title: P. sojae strain P6954 - race 1: Treated - 6 Hours post inoculation - rep 3

source_name: P.sojae strain P6954 - race 1: Treated - 6 Hours post inoculation

value: 6 h


status: Public on Jul 19 2010

type: RNA

city: Singapore

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

country: Singapore

institute: Genome Institute of Singapore

description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (3rd repeat)

hyb_protocol: Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly.  The slides were hybridized overnight for 16 hours at 42 degree Celsius under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2x SSC/0.1% SDS for 1 min, 1x SSC for 4 min, 0.2x SSC for 4 min, and 0.05x SSC for 1 min, and then spin-dried before scanning.

data_processing: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells

label_protocol: Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy5 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays

growth_protocol: Yeast cells were cultured at 30 degree Celsius

extract_protocol: cDNA of the Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point generated from total RNA as described in materials and methods

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point (3rd repeat)

source_name: cDNA from WT strain with no treatment

label_protocol: Approximately 30 ug of total RNA was used to synthesize cDNA coupled with aa-dUTP by reverse transcriptase. Approximately 1.5 ug of cDNA was coupled with Cy3 fluorescence dye and purified through a Microcon YM-30. Cy5- and Cy3-labeled cDNA were pooled and hybridized to the spotted S. pombe oligonucleotide (oligo)-based DNA microarrays

extract_protocol: total RNA of the WT cells were extracted as described in materials and methods

tag: Reference total RNA of the WT strain with no treatment


title: P. sojae strain P6954 - race 1: Treated - 6 Hours post inoculation - rep 2

city: Blacksburg

first: sucheta

last: Tripathy

state: VA

address: 1, Washington street

department: Virginia  Bioinformatics Institute

country: USA

institute: Virginia Tech

description: Data was collected from the hypocotyl regions of Soybean plants at different time points

hyb_protocol: hybridization cocktail is prepared, including the fragmented target, probe array controls, BSA, and herring sperm DNA. It is then hybridized to the probe array during a 16-hour incubation(Affymetrix technical manual - 2004)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000

data_processing: The data were analyzed with GCRMA suite from R package version 2.4.0. Background correction was using GCRMA followed by a modified quantile normalization routine where data from control chips are used to rank probes instead of averaging the probe values. Data was summarized using a memory efficient median polish method

label: biotin

organism: Phytophthora sojae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA. RNA is is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling. The biotinylated cRNA targets are then cleaned up, fragmented, and hybridized to GeneChip expression arrays(Affymetrix Technical manual - 2004)

growth_protocol: P.sojae mycelia were cultured in V8 media at 25C for 2 days prior to inoculation onto Soybean hypocotyl.

extract_protocol: QIAGEN RNeasy Kit : As recommended by manufacturer

treatment_protocol: Agar plugs of P. sojae isolate P6954 (race 1) were transferred to Petri dishes containing V8 liquid medium and incubated at 25C. P6954 is genetically near-identical to P6947 (Forster et al, 1994) but unlike P6947, P6954 expresses Avr1b. After 2 days the mycelia were transferred to Petri dishes with water to wash excess V8 medium. Seedlings of highly-susceptible soybean cultivar Sloan were grown in the greenhouse with natural light for 9 days.After harvesting, seedling roots were washed gently to remove soil and then placed on moist cloth. Washed P. sojae mycelia were used to inoculate seedling hypocotyls: a small (~1 cm long) longitudinal slit was cut near the top half of the hypocotyls and the mycelia were placed inside the cut. After 3, 6 or 12 h, the tissue surrounding the infected hypocotyl slits. As a 0 h control, pure P6954 mycelial inocula were also harvested right after the wash step (no infection).  All samples were      transferred to liquid nitrogen and frozen at 80C.  The entire experiment was replicated three times. .

tag: strain

tag: time


title: P. sojae strain P6954 - race 1: Treated - 3 Hours post inoculation - rep 2

source_name: P.sojae strain P6954 - race 1: Treated - 3 Hours post inoculation

value: 3 h


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (2nd repeat)

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point (2nd repeat)


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (1st repeat)

extract_protocol: cDNA of the Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point generated from total RNA as described in materials and methods

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point (1st repeat)


title: P. sojae strain P6954 - race 1: Treated - 12 Hours post inoculation - rep 1

source_name: P.sojae strain P6954 - race 1: Treated - 12 Hours post inoculation


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (2nd repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 30min time point (2nd repeat)


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (1st repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at 10min time point (1st repeat)


title: P. sojae strain P6954 - race 1: Control - zero time point - 0 Hours post inoculation - rep 1

source_name: P.sojae strain P6954 - race 1: Control - zero time point - 0 Hours post inoculation

value: 0 h


title: NSC-NP-iPSC-1 input, methyl-depleted

type: genomic

city: Baltimore

first: Akiko

last: Doi

state: MD

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

molecule: genomic DNA

organism: Mus musculus

source_name: Input fraction from NSC-NP-iPSC-1

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input, methyl-depleted  (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input, methyl-depleted  (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: cell type

value: iPS cells derived neural stem cells (that were differentiated NP-iPSC)

source_name: Methyl-depleted fraction from NSC-NP-iPSC-1


title: NSC-NP-iPSC-3 input, methyl-depleted

source_name: Input fraction from NSC-NP-iPSC-3

source_name: Methyl-depleted fraction from NSC-NP-iPSC-3


title: NP-iPSC-TSA-AZA3 input, methyl-depleted

source_name: Input fraction from NP-iPSC-TSA-AZA3

value: NP-iPSC treated with 5-azacytidine and Trichostatin A

source_name: Methyl-depleted fraction from NP-iPSC-TSA-AZA3


title: NSC-NP-iPSC-4 input, methyl-depleted

source_name: Input fraction from NSC-NP-iPSC-4

source_name: Methyl-depleted fraction from NSC-NP-iPSC-4


title: NSC-NP-iPSC-6 input, methyl-depleted

source_name: Input fraction from NSC-NP-iPSC-6

source_name: Methyl-depleted fraction from NSC-NP-iPSC-6


title: NSC-NP-iPSC-5 input, methyl-depleted

source_name: Input fraction from NSC-NP-iPSC-5

source_name: Methyl-depleted fraction from NSC-NP-iPSC-5


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (2nd repeat)

source_name: Fission yeast cells

extract_protocol: cDNA of the Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point generated from total RNA as described in materials and methods

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point (2nd repeat)


title: NP-iPSC-TSA-AZA2 input, methyl-depleted

source_name: Input fraction from NP-iPSC-TSA-AZA2

source_name: Methyl-depleted fraction from NP-iPSC-TSA-AZA2


title: NSC-NP-iPSC-2 input, methyl-depleted

source_name: Input fraction from NSC-NP-iPSC-2

source_name: Methyl-depleted fraction from NSC-NP-iPSC-2


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (1st repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point (1st repeat)

source_name: cDNA from WT strain with no treatment


title: P. sojae strain P6954 - race 1: Control - zero time point - 0 Hours post inoculation - rep 3

source_name: P.sojae strain P6954 - race 1: Control - zero time point - 0 Hours post inoculation


title: P. sojae strain P6954 - race 1: Treated - 3 Hours post inoculation - rep 1

source_name: P.sojae strain P6954 - race 1: Treated - 3 Hours post inoculation


title: P. sojae strain P6954 - race 1: Treated - 6 Hours post inoculation - rep 1

source_name: P.sojae strain P6954 - race 1: Treated - 6 Hours post inoculation


title: NP-iPSC-TSA-AZA1 input, methyl-depleted

source_name: Input fraction from NP-iPSC-TSA-AZA1

source_name: Methyl-depleted fraction from NP-iPSC-TSA-AZA1


title: P. sojae strain P6954 - race 1: Control - zero time point - 0 Hours post inoculation - rep 2


description: hybridization of Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (3rd repeat)

tag: cDNA from Pcr1 deletion strain treated with 0.5mM H2O2 at zero time point (3rd repeat)


title: NP-iPSC-5 input, methyl-depleted

source_name: Input fraction from NP-iPSC-5

value: Neural progenitor-derived iPS cells

source_name: Methyl-depleted fraction from NP-iPSC-5


title: NP-iPSC-6 input, methyl-depleted, 2

source_name: Input fraction from NP-iPSC-6

source_name: Methyl-depleted fraction from NP-iPSC-6


title: P. sojae strain P6954 - race 1: Treated - 12 Hours post inoculation - rep 2

source_name: P.sojae strain P6954 - race 1: Treated - 12 Hours post inoculation


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (2nd repeat)

extract_protocol: cDNA of the Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point generated from total RNA as described in materials and methods

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point (2nd repeat)


title: NP-iPSC-2 input, methyl-depleted, 2

source_name: Input fraction from NP-iPSC-2

source_name: Methyl-depleted fraction from NP-iPSC-2


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (1st repeat)

source_name: Fission yeast cells

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point (1st repeat)


title: NP-iPSC-4 input, methyl-depleted, 2

source_name: Input fraction from NP-iPSC-4

source_name: Methyl-depleted fraction from NP-iPSC-4


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (2nd repeat)

extract_protocol: cDNA of the Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point generated from total RNA as described in materials and methods

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point (2nd repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (3rd repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 120min time point (3rd repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (1st repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point (1st repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (3rd repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 60min time point (3rd repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (2nd repeat)

extract_protocol: cDNA of the Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point generated from total RNA as described in materials and methods

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point (2nd repeat)

tag: Reference total RNA of the WT strain with no treatment


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (3rd repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point (3rd repeat)


title: B-NP-iPSC-15-1 input, methyl-depleted

source_name: Input fraction from B-NP-iPSC-15-1

value: iPS cells derived blood (that was differentiated NP-iPSC)

source_name: Methyl-depleted fraction from B-NP-iPSC-15-1


title: B-NP-iPSC-14-1 input, methyl-depleted

source_name: Input fraction from B-NP-iPSC-14-1

source_name: Methyl-depleted fraction from B-NP-iPSC-14-1


title: B-NP-iPSC-1-2 input, methyl-depleted

source_name: Input fraction from B-NP-iPSC-1-2

source_name: Methyl-depleted fraction from B-NP-iPSC-1-2


title: B-NP-iPSC-15-2 input, methyl-depleted

source_name: Input fraction from B-NP-iPSC-15-2

source_name: Methyl-depleted fraction from B-NP-iPSC-15-2


title: Arabidopsis ATH1_SCR inducible line_time course_second biological replicate Time 0H after Dex treatment

city: Durham

first: Rosangela

last: Sozzani

state: NC

address: 124 Science Dr

department: Biology

institute: Duke University

description: Gene expression data from J0571 sorted cells under standard conditions for 5 days and transferred to dex containing plates

hyb_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: MAS 5.0

organism: Arabidopsis thaliana

source_name: J0571 sorted cells

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified at 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  Dex media is 1X Murashige and Skoog salt mixture in which 1micromolar of Dex is added. Nylon mesh was placed on top of the solidified media and seeds were planted at ~20 seeds/cm in two rows.

extract_protocol: Approximately 1000 roots were collected per replicate, with two biological replicates being performed per time point.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Plant Mini Kit (Qiagen).

treatment_protocol: Seedlings were grown for 5 days before transfer to Dex media.  Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer.

tag: ecotype

value: Columbia

tag: age

value: Seedling roots, 5 days after germination

tag: treatment

value: Dex media for 0 hours


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (2nd repeat)

extract_protocol: cDNA of the Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point generated from total RNA as described in materials and methods

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point (2nd repeat)

source_name: cDNA from WT strain with no treatment


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (3rd repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point (3rd repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (1st repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 10min time point (1st repeat)


title: Arabidopsis ATH1_cortex/endodermis initial cell type_CYCD6 marker GFP line_second biological replicate

description: Gene expression data from CEI sorted cells under standard conditions for 5 days

scan_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

source_name: CEI sorted cells

value: Standard media


title: ntESC-V6.5NSCB2 input, methyl-depleted

source_name: Input fraction from ntESC-V6.5NSCB2

tag: cell type

value: Nuclear transfer ES cells

tag: strain

source_name: Methyl-depleted fraction from ntESC-V6.5NSCB2


title: ntESC-V6.5 input, methyl-depleted

source_name: Input fraction from ntESC-V6.5

source_name: Methyl-depleted fraction from ntESC-V6.5


title: Arabidopsis ATH1_SCR inducible line_time course_second biological replicate Time 1H after Dex treatment

value: Dex media for 1 hour


title: NP-iPSC-1 input, methyl-depleted, 2

source_name: Input fraction from NP-iPSC-1

source_name: Methyl-depleted fraction from NP-iPSC-1


title: ntESC-Rag2 input, methyl-depleted

source_name: Input fraction from ntESC-Rag2

source_name: Methyl-depleted fraction from ntESC-Rag2


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (3rd repeat)

source_name: Fission yeast cells

extract_protocol: cDNA of the Atf1 deletion strain treated with 0.5mM H2O2 at zero time point generated from total RNA as described in materials and methods

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at zero time point (3rd repeat)


title: B-NP-iPSC-1-3 input, methyl-depleted

source_name: Input fraction from B-NP-iPSC-1-3

source_name: Methyl-depleted fraction from B-NP-iPSC-1-3


title: ntESC-NGFP input, methyl-depleted

source_name: Input fraction from ntESC-NGFP

source_name: Methyl-depleted fraction from ntESC-NGFP


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (2nd repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at zero time point (2nd repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (1st repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at 30min time point (1st repeat)


description: hybridization of Atf1 deletion strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (1st repeat)

tag: cDNA from Atf1 deletion strain treated with 0.5mM H2O2 at zero time point (1st repeat)


description: hybridization of WT strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the WT strain treated with 0.5mM H2O2 at 60min time point generated from total RNA as described in materials and methods

tag: cDNA from WT strain treated with 0.5mM H2O2 at 60min time point (3rd repeat)


description: hybridization of WT strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the WT strain treated with 0.5mM H2O2 at 120min time point generated from total RNA as described in materials and methods

tag: cDNA from WT strain treated with 0.5mM H2O2 at 120min time point (3rd repeat)


description: hybridization of WT strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (1st repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at 120min time point (1st repeat)


title: NP-iPSC-6 input, methyl-depleted

source_name: Input fraction from NP-iPSC-6

source_name: Methyl-depleted fraction from NP-iPSC-6


description: hybridization of WT strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (2nd repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at 60min time point (2nd repeat)

source_name: cDNA from WT strain with no treatment

tag: Reference total RNA of the WT strain with no treatment


title: ntESC-LN2 input, methyl-depleted

source_name: Input fraction from ntESC-LN2

source_name: Methyl-depleted fraction from ntESC-LN2


description: hybridization of WT strain treated with 0.5mM H2O2 at 60min time point and WT strain with no treatment (1st repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at 60min time point (1st repeat)


title: P06-0925B

city: Chapel Hill

first: Jen Jen

last: Yeh

address: LCCC, 450 West Drive

department: Surgical Oncology

institute: University of North Carolina at Chapel Hill

hyb_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent G2505C fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v10.5) software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken using Agilent Feature Extraction (v10.5) software.

organism: Homo sapiens

source_name: Human Reference

extract_protocol: Total RNA isolated by Qiagen

tag: tissue

value: Stratagene Human reference RNA

source_name: Pancreas Tissue

extract_protocol: Qiagen Rneasy Kit

value: Patient Primary Pancreatic Tumor

tag: tumor type


title: NP-iPSC-4 input, methyl-depleted

source_name: Input fraction from NP-iPSC-4

source_name: Methyl-depleted fraction from NP-iPSC-4


title: fESC-V6.5 input, methyl-depleted

source_name: Input fraction from fESC-V6.5

value: fES cells

source_name: Methyl-depleted fraction from fESC-V6.5


description: hybridization of WT strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the WT strain treated with 0.5mM H2O2 at 30min time point generated from total RNA as described in materials and methods

tag: cDNA from WT strain treated with 0.5mM H2O2 at 30min time point (3rd repeat)


title: NP-iPSC-1 input, methyl-depleted

source_name: Input fraction from NP-iPSC-1

source_name: Methyl-depleted fraction from NP-iPSC-1


description: hybridization of WT strain treated with 0.5mM H2O2 at 120min time point and WT strain with no treatment (2nd repeat)

source_name: Fission yeast cells

tag: cDNA from WT strain treated with 0.5mM H2O2 at 120min time point (2nd repeat)


title: fESC-PGEEE2-2 input, methyl-depleted

source_name: Input fraction from fESC-PGEEE2-2

source_name: Methyl-depleted fraction from fESC-PGEEE2-2


title: ntESC-LN3 input, methyl-depleted

source_name: Input fraction from ntESC-LN3

source_name: Methyl-depleted fraction from ntESC-LN3


title: P05-0268B

label_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]


title: P05-0175B


title: NP-iPSC-3 input, methyl-depleted

source_name: Input fraction from NP-iPSC-3

source_name: Methyl-depleted fraction from NP-iPSC-3


title: P04-0379B


description: hybridization of WT strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the WT strain treated with 0.5mM H2O2 at 10min time point generated from total RNA as described in materials and methods

tag: cDNA from WT strain treated with 0.5mM H2O2 at 10min time point (3rd repeat)

source_name: cDNA from WT strain with no treatment


title: Strain a710 replicate 3 (6 strain set)

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

description: replicate 3 of 3

hyb_protocol: The labelled DNA were mixed together with two volumes of hybridization buffer (Eurogentec, Belgium) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.

scan_protocol: The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma.

organism: Neisseria meningitidis

source_name: DNA from Strain_a710

label_protocol: 4 µg of chromosomal DNA and 4  µg of the pooled common reference were labelled with Cy3 dCTP and Cy5 dCTP using Klenow enzyme and random nonamers and the labelled DNA was precipitated and purified.

growth_protocol: The strains were cultivated on blood agar plates at 37°C

extract_protocol: Chromosomal DNA from the meningococcal strains were isolated using Genomic Tip 20/G (Qiagen, Germany).

source_name: Common Reference

tag: tag

value: Pool of all individual DNA´s


title: Bl-iPSC-K01-2 input, methyl-depleted

source_name: Input fraction from Bl-iPSC-K01-2

tag: cell type

value: Blood-derived iPS cells

tag: strain

source_name: Methyl-depleted fraction from Bl-iPSC-K01-2


title: Bl-iPSC-E3-1 input, methyl-depleted

source_name: Input fraction from Bl-iPSC-E3-1

source_name: Methyl-depleted fraction from Bl-iPSC-E3-1


description: hybridization of WT strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (2nd repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at 30min time point (2nd repeat)

extract_protocol: total RNA of the WT cells were extracted as described in materials and methods


title: Bl-iPSC-K02-2 input, methyl-depleted

source_name: Input fraction from Bl-iPSC-K02-2

source_name: Methyl-depleted fraction from Bl-iPSC-K02-2


description: hybridization of WT strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (2nd repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at 10min time point (2nd repeat)


description: hybridization of WT strain treated with 0.5mM H2O2 at 10min time point and WT strain with no treatment (1st repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at 10min time point (1st repeat)


title: Strain a710 replicate 2 (6 strain set)

description: replicate 2 of 3


title: P04-0234B

source_name: Human Reference

source_name: Pancreas Tissue


title: fESC-PGEEE2-1 input, methyl-depleted

source_name: Input fraction from fESC-PGEEE2-1

source_name: Methyl-depleted fraction from fESC-PGEEE2-1


title: Bl-iPSC-E2-1 input, methyl-depleted

source_name: Input fraction from Bl-iPSC-E2-1

source_name: Methyl-depleted fraction from Bl-iPSC-E2-1


title: Bl-iPSC-B-iPSC54 input, methyl-depleted

source_name: Input fraction from Bl-iPSC-B-iPSC54

source_name: Methyl-depleted fraction from Bl-iPSC-B-iPSC54


description: hybridization of WT strain treated with 0.5mM H2O2 at 30min time point and WT strain with no treatment (1st repeat)

source_name: Fission yeast cells

tag: cDNA from WT strain treated with 0.5mM H2O2 at 30min time point (1st repeat)

source_name: cDNA from WT strain with no treatment


title: P04-0316B


description: hybridization of WT strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (3rd repeat)

extract_protocol: cDNA of the WT strain treated with 0.5mM H2O2 at zero time point generated from total RNA as described in materials and methods

tag: cDNA from WT strain treated with 0.5mM H2O2 at zero time point (3rd repeat)


title: Strain a710 replicate 1 (6 strain set)

description: replicate 1 of 3

source_name: DNA from Strain_a710

source_name: Common Reference


title: Strain a275 replicate 3 (6 strain set)

description: replicate 3 of 3

source_name: DNA from Strain_a275


description: hybridization of WT strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (2nd repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at zero time point (2nd repeat)


title: NP-iPSC-2 input, methyl-depleted

source_name: Input fraction from NP-iPSC-2

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with McrBC, and fractionated on a 1% agarose gel alongside the sheared input, methyl-depleted  (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

source_name: Methyl-depleted fraction from NP-iPSC-2


title: P01-0505B


description: hybridization of WT strain treated with 0.5mM H2O2 at zero time point and WT strain with no treatment (1st repeat)

tag: cDNA from WT strain treated with 0.5mM H2O2 at zero time point (1st repeat)


title: Strain a275 replicate 1 (6 strain set)

description: replicate 1 of 3


title: Strain a153 replicate 3 (6 strain set)

description: replicate 3 of 3

source_name: DNA from Strain_a153


title: ntESC-F1 input, methyl-depleted

source_name: Input fraction from ntESC-F1

source_name: Methyl-depleted fraction from ntESC-F1


title: Strain a153 replicate 2 (6 strain set)

description: replicate 2 of 3


title: Glomerulus_LD9

city: Ann Arbor

first: Felix

last: Eichinger

state: MI

address: 1150 W Med Center Drive

department: Internal Medicine/Nephrology

institute: University of Michigan

hyb_protocol: The fragmentation, hybridization and staining were performed according the Affymetrix Expression Analysis Technical Manual

scan_protocol: The imaging was performed according the Affymetrix Expression Analysis Technical Manual

data_processing:
Background adjustment, quantile normalization and probeset summarization was performed using RMAexpress, Version 0.3 within a dataset of 88 samples for glomeruli and 83 samples for tubuli. The reported data are log2 transformed. A background filter cut-off was defined to lower the count of false positive calls using the highest signal value obtained from non-human Affymetrix control oligonucleotides multiplied by a factor of 1.2, following previous studies:

Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006

A linear model was fit to compensate differences in expression due to separate sample processing of the compartments. Subsequently, genes were selected based on foldchange.

label: Biotin

source_name: Transplant Living Donor, microdissected Glomerulus from kidney biopsy

label_protocol:
For probe labeling, a modification of the Eberwine protocol was used:
Phillips J, Eberwine JH: Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cells. Methods  10  : 283  –288,1996

extract_protocol:
RNA was isolated as described in:
Cohen CD, Frach K, Schlondorff D, et al.: Quantitative gene expression analysis in renal biopsies: a novel protocol for a high-throughput multicenter application. Kidney Int 61:133-140, 2002
Total RNA was reverse-transcribed (RT) and linearly amplified according to a protocol previously reported for tubulointerstitial specimen:
Schmid H, Boucherot A, Yasuda Y, et al.: Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 55:2993-3003, 2006
and glomeruli:
Cohen CD, Klingenhoff A, Boucherot A, et al.: Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 103:5682-5687, 2006

tag: gender

value: male

tag: age

value: 62 years


title: P03-0175AB

source_name: Human Reference

tag: tissue

source_name: Pancreas Tissue


title: Bl-iPSC-ABiPS input, methyl-depleted

source_name: Input fraction from Bl-iPSC-ABiPS

source_name: Methyl-depleted fraction from Bl-iPSC-ABiPS


title: ntESC-V1 input, methyl-depleted

source_name: Input fraction from ntESC-V1

source_name: Methyl-depleted fraction from ntESC-V1


title: F-iPSC-59 input, methyl-depleted

source_name: Input fraction from F-iPSC-59

value: Fibroblast-derived iPS cells

source_name: Methyl-depleted fraction from F-iPSC-59


title: ntESC-O input, methyl-depleted

source_name: Input fraction from ntESC-O

source_name: Methyl-depleted fraction from ntESC-O


title: Strain a153 replicate 1 (6 strain set)

description: replicate 1 of 3

source_name: Common Reference


title: Glomerulus_LD10

value: female

value: 58 years


title: Glomerulus_LD8

value: 41 years


title: ntESC-B3 input, methyl-depleted

source_name: Input fraction from ntESC-B3

source_name: Methyl-depleted fraction from ntESC-B3


title: ntESC-V3 input, methyl-depleted

source_name: Input fraction from ntESC-V3

source_name: Methyl-depleted fraction from ntESC-V3


title: F-iPSC-63 input, methyl-depleted

source_name: Input fraction from F-iPSC-63

source_name: Methyl-depleted fraction from F-iPSC-63


title: Strain a275 replicate 2 (6 strain set)

description: replicate 2 of 3

source_name: DNA from Strain_a275


title: Strain a14 replicate 3 (6 strain set)

description: replicate 3 of 3

source_name: DNA from Strain_a14


title: Strain a14 replicate 2 (6 strain set)

description: replicate 2 of 3


title: Strain a14 replicate 1 (6 strain set)

description: replicate 1 of 3


title: Glomerulus_LD5

source_name: Transplant Living Donor, microdissected Glomerulus from kidney biopsy

value: 35 years


title: Glomerulus_LD6

value: 39 years


title: Tubulus_LD10

source_name: Transplant Living Donor, microdissected Tubulus from kidney biopsy


title: Strain 2137 replicate 2 (6 strain set)

description: replicate 2 of 3

source_name: DNA from Strain_2137


title: Strain 2137 replicate 3 (6 strain set)

description: replicate 3 of 3


title: Glomerulus_LD7

value: 56 years


title: Tubulus_LD8


title: Tubulus_LD9


title: Tubulus_LD7


title: Tubulus_LD6


title: F-iPSC-16 input, methyl-depleted

source_name: Input fraction from F-iPSC-16

source_name: Methyl-depleted fraction from F-iPSC-16


title: F-iPSC-57 input, methyl-depleted

source_name: Input fraction from F-iPSC-57

source_name: Methyl-depleted fraction from F-iPSC-57


title: Strain 2135 replicate 2 (6 strain set)

description: replicate 2 of 3

source_name: DNA from Strain_2135


title: Tubulus_LD5


title: Strain 2135 replicate 1 (6 strain set)

description: replicate 1 of 3

source_name: Common Reference


title: F-iPSC-54 input, methyl-depleted

source_name: Input fraction from F-iPSC-54

source_name: Methyl-depleted fraction from F-iPSC-54


title: Strain 2137 replicate 1 (6 strain set)

description: replicate 1 of 3


title: Malme3M_PLX4032_1000

status: Public on Jul 18 2010

city: New York

first: Christine

middle: Anne

last: Pratilas

state: NY

address: 1275 York Avenue

department: Molecular Pharmacology

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data from BRAFV600E mutant cell line upon treatment with RAF inhibitor PLX4032

hyb_protocol: 10ug of labeled and fragmented cRNA were hybridized onto a U133A 2.0 expression array (Affymetrix)

scan_protocol: Microarrays were scanned using a high-numerical aperture and flying objective (FOL) lens in the GS300 scanner (Affymetrix)

data_processing: GeneChip Operating Software ver1.4 (GCOS, Affymetrix)

source_name: Malme3M, 1000nM PLX4032-treated, 8hrs

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol from 2ug total RNA.

growth_protocol: Cell lines were cultured in RPMI 1640 medium, supplemented with 10% fetal bovine serum.

extract_protocol: Total cellular RNA was extracted from harvested cells using the Qiagen RNeasy extraction kit, and methods provided by the manufacturer

treatment_protocol: Cells growing at 70% confluency were treated with 0.1% DMSO (control), or PLX4032 disolved in DMSO to reach a final concentration of 250nM  or 1000nM. Cells were washed with 1XPBS and harvested on ice, eight hours post treatment

tag: genotype

value: BRAFV600E mutant

tag: cell line


title: Malme3M_PLX4032_250

source_name: Malme3M, 250nM PLX4032-treated, 8hrs


title: F-iPSC-56 input, methyl-depleted

source_name: Input fraction from F-iPSC-56

source_name: Methyl-depleted fraction from F-iPSC-56


title: SkMel-19_PLX4032_1000

source_name: SkMel-19, 1000nM PLX4032-treated, 8hrs


title: SkMel-19_PLX4032_250

source_name: SkMel-19, 250nM PLX4032-treated, 8hrs


title: Malme3M_DMSO

description: Gene expression data from BRAFV600E mutant cell line upon treatment with DMSO

source_name: Malme3M, DMSO-treated, 8hrs


title: F-iPSC-13 input, methyl-depleted

source_name: Input fraction from F-iPSC-13

source_name: Methyl-depleted fraction from F-iPSC-13


title: SkMel-19_DMSO

source_name: SkMel-19, DMSO-treated, 8hrs


title: SkMel-28_PLX4032_250

source_name: SkMel-28, 250nM PLX4032-treated, 8hrs


title: SkMel-28_DMSO

source_name: SkMel-28, DMSO-treated, 8hrs


title: SkMel-5_PLX4032_250

source_name: SkMel-5, 250nM PLX4032-treated, 8hrs


title: SkMel-5_DMSO

source_name: SkMel-5, DMSO-treated, 8hrs


title: SkMel-1_DMSO

source_name: SkMel-1, DMSO-treated, 8hrs


title: fESC-E input, methyl-depleted

source_name: Input fraction from fESC-E

source_name: Methyl-depleted fraction from fESC-E


title: SkMel-1_PLX4032_250

source_name: SkMel-1, 250nM PLX4032-treated, 8hrs


title: fESC-I input, methyl-depleted

source_name: Input fraction from fESC-I

source_name: Methyl-depleted fraction from fESC-I


title: fESC-D input, methyl-depleted

source_name: Input fraction from fESC-D

source_name: Methyl-depleted fraction from fESC-D


title: fESC-G input, methyl-depleted

source_name: Input fraction from fESC-G

source_name: Methyl-depleted fraction from fESC-G


title: F-iPSC-1 input, methyl-depleted

source_name: Input fraction from F-iPSC-1

source_name: Methyl-depleted fraction from F-iPSC-1


title: Strain 2135 replicate 3 (6 strain set)

description: replicate 3 of 3

source_name: DNA from Strain_2135

source_name: Common Reference


title: Protoperithecia (Cy5) vs Mycelia (Cy3) replicate 1 [oligodT]

status: Public on Jul 17 2010

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers (53°C water bath). After hybridization, slides were washed sequentially.

scan_protocol: Hybridized microarrays were scanned and gridded with a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA)

data_processing: Normalized by background-subtracted mean-by-mean normalization of well measured spots, and statistically analyzed using a Bayesian analysis of gene expression levels with BAGEL software.

organism: Neurospora crassa

source_name: Reproductive structure

label_protocol: 2 µg of mRNA were primed with 0.5 µl of 100 µM MTP or Oligo-d(T) primer at 70°C for 10min, then reversed transcribed at 42°C for 2h in the presence of 400 U SuperScript II RTase (Invitrogen), and 0.8ul Amino-allyl dUTP/dNTP made from Sigma in mg aliquotes and dissolved in 20µl H2O-(DEPC) and mixed with 30µl of 100mM dATP, dTTP, dGTP, dCTP and 12µl 100mM dTTP;  25 µM Cy3/Cy5-label

growth_protocol: SCM media

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

treatment_protocol: Constant light

tag: developmental stage

value: Protoperithecia

value: mat A FGSC#2489

tag: primer type

value: oligodT

value: Myceilia


title: fESC-C input, methyl-depleted

source_name: Input fraction from fESC-C

value: fES cells

source_name: Methyl-depleted fraction from fESC-C


title: Protoperithecia (Cy5) vs Mycelia (Cy3) replicate 2 [oligodT]


title: Mycelia (Cy5) vs Protoperithecia (Cy3) [oligodT]


title: Patient 17, IDC, CNA

city: Augusta

first: Lesleyann

last: Hawthorn

state: GA

department: Molecular Oncology

institute: Medical College of Georgia Cancer Center

description: Hybridized to Sty1 mapping array.

hyb_protocol: Affymetrix hybridization oven (model #640), 16 hrs. Washing and staining were performed on an Affymetrix fluidics station 450.

scan_protocol: Scanning performed on Affymetrix 3000 scanner.

data_processing: RMA background-corrected, quantile normalization, genomic segmentation. Partek Genomics Suite version 6.0 was used to normalize the data. The HapMap 270 from CEPH (http://www.affymetrix.com/support/technical/sample_data/500k_data.affx) was used as reference.

source_name: Breast, IDC

label_protocol: 250 ng of genomic DNA was digested with Sty1. A custom adapter sequence was ligated to the end of the DNA fragments. PCR was performed to select for fragments ranging from 200-1100bp.  Amplicons were fragmented and 3' biotin labeled.

growth_protocol: N/A.

extract_protocol: Qiagen DNA extraction.

treatment_protocol: N/A.

value: breast cancer

tag: tissue type

value: infiltrating ductal carcinoma (IDC)

tag: patient


title: Patient 21, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 19, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 24, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 22, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 23, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 20, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: B-iPSC-10 input, methyl-depleted

source_name: Input fraction from B-iPSC-10

tag: cell type

value: Blood-derived iPS cells

tag: strain

source_name: Methyl-depleted fraction from B-iPSC-10


title: Patient 16, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 18, nodal metastasis, CNA

description: Hybridized to Sty1 mapping array.

source_name: Breast, nodal metastasis

value: nodal metastasis


title: B-iPSC-15 input, methyl-depleted

source_name: Input fraction from B-iPSC-15

source_name: Methyl-depleted fraction from B-iPSC-15


title: fESC-B input, methyl-depleted

source_name: Input fraction from fESC-B

source_name: Methyl-depleted fraction from fESC-B


title: Patient 9, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 15, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: fESC-A input, methyl-depleted

source_name: Input fraction from fESC-A

source_name: Methyl-depleted fraction from fESC-A


title: fESC-F input, methyl-depleted

source_name: Input fraction from fESC-F

source_name: Methyl-depleted fraction from fESC-F


title: Patient 8, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: B-iPSC-8 input, methyl-depleted

source_name: Input fraction from B-iPSC-8

source_name: Methyl-depleted fraction from B-iPSC-8


title: Patient 7, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 9, nodal metastasis, CNA

description: Hybridized to Sty1 mapping array.


title: Synthetic Medium (Cy5) vs Minimal Medium (Cy3) replicate 2 [MTP]

organism: Saccharomyces cerevisiae

source_name: cells

growth_protocol: Saccharomyces cerevisiae S288c was grown in synthetic complete medium (SC) at 30°C shaking at 160 rpm until mid log phase (OD600=0.4). For nitrogen depletion, cells were collected and resuspended in an equal volume of minimal medium (MM) without amino acids or adenine and with limiting concentrations (0.025%) of ammonium sulfate. Cultures were harvested after 12h incubation, flash frozen in liquid nitrogen and stored at -80°C [25].

tag: environment condition

value: nitrogen poor

value: MTP

value: Nitrogen rich


title: Patient 10, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: ntESC-V2 input, methyl-depleted

source_name: Input fraction from ntESC-V2

value: Nuclear transfer ES cells

source_name: Methyl-depleted fraction from ntESC-V2


title: hal4,5 pH6,0 W303 rep4

city: Barcelona

first: Jorge

last: Pérez-Valle

state: Barcelona

address: Parc Cientific de Barcelona, C/. Baldiri Reixac 10

department: RNA lab

country: Spain

institute: IBMB (CSIC)

description:
Biological replicate 1 of 4
cells grown in YPD pH 6.0 and W303 genetic background

hyb_protocol: Microarrays were hybridized according to UltraGAPS manual (Corning). Slides were prehybridized in 1% BSA, 5 x SSC, 0.1% SDS for 45 min at 42ºC, washed using water and dried prior to hibridization. Labeled probes were resuspended in 50% formamide, 5 x SSC, 0.1% SDS, 0.2 ug/uL salmon sperm DNA and hybridized overnight at 42ºC using a Hyb4 hybridization station (Genomic Solutions). Following hybridization, slides were sequentially washed with 2 x SSC, 0.1% SDS; then in 0.1 x SSC, 0.1% SDS and finally in 0.1 x SSC, and dried.

scan_protocol: Slide was scanned using an Axon 4000B microarray scanner (Molecular Devices), at 10 um resolution. PMT gains was adjusted so that the ratio of pixels intensity in both channels was 1.0  Image adquisition and processing was performed using GenePix 6.0 software (Molecular Devices)

data_processing: Replicates with valid data were merged using Acuity software. Slide was normalized by Lowess. VALUE column corresponds to the ratio of medians Cy5/Cy3, lowess-normalized, in log2 scale.

source_name: WT strain in log-phase culture

label_protocol: Fluorescent labeled cDNA was prepared from purified total RNA by the indirect method. Briefly, aminoallyl-cDNA was synthesised from 30 ug of total RNA using SuperScript II (InvitroGen) and poly-dT primer. Following removal of unincorporated nucleotides using Qiaquick columns (Qiagen), the reaction products were coupled to Cy5 NHS-ester fluorescent dye (GE). Cy-labelled probes were further purified using Qiaquick columns and lyophilized.

growth_protocol: Cells were grown at 28ºC in YPD rich medium until Ab660=1.0. 50 mL of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80ºC until RNA purification.

extract_protocol: Dried cell pellet was resuspended in 350 uL TCES buffer and 350 uL phenol:chloroforme:isoamylalcohol (25:24:1), together with 0.6 mL of 0.5 mm glass beads. Cells were vortex and centrifuged 5 min at 12.000 rpm, and upper phase was recovered and re-extracted using 0.3 mL chloloforme. RNA was precipitated overnight in 6 M LiCl, centrifuged 15 min, washed with 70% ethanol and resuspended in 30 uL water. RNA was purified using RNAeasy columns from Qiagen.

tag: growth media

value: YPD pH 6.0

tag: genotype/variation

value: wild type

source_name: hal4,5 strain in log-phase culture

value: hal4hal5 mutant


title: Patient 5, IDC, CNA

description: Hybridized to Sty1 mapping array.

source_name: Breast, IDC


title: hal4,5 pH6,0 W303 rep2


title: Patient 6, nodal metastasis, CNA

description: Hybridized to Sty1 mapping array.

source_name: Breast, nodal metastasis


title: Synthetic Medium (Cy5) vs Minimal Medium (Cy3) replicate 1 [MTP]


title: hal4,5 pH6,0 W303 rep1


title: hal4,5 pH6,0 W303 rep3


title: Patient 3, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: hal4,5 pH4,5 W303 rep4

description:
Biological replicate 1 of 4
cells grown in YPD pH 4.5 and W303 genetic background

growth_protocol: Cells were grown at 28ºC in YPD pH 4.5 rich medium until Ab660=1.0. 50 mL of yeast culture was harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80ºC until RNA purification.

value: YPD pH 4.5


title: Non-specific effects of Doxycycline treatment replicate 3

city: Iowa City

first: Ramakrishna

last: Sompallae

state: IA

address: 285 Newton Road, 5292 CBRB

department: Iowa Institute of Human Genetics

institute: University of Iowa

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol V5.0.1

scan_protocol: Agilent Technologies Scanner G2505B

data_processing: Agilent feature extraction software V9.1.3.1 was used for background subtraction and LOWESS normalization. Signal to noise ratio and relative error were calculated using Expressionist Pro software (Genedata AG, Basel, Switzerland)

source_name: BJAB cells transfected with only Tet vector cultered in absence of Doxycycline

label_protocol: Agilent's Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies - p/n 5188-5340) was used to generate the fluorescent cRNA (complimentary RNA).

growth_protocol: The cells were grown in RPMI-1640 complete medium supplemented with penicillin (100 U/ml), streptomycin (0.1 mg/ml), 10% fetal calf serum and the appropriate selection drugs for BJAB-E1 (200 mg/ml geneticin - Gibco, Darmstadt, Germany) or BJAB-tTA/BJAB-tTAE1 (0.5μg/ml hygromycin - Calbiochem, San Diego, CA, USA and 0.5 μg/ml puromycin - Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNA is extracted with the RNeasy mini kit from QIAGEN® as directed by the manufacturer.

treatment_protocol: One mg/ml of doxycycline was added to the BJAB-tTAE1 culture medium to repress the expression of EBNA-1.

value: BJAB-tTA

tag: doxycycline

value: Absent

tag: ebna-1 expression

value: Not expressed

source_name: BJAB cells transfected with only Tet vector cultered in presence of Doxycycline

value: Present


title: Minimal Medium (Cy5) vs Synthetic Medium (Cy3) replicate 2 [MTP]


title: Minimal Medium (Cy5) vs Synthetic Medium (Cy3) replicate 1 [MTP]


title: Non-specific effects of Doxycycline treatment replicate 2


title: B-iPSC-2 input, methyl-depleted

source_name: Input fraction from B-iPSC-2

source_name: Methyl-depleted fraction from B-iPSC-2


title: B-iPSC-18 input, methyl-depleted

source_name: Input fraction from B-iPSC-18

source_name: Methyl-depleted fraction from B-iPSC-18


title: Patient 1, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: Patient 2, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: EBNA-1 short-term inducible expression replicate 1

source_name: EBNA-1 inducible transfects of BJAB cells expressing EBNA-1

value: Expressed

source_name: EBNA-1 is repressed by doxycylinecycline


title: EBNA-1 short-term inducible expression replicate 3

source_name: EBNA-1 is repressed by Doxycycline


title: EBNA-1 short-term inducible expression replicate 2


title: EBNA-1 stable expression replicate 2

source_name: BJAB cells stably expressing EBNA-2

source_name: BJAB parental cells

value: BJAB


title: hal4,5 pH4,5 W303 rep3


title: B-iPSC-11 input, methyl-depleted

source_name: Input fraction from B-iPSC-11

source_name: Methyl-depleted fraction from B-iPSC-11


title: EBNA-1 longt-term inducible expression replicate 1

source_name: EBNA-1 inducible transfects of BJAB cells


title: EBNA-1 stable expression replicate 3

source_name: BJAB cells stably expressing EBNA-3


title: hal4,5 pH4,5 W303 rep1

source_name: WT strain in log-phase culture

source_name: hal4,5 strain in log-phase culture


title: hal4,5 pH4,5 BY4741 rep4

description:
Biological replicate 1 of 4
cells grown in YPD pH 4.5 and BY4741 genetic background


title: hal4,5 pH4,5 BY4741 rep3


title: 08SE1187

city: Santiago de Compostela

first: Carmen

last: Conde

state: A Coruña

address: Choupana s/n

institute: Hospital Clinico Universitario

description: Arthritis induced by transfer of K/BxN serum

hyb_protocol: Samples were hybridised to Affymetrix Mouse Gene 1.0 ST genechip using Affymetrix standard hybridization protocol  (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The chips were scanned using an Affymetrix  7G Genechip Scanner 3000 with GeneChip Command Console 1.1 software (Affymetrix)

data_processing: Data were processing by RMA algorithm using Partek Genomic Suite

source_name: MMP-8 KO arthritic mouse

label_protocol: Biotinylated cDNA were prepared from 300 ng of total RNA, using the WT cDNA synthesis and amplification kit (Affymetrix) following the GeneChip whole transcript (WT) sense target labelling assay manual of Affymetrix

extract_protocol: Ankle joints were pulverized in presence of liquid nitrogen and total RNA was extracted with Rneasy mini kit and QIAshredder (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Arthritic mice were intraperitoneally injected with 150 ul of K/BxN serum on days 0 and 2. Mice were killed for ankle RNA extraction on day 7 after serum injection.

value: ankle joint

value: MMP-8 KO


title: Patient 4, IDC, CNA

description: Hybridized to Sty1 mapping array.

source_name: Breast, IDC

value: breast cancer

value: infiltrating ductal carcinoma (IDC)


title: Non-specific effects of Doxycycline treatment replicate 1

source_name: BJAB cells transfected with only Tet vector cultered in absence of Doxycycline

source_name: BJAB cells transfected with only Tet vector cultered in presence of Doxycycline


title: 08SE1188


title: 08SE1186

source_name: MMP-8 wild type arthritic mouse

value: MMP-8 wild type


title: 08SE1185


title: EBNA-1 stable expression replicate 1

source_name: BJAB cells stably expressing EBNA-1


title: hal4,5 pH4,5 BY4741 rep2


title: 08SE1189


title: 08SE1184


title: 08SE1183

description: Mouse without arthritis

source_name: MMP-8 KO control mouse


title: 08SE1181

description: Mouse without arthritis


title: hal4,5 pH4,5 BY4741 rep1


title: 143B TK-ρ°_rep3

city: seoul

first: hyun-jung

last: koo

address: hoegi-dong,dongdaemun-gu

country: South Korea

institute: Kyung Hee University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization using the Avadis 4.3 software (Strand Genomics).

source_name: bone

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The cells were cultured in high glucose (4.5g/L) DMEM supplemented with 10% fetal bovine serum (FBS), antibiotics (100 µg/ml penicillin/streptomycin mix), and uridine (50 µg/ml) in a humidified atmosphere at 37℃ with 5% CO₂ .

extract_protocol: Total RNA from ρ+ or ρ0 cells (n=3) was isolated using TRIzol (Invitrogen, Karlsruhe, Germany) and quantified with NanoDrop spectrophotometer (NanoDrop Technologies, Inc.).

value: bone

tag: disease

value: osteosarcoma

value: 143B TK-ρ°


title: 143B TK-ρ+_rep2

description: replicate 2


title: 143B TK-ρ°_rep2

description: replicate 2


title: 08SE1180

description: Mouse without arthritis

source_name: MMP-8 wild type control mouse


title: 08SE1182

description: Mouse without arthritis


title: Patient 14, IDC, CNA

description: Hybridized to Sty1 mapping array.


title: 143B TK-ρ+_rep3

description: replicate 3


title: 08SE1179

description: Mouse without arthritis


title: D3 EB day 4 + 12h atra biological rep2

status: Public on Jul 16 2010

city: Debrecen

first: Zoltan

last: Simandi

address: Egyetem ter 1

department: BMBI

country: Hungary

institute: University of Debrecen

description:
biological rep2
Gene expression data from 12h atra treated embrioid bodies

hyb_protocol: 10 ug of ss cDNA was fragmented and labeled with biotin and were hybridized for 16 hr at 45C on GeneChip  1.0 ST Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX11 Software (Agilent). Cel files were imported using RMA16 algorithm and median normalization was performed.

source_name: D3 cell line

label_protocol: Biotinylated ss cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA using WT Expression kit (Ambion).

growth_protocol: mESCs (a clone of D3) were cultured as described in the article. ES medium contained 15% ES qualified FBS (Cat.no.: SH30070.03, HyClone Laboratories, Inc., Utah).

extract_protocol: RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

treatment_protocol: For induction of EB formation mES cells were aggregated in 100-mm bacteriological dishes (Greiner) at a specific density (4x106 cells/ 15 ml) in the abscence of LIF. Over the span of four days, embryoid bodies were treated for 12h with DMSO or ATRA (5 mikromol final concentration).


title: D3 EB day 4 + 12h atra biological rep3

description:
biological rep3
Gene expression data from 12h atra treated embrioid bodies


title: 08SE1178

description: Mouse without arthritis


title: D3 EB day 4 + 12h atra biological rep1

description:
biological rep1
Gene expression data from 12h atra treated embrioid bodies


title: D3 EB day 4 + 12h DMSO biological rep1

description:
biological rep1
Gene expression data from 12h DMSO treated embrioid bodies


title: D3 ES day 0 biological rep2

description:
biological rep2
Gene expression data from undifferentiated ES


title: D3 EB day 4 + 12h DMSO biological rep2

description:
biological rep2
Gene expression data from 12h DMSO treated embrioid bodies


title: D3 EB day 4 biological rep1

description:
biological rep1
Gene expression data from four day old embryoid bodies


title: D3 EB day 4 biological rep2

description:
biological rep2
Gene expression data from four day old embryoid bodies


title: D3 EB day 4 + 12h DMSO biological rep3

description:
biological rep3
Gene expression data from 12h DMSO treated embrioid bodies


title: D3 ES day 0 biological rep3

description:
biological rep3
Gene expression data from undifferentiated ES


title: 143B TK-ρ°_rep1

description: replicate 1


title: D3 EB day 4 biological rep3

description:
biological rep3
Gene expression data from four day old embryoid bodies


title: D3 ES day 0 biological rep1

description:
biological rep1
Gene expression data from undifferentiated ES


title: B-iPSC-12 input, methyl-depleted

source_name: Input fraction from B-iPSC-12

value: Blood-derived iPS cells

source_name: Methyl-depleted fraction from B-iPSC-12


title: Pol2 IP from wt cells 120 min 37C heat shock [time course 1]

type: other

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

description: BY4741 cells were grown to an OD of 0.5 in YPD shaking at 200 rpm at room temperature (25 degrees C).  An equal volume of YPD prewarmed to 49 degrees C was added to flasks, which were immediately transferred to a 37 degrees C incubator and incubated at the indicated times before harvesting.   Cells were then crosslinked with formaldehyde (1%) and washed with water. Cells were sonicated to shear DNA to ~500 bp, and subjected to immunoprecipitation with 5 ul anti-Rpb3 monoclonal antibody.  As a reference, DNA was obtained from the input sheared chromatin prior to antibody addition.  The ChIP and reference samples were amplified via Round A Round B amplification and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 Agilent S.cerevisiae whole genome arrays.

hyb_protocol: Amplified ChIP and ChIP input were mixed, purified by microcon, and hybridized to the microarrays in Agilent hybridization buffer for 16 hours at 65 degrees.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 6.0 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 expression ratios were calculated to produce the values given in the data table.

source_name: Pol2 IP

label_protocol: 3 ul of amplified DNA was combined with 20 ul random octamers from the Invitrogen BioPrime Labeling Kit and nuclease-free water to a volume of 41 ul.  This was boiled for 5 minutes at 100C, then incubated on ice for 5 minutes.  5 ul of a low-C dNTP mix (25 mM dATP, 15 mM dCTP, 25 mM dGTP and 25 mM dTTP) and 3 ul of 1 mM Cy3-dCTP (for IP) or Cy5-dCTP (for input) were added, along with 1 ul of exo- Klenow fragment DNA polymerase (from the BioPrime kit), and the samples were incubated for 2.5 hours at 37C. IP and input probes were combined and brought up to 500 ul volume with water in a YM-30 Microcon column, and spun at 14,000 x g until the volume reduced to <50 ul.  Water was added and the spin was repeated twice, with the final volume at 37.5 ul.  At this stage, samples were labeled and ready for hybridization onto Agilent 44K arrays.

extract_protocol: Chromatin associated with the target epitope was immunoprecipitated from mononucleosomal cell extract and amplified by TLAD.

value: wt

tag: stress

value: 37C heat shock

tag: time

value: 120 min

tag: antibody

value: anti-Rpb3 monoclonal antibody (Neoclone; catalog# W0012)

source_name: input

extract_protocol: DNA was isolated from mononucleosomal cell extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.


title: Pol2 IP from rpb1-1 cells 30 min 37C heat shock [time course 2]

description: BY4741 cells bearing a temperature-sensitive mutation in rpb1were grown to an OD of 0.5 in YPD shaking at 200 rpm at room temperature (25 degrees C).  An equal volume of YPD prewarmed to 49 degrees C was added to flasks, which were immediately transferred to a 37 degrees C incubator and incubated at the indicated times before harvesting.   Cells were then crosslinked with formaldehyde (1%) and washed with water. Cells were sonicated to shear DNA to ~500 bp, and subjected to immunoprecipitation with 5 ul anti-Rpb3 monoclonal antibody.  As a reference, DNA was obtained from the input sheared chromatin prior to antibody addition.  The ChIP and reference samples were amplified via Round A Round B amplification and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 Agilent S.cerevisiae whole genome arrays.

tag: genotype

value: rpb1-1 mutant

value: 30 min


title: Pol2 IP from rpb1-1 cells 10 min 37C heat shock, then 15 min diamide [time course 4]

description: BY4741 cells bearing a temperature-sensitive mutation in rpb1were grown to an OD of 0.5 in YPD shaking at 200 rpm at room temperature (25 degrees C).  An equal volume of YPD prewarmed to 49 degrees C was added to flasks, which were immediately transferred to a 37 degrees C incubator and incubated at the indicated time.  The cells were treated with diamide (1.5 mM final concentration) for the indicated time before harvesting.   Cells were then crosslinked with formaldehyde (1%) and washed with water. Cells were sonicated to shear DNA to ~500 bp, and subjected to immunoprecipitation with 5 ul anti-Rpb3 monoclonal antibody.  As a reference, DNA was obtained from the input sheared chromatin prior to antibody addition.  The ChIP and reference samples were amplified via Round A Round B amplification and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 Agilent S.cerevisiae whole genome arrays.

value: 37C heat shock, then diamide

value: 10 min heat shock, 15 min diamide


title: hal4,5 pH4,5 W303 rep2

description:
Biological replicate 1 of 4
cells grown in YPD pH 4.5 and W303 genetic background

value: YPD pH 4.5

value: hal4hal5 mutant

value: wild type


title: Pol2 IP from rpb1-1 cells 10 min 37C heat shock, then 60 min diamide [time course 4]

value: 10 min heat shock, 60 min diamide


title: Pol2 IP from rpb1-1 cells 60 min with diamide [time course 3]

description: BY4741 cells bearing a temperature-sensitive mutation in rpb1were grown to an OD of 0.5 in YPD shaking at 200 rpm at room temperature (25 degrees C).  The cells were treated with diamide (1.5 mM final concentration) for the indicated time before harvesting.   Cells were then crosslinked with formaldehyde (1%) and washed with water. Cells were sonicated to shear DNA to ~500 bp, and subjected to immunoprecipitation with 5 ul anti-Rpb3 monoclonal antibody.  As a reference, DNA was obtained from the input sheared chromatin prior to antibody addition.  The ChIP and reference samples were amplified via Round A Round B amplification and labeled with cy3 and cy5 respectively, and co-hybridized to 4x44 Agilent S.cerevisiae whole genome arrays.

value: diamide

value: 60 min


title: Pol2 IP from rpb1-1 cells 10 min 37C heat shock, then 30 min diamide [time course 4]

value: 10 min heat shock, 30 min diamide


title: Pol2 IP from rpb1-1 cells 120 min with diamide [time course 3]


title: Pol2 IP from rpb1-1 cells 15 min 37C heat shock [time course 2]

value: 15 min


title: Pol2 IP from rpb1-1 cells 30 min with diamide [time course 3]


title: Pol2 IP from rpb1-1 cells 120 min 37C heat shock [time course 2]


title: Pol2 IP from rpb1-1 cells 0 min with diamide [time course 3]

value: 0 min


title: Pol2 IP from wt cells 60 min 37C heat shock [time course 1]

value: wt


title: Pol2 IP from rpb1-1 cells 60 min 37C heat shock [time course 2]

value: 37C heat shock


title: Pol2 IP from wt cells 15 min 37C heat shock [time course 1]


title: Pol2 IP from wt cells 30 min 37C heat shock [time course 1]


title: Rat retina_Saffron + Light Damage_ rep1

city: Acton

first: Riccardo

last: Natoli

state: ACT

address: Sullivans Creek Road

department: CMBE

country: Australia

institute: ANU

description: Gene expression data from rat retina, pretreated with saffron (3 weeks of 1mg/kg/day) prior to light damage (1000lux for 24 hrs.).

hyb_protocol: Standard Affymetrix protocols were followed in the hybridisation, blocking and washing (GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)).

scan_protocol: Image analysis was performed using the standard Affymetrix protocols (GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)). Scanning was performed using the GeneChip® Scanner 3000 and  Affymetrix® GeneChip® Command Console® (AGCC).

data_processing: RMA expression values, log transformed (base 2) using Expression console (version 1.1.2800.19935). Normalized data were analyzed using GeneSpring GX v10 software.

organism: Rattus norvegicus

source_name: retina, pretreatment saffron then exposued to 24hrs 1000lux light, followed by 1000 lux light for 24hrs.

label_protocol: Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay 2009, Affymetrix, Inc.).

growth_protocol: All animals were raised in 5 lux cyclic light. They were routinely fed a vegetable (potato or rice) matrix, developed as a biodegradable packaging material, and we used the same matrix used as vehicle for feeding them with saffron.

extract_protocol: Total RNA was extracted from each retinal biopsy using Trizol and chloroform to separate the RNA from other cell components. The RNA was then purified and isolated using RNAqueous-Micro RNA isolation kit (Ambion, Inc., Austin, TX). In some cases where genomic DNA contamination was a concern, the RNA was DNAse treated.

treatment_protocol:
Animals were fed saffron at 1mg/kg/day, for 3w. Saffron (stigmata of Crocus sativus, from the Abbruzzo region in Italy) was soaked in water (at 2mg of spice/ml H2O) and 12h was allowed for the major anti-oxidants, which are water-soluble, to dissolve fully. The solute was then fed to the rats injecting a small volume into a piece of the vegetable matrix, which the animal readily ingested. The volume for each daily feed was calculated to provide the solutes from 1mg of saffron/kg body weight. Tissue was collected 24h after the last feed.
The animals were kept individually in plexiglass cages, with food kept on the floor of the cages and water offered from transparent containers, to ensure uniform exposure. After overnight dark adaptation, animals were exposed to bright (1000 lux) light for 24h, from a white fluorescent source. Exposure began and ended at 9.00am.

value: Sprague Dawley

tag: tissue

value: retina

value: Adult P80 - 120


title: Pol2 IP from wt cells 0 min 37C heat shock [time course 1]

value: anti-Rpb3 monoclonal antibody (Neoclone; catalog# W0012)


title: Rat retina_Saffron + Light Damage_ rep3

tag: developmental stage


title: Pol2 IP from rpb1-1 cells 0 min 37C heat shock [time course 2]

value: rpb1-1 mutant


title: Rat retina_Saffron + Light Damage_ rep2


title: Rat retina_PBM + Light Damage_ rep3

description: Gene expression data from rat retina, pretreated with PBM (5 days for 3mins) prior to light damage (1000lux for 24 hrs).

source_name: retina, pretreatment PBM, 3mins each day for 5 days, followed by 1000 lux light for 24hrs.

treatment_protocol:
Animals were exposed to 670nm red light from a WARP 75 source (Quantum Devices Inc, Barneveld, WI, USA). Animals were handled gently over several days until they were adapted to handling, Each was then gently restrained with a towel and held under a plexiglass platform with the head ~2.5cm below the platform. The WARP75 device was placed on top of the platform and turned on for 3 min. This arrangement provided a fluence of10J/cm2 at the eye. The animals did not hide from or appear agitated by the red light. Animals were treated in this way once daily for 5 days, at 9.00 am. Tissue was collected 24h after the last treatment.
The animals were kept individually in plexiglass cages, with food kept on the floor of the cages and water offered from transparent containers, to ensure uniform exposure. After overnight dark adaptation, animals were exposed to bright (1000 lux) light for 24h, from a white fluorescent source. Exposure began and ended at 9.00am.


title: Rat retina_PBM + Light Damage_ rep2


title: Rat retina_PBM + Light Damage_ rep1


title: Rat retina_Light Damage_ rep3

description: Gene expression data from rat retina. Animals were raised in normal 5lux light before being exposued to damaging 1000lux light for 24 hrs.

source_name: retina, exposed to 24hrs 100lux light

treatment_protocol: The animals were kept individually in plexiglass cages, with food kept on the floor of the cages and water offered from transparent containers, to ensure uniform exposure. After overnight dark adaptation, animals were exposed to bright (1000 lux) light for 24h, from a white fluorescent source. Exposure began and ended at 9.00am.


title: Ts1Cje neurospheres, biological rep3

city: East Melbourne

first: Chelsee

middle: A

last: Hewitt

state: VIC

address: St Andrews Place

department: Pathology

institute: The Peter MacCallum Cancer Centre

hyb_protocol: Labelled RNA samples were hybridised onto Affymetrix GeneChip Mouse Genome 430 2.0 Arrays according to the AGRFs protocol. Samples were prepared for hybridisation to the GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that included 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using a GeneChip scanner 3000 with the scanner operating software, GCOS.

data_processing: Expression data were pre-processed and normalized using the gcRMA algorithm.

source_name: Ts1Cje 7 day old neurosphere culture, generated from neural stem cells and progenitors isolated from adult lateral walls of the lateral ventricles

label_protocol: RNA was processed according to the Australian Genome Research Facility (AGRF) protocol using the Two-Cycle Target cDNA synthesis kit (Millenium Sciences cat no. 900432), GeneChip Eukaryotic poly-A RNA spikes (Millenium Sciences cat no. 900433), Affymetrix GeneChip Sample CLeanup kit (Millenium Sciences cat no. 900371) and Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449) according to the manufacturer's instructions.

growth_protocol: Neural stem cells and progenitors were isolated from the lateral walls of the lateral ventricles from 84 day year old Ts1Cje and littermate control C57BL/6 mice and cultured for 7 days in medium described previously in Merson et al., J Neurosci 2006; 26: 11359-70.

extract_protocol: Total RNA was extracted using a Qiagen Rneasy micro kit according to the manufacturer's instructions with a Dnase I digestion step.

tag: gender

value: Female

value: Ts1Cje on C57BL/6 background

tag: sample type

value: neurospheres

tag: culture age

value: 7 day


title: C57BL/6 neurospheres, biological rep3

source_name: C57BL/6 7 day old neurosphere culture, generated from neural stem cells and progenitors isolated from adult lateral walls of the lateral ventricles


title: Rat retina_Light Damage_ rep2


title: Rat retina_Light Damage_ rep1


title: C57BL/6 neurospheres, biological rep2


title: Ts1Cje neurospheres, biological rep2


title: BRCAx Breast tumor 60312 4302743297_B DNA

city: Brisbane

first: Nic

last: Waddell

address: St Lucia

institute: Queensland Centre for Medical Genomics

hyb_protocol: Standard Illumina hybridization protocol to CNV370 duo beadarrays

data_processing: The samples were preprocessed in Illumina's Genomestudio

label: C-Bio and A-DNP

source_name: kConFab

label_protocol: Standard Illumina Infinium protocol

extract_protocol: Frozen sections of 10 um were macrodissected with a needle to ensure that the neoplastic content was >75%. DNA was extracted by the salting-out method followed by a phenol chloroform extraction

value: Breast Tumour

tag: mutation status

value: BRCAx


title: BRCA2 Breast tumor 80654 4240263181_B DNA


title: BRCA1 Breast tumor 11396 4302743295_A DNA


title: BRCA1 Breast tumor 70441 4240263178_A DNA


title: BRCA1 Breast tumor 70672 4240263150_A DNA


title: BRCA1 Breast tumor 10164 4302743339_A DNA


title: Rat retina_Saffron_ rep3

description: Gene expression data from rat retina exposued to normal light levels and 3 weeks of 1mg/kg/day of saffron.

source_name: retina, pretreatment saffron, 1mg/kg/day for 3 weeks

treatment_protocol: Animals were fed saffron at 1mg/kg/day, for 3w. Saffron (stigmata of Crocus sativus, from the Abbruzzo region in Italy) was soaked in water (at 2mg of spice/ml H2O) and 12h was allowed for the major anti-oxidants, which are water-soluble, to dissolve fully. The solute was then fed to the rats injecting a small volume into a piece of the vegetable matrix, which the animal readily ingested. The volume for each daily feed was calculated to provide the solutes from 1mg of saffron/kg body weight. Tissue was collected 24h after the last feed.

tag: strain


title: BRCA1 Breast tumor 20034 4240263181_A DNA


title: BRCA2 Breast tumor 50642 4240263153_A DNA


title: Rat retina_Saffron_ rep2


title: pAGMK2 vs 10-87LP2

city: Bethesda

first: Andrew

middle: M

last: Lewis

address: 29 Lincoln Drive

department: Division of Viral products

institute: Food and Drug Adminstration

hyb_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2).  For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.

organism: Chlorocebus aethiops

source_name: African Green Monkey Kidney Cells

label_protocol: The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: Cells from the World Health Organization (WHO) VERO cell bank 10–87 (ATCC 10–87 VERO cells) were serially passaged in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) (DMEM-10) from p134 to p250 by sub-culturing VERO cells before they reached confluence

extract_protocol: Total RNA was extracted and purified using the miRNeasy mini kit according to the manufacturer’s procedures (Qiagen Inc., Valencia, CA).

treatment_protocol: The cell lines has been passed in culture under low density condition and Total RNA (including miRNAs) was extracted at passage 148.

tag: cell type

value: non-tumorigenic

tag: cell line

value: VERO

source_name: Primary African Green Monkey Kidney Cells

growth_protocol: The primary cells were seeded at 2 million cells and grown in Dulbeccoâ€™s Modified Eagleâ€™s Medium (DMEM) containing 10% fetal bovine serum (FBS) (DMEM-10) for 18 h.

treatment_protocol: Primary cells was purchased from Diagnostic Hybrids (Athens, Ohio) and Total RNA (including miRNAs) has been extracted up on arrival.

value: Primary cells

value: pAGMK


title: pAGMK3 vs 10-87LP3

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

source_name: Primary African Kidney Cells


title: Pol2 IP from rpb1-1 cells 15 min with diamide [time course 3]

value: diamide

value: 15 min


title: 10-87LP3 vs 10-87T3

source_name: African Green Monkey Kidney cells

treatment_protocol: The cell line has been passaged in culture under low density condition. Total RNA (including miRNAs) has been extracted up on arrival.

growth_protocol: Cells from the World Health Organization (WHO) VERO cell bank 10–87 (ATCC 10–87 VERO cells) were serially passaged in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) (DMEM-10) from p134 to p250 by sub-culturing VERO cells before they reached confluence.

treatment_protocol: The cell lines has been passed in culture under low density condition and Total RNA (including miRNAs) was extracted at passage 250.

value: tumorigenic


title: pAGMK1 vs 10-87LP1

growth_protocol: The primary cells were seeded at 2 million cells and grown in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) (DMEM-10) for 18 h.


title: BRCAx Breast tumor 20069 4239123864_A DNA


title: Ts1Cje neurospheres, biological rep1


title: C57BL/6 neurospheres, biological rep1


title: BRCAx Breast tumor 60681 4239123863_A DNA


title: 10-87LP3 vs 10-87HP3

treatment_protocol: The cell lines has been passaged in culture under low density condition. Total RNA (including miRNAs) has been extracted at passage 148.


title: BRCA2 Breast tumor 51010 1922058669_A DNA


title: Rat retina_PBM_ rep2

description: Gene expression data from rat retina exposued to normal light levels and 5 days of 3 mins/day PBM.

source_name: retina, pretreatment PBM, 3mins each day for 5 days

treatment_protocol: Animals were exposed to 670nm red light from a WARP 75 source (Quantum Devices Inc, Barneveld, WI, USA). Animals were handled gently over several days until they were adapted to handling, Each was then gently restrained with a towel and held under a plexiglass platform with the head ~2.5cm below the platform. The WARP75 device was placed on top of the platform and turned on for 3 min. This arrangement provided a fluence of10J/cm2 at the eye. The animals did not hide from or appear agitated by the red light. Animals were treated in this way once daily for 5 days, at 9.00 am. Tissue was collected 24h after the last treatment.

value: Sprague Dawley

value: retina


title: BRCA1 Breast tumor 20091 4239123862_A DNA


title: Rat retina_PBM_ rep3

value: Adult P80 - 120


title: Rat retina_Saffron_ rep1


title: Rat retina_PBM_ rep1


title: 10-87LP2 vs 10-87HP2

source_name: African Green Monkey Kdney cells

source_name: African Green Monkey Kideny Cells


title: Rat retina_Control_ rep3

description: Gene expression data from rat retina exposued to normal light levels

source_name: retina, control, no pretreatment and normal light


title: BRCAx Breast tumor 50467 1922058678_A DNA


title: 10-87LP1 vs 10-87T1

extract_protocol: Total RNA from pAGMK cells and the cell lines was extracted and purified using the miRNeasy mini kit according to the manufacturer’s procedures (Qiagen Inc., Valencia, CA).

source_name: A cell line was established from a tumor formed in newborn nude mouse following subcutaneous inoculation of 10-87HP cells

treatment_protocol: The cell lines has been established from tumor. Total RNA (including miRNAs) has been extracted.


title: BRCA1 Breast tumor 30130 4239123853_A DNA


title: BRCAx Breast tumor 20031 1922058656_A DNA


title: Dreducens_Ureduction_T3_R3

status: Public on Jul 15 2010

city: Neuchâtel

first: Pilar

last: Junier

address: Rue Emile-Argand 11

department: Institute of Biology

country: Switzerland

institute: University of Neuchâtel

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the third of three biological replicates used in this experiment, each from separate cultures. RNA extracted after exponential phase (T3= 44 hours)

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

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

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

organism: Desulforamulus reducens MI-1

source_name: Desulfotomaculum reducens MI-1

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

growth_protocol: Standard anaerobic conditions were used throughout the study (Balch et al., 1979). Widdel low phosphate (WLP) medium, modified from Widdel and Bak (1992), was used for all the experiments. The constituents of the WLP medium were as follows (per liter): NH4Cl, 0.25 g; CaCl2.2H2O, 0.1 g; MgCl2.6H2O, 0.5 g; NaCl, 5 g; KCl, 0.5 g; and KH2PO4, 0.03 g, vitamins and trace elements. The medium was dispensed in 100 mL volumes into 200 mL glass serum bottles and autoclaved. The following solutions were added from sterile anaerobic stocks (final concentration): yeast extract, 0.05%; NaHCO3, 30 mM; 1,4-piperazinediethane sulfonic acid disodium salt monohydrate (PIPES), 20 mM; pyruvic acid, 20 mM (unless indicated otherwise). The final pH of the medium was 7.2 ± 0.2.  All cultures were grown in a 100% N2 atmosphere.

extract_protocol: The cultures were sampled (16 mL) for RNA extraction at the time point targeted for the expression analysis.  Samples were collected in a RNAse-free 50 mL Falcon tube by centrifugation at 7000xg for 7 minutes and resuspended in 400 µL of 3 mg/ml lysozyme in TE buffer (pH 8.0) and mixed by vortexing. After digestion for 10 minutes at room temperature 1.4 mL of Buffer RLT (Qiagen) containing freshly added 0.01% vol/vol β-mercaptoethanol, was added to the sample and mixed vigorously by vortexing. The homogenized cell lysates were stored at –80oC. After all the samples were collected, the cell lysates were thawed for 15 min at 37 oC in a water bath to dissolve salts. The samples were separated into four equal aliquots of 450 µL. RNA extraction was carried out using the RNeasy extraction kit (Qiagen) with on column DNAse treatment (Qiagen). The quantity and quality of the RNA were evaluated with a Nanodrop spectrophotometer (Thermo Scientific). RNA from the four aliquots was combined and precipitated using 0.1 volume of 1M sodium acetate and 2.5 volumes cold 95% ethanol, incubating overnight at –20oC. RNA was collected by centrifugation for 15 min at 12,000xg at 4oC and washed with 75% ethanol. RNA was dried at 37oC for 20 min and resuspended in 30 µL RNAse free water. RNA concentration and quality were re-measured using the Nanodrop and the Bioanalyzer (Agilent). A total of 20 µg of total RNA per sample was sent to Nimblegen Systems (Roche) for cDNA synthesis, labeling with Cy3, and hybridization onto a custom-designed 4x77K microarrays

treatment_protocol: For experiments with U(VI) and sulfate, 100 µM U(VI) (as uranyl acetate) and 20 mM sulfate (as Na2SO4) were added, respectively.

tag: growth condition

value: Uranium reduction


title: 10-87LP2 vs 10-87T2

source_name: cell line  established from a tumor formed in newborn nude mouse following subcutaneous inoculation of 10-87 HP cells

treatment_protocol: The cell lines has been established from tumor and Total RNA (including miRNAs).


title: 10-87LP1 vs 10-87HP1

source_name: African green monkey kidney cell line

treatment_protocol: The cell lines has been passaged in culture under low density condition. Total RNA (including miRNAs) has been extracted at passage 250.


title: Rat retina_Control_ rep2


title: Dreducens_Ureduction_T3_R2

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the second of three biological replicates used in this experiment, each from separate cultures. RNA extracted after exponential phase (T3= 44 hours)


title: Dreducens_Ureduction_T3_R1

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the first of three biological replicates used in this experiment, each from separate cultures. RNA extracted after exponential phase (T3= 44 hours)


title: BRCAx Breast tumor 12655 1922058667_A DNA


title: Dreducens_Ureduction_T2_R3

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the third of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2=30 hours)


title: Dreducens_fermentation_T3_R1

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the first biological replicate used in this experiment. RNA extracted after exponential phase (T3= 44 hours)

value: Pyruvate fermentation


title: Rat retina_Control_ rep1


title: Dreducens_Ureduction_T2_R1

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the first of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2=30 hours)


title: Dreducens_Ureduction_T2_R2

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the second of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2=30 hours)


title: BRCA2 Breast tumor 20444 1922058585_A DNA


title: Dreducens_fermentation_T2_R2

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the second of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2= 30 hours)


title: Dreducens_fermentation_T2_R1

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the first of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2= 30 hours)


title: BRCAx Breast tumor 90473 1922058585_B DNA


title: Dreducens_fermentation_T2_R4

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the fourth of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2= 30 hours)


title: BRCAx Breast tumor 61761 4240263194_A DNA


title: BRCA1 Breast tumor 70020 1922058555_A DNA


title: BRCAx Breast tumor 21349 4240263189_A DNA


title: BRCA1 Breast tumor 80553 1922058584_A DNA


title: Dreducens_SO4reduction_T4_R4

description: This sample is of Desulftomaculum reducens MI-1 growing by sulfate respiration (20 mM of SO4-2) using pyruvate as an electron donor. It is the fourth of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T4= 10 hours)

value: Sulfate reduction


title: BRCAx Breast tumor 60584 1922058554_A DNA


title: Dreducens_Ureduction_T2_R4

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the fourth of four biological replicates used in this experiment, each from separate cultures. RNA extracted in late exponential phase (T2=30 hours)


title: Dreducens_SO4reduction_T4_R3

description: This sample is of Desulftomaculum reducens MI-1 growing by sulfate respiration (20 mM of SO4-2) using pyruvate as an electron donor. It is the third of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T4= 10 hours)


title: Dreducens_SO4reduction_T4_R2

description: This sample is of Desulftomaculum reducens MI-1 growing by sulfate respiration (20 mM of SO4-2) using pyruvate as an electron donor. It is the second of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T4= 10 hours)


title: Dreducens_SO4reduction_T4_R1

description: This sample is of Desulftomaculum reducens MI-1 growing by sulfate respiration (20 mM of SO4-2) using pyruvate as an electron donor. It is the first of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T4= 10 hours)


title: Dreducens_Ureduction_T1_R4

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the fourth of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)


title: Dreducens_Ureduction_T1_R3

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the third of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)


title: Dreducens_Ureduction_T1_R1

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the first of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)


title: Dreducens_fermentation_T1_R4

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the fourth of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)


title: Dreducens_Ureduction_T1_R2

description: This sample is of Desulftomaculum reducens MI-1 growing in the presence of 100 uM U(VI) using pyruvate as an electron donor. It is the second of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)


title: Dreducens_fermentation_T1_R3

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the third of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)


title: Dreducens_fermentation_T1_R2

description: This sample is of Desulftomaculum reducens MI-1 growing by fermentation of pyruvate. It is the second of four biological replicates used in this experiment, each from separate cultures. RNA extracted in mid-exponential phase (T1= 26 hours)