title: Aedes, infected vs. uninfected, rep 3

city: Oxford

first: Steven

last: Sinkins

address: South Parks Rd

department: Department of Zoology

institute: University of Oxford

description:
Biological replicate 3 of 4
Day 2 and day 15 adults were pooled.

hyb_protocol: Labelled cRNA samples were prepared and hybridized using the Gene Expression Hybridisation Kit (Agilent Technologies) and the manufacturer's protocols for 4 x 44k arrays. Hybridized arrays were washed in sequential wash solutions before being protected from ozone with a stabilization and drying solution (Agilent Technologies).

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner at 5 µm resolution and using the extended dynamic range feature (PMT 100% and 10%).

data_processing:
Agilent Feature Extraction Software (v 9.5.3) was used to quantify fluoresence dats using the Agilent Technologies GE2-v5_95 protocol.
VALUEs represent Lowess-normalized log2 (infected/uninfected) ratios.

organism: Aedes aegypti

source_name: Ae. aegypti PGYP1 adult females, 2 & 15 day

label_protocol: All array experiments were conducted according to Agilent Technologies' Two-colour Microarray-based Gene Expression Analysis protocol (version 5.5). 1.5 µg total RNA was amplified and labelled using the Low RNA Linear Amplification Kit PLUS Two-colour (Agilent Technologies), following manufacturer's protocols.

growth_protocol: Aedes aegypti strains PGYP1 and PGYP1.tet were maintained under standard mosquito insectary conditions. Adults were collected at age 2 day and 15 day.

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

tag: wmelpop infection

value: Infected

tag: sex

value: Female

tag: age

value: day 2 adult, day 15 adult

source_name: Ae. aegypti PGYP1.tet adult females, 2 & 15 day

value: Uninfected


title: MEF-rep1

status: Public on Aug 03 2009

type: RNA

city: Shanghai

first: Fanyi

last: Zeng

address: 24/1400 West Beijing Road

department: Institute of Medical Genetics

country: China

institute: Shanghai Jiao Tong University

description: Gene expression data from Mouse Embryonic Fibroblast cells that was used to generate iPS cells.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: Expression Console (with MAS5.0) was used to quantify microarray signals with default analysis parameters and global scaling to target mean=150.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryo fibroblast

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: ES cells and iPS cells were cultured on mitomycin C treated MEF cells with DMEM plus 15% FBS or 20% Knockout serum replacement (KOSR), 1000u/ml LIF, 2 mM glutamine, 1 mM sodium pyruvate, 0.1 mM β-mercaptoethanol and 0.1 mM nonessential amino acid (NEAA).

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

treatment_protocol: Cells were collected and pelleted before Trizol was added and stored in -80oC before extraction.

tag: cell type

value: MEF

tag: genetic background


title: IP14D-101-rep1

description: Gene expression data from iPS cell line IP14D-101.

source_name: Induced pluripotent stem cells

tag: cell line

value: iPS


title: Aedes, infected vs. uninfected, rep 1

country: United Kingdom

description:
Biological replicate 1 of 4
Day 2 and day 15 adults were pooled.

tag: strain


title: Exp-rpoS-rep3

city: Hamilton

first: Herb

middle: E

last: Schellhorn

state: ON

address: 1280 Main St. W.,

department: Biology

country: Canada

institute: McMaster University

description: no additional information

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GCRMA method

organism: Escherichia coli O157:H7 str. EDL933

source_name: Exponential phase culture of EDL933 rpoS mutants in LB at OD600 of 0.3

label_protocol: Affymetrix protocol

growth_protocol: Cells were grown in Luria Bertani (LB) media at 37C at 200 rpm. Overnight cultures were inoculated with single, independent colonies in triplicate, incubated aerobically overnight at 37oC, and sub-cultured to a starting OD600 of 0.0001. Cultures were harvested at OD600 = 0.3 in exponential phase and at OD600 = 1.5 in stationary phase.

extract_protocol: Acidic Hot Phenol

tag: growth phase

value: Exponential

tag: genotype

value: rpoS


title: Exp-WT-rep2

description: no additional information

source_name: Exponential phase culture of EDL933 wild type in LB at OD600 of 0.3

value: WT


title: Aedes, infected vs. uninfected, rep 2

description:
Biological replicate 2 of 4
Day 2 and day 15 adults were pooled.


title: Exp-WT-rep1

description: no additional information


title: CL11-rep3

description: Gene expression data from ES cell line CL11.

source_name: Mouse ES cells

value: ES


title: miRNA_human reprogrammed cell line 2 (hiPSC2p54_2)

status: Public on Jul 28 2009

type: other

city: Los Angeles

first: Mark

middle: H.

last: Chin

state: CA

address: 650 Charles E. Young Dr

department: Human Genetics

country: USA

institute: UCLA

description: miRNA expression data

hyb_protocol: The chips were hybridized on Tecan HS 4800 hybridization station.

scan_protocol: The chips were scanned using an Axon 4200A Microarray Scanner

data_processing:
Quantiles normalization was implemented using Bioconductor 1.8 affy 1.1.2.
MiRNAs were retained when thy were present in at least 20% of samples and when they had fold change of more than 1.5 from the gene median in at least 20% of samples. Absent calls were thresholded to 22 (4.5 in log2 scale) prior to statistical analysis with BRB 3.5.0 (class comparison and class prediction).

label: Biotin

molecule: other

organism: Homo sapiens

source_name: hiPSC line 2 (p54)

label_protocol: The biotin-labeled cDNA targets are prepared by a simple reverse transcription into first strand cDNA.

growth_protocol: Cell lines were cultured in ES cell media (Lowry, et al. PNAS, 2008)

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

treatment_protocol: Reprogrammed Cell lines were created as described in Lowry, et al. (PNAS, 2008)

value: hiPSC line 2


title: CL11-rep2


title: IP14D-1-rep2

description: Gene expression data from iPS cell line IP14D-1.


title: miRNA_human reprogrammed cell line 2 (hiPSC2p54_1)

description: miRNA expression data


title: MEF-rep3


title: miRNA_human reprogrammed cell line 1 (hiPSC1p61_3)

description: miRNA expression data

source_name: hiPSC line 1 (p61)

value: hiPSC line 1


title: miRNA_human reprogrammed cell line 1 (hiPSC1p61_2)

description: miRNA expression data


title: miRNA_hESC line (H9p36_3)

description: miRNA expression data

source_name: HESC H9 (p36)


title: A2780 DMSO/BIO treatment 2 rep 1

city: Glasgow

first: W.

middle: Nicol

last: Keith

state: Lanarkshire

address: Center for Oncology and Applied Pharmacology, University of Glasgow, CRUK Beatson Laboratories, Garscube Estate, Switchback Road

institute: The University of Glasgow

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm as per manufacturor's instructions.

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: All data was analysed within Genespring GX version 7.3.1. Data was normalised using a Lowess intensity dependant normalisation.

source_name: A2780 ovarian adenocarcinoma cells, treated with DMSO

label_protocol: 800 ng of total RNA was labelled with Cy3 (DMSO treated cells) or Cy5 (BIO treated cells) using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.

growth_protocol: A2780 ovarian adenocarcinoma cells were cultured in RPMI medium containing 10 % Fetal Bovine Serum and 1 % L-glutamine.

extract_protocol: Cells were rinsed in PE, trypsanised and total RNA was extracted using Nucleospin II RNA extraction kit (Macherey-Nagel) as per manufacutor's instructions.

treatment_protocol: 21 day continual culture in the presence of DMSO or 2.5mM GSK3 inhibitor 6-bromoindirubin-3’-oxime (BIO) with replenishment weekly on days 1 and 4.

source_name: A2780 ovarian adenocarcinoma cells, treated with 2.5mM GSK3 inhibitor 6-bromoindirubin-3’-oxime (BIO)


title: miRNA_hESC line (HSF1p49_3)

description: miRNA expression data

source_name: HESC HSF1 (p49)


title: CL11-rep1


title: miRNA_hESC line (H9p36_1)

description: miRNA expression data


title: Stat-rpoS-rep3

description: no additional information

source_name: Stationary phase culture of EDL933 rpoS mutants in LB at OD600 of 1.5

value: Stationary


title: miRNA_hESC line (HSF1p75_3)

description: miRNA expression data

source_name: HESC HSF1 (p75)


title: miRNA_hESC line (HSF1p75_1)

description: miRNA expression data


title: miRNA_hESC line (HSF1p49_1)

description: miRNA expression data


title: miRNA_human reprogrammed cell line 2 (hiPSC2p54_3)

description: miRNA expression data


title: WT1 Control

status: Public on Aug 04 2009

city: Copenhagen

first: Morten

last: Alhede

address: Blegdamsvej 3B

department: International Health, Immunology and Microbiology

country: Denmark

institute: University of Copenhagen

description: Gene expression in Pseudomonas aeruginosa biofilm exposed to PMNs for 2 hours

hyb_protocol: Following fragmentation,  cDNA were hybridized for 16 hr at 55C on GeneChip P. aeruginosa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas Genetic Stock Center

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

growth_protocol: Biofilms were grown at 37 ºC in continuous-culture silicon tubing, as previously described by (Hentzer et al., 2003; Hentzer, 2005), perfused with ABT minimal media supplemented with 0.5 w/v % glucose (AB medium (Clark & Maaløe, 1967)). Media were supplemented with antibiotics where appropriate. Unless otherwise stated, all strains were incubated in growth media at 37 ºC. Due to the need of a large quantity of cells for the transcriptomic analysis the volume of the biofilm flow chambers had to be fairly large. A biofilm flow chamber consisted of a 12 cm long silicon tube (inner diameter: 0.8 cm) with a total volume of 6 ml. The flow chamber was connected to a media reservoir with silica tubing of smaller dimension, with the inclusion of a peristaltic pump creating the liquid flow. Furthermore, a bubble trap was included between the flow cell and the pump and the effluent was collected in a waste flask that was connected via silica tubing to the distal end of the flow cell. 100 µl of wild type or lasRrhlR deletion mutant O/N cultures was diluted in 10 ml fresh medium. Six ml was then injected into each of six channels (3 of each strain). To allow cell attachment the flow into the chamber was halted for one hour, by clamping both the influent and effluent tubes. Sterile ABTG minimal medium were then pumped through the chamber. The medium flow was set to 23 rpm (60 ml hour-1) using a Watson Marlow 205S pump. The relatively high flow rate is maintained to ensure that planktonic bacteria were washed out of the setting.

extract_protocol: RNeasy Mini Kits (QIAGEN)

treatment_protocol: The biofilms were allowed to grow and develop in the biofilm flow chambers for 3 days before challenge with PMNs. Fresh PMNs from human volunteers were isolated and resuspended in RPMI-1640 medium (BIOCHROM AG) as previously described by Bjarnsholt et al. 2005 (Bjarnsholt et al., 2005). Prior to PMN injection the flow was halted. Ten million PMNs were resuspended in 6 ml of RPMI media and injected into the flow chamber. The concentration of PMNs was found by microscopy to be approximately 1 PMN per 1000 bacterial cells. PMNs and biofilm were incubated for 2 hours. The flow chambers were rolled every 15 minutes to ensure that the entire biofilm was exposed to the PMNs. After incubation the fluid inside the chamber was discarded and the attached biofilm cells were loosened by rolling. The cells were then mechanically removed and collected in 6 ml of RNAlater®.

tag: Biofilm - PMNs

tag: Age


title: miRNA_hESC line (HSF1p75_2)

description: miRNA expression data


title: miRNA_human reprogrammed cell line 18 (hiPSC18p52_3)

description: miRNA expression data

source_name: hiPSC line 18 (p52)

value: hiPSC line 18


title: miRNA_human reprogrammed cell line 18 (hiPSC18p52_2)

description: miRNA expression data


title: miRNA_human reprogrammed cell line 18 (hiPSC18p52_1)

description: miRNA expression data


title: miRNA_human reprogrammed cell line 1 (hiPSC1p59_2)

description: miRNA expression data

source_name: hiPSC line 1 (p59)


title: Stat-WT-rep2

description: no additional information

source_name: Stationary phase culture of EDL933 wild type in LB at OD600 of 1.5


title: miRNA_human reprogrammed cell line 2 (hiPSC2p51_2)

description: miRNA expression data

source_name: hiPSC line 2 (p51)


title: miRNA_human reprogrammed cell line 2 (hiPSC2p51_3)

description: miRNA expression data


title: Sample NA19238_R

status: Public on Jul 27 2009

type: genomic

city: San Diego

last: Illumina Inc.

address: 9885 Towne Centre Drive

institute: Illumina Inc.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: Sample NA18856_R


title: GM06990_RCyP+

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description:
includes cytoplasmic RNA
Single chip x 2 tech reps, each chromosome placed in separate file

hyb_protocol: 2 micrograms of  double-stranded cDNA were labeled and hybridized to Affymetrix tiling arrays containing probes against non-repepetitive portions of human chromosomes 21 and 22 essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

scan_protocol: Arrays were scanned on Affymetrix GCS3000 scanner

data_processing:
See supplement materials of Djebali, S, et al (2009) Nature in press
Bar files generated with proprietary software (almost identical to Affymetrix TAS). Bandwidth = 0, Normalization target= 330

molecule: polyA RNA

source_name: BD SMARTTM RACE cDNA – GM06990

label_protocol: 2 micrograms of polyA+ RNA were converted into double-stranded cDNA essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

growth_protocol: 11 tissues poly A+ RNA was purchased and 5 cell lines were grown as suggested by ATCC

extract_protocol: see Kapranov, et al Science 2002

tag: tissue

value: GM06990 cell line


title: miRNA_human reprogrammed cell line 1 (hiPSC1p59_1)

description: miRNA expression data


title: miRNA_human Fibroblast line (NHDF1p9_1)

description: miRNA expression data

source_name: NHDF1 (p9)


title: miRNA_human reprogrammed cell line 2 (hiPSC2p51_1)

description: miRNA expression data


title: miRNA_human Fibroblast line (NHDF1p9_3)

description: miRNA expression data


title: Sample NA18951_R


title: Sample NA18609_R


title: miRNA_hESC line (H9p67_3)

description: miRNA expression data

source_name: HESC H9 (p67)


title: Sample NA12248_R2


title: miRNA_human Fibroblast line (NHDF1p9_2)

description: miRNA expression data


title: miRNA_hESC line (H9p67_1)

description: miRNA expression data


title: miRNA_hESC line (H9p67_2)

description: miRNA expression data


title: Sample NA06993_R


title: miRNA_human reprogrammed cell line 1 (hiPSC1p59_3)

description: miRNA expression data


title: Aedes, infected vs. uninfected, rep 4

description:
Biological replicate 4 of 4
Day 2 and day 15 adults were pooled.

source_name: Ae. aegypti PGYP1 adult females, 2 & 15 day

source_name: Ae. aegypti PGYP1.tet adult females, 2 & 15 day


title: Sample NA12891


title: miRNA_hESC line (HSF1p49_2)

description: miRNA expression data


title: Sample NA12878


title: Sample NA12875


title: miRNA_human reprogrammed cell line 1 (hiPSC1p61_1)

description: miRNA expression data

source_name: hiPSC line 1 (p61)


title: Sample NA12812


title: Sample NA12874


title: Sample NA12813


title: Sample NA12801


title: Sample NA12751


title: miRNA_hESC line (H9p36_2)

description: miRNA expression data

source_name: HESC H9 (p36)


title: Sample NA11993_R


title: Sample NA19240


title: Sample NA19239


title: Sample NA12740


title: Sample NA12249


title: Sample NA12248_R2


title: Sample NA19173


title: Sample NA12248_R


title: Sample NA12248


title: Sample NA19192


title: Sample NA19172


title: Sample NA12239


title: Sample NA19193


title: Sample NA19161


title: Sample NA19145


title: Sample NA19160


title: Sample NA19143


title: Sample NA12264


title: Sample NA12750


title: Sample NA12236


title: Sample NA12154


title: Sample NA19238_R


title: Sample NA12234


title: Sample NA19194


title: Sample NA19159


title: Sample NA19141


title: Sample NA19138


title: Sample NA12057


title: Sample NA19142


title: Sample NA19120


title: Sample NA19139


title: Sample NA19140


title: Sample NA19119


title: Sample NA19116


title: Sample NA12056


title: Sample NA12865


title: Sample NA19094


title: Sample NA12146


title: Sample NA19092


title: Sample NA12043


title: Sample NA19093


title: Sample NA12044


title: Sample NA18994


title: Sample NA19003


title: Sample NA18999


title: Sample NA11995


title: Sample NA18992


title: Sample NA18971


title: Sample NA11994


title: Sample NA18968


title: Sample NA11993


title: Sample NA18978


title: Sample NA11993_R


title: Sample NA11992


title: Sample NA18987


title: Sample NA18953


title: Sample NA18960


title: Sample NA11882


title: Sample NA18965


title: Sample NA18951_R


title: Sample NA19238


title: Sample NA18952


title: Sample NA11881


title: Sample NA18951


title: Sample NA10863


title: Sample NA18949


title: Sample NA18857


title: Sample NA18944


title: Sample NA10861


title: Sample NA18856


title: Sample NA19171


title: Sample NA18856_R


title: Sample NA18972


title: Sample NA18855


title: Sample NA10859


title: Sample NA10860


title: Sample NA18854


title: Sample NA18852


title: Sample NA18853


title: Sample NA10851


title: Sample NA18612


title: Sample NA18609_R


title: Sample NA18593


title: Sample NA18608


title: Sample NA18576


title: Sample NA10847


title: Sample NA18577


title: Sample NA18547


title: Sample NA10835


title: Sample NA07357


title: Sample NA18558


title: Sample NA18550


title: Sample NA07345


title: Sample NA18516


title: Sample NA18542


title: Sample NA18529


title: Sample NA18517


title: Sample NA18515


title: Sample NA07029


title: Sample NA18609


title: Sample NA07000


title: Sample NA12891


title: Sample NA06994


title: Sample NA12878


title: Sample NA12875


title: Sample NA12874


title: Sample NA12865


title: Sample NA18537


title: Sample NA12813


title: Sample NA06993_R


title: Sample NA12751


title: Sample NA12750


title: Sample NA06993


title: Sample NA07348


title: Sample NA06985


title: Sample NA12892


title: Sample NA12264


title: Sample NA12249


title: Sample NA12239


title: Sample NA12234


title: Sample NA12248


title: Sample NA12248_R2


title: Sample NA12236


title: Sample NA10830


title: Sample NA06991


title: Sample NA12056


title: Sample NA12154


title: Sample NA12146


title: Sample NA12057


title: Sample NA12043


title: Sample NA12812


title: Sample NA12801


title: Sample NA12044


title: Sample NA11994


title: Sample NA11993_R


title: Sample NA12740


title: Sample NA11995


title: Sample NA11992


title: Sample NA11993


title: Sample NA12248_R


title: Sample NA11881


title: Sample NA11882


title: Sample NA10860


title: Sample NA10859


title: Sample NA10863


title: Sample NA10835


title: Sample NA10857


title: Sample NA10851


title: Sample NA10861


title: Sample NA07357


title: Sample NA07000


title: Sample NA07345


title: Sample NA10830


title: Sample NA07348


title: Sample NA10847


title: Sample NA06991


title: Sample NA06993


title: Sample NA06993_R


title: Sample NA06985


title: Sample NA06994


title: Sample NA18951_R


title: Sample NA19238_R


title: Sample NA19240


title: Sample NA19239


title: Sample NA19238


title: Sample NA19194


title: Sample NA19192


title: Sample NA19160


title: Sample NA18856_R


title: Sample NA19161


title: Sample NA19159


title: Sample NA07029


title: Sample NA19172


title: Sample NA18609_R


title: Sample NA19141


title: Sample NA19171


title: Sample NA19145


title: Sample NA19140


title: Sample NA19138


title: Sample NA19143


title: Sample NA19173


title: Sample NA19142


title: Sample NA19120


title: Sample NA19137


title: Sample NA19193


title: Sample NA19119


title: Sample NA19092


title: Sample NA19093


title: Sample NA19003


title: Sample NA18999


title: Sample NA18994


title: Sample NA18978


title: Sample NA18992


title: Sample NA18972


title: Sample NA18987


title: Sample NA19144


title: Sample NA18971


title: Sample NA19139


title: Sample NA18968


title: Sample NA19094


title: Sample NA18965


title: Sample NA12248_R2


title: Sample NA18953


title: Sample NA18951


title: Sample NA18960


title: Sample NA12248_R


title: Sample NA19116


title: Sample NA18856


title: Sample NA18857


title: Sample NA18944


title: Sample NA18856_R


title: Sample NA18854


title: Sample NA18852


title: Sample NA18855


title: Sample NA18952


title: Sample NA18609_R


title: Sample NA18949


title: Sample NA18853


title: Sample NA18608


title: Sample NA18577


title: Sample NA18593


title: Sample NA18558


title: Sample NA18609


title: Sample NA18542


title: Sample NA18550


title: Sample NA18951_R


title: Sample NA18537


title: Sample NA18547


title: Sample NA11993_R


title: Sample NA18529


title: Sample NA18576


title: Sample NA18612


title: Sample NA18517


title: Sample NA18516


title: Sample NA12892


title: Sample NA18515


title: Sample NA06993_R


title: GI-ME-N_normoxia

status: Public on Apr 11 2009

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

country: Italy

institute: Istiuto Giannina Gaslini

description: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, and 100 ug/mL streptomycin (Euroclone Ltd), at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2.

hyb_protocol: Fragmented cRNA was used for hybridization to Affymetrix HG-U133 plus 2.0 arrays according to the Affymetrix’s instructions.

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

data_processing: Expression values were quantified and array quality control was performed with the statistical algorithms implemented in Affymetrix Microarray Suite 5.0.

source_name: neuroblastoma cell line under normoxic conditions

label_protocol: The RNA was reverse-transcribed into cDNA and biotin labeled according to the Affymetrix’s instructions.

extract_protocol: Total RNA was extracted from cell lines using Trizol (Invitrogen Life technologies, Irvine, CA) according to the manufacturer's instructions.

value: GI-ME-N

tag: condition

value: normoxia


title: Rice wild-type panicle rep2

status: Public on Jul 22 2009

city: Beijing

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

description:
the panicle (9cm-12cm) was collected directly
Gene expression data from rice mutant phoenix (pho)  panicle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner

data_processing: The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa

source_name: rice wild-type panicle Rep2

growth_protocol: plants were grown in paddy fields in Beijing

extract_protocol: total RNA was isolated by  TRIZOL and  purified by Qiagen RNeasy kit.

value: Oryza sativa L. ssp. Indica, Zhongxian 3037

value: rice panicle (9cm-12cm)


title: LAN-1_normoxia

growth_protocol: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, and 100 ug/mL streptomycin (Euroclone Ltd), at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2.


title: SK-N-F1_normoxia


title: Sakai, control, biological rep2

status: Public on Apr 04 2009

city: SUMMIT

first: SIYUN

last: WANG

state: IL

address: 6502 S ARCHER ROAD

institute: ILLINOIS INSTITUTE OF TECHNOLOGY

description: Gene expression data from E. coli Sakai cells without oxidative stress

hyb_protocol: The arrays were hybridized for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640

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

data_processing: The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix).

organism: Escherichia coli O157:H7

source_name: Escherichia coli cells with 30 min incubation in BHI broth

label_protocol: The target preparation followed the Affymetrix GeneChip Expression Analysis Manual (Santa Clara, CA).

growth_protocol: E.coli cells were growed overnight (37 C) and incubate to log phase on the next day.

extract_protocol: Extraction of total RNA was performed using Rneasy Midi kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were incubated with chlorine or H2O2 treated broth or non-treated broth for 30 minutes.

value: Sakai


title: SK-N-BE2(C)_normoxia


title: TW, control, biological rep2

description: Gene expression data from E. coli TW14359 cells without oxidative stress


title: Rice mutant phoenix (pho) panicle rep 2

source_name: rice mutant phoenix (pho) panicle rep 2

value: Oryza sativa L. ssp. Indica, mutant phoenix (pho)


title: Rice mutant phoenix (pho) panicle rep1

description:
the panicle (5cm-8cm) was collected directly
Gene expression data from rice mutant phoenix (pho)  panicle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degee on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner .  .

source_name: rice mutant phoenix (pho)  panicle Rep1

value: rice panicle (5cm-8cm)


title: SK-N-F1_hypoxia

description: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, and 100 ug/mL streptomycin (Euroclone Ltd), at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2. Hypoxic conditions (1% O2) were achieved by culturing the cells in an anaerobic workstation incubator (BUG BOX, Jouan, ALC International S.r.l., Cologno Monzese, Milano, Italy) flushed with a gas mixture containing 1% O2, 5% CO2, and balanced N2 at 37°C in a humidified atmosphere. Oxygen tension in the medium was measured with a portable, trace oxygen analyzer (Oxi 315i/set, WTW; VWR International, Milano, Italy).

source_name: neuroblastoma cell line under hypoxic conditions

value: hypoxia


title: TW, H2O2, biological rep2

description: Gene expression data from E. coli TW14359 cells with H2O2 treatment

source_name: Escherichia coli cells with 30 min incubation in H2O3


title: Rice wild-type panicle rep1

description:
the panicle (5cm-8cm) was collected directly
Gene expression data from  rice wild-type panicle

scan_protocol: GeneChip were scanned using the Affymetrix GeneChip Scanner .

source_name: rice wild-type panicle Rep1


title: TW, chlorine, biological rep2

description: Gene expression data from E. coli TW14359 cells with chlorine treatment

source_name: Escherichia coli cells with 30 min incubation in chlorine


title: GI-ME-N_hypoxia

treatment_protocol: Hypoxic conditions (1% O2) were achieved by culturing the cells in an anaerobic workstation incubator (BUG BOX, Jouan, ALC International S.r.l., Cologno Monzese, Milano, Italy) flushed with a gas mixture containing 1% O2, 5% CO2, and balanced N2 at 37°C in a humidified atmosphere. Oxygen tension in the medium was measured with a portable, trace oxygen analyzer (Oxi 315i/set, WTW; VWR International, Milano, Italy).


title: IMR-32_hypoxia


title: GI-LI-N_normoxia

value: GI-LI-N


title: ACN_hypoxia

value: ACN


title: Sakai, H2O2, biological rep2

description: Gene expression data from E. coli Sakai cells with H2O2 treatment

source_name: Escherichia coli cells with 30 min incubation in H2O2


title: IMR-32_normoxia


title: SK-N-SH_hypoxia

value: SK-N-SH


title: ACN_normoxia


title: SHEP-2_normoxia


title: SHEP-2_hypoxia


title: SK-N-BE2(C)_hypoxia


title: LAN-1_hypoxia


title: GI-LI-N_hypoxia


title: SK-N-SH_normoxia


title: TW, control, biological rep1


title: 13705887 - bou homozygote 8 days cotyledons set2 vs Col 0 8 days cotyledons set2

status: Public on Feb 05 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth.

hyb_protocol: Col 0 8 days cotyledons set2 Cy5 / bou homozygote 8 days cotyledons set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Col 0 8 days cotyledons set2

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

growth_protocol: whole plant - Media=MS 1/2	 hygrometry=100%	 Temperature=21°C	 Light=continuous

extract_protocol: Col 0 8 days cotyledons set2:20ug.

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: bou homozygote 8 days cotyledons set2

extract_protocol: bou homozygote 8 days cotyledons set2:25.54ug.

tag: Arabidopsis thaliana (col-0)  mutant (AT5G46800 = BOU (A BOUT DE SOUFFLE) ) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13705889 - bou homozygote 8 days cotyledons set1 vs Col 0 8 days leaves

hyb_protocol: Col 0 8 days leaves Cy5 / bou homozygote 8 days cotyledons set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col 0 8 days leaves

extract_protocol: Col 0 8 days leaves:68.95ug.

source_name: bou homozygote 8 days cotyledons set1

extract_protocol: bou homozygote 8 days cotyledons set1:19.45ug.


title: Sakai, chlorine, biological rep1

description: Gene expression data from E. coli Sakai cells with chlorine treatment


title: Sakai, chlorine, biological rep2


title: TW, chlorine, biological rep1


title: 13705718 - bou homozygote 8 days cotyledons set1 vs bou heterozygote 8 days leaves

hyb_protocol: bou heterozygote 8 days leaves Cy5 / bou homozygote 8 days cotyledons set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: bou heterozygote 8 days leaves

extract_protocol: bou heterozygote 8 days leaves:27.69ug.


title: 13705883 - Col 0 5 days cotyledons  vs bou homozygote 5 days cotyledons

hyb_protocol: bou homozygote 5 days cotyledons  Cy5 / Col 0 5 days cotyledons  Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: bou homozygote 5 days cotyledons

extract_protocol: bou homozygote 5 days cotyledons :20ug.

source_name: Col 0 5 days cotyledons

extract_protocol: Col 0 5 days cotyledons :20ug.


title: TW, H2O2, biological rep1


title: Sakai, H2O2, biological rep1


title: 13705888 - Col 0 8 days leaves vs bou homozygote 8 days cotyledons set1

hyb_protocol: bou homozygote 8 days cotyledons set1 Cy5 / Col 0 8 days leaves Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13705732 - Col 0 8 days cotyledons set1 vs bou homozygote 8 days cotyledons set1

hyb_protocol: bou homozygote 8 days cotyledons set1 Cy5 / Col 0 8 days cotyledons set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col 0 8 days cotyledons set1

extract_protocol: Col 0 8 days cotyledons set1:46.32ug.


title: 13705885 - bou homozygote 5 days cotyledons  vs Col 0 5 days cotyledons

hyb_protocol: Col 0 5 days cotyledons  Cy5 / bou homozygote 5 days cotyledons  Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: YJM789 vs DBY8268 #3

status: Public on Sep 05 2008

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

description:
Comparison of Strain YJM789 to Strain DBY8268
yG6-78b

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: YJM789 grown in YPD medium

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology 350: 393-414

growth_protocol: Unless otherwise noted, cells were grown 3 doublings in YPD  at 30C to OD600 ~0.5

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology 350: 393-414

treatment_protocol: No treatment

tag: Strain YJM789

label: Oyster 650 cyanine dye

source_name: DBY8268 grown in YPD medium

tag: Strain DBY8268


title: YPS1009 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain YPS1009
yG5-39a

source_name: YPS1009 grown in YPD medium

tag: Strain YPS1009


title: YPS163 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain YPS163
yG5-100b

source_name: YPS163 grown in YPD medium

tag: Strain YPS163


title: YPS163 vs DBY8268 #3

description:
Comparison of Strain DBY8268 to Strain YPS163
yG5-60a


title: YPS1009 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain YPS1009
yG5-53a


title: YPS1009 vs DBY8268 #3

description:
Comparison of Strain YPS1009 to Strain DBY8268
yG6-25a


title: YJM789 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain YJM789
yG6-77b


title: YJM789 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain YJM789
yG6-80b


title: YPS163 vs DBY8268 #4

description:
Comparison of Strain YPS163 to Strain DBY8268
yG6-11b


title: YPS163 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain YPS163
yG4-2b


title: Sakai, control, biological rep1

description: Gene expression data from E. coli Sakai cells without oxidative stress

source_name: Escherichia coli cells with 30 min incubation in BHI broth


title: 13697304 - bou heterozygote 8 days leaves vs bou homozygote 8 days cotyledons set1

hyb_protocol: bou homozygote 8 days cotyledons set1 Cy5 / bou heterozygote 8 days leaves Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13705736 - bou homozygote 8 days cotyledons set1 vs Col 0 8 days cotyledons set1

hyb_protocol: Col 0 8 days cotyledons set1 Cy5 / bou homozygote 8 days cotyledons set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13705886 - Col 0 8 days cotyledons set2 vs bou homozygote 8 days cotyledons set2

hyb_protocol: bou homozygote 8 days cotyledons set2 Cy5 / Col 0 8 days cotyledons set2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: YJM308 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain YJM308
yG5-29a

source_name: YJM308 grown in YPD medium

tag: Strain YJM308


title: YJM269 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain YJM269
yG5-61b

source_name: YJM269 grown in YPD medium

tag: Strain YJM269


title: YJM308 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain YJM308
yG5-51a


title: YJM269 vs DBY8268 #3

description:
Comparison of Strain YJM269 to Strain DBY8268
yG6-13a


title: YJM308 vs DBY8268 #3

description:
Comparison of Strain YJM308 to Strain DBY8268
yG6-13b


title: Y12 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain Y12
yG5-33b

source_name: Y12 grown in YPD medium

tag: Strain Y12


title: YJM269 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain YJM269
yG5-30b


title: Y12 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain Y12
yG5-64b


title: Y10 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain Y10
yG4-18b

source_name: Y10 grown in YPD medium

tag: Strain Y10


title: Y12 vs DBY8268 #3

description:
Comparison of Strain Y12 to Strain DBY8268
yG6-12b


title: RM11a vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain RM11a
yG6-80a

source_name: RM11a grown in YPD medium

tag: Strain RM11a


title: Y1 vs DBY8268 #3

description:
Comparison of Strain Y1 to Strain DBY8268
yG6-12a

source_name: Y1 grown in YPD medium

tag: Strain Y1


title: Y10 vs DBY8268 #4

description:
Comparison of Strain Y10 to Strain DBY8268
yG6-27a


title: Y10 vs DBY8268 #3

description:
Comparison of Strain DBY8268 to Strain Y10
yG5-64a


title: SB vs DBY8268 #3

description:
Comparison of Strain SB to Strain DBY8268
yG6-11a

source_name: SB grown in YPD medium

tag: Strain SB


title: Y10 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain Y10
yG5-100a


title: PR vs DBY8268 #3

description:
Comparison of Strain PR to Strain DBY8268
yG6-25b

source_name: PR grown in YPD medium

tag: Strain PR


title: RM11a vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain RM11a
yG6-77a


title: Y1 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain Y1
yG4-18a


title: Y1 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain Y1
yG5-97b


title: M8 vs DBY8268 #4

description:
Comparison of Strain M8 to Strain DBY8268
yG6-32a

source_name: M8 grown in YPD medium

tag: Strain M8


title: PR vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain PR
yG5-37a


title: SB vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain SB
yG5-30a


title: RM11a vs DBY8268 #3

description:
Comparison of Strain RM11a to Strain DBY8268
yG6-78a


title: SB vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain SB
yG5-37b


title: M8 vs DBY8268 #3

description:
Comparison of Strain M8 to Strain DBY8268
yG6-22b


title: M8 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain M8
yG5-97a


title: M8 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain M8
yG3-36b


title: M22 vs DBY8268 #3

description:
Comparison of Strain M22 to Strain DBY8268
yG6-93b

source_name: M22 grown in YPD medium

tag: Strain M22


title: M22 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain M22
yG6-93a


title: M22 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain M22
yG6-91b


title: K9 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain K9
yG5-51b

source_name: K9 grown in YPD medium

tag: Strain K9


title: K9 vs DBY8268 #3

description:
Comparison of Strain K9 to Strain DBY8268
yG6-27b


title: B1 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain B1
yG5-61a

source_name: B1 grown in YPD medium

tag: Strain B1


title: K1 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain K1
yG5-72b

source_name: K1 grown in YPD medium

tag: Strain K1


title: K9 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain K9
yG3-36a

source_name: DBY8268 grown in YPD medium


title: K1 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain K1
yG5-33a


title: I14 vs DBY8268 #2

description:
Comparison of Strain DBY8268 to Strain I14
yG5-60b

source_name: I14 grown in YPD medium

tag: Strain I14


title: I14 vs DBY8268 #3

description:
Comparison of Strain I14 to Strain DBY8268
yG6-32b

tag: Strain DBY8268


title: K1 vs DBY8268 #3

description:
Comparison of Strain K1 to Strain DBY8268
yG6-28b


title: I14 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain I14
yG5-39b


title: B1 vs DBY8268 #3

description:
Comparison of Strain B1 to Strain DBY8268
yG6-28a


title: B1 vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain B1
yG5-27a


title: Schizosaccharomyces Pombe gcn5 mutant compared to wt no treatment,replicate 4  (slide 21)

status: Public on Jul 06 2006

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Schizosaccharomyces Pombe gcn5 mutant strain compared to  wild type strain in rich medium at 25C, no treatment.

hyb_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

scan_protocol: Slides were scanned using Bio-rad Vers-Array ChipReader.

data_processing: Scanned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.

organism: Schizosaccharomyces pombe

growth_protocol: Schizosaccharomyces Pombe gcn5 mutant strain Hu0984 grows in rich medium.

treatment_protocol: Schizosaccharomyces Pombe gcn5 mutant strain Hu0984 grows in rich medium at 25C, no treatment.

growth_protocol: Schizosaccharomyces Pombe wild type strain 972 h- grows in rich medium at 25C.

treatment_protocol: Schizosaccharomyces Pombe wild type strain 972 h- grows in rich medium at 25C, no treatment


title: Schizosaccharomyces Pombe gcn5 mutant compared to wt no treatment,replicate 6  (slide 23)

source_name: Schizosaccharomyces Pombe gcn5 mutant strain Hu0985

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

source_name: Schizosaccharomyces Pombe wild type strain 972 h-


title: Schizosaccharomyces Pombe gcn5 mutant compared to wt no treatment,replicate 5  (slide 22)

source_name: Schizosaccharomyces Pombe gcn5 mutant strain Hu0984

extract_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

tag: Schizosaccharomyces Pombe wild type strain 972 h-


title: Schizosaccharomyces pombe gcn5 mutant compared to wt no treatment,replicate 3  (slide 18)

description: Schizosaccharomyces pombe gcn5 mutant strain compared to  wild type strain in rich medium at 25C, no treatment.

growth_protocol: Schizosaccharomyces pombe gcn5 mutant strain Hu0985 grows in rich medium.

treatment_protocol: Schizosaccharomyces pombe gcn5 mutant strain Hu0985 grows in rich medium at 25C, no treatment.

growth_protocol: Schizosaccharomyces pombe wild type strain 972 h- grows in rich medium at 25C.

treatment_protocol: Schizosaccharomyces pombe wild type strain 972 h- grows in rich medium at 25C, no treatment


title: Schizosaccharomyces Pombe gcn5 mutant compared to wt no treatment,replicate 1 (slide 13)

tag: Schizosaccharomyces Pombe gcn5 mutant strain Hu0984


title: Schizosaccharomyces Pombe gcn5 mutant compared to wt, KCl treatment,replicate 1  (slide 5)

description: Expression profile of Schizosaccharomyces pombe gcn5 mutant strain was compared to  wild type strain, both treated with 1M KCl in rich medium at 25C.

source_name: Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with KCl

growth_protocol: Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.

treatment_protocol: Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with 1M KCl for 60min at 25C.

source_name: Schizosaccharomyces pombe wild type strain fy368 treated with KCl for 60min

treatment_protocol: Schizosaccharomyces pombe wild type strain fy368 treated with 1M KCl for 60min.


title: Schizosaccharomyces Pombe wild type strain KCl treatment, replicate 1 (slide 19)

description: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min compared to non-treated sample at 25C.

source_name: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min.

treatment_protocol: Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.

tag: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min at 25C.

growth_protocol: Strain was grown on YEA medium at 25C to log phase.

treatment_protocol: Schizosaccharomyces Pombe wild type strain Fy368 was grown in rich medium at 25C.

tag: Schizosaccharomyces Pombe wild type strain Fy368 was grown in rich medium at 25C as control.


title: Corticotectal Neurons P14 2

status: Public on Jan 19 2005

city: Boston

first: Bradley

last: Molyneaux

state: MA

department: MGH-HMS Center For Nervous System Repair

institute: Harvard Medical School

description: Postnatal day 14 corticotectal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P14 FACS-purified corticotectal projection neurons

tag: strain

tag: tissue type

value: neuronal

tag: cell type

value: corticotectal neurons

tag: age

value: Postnatal day 14


title: Schizosaccharomyces Pombe wild type strain KCl treatment, replicate 2 (slide 17)

scan_protocol: Slides were scanned using Scan Express laser scanner

source_name: Schizosaccharomyces Pombe wild type strain Fy368


title: Corticotectal Neurons P14 1


title: Schizosaccharomyces Pombe gcn5 mutant compared to wt no treatment,replicate 2  (slide 9)


title: Schizosaccharomyces pombe gcn5 mutant compared to wt KCl treatment,replicate 1  (slide 6)

description: Schizosaccharomyces pombe gcn5 mutant strain compared to  wild type strain, both treated with 1M KCl in rich medium at 25C.

source_name: Schizosaccharomyces Pombe gcn5 mutant Hu0799 treated with KCl

tag: Schizosaccharomyces pombe gcn5 mutant Hu0799 treated with 1M KCl for 60min at 25C.

source_name: Schizosaccharomyces pombe wild type strain Fy368 treated with KCl for 60min


title: Corticospinal Motor Neurons P14 1

description: Postnatal day 14 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P14 FACS-purified corticospinal motor neurons

value: corticospinal motor neurons


title: Corticospinal Motor Neurons P6 2

description: Postnatal day 6 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P6 FACS-purified corticospinal motor neurons

value: Postnatal day 6


title: Corticospinal Motor Neurons P14 2


title: Corticospinal Motor Neurons P3 2

description: Postnatal day 3 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P3 FACS-purified corticospinal motor neurons

value: Postnatal day 3


title: Corticospinal Motor Neurons P3 3


title: Corticospinal Motor Neurons P6 1


title: Callosal Neurons P14 1

description: Postnatal day 14 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P14 FACS-purified callosal projection neurons

value: callosal projection neurons


title: Corticospinal Motor Neurons P3 1

description: Postnatal day 3corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.


title: Callosal Neurons P6 2

description: Postnatal day 6 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P6 FACS-purified callosal projection neurons


title: Corticospinal Motor Neurons E18 2

description: Embryonic day 18.5 corticospinal motor neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: E18 FACS-purified corticospinal motor neurons

value: Embryonic day 18


title: Corticospinal Motor Neurons E18 1


title: Callosal Neurons P6 1


title: Callosal Neurons P3 1

description: Postnatal day 3 callosal projection neurons purified by fluorescence-activated cell sorting. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: P3 FACS-purified callosal projection neurons


title: Callosal Neurons E18 1

description: Embryonic day 18 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.

source_name: E18 FACS-purified callosal projection neurons


title: Callosal Neurons P3 2

description: Postnatal day 3 callosal projection neurons purified by fluorescence-activated cell sorting from murine (C57BL/6) cortex. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.


title: Callosal Neurons E18 2

description: Embryonic day 18 callosal projection neurons purified by fluorescence-activated cell sorting. RNA extracted using StrataPrep Total RNA Micro Kit (Stratagene). RNA amplified according to Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription.


title: Callosal Neurons P14 2


title: f2#345 versus pool Mouse Liver tissue

status: Public on Aug 10 2009

first: Leslie

last: Ingram-drake

department: Medicine/MIMG/Human Genetics

description: Liver tissue from 302 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

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

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

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

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Male

source_name: pool

tag: Strain:C57BL/6J and C3H/HeJ  Age:20 weeks (150 randomly selected F2)


title: Normal_CD34(+)_#2

status: Public on Aug 05 2009

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

institute: University of Miiami

description: MspI representation of genomic DNA vs. HpaII representation of genomic DNA.

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. , genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.

source_name: Bone marrow CD34+ cells

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5.

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55).

tag: tissue

value: bone marrow

value: CD34+ cells

tag: restriction enzyme

value: MspI

value: HpaII


title: Sample NA12248_R1

hyb_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: PR vs DBY8268 #1

description:
Comparison of Strain DBY8268 to Strain PR
yG5-27b

source_name: DBY8268 grown in YPD medium

source_name: PR grown in YPD medium

tag: Strain PR