8519 G1

source_name: IP fraction of Rpb3-PK wt CY8519 G1

source_name: SUP of Rpb3-PK wt CY8519 G1


title: Rpb3

description: Rpb3-PK wt CY8592 S GLU

source_name: IP fraction of Rpb3-PK wt CY8592 S GLU

value: anti-V5-TAG (Abd serotec)

source_name: SUP of Rpb3-PK wt CY8592 S GLU


title: Hmo1

description: Hmo1-PK wt CY8516 S

source_name: IP fraction of Hmo1-PK wt CY8516 S

source_name: SUP of Hmo1-PK wt CY8516 S


title: Gene expression analysis of TT2-G9aflox/delta ESC, +OHT, replicate 1

description: submitted as of 9/6/09

source_name: Total RNA extracted from TT2-G9aflox/delta ESC, +OHT

tag: cell line


title: Rpb3-GAL

description: Rpb3-PK wt CY8592 S GAL

source_name: IP fraction of Rpb3-PK wt CY8592 S GAL

source_name: SUP of Rpb3-PK wt CY8592 S GAL


title: Hmo1-G1

description: Hmo1-PK wt CY8516 G1

source_name: IP fraction of Hmo1-PK wt CY8516 G1

source_name: SUP of Hmo1-PK wt CY8516 G1


title: small airways, non-smoker 022

status: Public on Jul 13 2009

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: age

tag: sex

value: M

tag: ethnic group

value: white

tag: smoking status


title: small airways, non-smoker 066

value: black


title: small airways, smoker 176

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

value: smoker, 33 pack-years


title: small airways, smoker 159

value: F

value: smoker, 3.8 pack-years


title: small airways, smoker 155

value: smoker, 7.6 pack-years


title: small airways, smoker 195

value: smoker, 38 pack-years


title: small airways, smoker 136

value: hispanic

value: smoker, 26 pack-years


title: small airways, smoker 164

value: smoker, 44.3 pack-years


title: small airways, smoker 177


title: small airways, non-smoker 083

value: non-smoker


title: stageII colorectal cancer patient12 with no recurrence in validation phase

status: Public on Jul 02 2009

description: no additional information

source_name: 40 Total RNA mixture from normal colorectal mucosa labeled with Cyanine-3 (green).

treatment_protocol: no treatment

tag: Tissue

value: mixture of normal colorectal mucosa

source_name: Total RNA from primary colorectal cancer of stageII patient with no recurrence labeled with Cyanine-5 (red).

extract_protocol:
Tumor samples were collected within 30 minutes from the time of resection, cut in 5-mm cubes, and immediately stored with RNAase inhibitor and stored at -85°C until RNA extraction.
Total RNA was purified from the clinical samples utilizing TRIzol reagent (Invitrogen, San Diego, CA) using the protocol supplied by the manufacturer.

value: stageII colorectal cancer with no recurrence


title: small airways, smoker 122

value: smoker, 3 pack-years


title: small airways, smoker 123

value: smoker, 22.5 pack-years


title: small airways, smoker 120

value: smoker, 30 pack-years


title: small airways, smoker 087

value: M


title: small airways, non-smoker 050


title: small airways, smoker 130

value: white

value: smoker, 12 pack-years


title: small airways, smoker 134

value: smoker, 20 pack-years


title: small airways, smoker 102

value: F

value: smoker, 45 pack-years


title: small airways, non-smoker 047


title: Never Smoker 5 Sample 311

status: Public on Apr 10 2009

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: RNA isolated from bronchial epithelial cells obtained during bronchoscopy

hyb_protocol: Affymetrix Suggested Protocol

scan_protocol: Affymetrix Suggested Protocol

data_processing: MAS5 generated expression value

source_name: Bronchial epithelium, never smoker

label_protocol: Affymetrix Suggested Protocol

extract_protocol: RNA was extracted by using TRIzol Reagent (Invitrogen) according to the manufacturer's protocol

tag: Never Smoker


title: small airways, non-smoker 065

value: black


title: small airways, non-smoker 039


title: small airways, non-smoker 048


title: Never Smoker 1 Sample 293


title: Never Smoker 2 Sample 254

description: RNA isolated from bronchial epithelial cells obtained during bronchscopy


title: Smoker with suspect lung cancer Sample 180

status: Public on Mar 06 2007

description: RNA isolated from bronchial epithelial cells obtained during time of clinical bronchoscopy of cigarette smoking patients with suspect lung cancer

data_processing: RMA (Robust Multichip Average) generated expression value

source_name: Bronchial Epithelium

tag: Sample from smoker with suspect lung cancer


title: Current Smoker 4 Sample 292

source_name: Bronchial epithelium, current smoker

tag: Current Smoker


title: Smoker with suspect lung cancer Sample 179


title: small airways, non-smoker 001

status: Public on Dec 19 2008

description: Comparison of gene expression in airway epithelial cells of normal non-smokers, phenotypic normal smokers, smokers with early COPD, and smokers with COPD.


title: Current Smoker 1 Sample 283


title: Sample_286_current smoker without cancer

data_processing: MAS5.0 Scaled 100 generated expression value

source_name: current smoker without cancer

tag: tissue

value: Bronchial Epithelium

value: Female

tag: race

value: AFA

tag: pkyrs

tag: history

value: current smoker without cancer

tag: status

value: SNC


title: Current Smoker 5 Sample 307


title: Smoker NOT diagnosed with cancer Sample 317

tag: Sample from smoker NOT diagnosed with cancer

tag: gender

value: CAU

value: No Cancer

value: quit less than 10 years

tag: packyears

value: non-diagnostic

value: Medium


title: Smoker NOT diagnosed with cancer Sample 286

value: OTHER

value: Low


title: Smoker NOT diagnosed with cancer Sample 265


title: Smoker with suspect lung cancer Sample 251


title: Smoker NOT diagnosed with cancer Sample 292

value: M


title: Smoker NOT diagnosed with cancer Sample 296


title: Smoker NOT diagnosed with cancer Sample 304

value: High


title: Smoker NOT diagnosed with cancer Sample 316


title: Smoker NOT diagnosed with cancer Sample 301


title: Smoker NOT diagnosed with cancer Sample 263

value: F


title: Smoker NOT diagnosed with cancer Sample 244


title: Smoker with suspect lung cancer Sample 295


title: Smoker NOT diagnosed with cancer Sample 326

value: quit for 10 years or greater


title: Smoker NOT diagnosed with cancer Sample 119


title: Smoker NOT diagnosed with cancer Sample 262


title: Smoker with suspect lung cancer Sample 294


title: Smoker NOT diagnosed with cancer Sample 300


title: Smoker NOT diagnosed with cancer Sample 307


title: Smoker NOT diagnosed with cancer Sample 309


title: Smoker NOT diagnosed with cancer Sample 282


title: Smoker diagnosed with cancer Sample 302

tag: Sample from smoker diagnosed with cancer

value: Cancer

value: diagnostic


title: Smoker diagnosed with cancer Sample 285

tag: age


title: Smoker diagnosed with cancer Sample 312


title: Smoker diagnosed with cancer Sample 321


title: Smoker diagnosed with cancer Sample 201


title: Smoker diagnosed with cancer Sample 308


title: Smoker diagnosed with cancer Sample 297


title: Smoker diagnosed with cancer Sample 252


title: Smoker diagnosed with cancer Sample 315


title: Smoker diagnosed with cancer Sample 274


title: Smoker diagnosed with cancer Sample 215


title: Smoker diagnosed with cancer Sample 325


title: Smoker diagnosed with cancer Sample 299


title: Jurkat+Globin, cDNA target, replicate 3

status: Public on Sep 08 2006

city: Lyngby

first: Aron

middle: C

last: Eklund

address: Kemitorvet, Building 208

department: Center for Biological Sequence Analysis

country: Denmark

institute: Technical University of Denmark

description: Jurkat + Globin RNA, from GeneChip Globin-Reduction RNA Controls (Affymetrix P/N 900586)

hyb_protocol: cDNA was hybridized according to the Ovation Biotin RNA Amplification and Labeling System User Guide (rev. 1, NuGEN Technologies). Briefly, cDNA was hybridized at 10 ng/ul for 18 hours at 45 C.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000.

data_processing: The data were analyzed with the MAS 5 algorithm in the R statistical environment using default settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Jurkat cells, hemoglobin spikes added

label_protocol: Biotinylated cDNA was prepared using the Ovation Biotin System (NuGEN Technologies, Inc.) from 50 ng starting RNA.

value: T-lymphocyte leukemia cell line


title: Smoker diagnosed with cancer Sample 271


title: Jurkat, cDNA target, replicate 3

description: Jurkat RNA, from GeneChip Globin-Reduction RNA Controls (Affymetrix P/N 900586)

source_name: Jurkat cells


title: Smoker diagnosed with cancer Sample 322


title: Jurkat, cDNA target, replicate 2


title: Smoker diagnosed with cancer Sample 328


title: Jurkat+Globin, cRNA target, replicate 3

hyb_protocol: cRNA was hybridized according to the GeneChip Expression Analysis Technical Manual (rev. 4, Affymetrix).  Briefly, cRNA was hybridized at 50 ng/ul for 16 hours at 45 C.

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II kit (Ambion).


title: Jurkat+Globin, cDNA target, replicate 1


title: Smoker diagnosed with cancer Sample 290


title: Jurkat+Globin, cRNA target, replicate 2


title: Jurkat, cRNA target, replicate 2


title: Jurkat, cDNA target, replicate 1


title: Jurkat, cRNA target, replicate 3


title: Jurkat, cRNA target, replicate 1


title: Jurkat+Globin, cRNA target, replicate 1


title: Smoker diagnosed with cancer Sample 209

status: Public on Feb 27 2006


title: Smoker diagnosed with cancer Sample 243


title: Smoker diagnosed with cancer Sample 216


title: Smoker diagnosed with cancer Sample 236


title: Smoker diagnosed with cancer Sample 231


title: Smoker diagnosed with cancer Sample 213


title: Smoker diagnosed with cancer Sample 233


title: Smoker diagnosed with cancer Sample 235


title: Smoker diagnosed with cancer Sample 212


title: Smoker diagnosed with cancer Sample 219


title: Smoker diagnosed with cancer Sample 214


title: Smoker diagnosed with cancer Sample 221


title: Smoker diagnosed with cancer Sample 208


title: Smoker diagnosed with cancer Sample 234


title: Smoker diagnosed with cancer Sample 202


title: Smoker diagnosed with cancer Sample 237


title: Smoker diagnosed with cancer Sample 203


title: Smoker diagnosed with cancer Sample 239


title: Smoker diagnosed with cancer Sample 200


title: Smoker NOT diagnosed with cancer Sample 247


title: Smoker NOT diagnosed with cancer Sample 223


title: Smoker NOT diagnosed with cancer Sample 220


title: Smoker diagnosed with cancer Sample 229


title: Smoker diagnosed with cancer Sample 211


title: Smoker diagnosed with cancer Sample 228


title: Smoker NOT diagnosed with cancer Sample 241


title: Smoker NOT diagnosed with cancer Sample 101


title: Smoker NOT diagnosed with cancer Sample 238


title: Smoker NOT diagnosed with cancer Sample 246


title: Smoker NOT diagnosed with cancer Sample 225


title: Smoker NOT diagnosed with cancer Sample 196


title: Smoker NOT diagnosed with cancer Sample 151


title: Smoker NOT diagnosed with cancer Sample 240


title: Smoker NOT diagnosed with cancer Sample 195


title: Smoker NOT diagnosed with cancer Sample 173


title: Smoker NOT diagnosed with cancer Sample 140


title: Smoker NOT diagnosed with cancer Sample 226


title: Smoker NOT diagnosed with cancer Sample 207


title: Smoker NOT diagnosed with cancer Sample 113


title: Smoker NOT diagnosed with cancer Sample 109


title: Smoker NOT diagnosed with cancer Sample 134


title: Smoker NOT diagnosed with cancer Sample 112


title: Smoker NOT diagnosed with cancer Sample 176


title: Smoker NOT diagnosed with cancer Sample 185


title: Smoker NOT diagnosed with cancer Sample 128


title: Smoker NOT diagnosed with cancer Sample 120


title: Smoker NOT diagnosed with cancer Sample 147


title: Smoker NOT diagnosed with cancer Sample 161


title: Smoker NOT diagnosed with cancer Sample 110


title: Smoker NOT diagnosed with cancer Sample 141


title: Smoker NOT diagnosed with cancer Sample 107


title: Smoker NOT diagnosed with cancer Sample 125


title: Smoker NOT diagnosed with cancer Sample 157


title: Smoker NOT diagnosed with cancer Sample 143


title: Smoker NOT diagnosed with cancer Sample 106


title: Smoker diagnosed with cancer Sample 222


title: Smoker NOT diagnosed with cancer Sample 116


title: Smoker NOT diagnosed with cancer Sample 124


title: Smoker NOT diagnosed with cancer Sample 104


title: Smoker NOT diagnosed with cancer Sample 102


title: Jurkat+Globin, cDNA target, replicate 2


title: Smoker NOT diagnosed with cancer Sample 86


title: Smoker NOT diagnosed with cancer Sample 56


title: Smoker NOT diagnosed with cancer Sample 131


title: Smoker NOT diagnosed with cancer Sample 76


title: Smoker NOT diagnosed with cancer Sample 73


title: Smoker NOT diagnosed with cancer Sample 98


title: Smoker NOT diagnosed with cancer Sample 89


title: Smoker NOT diagnosed with cancer Sample 75


title: Smoker NOT diagnosed with cancer Sample 162


title: Smoker NOT diagnosed with cancer Sample 92


title: Smoker NOT diagnosed with cancer Sample 69


title: Smoker NOT diagnosed with cancer Sample 97


title: Smoker NOT diagnosed with cancer Sample 61


title: Smoker NOT diagnosed with cancer Sample 81


title: Smoker NOT diagnosed with cancer Sample 95


title: Smoker NOT diagnosed with cancer Sample 85


title: Smoker NOT diagnosed with cancer Sample 84


title: Smoker NOT diagnosed with cancer Sample 82


title: Smoker NOT diagnosed with cancer Sample 58


title: Smoker NOT diagnosed with cancer Sample 74


title: Smoker NOT diagnosed with cancer Sample 72


title: Smoker NOT diagnosed with cancer Sample 87


title: Smoker NOT diagnosed with cancer Sample 99


title: Smoker NOT diagnosed with cancer Sample 77


title: Smoker NOT diagnosed with cancer Sample 79


title: Smoker NOT diagnosed with cancer Sample 68


title: Smoker NOT diagnosed with cancer Sample 83


title: Smoker NOT diagnosed with cancer Sample 88


title: Smoker NOT diagnosed with cancer Sample 67


title: Smoker diagnosed with cancer Sample 270


title: Smoker NOT diagnosed with cancer Sample 71


title: Smoker NOT diagnosed with cancer Sample 63


title: Smoker diagnosed with cancer Sample 269


title: Smoker diagnosed with cancer Sample 275


title: Smoker NOT diagnosed with cancer Sample 80


title: Smoker diagnosed with cancer Sample 255


title: Smoker diagnosed with cancer Sample 257


title: Smoker diagnosed with cancer Sample 281


title: Smoker diagnosed with cancer Sample 279


title: Smoker diagnosed with cancer Sample 273


title: Smoker diagnosed with cancer Sample 258


title: Smoker diagnosed with cancer Sample 266


title: Smoker diagnosed with cancer Sample 187


title: Smoker diagnosed with cancer Sample 199


title: Smoker diagnosed with cancer Sample 280


title: Smoker diagnosed with cancer Sample 267


title: Smoker diagnosed with cancer Sample 150


title: Smoker diagnosed with cancer Sample 192


title: Smoker diagnosed with cancer Sample 175


title: Smoker diagnosed with cancer Sample 156


title: Smoker diagnosed with cancer Sample 159


title: Smoker diagnosed with cancer Sample 177


title: Smoker diagnosed with cancer Sample 184


title: Smoker diagnosed with cancer Sample 163


title: Smoker NOT diagnosed with cancer Sample 121


title: Smoker diagnosed with cancer Sample 168


title: Smoker diagnosed with cancer Sample 190


title: Smoker diagnosed with cancer Sample 178


title: Smoker diagnosed with cancer Sample 160


title: Smoker diagnosed with cancer Sample 197


title: Smoker diagnosed with cancer Sample 154


title: Smoker diagnosed with cancer Sample 193


title: Smoker diagnosed with cancer Sample 188


title: Smoker diagnosed with cancer Sample 181


title: Smoker diagnosed with cancer Sample 174


title: Smoker diagnosed with cancer Sample 206


title: Smoker NOT diagnosed with cancer Sample 172


title: Smoker diagnosed with cancer Sample 152


title: Smoker diagnosed with cancer Sample 155


title: Smoker diagnosed with cancer Sample 204


title: Smoker diagnosed with cancer Sample 148


title: Smoker diagnosed with cancer Sample 198


title: Smoker diagnosed with cancer Sample 145


title: Smoker diagnosed with cancer Sample 117


title: Smoker diagnosed with cancer Sample 138


title: Smoker diagnosed with cancer Sample 146


title: Smoker diagnosed with cancer Sample 115


title: Smoker diagnosed with cancer Sample 135


title: Smoker diagnosed with cancer Sample 114


title: Smoker diagnosed with cancer Sample 123


title: Smoker diagnosed with cancer Sample 136


title: Smoker diagnosed with cancer Sample 133


title: Smoker diagnosed with cancer Sample 126


title: Smoker NOT diagnosed with cancer Sample 250


title: Smoker diagnosed with cancer Sample 137


title: Smoker diagnosed with cancer Sample 144


title: Smoker diagnosed with cancer Sample 122


title: Smoker diagnosed with cancer Sample 142


title: Smoker diagnosed with cancer Sample 139


title: Smoker diagnosed with cancer Sample 130


title: Smoker diagnosed with cancer Sample 62


title: Smoker diagnosed with cancer Sample 57


title: SCARKO d 10 (3)

status: Public on Oct 04 2005

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
RNA from 1 testis from three 10 day old control (AMHCre) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor

hyb_protocol: After purification (GeneChip Sample Cleanup Module, Affymetrix), yield (30–120 µg) and purity (260/280 and 260/230 nm ratios, >1.8) of the labeled amplified RNA were analyzed, 20 µg quality-controlled amplified RNA was fragmented by alkaline hydrolysis and resuspended with control spikes in 300 µl hybridization buffer (Eukaryotic Hybridization Control Kit, Affymetrix).  Of this probe solution, 200 µl was used for hybridization in a rotisserie oven at 45 C.

scan_protocol: After hybridization, gene chips were washed and stained in the GeneChip Fluidics Workstation 400 (Affymetrix) using the EukGE-WS2v4 protocol and subsequently scanned with the GeneChip Scanner 3000 (Affymetrix). Image analysis was performed by use of Affymetrix GeneChip operating software.

data_processing: Expression values were computed with the Affymetrix Microarray Suite (MAS) 5.0 software. The amount of transcripts in a sample that scored present, absent, or marginally detectable was assessed, also with the MAS 5.0 software.

source_name: testis

label_protocol: Before target synthesis, RNA extracts from one testis of three control or three SCARKO littermates were pooled, creating paired control and SCARKO samples optimally adjusted for potential variation between litters. Five micrograms of polyadenylated RNA from each pool was reverse transcribed into double-stranded DNA with a polydeoxythymidine-T7 primer using SuperScript II RT, ribonuclease H, and DNA polymerase I (Invitrogen Life Technologies, Inc., Carlsbad, CA). From this double-stranded DNA, biotin-labeled target aRNA was generated in a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit (Affymetrix, High Wycombe, UK).

extract_protocol:
Whole testes were obtained from animals at different ages depending on the experiment. Immediately after removal, testis samples
were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer (Kontes Co., Vineland, NJ). Thereafter, RNA was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer’s instructions, encompassing an on-column deoxyribonuclease I (DNase I) treatment of the RNA. For quantitative RT-PCR analyses, 5ng luciferase mRNA (Promega Corp., Madison, WI) were added to each testis sample before RNA preparation as an external standard.
The quality of all testis RNA samples was monitored by measuring the 260/280 and 260/230 nm ratios with a Nano-Drop spectrophotometer (NanoDrop Technologies, Centreville, DE) and by means of the Agilent 2100 BioAnalyzer (Agilent, Palo Alto, CA). Only RNA showing no signs of degradation or impurities (260/280 and 260/230 nm ratios, larger than 1.8) was considered suitable for microarray analysis.


title: SCARKO d10 (1)


title: Control d10 (3)

description:
RNA from 1 testis from three 10 day old Sertoli cell-selective androgen receptor knockout (SCARKO) mice. Immediately after removal, testis samples were snap-frozen and stored in liquid nitrogen. Before RNA extraction, testis samples were weighed and homogenized in a Dounce homogenizer. Thereafter RNA was isolated with the QIAGEN RNeasy Kit (Chatsworth, CA) according to the manufacturers instructions, encompassing an on-column DNaseI-treatment of the RNA.
Keywords = SCARKO
Keywords = testis
Keywords = spermatogenesis
Keywords = androgens
Keywords = microarray
Keywords = Pem
Keywords = serine protease inhibitor


title: Control d10 (2)


title: Smoker NOT diagnosed with cancer Sample 283

description: RNA isolated from Bronchial Epithelial cells obtained during time of bronchoscopy

data_processing: RMA generated expression value


title: SCARKO d10 (2)


title: Control d10 (4)


title: Control d10 (1)


title: SCARKO d10 (4)


title: MCC Patient 159

status: Public on Nov 14 2009

city: Nashville

first: Pengcheng

last: Lu

state: TN

address: 2200 Pierce Avenue

institute: Vanderbilt University

description: Gene expression

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: Bioconductor's affy package was used for RMA normalization and raw data processing using default settings for background correction and normalization. Cox regression hazards model was applied to the processed data using the survival package. All analyses were performed using R software.

source_name: Moffitt Cancer Center

label_protocol: Standard Affymetrix protocols were used.

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

value: male

tag: ethnicity

value: caucasian

tag: grade

value: 2 - Moderately differentiated (MD)

tag: overall_event (death from any cause)

value: death

tag: dss_event (disease specific survival; death from cancer)

tag: dfs_event (disease free survival; cancer recurrence)

tag: overall survival follow-up time


title: Wild type + NaClO3- (20mM)  rep2

status: Public on Nov 13 2009

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: Biological replicate 2

hyb_protocol: 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina, USA) as per manufacturer specifications.

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

data_processing: The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina, USA) and normalized using the Cross-correlation method (Chua et al., 2006). Differentially expressed transcripts were identified based on the mean Log2 fold change in expression values compared to the wild type ES cell controls with a cutoff at 1.5-fold change. Reference: Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: Wild type + NaClO3- (20mM)

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

growth_protocol: Cells were cultured on gelatin coated plates in Glascow MEM (Sigma-Aldrich) supplemented with 15% FBS (Hyclone), 1000 IU/ml LIF, 2-mercaptoethanol, and Non-Essential Amino Acids (Gibco). Medium was changed daily and cells passaged every second day.

extract_protocol: Total RNA was extracted from 3 biological replicates of wild-type and Ndst1/2 - /- ES cells subjected to NaCIO3-, SU5402 or control treatments using the RNeasy Mini kit (Qiagen, Germany) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent, USA) using the RNA 6000 Nano Chip kit (Agilent, USA) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

treatment_protocol: Cells were treated 24h with either heparan sulfation inhibitor (NaClO3-, 20mM) or FGFR inhibitor (SU5402, 5μM)

tag: cell line

value: Wild type ES cells

tag: treatment

value: NaClO3- (20mM) 24 hours


title: Control_line6_3

status: Public on Nov 12 2009

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: SY5Y cells overexpressing empty vector

hyb_protocol: Manufacturer's instructions

scan_protocol: Manufacturer's instructions

data_processing: Quantile normalization; please see associated published manuscript

source_name: SY5Y cells, line 6, control 3

label_protocol: Manufacturer's instructions

extract_protocol: Qiagen RNeasy kit


title: Liver_myocardial ischemia-reperfusion_24hour_rep4

city: Kanazawa

first: Hiroshi

last: Ootsuji

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Disease Control and Homeostasis

institute: Kanazawa University Graduate School of Medical Science

description: Liver or heart samples were amplified individually without mixing. As a reference for hybridization, we used mixed RNA samples from the sham group at various time-points. Test and reference samples were labeled with fluorescent Cy5 and Cy3, respectively, mixed, and hybridized on a microarray. Supplementary txt file: our nomalized values are in column AI. But, if signal intensity of Cy3 or Cy5 is less than 100, the column AI is blank. In this situation, normalized values is in column AL or AO.

hyb_protocol: Incubate at 50°C for 20 hour in a humid chamber.

scan_protocol: The microarrays were then scanned using ScanArray GX (PerkinElmer, Wellesley, MA) and signal values were calculated using GenePix Pro 4.0 software (Axon Instruments, Union City, CA). Image output files were examined visually for major defects and hybridization artifacts.

data_processing: The signal intensity of each spot was corrected by subtracting adjacent background signals. To normalize the data, we averaged the intensities of all spots obtained with Cy3 and Cy5 in each of the 48 rectangles, and adjusted the intensity of each corrected DNA spot by the average intensity ratio of Cy5:Cy3 (equal to 1.0). This global normalization of intensity provided a smaller variance of the Cy5:Cy3 ratio and results similar to those obtained via normalization using housekeeping genes.

label_protocol: Dissolve aRNA sample in 5μl of 0.2M Sodium bicarbonate buffer(pH9.0). Add 5μl of CyDye (dissolved in 45μl of DMSO/vial ;Amersham Bioscience) to sample. Mix well  by vortex. Incubate for 1hour at 40°C keep in dark.

extract_protocol: Total RNA was extracted individually using the RNeasy Mini Kit for liver tissue and RNeasy Fibrous Tissue Mini Kit for myocardium (QIAGEN, Chatsworth, CA), according to the manufacturer’s protocol. RNA was analyzed to determine if it met the minimum purity and integrity standards for total RNA quality (i.e., OD 260/280>1.8, OD 260/230>2.0, and minimal degradation as determined using a NanoDrop 1000A spectrophotometer; NanoDrop Technologies, Wilmington, DE). The quality and degradation of the isolated RNA were estimated after electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Heart or liver samples were pooled in each group at the indicated time-points and amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Austin, TX), as recommended by the manufacturer.

tag: strain

tag: tissue

value: Liver

source_name: Liver,sham operation,24hour


title: Chimp_FP_4

description:
Adult chimpanzee brain
Identifier #Y04-04

organism: Pan troglodytes

source_name: Chimpanzee frontal pole

extract_protocol: Qiagen miRNeasy kit

value: Chimpanzee frontal pole


title: Whole-Body_Day 3 of the first instar larva

status: Public on Nov 05 2009

city: Beibei

first: Jiubo

last: Liang

state: Chongqing

address: Tiansheng Road No. 2

department: Molecular Biology

country: China

hyb_protocol: Cy5-dCTP-labeled (test samples) and Cy3-dCTP-labeled (reference samples) double-stranded cDNA were dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from images using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing:
LOWESS-normalized, background-subtracted data obtained from log2 of processed Red signal/processed Green signal. The software from CapitalBio Crop was used. Cluster 3.0 and Mev software (version 4.2.01) were also used in further data processing.
Probes with signal intensity lower than 800 after subtracting the background were considered as unexpressed genes since signals at that detection level are not reliable.

organism: Bombyx mori

source_name: Whole body of day 3 of the first instar larva

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: Silkworm larvae (p50 strain) maintained at the Institute of Sericulture and System Biology (Southwest University, China) were reared on mulberry leaves at 25°C-26°C.

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

value: mixed-sex

value: whole body

tag: developmental stage

value: larva

source_name: Whole body of day 3 of the fifth instar larva