title: chd1D_H3K36me3

hyb_protocol: Labeled probes (a mixture of Cy5 labeled input and Cy3 labeled ChIPed material) were hybridized onto an Agilent yeast 4x44 whole genome array. The arrays were scanned at 5 micron resolution with the Agilent array scanner. Image analysis and data normalization were performed as previously described [1].

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent High Resolution C fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy3/Cy5) were calculated to produce the values given in the data table.

growth_protocol: WT and mutant cells were grown to log phase in YPD media at 30°C

extract_protocol: Cells were washed in water, digested with zymolyase and then treated with micrococcal nuclease.  Immunoprecipitations were performed with extract equivalent to 100 ml of cell culture in the following volumes: 10μl anti-H3K36me3 (Abcam polyclonal), or 7μl anti-H3K4me3 (Millipore monoclonal). Immunoprecipitation, washing, protein degradation, and DNA isolation were performed as previously described [2].

tag: antibody/vendor

value: Abcam


title: WT_H3K36me3

status: Public on Jun 08 2012

type: genomic

city: Santa Cruz

first: Grant

middle: A

last: Hartzog

state: CA

address: 349 Sinsheimer Labs

department: MCD Biology

country: USA

institute: UC Santa Cruz

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: DNA samples were amplified, with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification method described previously [1].  2.5 micrograms of aRNA produced from the linear amplification were labeled via the amino-allyl method as described on www.microarrays.org.

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: strain

tag: genotype/variation

value: wild type

tag: antibody


title: Primary_melanoma MEL176

type: RNA

city: Nashville

first: Leon

last: Raskin

state: TN

address: 2525 West End Avenue, Suite 300

department: Medicine

institute: Vanderbilt University

description: amplified using Nugen WT-Ovation™

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Expression data on 76 samples and 54,675 probes on U133 Plus 2.0 array were first subjected for quality assessment by creating the density plot of the log-intensity and RNA degradation plot corresponding to each sample. For all 76 samples, MAS 5.0-calculated signal intensities were normalized using the quantile normalization procedure implemented in robust multiarray analysis and the normalized data were log 2 transformed. Filtering was done to exclude probe sets that were not expressed or probe sets that exhibited low variability across samples. Expression values were required to be above the lower quartile of all expression measurements in at least 25% of samples, and the interquartile range across the samples on log 2 scale was required to be at least 0.5. After preprocessing and quality assessment, 74 samples and 44,137 probe sets were subjected to further analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Frozen half of the melanoma punch biopsy

label_protocol: The RNA samples were labeled with IVT labelling kit according to manufacturer's instructions.

extract_protocol: Frozen blocks were microdissected and total RNA was extracted using TRIzol protocol and Qiagen RNeasy purification kit according to the manufacturer's instructions.

tag: gender

value: m

tag: age at diagnosis

tag: diagnosis

value: SSM

tag: regional metastases

value: NO

tag: distant metastases

value: YES

tag: braf mutation status

tag: nras mutation status

value: WT


title: wt_Rpb3 dye flip

hyb_protocol: Labeled probes were hybridized onto an Agilent yeast 4x44 whole genome array. The arrays were scanned at 5 micron resolution with the Agilent array scanner. Image analysis and data normalization were performed as previously described [1].

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent High resolution C fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

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

source_name: WT_Rpb3_input dye flip

growth_protocol: WT and mutant cells were grown to an OD of 0.5 in YPD media at 30°C.

extract_protocol: DNA was isolated from mononucleosomal cell extract or from an anti-Rpb3 immunoprecipitate of that extract via proteinase K digestion and phenol:chloroform extraction, and amplified by TLAD.

source_name: WT_Rpb3_IP dye flip


title: chd1D_H3K4me3

value: Millipore


title: BC180_SCNT7711

city: Jouy en Josas

first: Isabelle

last: Hue

address: Domaine de Vilvert

department: PHASE

country: France

institute: INRA

description: Embryonic stage was defined by "Brachuyry" ISH on the embryonic disc (Hue et al. 2001). SCNT: somatic cell nuclear transfer. Donor cells: skin-ear fibroblasts from 3 different Holstein cows: 5538, 7711, 029. Syntax of the sample names: embryoName_ReproductionMode. Where the reproduction mode is either IVP, SCNT-0029, SCNT-771 and SCNT-5538.

hyb_protocol: Prehybridisation in ExpressHybTM Hybridization Solution (Clontech) at 68°C during 1h (14ml). Hybridisation using new ExpressHybTM Hybridization Solution (Clontech) at 68°C overnight (10ml). Arrays were washed four times in 2X SSC, 1% SDS and once in 0.1X SSC, 0.5% SDS at 68°C for 30 min each. They were then exposed to phosphor-screens (Amersham) for 5 days.

scan_protocol: Scanner: STORM 760 from Molecular Dynamics - Raw data set : Feature extraction with Imagene 5.1 software from BioDiscovery (Proteigene)

data_processing: Intensity = Signal Mean - Normalization = Signal mean were log2 transformed and normalized by the mean of the all intensities on the array

organism: Bos taurus

source_name: reproduction mode: SCNT-7711

label_protocol: aRNA was retro-transcribed and directly labelled with [alpha-33P]dATP as described  (Degrelle et al., 2008). 500ng of aRNA was mixed with 500ng of random hexamers in a volume of 25µl. The mixture was incubated at 70°C for 10 min and chilled on ice. cDNA was synthesised by the addition of 5µl 10X PCR buffer, 5µl 25mM MgCl2, 5 µl 0,1 mM DTT, 2,5µl 10mM mix dGTP, dCTP and dTTP, 2,5µl water, 50 µCi [alpha-33P]dATP and 200U Superscript II (Invitrogen) at 42°C for 50min. The RNA template was removed by the addition of 1µl RNAse H- and incubation at 37°C for 20 min. Labelled targets were then purified on Sephadex columns (G-50).

extract_protocol: IVT amplified RNA from each sample was synthesized with the MessageAmpTM aRNA Kit (Ambion) according to Degrelle et al., 2008 (RT on 1µg total RNA, IVT during 10h). aRNA was purified on Mini Quick Spin RNA columns (Roche Diagnostic).

treatment_protocol: Tissues were collected and immediately snap-frozen. Total RNA from IVP and SCNT embryos were extracted with TrizolTM (Invitrogen). RNA quality was first verified by A260/280 absorbance ratios.

tag: embryo name

tag: Stage

value: embryonic

tag: somatic tissue

value: no

tag: reproduction mode


title: BC183_SCNT7711


title: Primary_melanoma MEL185

description: amplified using Nugen WT-Ovation™

value: f


title: Week 10 2 aortic arch

city: Stockholm

first: Johan

middle: Lars Markus

last: Björkegren

state: Stockholm

address: Scheelesv. 2

department: The Department of Medical Biophysics and Biochemistry

country: Sweden

institute: The Vascular Biology Unit

description: Gene expression data from aortic arch at week 10

hyb_protocol: According to the standard Affymetrix protocols.

scan_protocol: According to the standard Affymetrix protocols using GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (Affymetrix) using default analysis settings.

organism: Mus musculus

source_name: Week 10 2 aortic arch

label_protocol: Biotinylated cRNA were prepared using the 2-cycle protocol according to the standard Affymetrix protocols.

extract_protocol: Aortas were perfused with RNAlater (Qiagen), and the aortic arch from above the third rib to the aortic root was removed and homogenized with FastPrep (Qbiogene). Total RNA was isolated with RNeasy Mini Kit (Qiagen) using a DNAse I treatment step. RNA quality was assessed with a Bioanalyzer 2100 (Agilent Technologies).

tag: tissue

value: Atherosclerotic aortic arch

tag: age

value: 10 wk

tag: genotype

value: Ldlr-/-, Apob100/100, Mttp flox/flox Mx1-Cre

tag: genetic background

value: mixed C57BL/6


title: top1Dchd1D_H3K36me3

tag: strain

tag: genotype/variation

tag: antibody/vendor


title: Primary_melanoma MEL173

description: amplified using Nugen WT-Ovation™

tag: gender

tag: age at diagnosis


title: NR4 B cells, 2h anti-IgM stimulation, biological replicate 3

city: Darlinghurst

first: Pablo

middle: Alejandro

last: Silveira

state: NSW

address: 384 Victoria St

department: Immunology Program

country: Australia

institute: Garvan Institute

description: Gene expression data from splenic NR4 B cells cultured for 2h with anti-IgM stimulation

hyb_protocol: 10ug of fragmented RNA was hybridised for 16h at 45C on Affymetrix Mouse Genome 4.30 2.0 Arrays. Washing and staining performed as per manufacturer's instruction on Affymetrix Fludics Station 450 instrument.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 laser confocal slide scanner (Affymetrix).

data_processing: Analysis of data was performed using GeneSpring 12.0 software (Agilent).  Samples were preprocessed with RMA. All samples were normalised on a per gene basis to the median of total samples. The data was filtered for genes which had a raw expression level of >50 in at least one sample.

source_name: Splenic NR4 B cells, 2h culture with anti-IgM stimulation

label_protocol: Following reverse transcription with an Oligo(dT)-T7 primer (Affymetrix, Santa Clara, Ca), double stranded stranded cDNA was synthesized with the GeneChip® Expression 3’-Amplification One-cycle kit (Affymetrix, Santa Clara, Ca).  In an in vitro (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified and labeled with biotinylated nucleotides (Affymetrix).

extract_protocol: Trizol extraction of total RNA from cultured cells was performed according to the manufacturer's instructions and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Purified B cells from each lot were resuspended at 1x10<7> cells/ml for 2h in complete RPMI media alone or with 10µg/ml AffiniPure goat anti-mouse IgM F(ab’)2 fragments.

value: female

value: NOD.NOR-Chr4/DvsJ (NR4)

value: 6 weeks

tag: cell type

value: splenic B cells

tag: stimulation

value: anti-IgM stimulated


title: Primary_melanoma MEL190

description: amplified using Nugen WT-Ovation™

value: m

tag: diagnosis

value: MIS

tag: regional metastases

tag: distant metastases

tag: braf mutation status


title: WT_H3K4me3

value: wild type

tag: antibody


title: NR4 B cells, 2h anti-IgM stimulation, biological replicate 1


title: NR4 B cells, 2h anti-IgM stimulation, biological replicate 2


title: Primary_melanoma MEL157

description: amplified using Nugen WT-Ovation™

value: NODULAR MELANOMA

value: WT

tag: nras mutation status


title: BC192_SCNT7711

tag: embryo name

tag: Stage

value: embryonic

tag: somatic tissue

tag: reproduction mode


title: NR4 B cells, 2h unstimulated, biological replicate 3

description: Gene expression data from splenic NR4 B cells cultured for 2h without stimulation

source_name: Splenic NR4 B cells, 2h culture without stimulation

tag: strain

tag: age

value: unstimulated


title: NR4 B cells, 2h unstimulated, biological replicate 1


title: top1Dchd1D_H3K4me3

tag: genotype/variation

tag: antibody/vendor

value: Millipore


title: NR4 B cells, 2h unstimulated, biological replicate 2

tag: gender


title: top1d_H3K36me3

value: Abcam


title: Primary_melanoma MEL142

description: amplified using Nugen WT-Ovation™

tag: age at diagnosis

value: SSM


title: BC160_SCNT7711

value: no


title: BC158_SCNT7711


title: BC123_SCNT7711


title: top1d_H3K4me3


title: wtFlagH3overH3 bio rep 2

description: biological replicate

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 5.1 analysis software.

data_processing: After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (FlagH3/TotalH3) were calculated to produce the values given in the data table.

growth_protocol: Strains transformed with pGAL-H4-FlagH3 were grown to ~1.2x107 cells/ml in SC-Ura media with raffinose as the carbon source. Cells were G1 arrested with alpha factor and Flag-H3/H4WT expression was induced by addition of galactose (2% final concentration) for 60 minutes.

extract_protocol: Fixed cells were disrupted by bead beating and chromatin was sonicated using a Diagenode Bioruptor to obtain an average size of 500 bp. Chromatin was immunoprecipitated using 40 Microliter (1:2 slurry) Anti-Flag M2 Affinity gel (A2220; Sigma) or 1 ug of a rabbit polyclonal antibody against the C- terminus of H3 (ab1791; Abcam). Chelex 100 resin (BioRad) was added to the immunoprecipitated material and Input-DNA samples, and the suspensions were placed at 100°C for 10 minutes to reverse crosslinks. Samples were treated with proteinase K and DNA was recovered.  The immunoprecipitated DNA was initially PCR amplified using random hexamer primers as described in [1]. The number of cycles used to amplify the samples was adjusted to between 28 and 37 so that there was equal amplification of DNA in the IP vs. Flag-tagged H3 and the IP vs. total H3 samples. Amplified DNA was visualized on a 1% agarose gel and checked for a visible smear of DNA between 500 and 1.2 kB.

value: Anti-Flag M2

tag: antibody vendor/catalog#


title: Primary_melanoma MEL135

description: amplified using Nugen WT-Ovation™

tag: diagnosis

value: NO


title: chd1DFLAGH3overH3 bio rep 2

description: biological replicate

value: polyclonal antibody against the C- terminus of H3


title: BC107_SCNT7711


title: BC122_SCNT7711


title: chd1DH3overFLAGH3 tech rep 1

description: technical replicate of 11335d_chd1dH3overFLAGH3


title: Primary_melanoma MEL131

description: amplified using Nugen WT-Ovation™

tag: regional metastases

value: YES


title: Primary_melanoma MEL128

description: amplified using Nugen WT-Ovation™

tag: distant metastases


title: NOD B cells, 2h unstimulated, biological replicate 3

description: Gene expression data from splenic NOD B cells cultured for 2h without stimulation

source_name: Splenic NOD B cells, 2h culture without stimulation

value: female

value: NOD/ShiLtJ (NOD)

value: 6 weeks

tag: cell type

value: splenic B cells

tag: stimulation


title: NOD B cells, 2h anti-IgM stimulation, biological replicate 2

description: Gene expression data from splenic NOD B cells cultured for 2h with anti-IgM stimulation

source_name: Splenic NOD B cells, 2h culture with anti-IgM stimulation

value: anti-IgM stimulated


title: NOD B cells, 2h anti-IgM stimulation, biological replicate 1


title: Normal_skin N356

description: amplified using Nugen WT-Ovation™

source_name: Frozen tip of melanoma excision

value: m

value: NORMAL SKIN

value: not applicable

tag: braf mutation status

tag: nras mutation status


title: Primary_melanoma MEL145

description: amplified using Nugen WT-Ovation™

value: WT


title: NOD B cells, 2h unstimulated, biological replicate 2

value: unstimulated


title: cdc55 msn24 20min

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

hyb_protocol: 325ng of both Cy3 and Cy5 labeled cRNA were hybridized to the S. cerevisiae AMADID GE 8x15K G4813A arrays. Samples were hybridized for 17 hours in G2545A Hybridization Oven.

scan_protocol: Agilent G2565A Microarray Scanner System was used to scan the arrays.

data_processing: Agilent Feature Extraction program (Version FE 10.5.1.1), separation of red and green gPS data for further evaluation. Features with signals below 100 units were discarded.

source_name: whole cell extract

label_protocol: 1 µg of total RNA was used for labeling reaction (Agilent Quick Amp Labeling Kit, two-color, Cat.Nr. 5190-0444). The standard Agilent Protocol for two-color labeling was used, Publication Number: G4140-90050 v.6.0).

growth_protocol: Cells were grown for 4 generations in 50ml cultures in YPD at 30°C to OD600nm of about 1. before NaCl was added to a final concentration of 0.4M. After 10, 20 and 30 minutes cells were harvested and immediately frozen.

extract_protocol: Total RNA was isolated using glass beads and phenol/chloroform extraction.

treatment_protocol: Hyperosmotic stress: NaCl was added to a final concentration of 0.4M.

tag: treatment

value: 0.4M NaCl

tag: time

tag: genotype

value: cdc55 msn24


title: cdc55 msn24 30min


title: cdc55 msn24 10min


title: wtFLAGH3overH3 bio rep 1

description: biological replicate

tag: strain

tag: antibody

value: wild type


title: chd1DFLAGH3overH3 bio rep 1

description: biological replicate

value: Anti-Flag M2

tag: genotype/variation


title: Normal_skin N307

description: amplified using Nugen WT-Ovation™


title: Primary_melanoma MEL101

description: amplified using Nugen WT-Ovation™

value: DESMOPLASTIC MELANOMA

value: NO


title: wtH3overFLAGH3 tech rep 1

description: technical replicate of 11335a_wtFLAGH3overH3

value: polyclonal antibody against the C- terminus of H3


title: msn24 20min


title: msn24 30min


title: cdc55 msn24 0min


title: Normal_skin N298

description: amplified using Nugen WT-Ovation™


title: Normal_skin N290

description: amplified using Nugen WT-Ovation™

value: f


title: NOD B cells, 2h unstimulated, biological replicate 1

value: female

value: NOD/ShiLtJ (NOD)

tag: age


title: msn24 10min


title: cdc55 30min


title: Normal_skin N287

description: amplified using Nugen WT-Ovation™

tag: gender


title: Normal_skin N280

description: amplified using Nugen WT-Ovation™

tag: age at diagnosis


title: cdc55 20min


title: msn24 0min


title: Normal_skin N288

description: amplified using Nugen WT-Ovation™


title: Normal_skin N275

description: amplified using Nugen WT-Ovation™


title: Normal_skin N236

description: amplified using Nugen WT-Ovation™


title: Normal_skin N273

description: amplified using Nugen WT-Ovation™


title: Normal_skin N206

description: amplified using Nugen WT-Ovation™


title: bcl6 knockout macrophages, biological rep2

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description:
Age: 16 wks old, 6 weeks post-bone marrow transplant with Bcl6-/- marrow, male
Gene expression data from BCL6 KO macrophages

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with MG430 2.0 arrays, washed and processed in accordance with standard Affymetrix protocols.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: BCL6 KO bone marrow-derived macrophages

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

growth_protocol: Bone marrow was purified and differentiated in DMEM containing 20% fetal bovine serum, 30% L929 conditioned media, and antibiotics for 5 days, then re-plated in macrophage serum free media (Invitrogen) overnight prior to harvesting via Trizol lysis.

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

value: BCL6 knockout

tag: genetic background

tag: tissue

value: bone marrow-derived macrophages


title: Wild-type macrophages, biological rep2

description:
Age: 16 wks old, 6 weeks post-bone marrow transplant with Bcl6+/+ marrow, male
Gene expression data from WT macrophages

source_name: C57/BL6 bone marrow-derived macrophages

value: wild-type


title: Normal_skin N243

description: amplified using Nugen WT-Ovation™

value: m

tag: diagnosis

value: NORMAL SKIN

tag: regional metastases


title: bcl6 knockout macrophages, biological rep1


title: Normal_skin N201

description: amplified using Nugen WT-Ovation™

value: not applicable

tag: distant metastases


title: cdc55 0min


title: WT 0min

value: WT


title: WT 10min

value: 0.4M NaCl


title: WT 20min


title: cdc55 10min


title: Normal_skin N157

description: amplified using Nugen WT-Ovation™


title: Normal_skin N173

description: amplified using Nugen WT-Ovation™


title: WT 30min


title: Wild-type macrophages, biological rep1


title: Normal_skin N118

description: amplified using Nugen WT-Ovation™


title: Antirrhinum_majus_sepal_day-3_rep1

status: Public on Jun 07 2012

city: West Lafayette

first: Natalia

last: Dudareva

state: Indiana

address: 625 Agriculture Mall Drive

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested three days before anthesis. It is the first of three biological replicates used in this experiment.

hyb_protocol: Hybridization was performed by MOgene LC (St. Louis, MO, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by MOgene LC (St. Louis, MO, USA), using the NimbleScan 2.3 extraction software and 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 2.3 (Roche NimbleGen, Inc.).

organism: Antirrhinum majus

source_name: Antirrhinum majus cv. Maryland True Pink sepal d-3

label_protocol: Labeling was performed by MOgene LC (St. Louis, MO, USA), using Cy3-labeled 9-mer probes as a dye and following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Antirrhinum majus cv. Maryland True Pink was grown under standard greenhouse condition.

extract_protocol: Total RNA was extracted from ground frozen tissue using the RNeasy  Plant Mini kit (Qiagen Inc., Valencia, CA, USA) and sent overnight on dry ice to MOgene LC (St. Louis, MO, USA).

tag: cultivar

value: Maryland True Pink

value: Wild-type

value: Sepal

tag: developmental stage

value: Three days before anthesis


title: Antirrhinum_majus_sepal_day-3_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested three days before anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_sepal_day4_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested four days after anthesis. It is the first of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink sepal d4

value: Four days after anthesis


title: Antirrhinum_majus_sepal_day7_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested seven days after anthesis. It is the third of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink sepal d7

value: Seven days after anthesis


title: Antirrhinum_majus_sepal_day4_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested four days after anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_sepal_day1_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested the day of anthesis. It is the first of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink sepal d1

value: Day of anthesis


title: Antirrhinum_majus_petal_day1_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested the day of anthesis. It is the first of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink petal d1

value: Petal


title: Antirrhinum_majus_sepal_day7_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested seven days after anthesis. It is the first of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day4_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested four days after anthesis. It is the first of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink petal d4


title: Antirrhinum_majus_sepal_day1_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested the day of anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day7_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested seven days after anthesis. It is the first of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink petal d7


title: Antirrhinum_majus_petal_day1_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested the day of anthesis. It is the second of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day-3_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested three days before anthesis. It is the second of three biological replicates used in this experiment.

source_name: Antirrhinum majus cv. Maryland True Pink petal d-3


title: Antirrhinum_majus_petal_day-3_rep1

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested three days before anthesis. It is the first of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day1_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested the day of anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_sepal_day-3_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested three days before anthesis. It is the second of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day4_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested four days after anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_sepal_day1_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested the day of anthesis. It is the second of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day7_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested seven days after anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day4_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested four days after anthesis. It is the second of three biological replicates used in this experiment.


title: Antirrhinum_majus_petal_day-3_rep3

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested three days before anthesis. It is the third of three biological replicates used in this experiment.


title: Antirrhinum_majus_sepal_day4_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested four days after anthesis. It is the second of three biological replicates used in this experiment.


title: Antirrhinum_majus_sepal_day7_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink sepal tissue harvested seven days after anthesis. It is the second of three biological replicates used in this experiment.


title: WT.MEFs5

city: San Francisco

first: Yadong

last: Huang

address: 1650 Owens Street

institute: Gladstone Institute of Neurological Disease

description: Gene expression data from mouse embyronic fibroblasts

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 18 hr at 45C on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000 and processed using GCOS1.4.

data_processing: Raw intensities from the CEL files were analyzed using Affymetrix Power Tools (APT, version 1.10.1) to generate a RMA (robust multi-array average; Irizarry et al 2003) intensity on a log2 scale for each probe set and various quality metrics. The perfect match (PM) intensities per probe set were (i) background corrected; (ii) quantile-normalized (to make the distribution of intensities the same for all arrays); and (iii) summarized for each probe set using a robust fit of linear models.

label: Biotin

source_name: WT mouse embyronic fibroblast.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA according to the Expression Analysis Technical Manual of Affymetrix.

growth_protocol: Mouse iNSCs and NSC were cultured in NSC basal medium containing EGF (20 ng/ml), FGF-2 (20 ng/ml), and heparin (2 μg/ml). MEFs were cultured in DMEM +10% FBS.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The extracted total RNA was further purified with a Qiagen Rneasy Mini Kit.

treatment_protocol: All cells were washed with serum-free medium before collection

tag: cell type

value: mouse embryonic fibroblast


title: WT.NSC3

description: Gene expression data from mouse wildtype neural stem cells

source_name: WT mouse neural stem cell.3

value: neural stem cell


title: Antirrhinum_majus_petal_day7_rep2

description: This sample is of Antirrhinum majus cv. Maryland True Pink petal tissue harvested seven days after anthesis. It is the second of three biological replicates used in this experiment.


title: WT.MEFs1

source_name: WT mouse embyronic fibroblast.1


title: WT.MEFs3

source_name: WT mouse embyronic fibroblast.3


title: miNSC2.2

description: Gene expression data from mouse induced neural stem cells

source_name: Mouse induced neural stem cell.2.2

value: induced neural stem cell


title: miNSC1.2

source_name: Mouse induced neural stem cell.1.2


title: miNSC2.1

source_name: Mouse induced neural stem cell.2.1


title: miNSC1.3

source_name: Mouse induced neural stem cell.1.3


title: WT.NSC1

source_name: WT mouse neural stem cell.1


title: SCD 52

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from PBMC total RNA from sickle cell disease patients.

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Exon 1.0 ST Arrays per manufacturer’s instructions.

scan_protocol: Array scanning was performed according to the manufacturer's instruction by the Core Genomics Facility of  the University of Illinois at Chicago.

data_processing: The transcript expression data were summarized by RMA using the Affymetrix Power Tools v.1.12.0 and were later corrected for batch effect using the R COMBAT script.

source_name: Human peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

tag: ethnicity

value: African American

value: sickle cell disease

tag: right ventricular systolic pressure (mmhg)

tag: maximum tricuspid regurgitation jet velocity (m/s)


title: SCD 44


title: SCD 73


title: WT.NSC2

source_name: WT mouse neural stem cell.2


title: SCD 58


title: SCD 35


title: SCD 42


title: SCD 30


title: SCD 48


title: miNSC2.3

source_name: Mouse induced neural stem cell.2.3


title: SCD 34


title: SCD 37


title: SCD 32


title: miNSC1.1

source_name: Mouse induced neural stem cell.1.1


title: SCD 43


title: SCD 33


title: SCD 27


title: SCD 28


title: SCD 21


title: SCD 24


title: SCD 20


title: SCD 18


title: SCD 22


title: SCD 05


title: SCD 16


title: SCD 13


title: SCD 10


title: SCD 07


title: SCD 14


title: SCD 25


title: Avian influenza infected lung A1

city: Davis

first: Huaijun

address: RM 3307 Meyer Hall

institute: UC Davis

description: Four arrays are included in one slide

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program

organism: Gallus gallus

source_name: Lung

label_protocol: A 500 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

growth_protocol: The chickens were housed in negative pressure Horsfall-Bauer, temperature control isolation units and provided with water and commercial feed ad libitum.

extract_protocol: Lung samples were homogenized by tissue miser (Fisher Scientific, Houston, TX). Total RNA was isolated using Trizol (Invitrogen, CA)

treatment_protocol: The chicken was inoculated with 0.1 ml of CK/TX/02/H5N3 virus containing107.5 EID50/ml as infected group on day 7.

tag: breed

value: Broiler

value: day 7

tag: infection

value: CK/TX/02/H5N3 virus

value: lung

treatment_protocol: The chicken was inoculated with PBS as non-infected group on day 7.

value: Non-infected group


title: Avian influenza infected lung A2

description: Four arrays are included in one slide

value: Non-Infected group


title: HUVEC KDM3Aarray_KDM3AsiRNA_Normoxia

city: Tokyo

first: Imari

last: Mimura

address: 4-6-1 Komaba Meguro-ku

department: Laboratory for Systems Biology and Medicine

country: Japan

institute: Research Center for Advanced Science and Technology

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Affymetrix GeneChip Operating Software (GCOS) Version 1.0. with target intensity=100.

source_name: HUVEC KDM3Aarray_KDM3AsiRNA_Normoxia

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using Trizol (Invitrogen). 2 micrograms of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

tag: cell line

value: HUVEC

tag: sirna

tag: treatment

value: absensce of hypoxia


title: Avian influenza infected lung A3

description: Four arrays are included in one slide

tag: age


title: HUVEC KDM3Aarray_CtlsiRNA_Normoxia

source_name: HUVEC KDM3Aarray_CtlsiRNA_Normoxia

value: CtlsiRNA


title: Hypoxia profile 12hrs

source_name: HUVEC, hypoxia 12hrs

value: hypoxia

tag: time period


title: HUVEC HIF1array_HIF1siRNA_Hypoxia

source_name: HUVEC HIF1array_HIF1siRNA_Hypoxia

value: presence of hypoxia


title: HUVEC KDM3Aarray_CtlsiRNA_Hypoxia

source_name: HUVEC KDM3Aarray_CtlsiRNA_Hypoxia


title: Hypoxia profile 2hrs

source_name: HUVEC, hypoxia 2hrs


title: Hypoxia profile

source_name: HUVEC, hypoxia 1hr


title: HIF1array_HIF1siRNA_Normoxia

source_name: HUVEC, HIF1array_HIF1siRNA_Normoxia


title: T47D_iKR_noAP_yesR5020_6h_rep1

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description: Gene expression data from T47D cells stably expressing inducible K388R mutant PR vectors, no dimerizer AP21967 treatment but added PR ligand treatment. Replicate 1.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133A 2.0

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

data_processing: The data were analyzed with Bioconductor package simpleaffy in R using rma as normalization method.

source_name: iKR (inducible K388R mutant PR) cells treated with AP21967 vehicle (ethanol) and R5020 for 6 h

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

growth_protocol: T47D cells expressing inducible constructs were grown in minimal essential medium (5% FBS, 1% NEAA, 1% pennicilin/streptomycin, 6 ng/ml insulin, 200 ug/ml G418, 200 ug/ml hygromycin B) before being serum starved and AP21967 treated for 2 d, then treated with R5020

treatment_protocol: Cells were treated with 10e-9 M AP21967 durring the starvation with modified IMEM, and treated with 10e-8 M R5020 for 6 h

tag: tissue

value: breast

tag: genotype

value: mutant K388R PR

tag: parental cell line

tag: inducer treatment

value: vehicle

tag: ligand treatment


title: HUVEC profile 24hrs

source_name: HUVEC, hypoxia 24hrs


title: HIF1array_CtlsiRNA_Normoxia

source_name: HUVEC, HIF1array_CtlsiRNA_Normoxia


title: Avian influenza infected lung A4

description: Four arrays are included in one slide


title: Hypoxia profile 8hrs

source_name: HUVEC, hypoxia 8hrs


title: HUVEC HIF1array_CtlsiRNA_Hypoxia

source_name: HUVEC HIF1array_CtlsiRNA_Hypoxia


title: T47D_iKR_yesAP_yesR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible K388R mutant PR vectors, added dimerizer AP21967 treatment but added PR ligand treatment. Replicate 1.

source_name: iKR (inducible K388R mutant PR) cells treated with AP21967 and R5020 for 6 h


title: T47D_iKR_yesAP_noR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible K388R mutant PR vectors, added dimerizer AP21967 treatment and no PR ligand treatment. Replicate 1.

source_name: iKR (inducible K388R mutant PR) cells treated with AP21967 and R5020 vehicle (ethanol) for 6 h


title: T47D_iKR_noAP_noR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible K388R mutant PR vectors, no dimerizer AP21967 treatment and no PR ligand treatment. Replicate 1.

source_name: iKR (inducible K388R mutant PR) cells treated with AP21967 vehicle (ethanol) and R5020 vehicle (ethanol) for 6 h


title: HUVEC KDM3Aarray_KDM3AsiRNA_Hypoxia

source_name: HUVEC KDM3Aarray_KDM3AsiRNA_Hypoxia


title: Hypoxia profiles 4hrs

source_name: HUVEC, hypoxia 4hrs


title: Human endothelial cell Hypoxia 0hr

source_name: HUVEC, Hypoxia 0hr

value: Hypoxia


title: T47D_iWT_yesAP_noR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible WT PR vectors, added dimerizer AP21967 treatment and no PR ligand treatment. Replicate 1.

source_name: iWT (inducible wild type PR) cells treated with AP21967 and R5020 vehicle (ethanol) for 6 h

value: wild type PR


title: T47D_iWT_yesAP_yesR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible WT PR vectors, added dimerizer AP21967 treatment but added PR ligand treatment. Replicate 1.

source_name: iWT (inducible wild type PR) cells treated with AP21967 and R5020 for 6 h


title: PDCCETumor_FreshFrozen_CRC162X1A

city: Durham

first: David

last: Hsu

state: NC

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

institute: Duke University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.

source_name: mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.

extract_protocol: Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).

tag: primary tumor site

value: colorectal

tag: sample type

value: PDCCE tumor

tag: metastatic tumor site

value: liver


title: PDCCETumor_FreshFrozen_CRC149X5A


title: PDCCETumor_FreshFrozen_CRC170X2A


title: PDCCETumor_FreshFrozen_CRC159X1A


title: PDCCETumor_FreshFrozen_CRC149X1A


title: T47D_iWT_noAP_yesR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible WT PR vectors, no dimerizer AP21967 treatment but added PR ligand treatment. Replicate 1.

source_name: iWT (inducible wild type PR) cells treated with AP21967 vehicle (ethanol) and R5020 for 6 h


title: T47D_iEV_noAP_noR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible empty vectors, therefore are PR-null expressing cells, no dimerizer AP21967 treatment and no PR ligand treatment. Replicate 1.

source_name: iEV (inducible empty vector) cells treated with AP21967 vehicle (ethanol) and R5020 vehicle (ethanol) for 6 h

value: PR null


title: PDCCETumor_FreshFrozen_CRC133X7A


title: PDCCETumor_FreshFrozen_CRC043X1A

value: lung


title: T47D_iEV_yesAP_noR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible empty vectors, therefore are PR-null expressing cells, with dimerizer AP21967 treatment and no PR ligand treatment. Replicate 1.

source_name: iEV (inducible empty vector) cells treated with AP21967 and R5020 vehicle (ethanol) for 6 h


title: PDCCETumor_FreshFrozen_CRC133X1A


title: PDCCETumor_FreshFrozen_CRC167X1B


title: T47D_iWT_noAP_noR5020_6h_rep1

description: Gene expression data from T47D cells stably expressing inducible WT PR vectors, no dimerizer AP21967 treatment and no PR ligand treatment. Replicate 1.

source_name: iWT (inducible wild type PR) cells treated with AP21967 vehicle (ethanol) and R5020 vehicle (ethanol) for 6 h


title: PDCCETumor_FreshFrozen_CRC167X3A


title: PDCCETumor_FreshFrozen_CRC103X1A


title: PDCCETumor_FreshFrozen_CRC066X1A


title: PDCCETumor_FreshFrozen_CRC096X14A3


title: Patient PR72B

first: Bing

last: Sun

address: B1, R103, 4150 Clement St

institute: San Francisco VA Medical Center

description: GE Human Whole Genome

hyb_protocol: Biotin labeled fragmented aRNA was sealed in the chamber of the microarray slide. Hybridized for 17 hours at 37C on a horizontal rocking platform at 300 rmp. The slides were then washed  and stained with Steptavidin Alexa Fluor-647. The slides were washed after staining.

scan_protocol: The arrays were then scanned on a Axon GenePix 4000B Scanner with PMT 600, single color.

data_processing: The raw data were normalized with loess normalization method.

label: Steptavidin Alexa Fluor-647

source_name: primary blood monocytes

label_protocol: Half microgram of total RNA was amplified and labelled with Ambion MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (AM1790) using biotin-UTP.

extract_protocol: A total of 30ml blood was drawn and subjected to Ficoll seperation to obtain PBMCs. CD14+ monocytes were isolated from PBMC with CD14-conjugated magnetic bead. Total RNA was isolated from 1-2x10^6 monocytes with Qiagen Rneasy mini kit.

value: Blood monocytes

tag: group

value: C

tag: ethnicity

value: Caucasian


title: Patient PR110

description: GE Human Whole Genome


title: Patient PR79B

description: GE Human Whole Genome

value: HCV

value: Black


title: Patient PR57B

description: GE Human Whole Genome


title: Patient PR27B

description: GE Human Whole Genome

value: Hispanic


title: Patient PR88B

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC108X1A


title: Patient PR48B

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC120X1A

value: omentum


title: Patient PR97

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC170X1A


title: Patient PR98

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC119X1A


title: Patient PR19B

description: GE Human Whole Genome


title: Patient PR109

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC103X4A


title: PDCCETumor_FreshFrozen_CRC096X1A


title: Patient PR29B

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC093X1A


title: PDCCETumor_FreshFrozen_CRC030X5A


title: PDCCETumor_FreshFrozen_CRC040X5A


title: Patient PR108

description: GE Human Whole Genome


title: Patient PR105

description: GE Human Whole Genome


title: Patient PR103

description: GE Human Whole Genome

value: Asian/Pacific


title: Patient PR99

description: GE Human Whole Genome


title: Patient PR96

description: GE Human Whole Genome


title: Patient PR104

description: GE Human Whole Genome


title: Patient PR100

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC057XC


title: PDCCETumor_FreshFrozen_CRC083X1A

value: peritoneal


title: PDCCETumor_FreshFrozen_CRC102XA


title: Patient PR102

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC054XA


title: PDCCETumor_FreshFrozen_CRC034XA


title: Patient PR101

description: GE Human Whole Genome


title: Patient PR94

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC025XA


title: PDCCETumor_FreshFrozen_CRC167X


title: Patient PR107

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC030X1A


title: Patient PR106

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC025X2A


title: Patient PR93

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC075XB


title: PDCCETumor_FreshFrozen_CRC020XA


title: PDCCETumor_FreshFrozen_CRC039XA


title: PDCCETumor_FreshFrozen_CRC028XA


title: Patient PR92

description: GE Human Whole Genome


title: PDCCETumor_FreshFrozen_CRC105X11A


title: Patient PR89

description: GE Human Whole Genome


title: Patient PR85

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC043A

source_name: human tumor, colorectal primary, fresh frozen tissue

value: patient tumor


title: Patient PR91

description: GE Human Whole Genome


title: Patient PR71

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC159


title: Patient PR68

description: GE Human Whole Genome


title: Patient PR84

description: GE Human Whole Genome


title: Patient PR87

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC149A


title: Patient PR90

description: GE Human Whole Genome


title: Patient PR67

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC103


title: Patient PR86

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC162A


title: HumanTumor_FreshFrozen_CRC025


title: Patient PR69

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC108


title: HumanTumor_FreshFrozen_CRC093A


title: Patient PR73

description: GE Human Whole Genome


title: Patient PR74

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC133A


title: HumanTumor_FreshFrozen_CRC096


title: HumanTumor_FreshFrozen_CRC083A


title: Patient PR66

description: GE Human Whole Genome


title: Patient PR64

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC066A


title: Patient PR77

description: GE Human Whole Genome


title: Patient PR83

description: GE Human Whole Genome


title: Patient PR80

description: GE Human Whole Genome


title: Patient PR76

description: GE Human Whole Genome


title: Patient PR82

description: GE Human Whole Genome


title: Patient PR81

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC167


title: Patient PR44B

description: GE Human Whole Genome


title: Patient PR78

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC120A


title: HumanTumor_FreshFrozen_CRC170


title: Patient PR61

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC119A


title: HumanTumor_FreshFrozen_CRC075A


title: Patient PR75

description: GE Human Whole Genome


title: Patient PR36B

description: GE Human Whole Genome


title: HumanTumor_FreshFrozen_CRC054


title: HumanTumor_FreshFrozen_CRC102A


title: HumanTumor_FreshFrozen_CRC105B


title: HumanTumor_FreshFrozen_CRC040


title: HumanTumor_FreshFrozen_CRC020


title: HumanTumor_FreshFrozen_CRC034


title: HumanTumor_FreshFrozen_CRC039A


title: HumanTumor_FreshFrozen_CRC057A


title: HumanTumor_FreshFrozen_CRC028A


title: Patient PR56

description: GE Human Whole Genome


title: Desulfovibrio_africanus_strain_Walvis_Bay-Control_Stationary-rep6

city: Oak Ridge

first: James

middle: G

last: Moberly

address: 1 Bethel Valley Rd

department: Biosciences Division

institute: Oak Ridge National Laboratory

hyb_protocol: Hybridization was performed following Nimblegen 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 analyzed using JMPgenomics software package. Data was standardized, normalized using Lsmeans, and log2 transformed.

organism: Desulfocurvibacter africanus subsp. africanus str. Walvis Bay

label_protocol: Labeling was performed using standard protocols from Nimblegen, with QIAquick kit (Qiagen) for purification of probes

growth_protocol: D.africanas was grown anaerobically under N2 in MOYLS4 medium (Zane et al. 2010 AEM. 76(16):5500) modified as follows: Oak Ridge National Laboratory vitamin and mineral solutions (Phelps et al. 1989 Geomicrobiol J 7(1):79) were used in place of Thauers vitamin and trace metals, FeEDTA was removed from the medium, and 60 mM sodium lactate and 30 mM sodium sulfate added as electron donor and acceptor, respectively. 5 ug/L of Hg2+ (as NgNO3) was added at time zero of the cultuivation for Hg containing cultures. Subsamples were taking at 24 and 48 hrs from both Hg containing and Hg-free cultures conrresponding to mid-exponential and early stationary phase cultures.

extract_protocol: Total RNA was extracted using Trisol lysis followed by chloroform extraction and isopropyl precipitation. DNA was removed byRNeasy Kit (Qiagen). RNA quality and concentration was determined by nano drop.

tag: accession


title: Desulfovibrio_africanus_strain_Walvis_Bay-Control_Exponential-rep6


title: CH34_Ca_5mM_rep3

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description:
Ca5mM_3
induction with 5 mM calcium (II)

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42°C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit's protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices©, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50. Data were normalized within each array using the printing-tip loess normalization algorithm. The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package. The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method. P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate.

organism: Cupriavidus metallidurans CH34

source_name: non-induced culture

label_protocol: Ten micrograms of RNA were reverse transcribed following the instructions provided with the Pronto kit (Promega, United States). Two color labeling, green for control samples and red for condition (metal challenge) samples, was performed using respectively Cy™3-dCTP and Cy™5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: Cultivating C. metallidurans CH34 for studying the gene expression during a defined chemical compound stress was done in by first inoculating 40 ml TrisMMM-gluconate with 500 microliter of a stationary C. metallidurans CH34 culture. These subcultures were allowed to grow until a cell density of 5.108 [CFU.ml-1] was reached. Cell density was controlled by regular OD600 measurements on aliquots of growing C. metallidurans CH34 subcultures with a biological spectrophotometer (biophotometer, Eppendorf). A bacterial density of 5.108 [CFU.ml-1] corresponds with an OD600 value of 0.5. This cell density in trisMMM-gluconate medium is typical reached after 20 hours of incubation at 30°C.

extract_protocol: Total RNA extraction was performed using the SV Total RNA Isolation system (Promega Corporation). The RNA isolation protocol used was optimized for RNA-extraction from C. metallidurans CH34 bacterial cells. A -80°C frozen bacterial pellet (approx 109 cells) was unfrozen at room temperature suspended in 100 microliter of RNA-stabilizing solution (RNAlater®, Ambion Inc.) and maintained at room temperature for approximately one hour. Afterwards, this cell suspension was centrifuged for 2 minute at 10 000 g and the supernatants was discarded. Lysis of the bacterial cell walls of C. metallidurans CH34 was performed by resuspending the recovered bacterial pellet in a solution containing 3 [mg.ml-1] (i.e. ≥ 120 000 [units.ml-1]) lysozyme (Sigma-Aldrich®)at room temperature. The lysis reaction was stopped after ten minutes. After this lysis, the standard microbial RNA isolation protocol of SV Total RNA Isolation system was resumed according to the centrifugation method. The quantity of extracted RNA was measured using a NanoDrop™ 1000 spectrophotometer (Thermo Scientific, USA). The RNA quality was determined with a bioanalyzer (Agilent 2100 Electrophoresis Bioanalyzer, Agilent Technologies). Only extracted RNA with a RNA integrity number (RIN-number) of higher than 8 was accepted for further micro array gene expression analysis

treatment_protocol: After growth, the subculture was divided in two equal portions of 20 ml in two new falcon tubes. One tube was used as condition (i.e. challenged with the defined amount of a chemical compound – see samples) while the other flask served as control (i.e. same amount of sterile water added). Immediately after addition, the tubes were incubated at the same conditions as before for the needed duration for chemical compound challenges (i.e. 30 min). After this challenge, each 20 ml culture was immediately subdivided in 10 eppendorfs of 2 ml, and the cells were harvested by centrifugation for 1 minute at 10 000 g. Supernatans was removed and the eppendorfs containing only the centrifuged bacterial pellets (each containing ca. 109 bacterial cells) were flash frozen by immersion into liquid nitrogen. Pellets were kept frozen at -80°C at all times. Each challenge condition (i.e. each of the different tested chemical compounds) was performed in biological quadruplicate, using 4 independent bacterial cultures.

tag: metal

source_name: induction with 5mM calcium (II)

value: calcium(II)

tag: metal concentration

value: 5 mM


title: CH34_Sr_60mM_rep3

description:
Sr60mM_3
induction with 60 mM strontium (II)

source_name: induction with 60mM strontium (II)

value: strontium (II)

value: 60 mM


title: CH34_Ca_5mM_rep1

description:
Ca5mM_1
induction with 5 mM calcium (II)


title: CH34_Ca_5mM_rep2

description:
Ca5mM_2
induction with 5 mM calcium (II)


title: CH34_Sr_60mM_rep2

description:
Sr60mM_2
induction with 60 mM strontium (II)


title: Desulfovibrio_africanus_strain_Walvis_Bay-Control_Stationary-rep4


title: PDCCETumor_FreshFrozen_CRC105XB

value: colorectal

value: PDCCE tumor

value: liver


title: NSP cells 6 days after lentivirus infection REST shRNA 3

city: Stony Brook

first: Matthew

last: Covey

state: New York

address: 350 CMM Building

department: Biochemistry

institute: Stony Brook University

hyb_protocol: The labeled samples were hybridized to Affymetrix GeneCHip Mouse Genome 430 2.0 Array

scan_protocol: The detection and quantitation of target hybridization was performed with an Affymetrix GeneChip Scanner

data_processing: Data analysis was performed using Agilent Genespring GX Software

source_name: NSP cells, REST shRNA 6 days

label_protocol: The amplified cDNA was fragmented and labeled with biotin using Encore Biotin Module (NuGEN, Cat#4200-A01)

growth_protocol: E12.5 brains were dissected, dissociated and plated on PDL/Lam 60mm dishes and grown until confluent. Cells were dissociated and split prior to lentiviral infection

extract_protocol: Trizol extraction of total RNA was performed as per manufacturers instructions

treatment_protocol: Cells were infected with either CTL or REST shRNA lentivirus overnight, the lentivirus was removed and the cells regrown for 6 days with media changes every other day

tag: cell type

value: NSP

tag: infection

value: REST shRNA lentivirus


title: NSP cells 6 days after lentivirus infection CTL3

source_name: NSP cells, CTL lentivirus 6 days

tag: age

value: CTL shRNA lentivirus


title: NSP cells 6 days after lentivirus infection REST shRNA 2


title: CH34_Sr_5mM_rep3

description:
Sr5mM_3
induction with 5 mM strontium (II)

source_name: induction with 5mM strontium (II)


title: CH34_Sr_60mM_rep1

description:
Sr60mM_1
induction with 60 mM strontium (II)


title: Desulfovibrio_africanus_strain_Walvis_Bay-Control_Stationary-rep5


title: NSP cells 6 days after lentivirus infection CTL2


title: NSP cells 6 days after lentivirus infection CTL1


title: NSP cells 6 days after lentivirus infection REST shRNA 1


title: Desulfovibrio_africanus_strain_Walvis_Bay-Control_Exponential-rep5


title: Desulfovibrio_africanus_strain_Walvis_Bay-Control_Exponential-rep4


title: Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Stationary-rep3


title: Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Stationary-rep2


title: Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Exponential-rep3


title: CH34_Sr_5mM_rep2

description:
Sr5mM_2
induction with 5 mM strontium (II)


title: CH34_Sr_5mM_rep1

description:
Sr5mM_1
induction with 5 mM strontium (II)


title: Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Stationary-rep1


title: 4T1-regular

city: Taipei

first: Oscar

middle: K.

last: Lee

address: No. 155, Li-Long St.

country: Taiwan

institute: National Yang Ming University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

source_name: 4T1 cells cultured with regular medium

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

growth_protocol: 4T1 cells are cultured in RPMI-1640 supplemented with 10% FBS

treatment_protocol: 4T1 cells are either cultured with MSC-CM or contact co-cultured with MSCs for 1 week

value: 4T1 mammary cancer cells

tag: growth condition

value: cultured with regular medium


title: Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Exponential-rep2


title: 4T1-CM

source_name: 4T1 cells cultured with MSC-CM

value: cultured with MSC-CM


title: Desulfovibrio_africanus_strain_Walvis_Bay-Hg_Exponential-rep1


title: H1N1 O+ CA BAL 17533 d10

status: Public on Jun 06 2012

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014850) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.
For the creation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1).

organism: Macaca mulatta

source_name: Ilhem H1N1 O+ CA BAL 17533 d10

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: The study was carried out in strict accordance with the recommendations described in the Guide for the Care and Use of Laboratory Animals of the National Institute of Health, the Office of Animal Welfare and the United States Department of Agriculture. All animal work was approved by the Oregon National Primate Research Center (ONPRC) Institutional Animal Care and Use Committee, which is accredited by the American Association for Accreditation of Laboratory Animal Care (PHS/OLAW Animal Welfare Assurance # A3304-01). All procedures were carried out under Ketamine anesthesia by trained personnel under the supervision of veterinary staff and all efforts were made to ameliorate the welfare and to minimize animal suffering in accordance with the “Weatherall report for the use of non-human primates” recommendations. Animals were housed in adjoining individual primate cages allowing social interactions, under controlled conditions of humidity, temperature and light (12-hour light/12-hour dark cycles). Food and water were available ad libitum. Animals were monitored and fed commercial monkey chow, treats and fruit twice daily by trained personnel. Environmental enrichment consisted of commercial toys. Sixteen female rhesus macaques (Macaca Mulatta) 10-12 (Adult) and 20-24 years (Old/Aged) of age were used in these studies. Animals were infected using a combinatory of intra-tracheal (4ml), intranasal (0.5 ml/nostril), and conjunctival (0.5 ml/eyelid) routes for a total dose of 7x106 TCID50 dose. Microarray analysis was performed on Bronchoalveolar lavage (BAL) samples collected on days 0, 4, 7, 10 and 14.

extract_protocol: All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Microarray analysis was performed on Bronchoalveolar lavage (BAL) samples collected on days 0, 4, 7, 10 and 14.  Note: One of the Day 0 array did not pass QC metrics so for this animal the average of the other Day 0 samples from that group was utilized.1 million BAL cells were resuspended in Trizol (Invitrogen) and frozen until RNA was extracted.

value: 20-24 years old

tag: gender

value: female

tag: time (post-infection)

value: day 10

value: A/California/04/2009 H1N1

value: bronchial lavage

tag: subject


title: H1N1 O- CA BAL 15753 d0

source_name: Ilhem H1N1 O- CA BAL 15753 d0

value: day 0


title: H1N1 O- CA BAL 15452 d4

source_name: Ilhem H1N1 O- CA BAL 15452 d4

value: day 4


title: H1N1 O+ CA BAL 17533 d4

source_name: Ilhem H1N1 O+ CA BAL 17533 d4


title: H1N1 A+ CA BAL 24855 d0

source_name: Ilhem H1N1 A+ CA BAL 24855 d0

value: 10-12 years old


title: H1N1 A- CA BAL 22315 d10

source_name: Ilhem H1N1 A- CA BAL 22315 d10


title: H1N1 O+ CA BAL 15938 d0

source_name: Ilhem H1N1 O+ CA BAL 15938 d0


title: H1N1 A+ CA BAL 20303 d10

source_name: Ilhem H1N1 A+ CA BAL 20303 d10


title: H1N1 O- CA BAL 14623 d14

source_name: Ilhem H1N1 O- CA BAL 14623 d14

value: day 14


title: H1N1 O+ CA BAL 14171 d4

source_name: Ilhem H1N1 O+ CA BAL 14171 d4


title: H1N1 A- CA BAL 22179 d10

source_name: Ilhem H1N1 A- CA BAL 22179 d10


title: 4T1-coculture

source_name: 4T1 cells (isolated from co-culture)

value: isolated from co-culture


title: H1N1 O- CA BAL 16187 d0

source_name: Ilhem H1N1 O- CA BAL 16187 d0


title: H1N1 O- CA BAL 16187 d7

source_name: Ilhem H1N1 O- CA BAL 16187 d7

value: day 7


title: H1N1 O+ CA BAL 17533 d14

source_name: Ilhem H1N1 O+ CA BAL 17533 d14


title: H1N1 A+ CA BAL 20303 d4

source_name: Ilhem H1N1 A+ CA BAL 20303 d4


title: H1N1 A+ CA BAL 21864 d4

source_name: Ilhem H1N1 A+ CA BAL 21864 d4


title: HumanTumor_FreshFrozen_CRC030A

source_name: human tumor, colorectal primary, fresh frozen tissue

value: colorectal

value: patient tumor


title: H1N1 A- CA BAL 22179 d14

source_name: Ilhem H1N1 A- CA BAL 22179 d14


title: H1N1 A+ CA BAL 24855 d10

source_name: Ilhem H1N1 A+ CA BAL 24855 d10


title: H1N1 O+ CA BAL 14171 d7

source_name: Ilhem H1N1 O+ CA BAL 14171 d7


title: H1N1 A- CA BAL 22315 d0

source_name: Ilhem H1N1 A- CA BAL 22315 d0


title: H1N1 A- CA BAL 22179 d4

source_name: Ilhem H1N1 A- CA BAL 22179 d4


title: H1N1 A+ CA BAL 21864 d10

source_name: Ilhem H1N1 A+ CA BAL 21864 d10


title: H1N1 O+ CA BAL 15938 d10

source_name: Ilhem H1N1 O+ CA BAL 15938 d10


title: H1N1 O- CA BAL 16187 d10

source_name: Ilhem H1N1 O- CA BAL 16187 d10


title: H1N1 O- CA BAL 14623 d7

source_name: Ilhem H1N1 O- CA BAL 14623 d7


title: H1N1 O+ CA BAL 15938 d4 2

source_name: Ilhem H1N1 O+ CA BAL 15938 d4 2


title: H1N1 A+ CA BAL 21864 d14 2

source_name: Ilhem H1N1 A+ CA BAL 21864 d14 2


title: H1N1 O+ CA BAL 14171 d10

source_name: Ilhem H1N1 O+ CA BAL 14171 d10


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipB

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression data was processed with our novel permutation algorithm TileShuffle.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

tag: cell line

value: HFF

tag: data processing

value: TileShuffle


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipB

description: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with our new permutation approach TileShuffle.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.). Analysis of differential expression was performed with the same parameters, except of 100000 permutations, aiming at accommodating the more rugged nature of expression difference signal. Here we use variant B to detect differentially expressed segments, i.e. it is assumed that entire windows are either up- or downregulated between two conditions and converse behaviour of neighboring probes is a consequence of non-specific hybridization. In order to correct for this bias, the presumed direction of regulation is initially assigned to each window on the basis of the sign of its expression scores. Subsequently, all converse probes, i.e. probes with negative log-fold change within positive windows or vice versa, are ignored and neither permuted nor incorporated into the score calculation for differential expression. Consequently, positive and negative windows are compared to different background distributions. To asses the significance of a window score a one-tailed empirical p-value is estimated (according to the corresponding background distribution) and corrected for multiple testing, similar to the one-state analysis. Here we use a q-value < 0.1 which results in an FDR of 18%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, TileShuffle takes regions found to be significantly high expressed in at least one of the compared states as input for the two-state analysis, and assesses differential expression solely on the expressed segments.

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle


title: H1N1 O- CA BAL 15753 d4

source_name: Ilhem H1N1 O- CA BAL 15753 d4


title: H1N1 A- CA BAL 22315 d7

source_name: Ilhem H1N1 A- CA BAL 22315 d7


title: H1N1 O- CA BAL 15452 d0

source_name: Ilhem H1N1 O- CA BAL 15452 d0


title: H1N1 O- CA BAL 14623 d4

source_name: Ilhem H1N1 O- CA BAL 14623 d4


title: H1N1 O- CA BAL 14623 d0

source_name: Ilhem H1N1 O- CA BAL 14623 d0


title: H1N1 O- CA BAL 16187 d4

source_name: Ilhem H1N1 O- CA BAL 16187 d4


title: H1N1 O- CA BAL 22098 d14

source_name: Ilhem H1N1 O- CA BAL 22098 d14


title: H1N1 A- CA BAL 22315 d4

source_name: Ilhem H1N1 A- CA BAL 22315 d4


title: H1N1 A- CA BAL 22315 d14

source_name: Ilhem H1N1 A- CA BAL 22315 d14


title: H1N1 O- CA BAL 15452 d14

source_name: Ilhem H1N1 O- CA BAL 15452 d14


title: H1N1 O- CA BAL 22098 d7

source_name: Ilhem H1N1 O- CA BAL 22098 d7


title: H1N1 O- CA BAL 22098 d0

source_name: Ilhem H1N1 O- CA BAL 22098 d0


title: H1N1 O+ CA BAL 17533 d7

source_name: Ilhem H1N1 O+ CA BAL 17533 d7


title: H1N1 A- CA BAL 22203 d0

source_name: Ilhem H1N1 A- CA BAL 22203 d0


title: H1N1 O- CA BAL 15753 d10

source_name: Ilhem H1N1 O- CA BAL 15753 d10


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipB

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression data was processed with our novel permutation approach TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: H1N1 A+ CA BAL 20766 d10

source_name: Ilhem H1N1 A+ CA BAL 20766 d10


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipB

description: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with TAS.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The data were processed with Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). In order to identify highly expressed segments we set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150. Differentially expressed segments were identified with the following parameters: Signal intensities of chips of the same type were normalized across the two different biological conditions and log fold changes were calculated. We set bandwith=150 and the maximal gap between probes to be included in a differentially expressed interval was set to maxgap=40. The minimal length of differentially expressed segments was set to minrun=90. Here we use a q-value < 0.05 which results in an FDR of 18%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, we identify highdiff intervals by intersecting intervals identified as differentially expressed with those intervals deemed as 'expressed' in at least one of the compared biological states.

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle

value: TAS


title: H1N1 A- CA BAL 22179 d0

source_name: Ilhem H1N1 A- CA BAL 22179 d0


title: H1N1 O- CA BAL 22098 d10

source_name: Ilhem H1N1 O- CA BAL 22098 d10


title: H1N1 A- CA BAL 26303 d14

source_name: Ilhem H1N1 A- CA BAL 26303 d14


title: H1N1 A- CA BAL 26303 d10

source_name: Ilhem H1N1 A- CA BAL 26303 d10


title: H1N1 O+ CA BAL 15938 d14

source_name: Ilhem H1N1 O+ CA BAL 15938 d14


title: H1N1 A- CA BAL 26303 d4

source_name: Ilhem H1N1 A- CA BAL 26303 d4


title: H1N1 A+ CA BAL 20766 d14

source_name: Ilhem H1N1 A+ CA BAL 20766 d14


title: H1N1 O- CA BAL 15452 d7

source_name: Ilhem H1N1 O- CA BAL 15452 d7


title: H1N1 A+ CA BAL 24855 d14

source_name: Ilhem H1N1 A+ CA BAL 24855 d14


title: H1N1 A+ CA BAL 21864 d7

source_name: Ilhem H1N1 A+ CA BAL 21864 d7


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipB

description: Whole transcriptome differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with MAT.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 5e-2 which yielded the best results from the set of tested parameter values. Differentially expressed segments were identified with the following parameters: We set bandwith=150 and the maximal gap between probes to be included in a differentially expressed interval was set to maxgap=40. The minimal length of differentially expressed segments was set to minprobe=3. Here we use a q-value < 1e-6 which results in an FDR of 17%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, we identify highdiff intervals by intersecting intervals identified as differentially expressed with those intervals deemed as 'expressed' in at least one of the compared biological states.

value: MAT


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipB

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression data was processed with MAT.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 5e-2 which yielded the best results from the set of tested parameter values.


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipC


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipC


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipC

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipC


title: HFF cells using TAS (G0 phase) ChipB

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression data was processed with TAS.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). We set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150.

tag: phase


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipC


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipC

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression data was processed with MAT.


title: HFF cells using TAS (G1 phase) ChipB

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression data was processed with TAS.


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipB


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipA


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipC


title: HFF cells using TAS (G0 phase) ChipC


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipA


title: H1N1 A+ CA BAL 20766 d0

source_name: Ilhem H1N1 A+ CA BAL 20766 d0

tag: sample type


title: H1N1 O- CA BAL 15452 d10

source_name: Ilhem H1N1 O- CA BAL 15452 d10

value: 20-24 years old


title: H1N1 O- CA BAL 22098 d4

source_name: Ilhem H1N1 O- CA BAL 22098 d4

value: female


title: H1N1 A- CA BAL 22203 d4

source_name: Ilhem H1N1 A- CA BAL 22203 d4


title: H1N1 A- CA BAL 22203 d7

source_name: Ilhem H1N1 A- CA BAL 22203 d7


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipA

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle


title: HFF cells using TAS (G1 phase) ChipC


title: H1N1 O+ CA BAL 17533 d0

source_name: Ilhem H1N1 O+ CA BAL 17533 d0


title: H1N1 O+ CA BAL 15938 d7

source_name: Ilhem H1N1 O+ CA BAL 15938 d7


title: H1N1 A+ CA BAL 20766 d7

source_name: Ilhem H1N1 A+ CA BAL 20766 d7


title: H1N1 O- CA BAL 15753 d7

source_name: Ilhem H1N1 O- CA BAL 15753 d7


title: H1N1 O- CA BAL 15753 d14

source_name: Ilhem H1N1 O- CA BAL 15753 d14


title: H1N1 A+ CA BAL 24855 d7

source_name: Ilhem H1N1 A+ CA BAL 24855 d7


title: H1N1 A+ CA BAL 24855 d4

source_name: Ilhem H1N1 A+ CA BAL 24855 d4


title: H1N1 O+ CA BAL 14171 d0

source_name: Ilhem H1N1 O+ CA BAL 14171 d0


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipA


title: H1N1 A- CA BAL 26303 d0

source_name: Ilhem H1N1 A- CA BAL 26303 d0


title: HFF cells using TAS (G1 phase) ChipA


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipA

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipA


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipI


title: HFF cells using TAS (G0 phase) ChipA


title: H1N1 A+ CA BAL 20303 d14

source_name: Ilhem H1N1 A+ CA BAL 20303 d14


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipI


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipI


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipI

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipA


title: H1N1 A+ CA BAL 20303 d7

source_name: Ilhem H1N1 A+ CA BAL 20303 d7


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipI


title: H1N1 A+ CA BAL 21864 d0

source_name: Ilhem H1N1 A+ CA BAL 21864 d0


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipI


title: H1N1 A+ CA BAL 20766 d4

source_name: Ilhem H1N1 A+ CA BAL 20766 d4


title: H1N1 A- CA BAL 22179 d7

source_name: Ilhem H1N1 A- CA BAL 22179 d7


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipJ

source_name: Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle


title: HFF cells using TAS (G0 phase) ChipI


title: BW25113 cobB/pCA24N under stress conditions

city: college station

first: Qun

last: Ma

address: 3122 TAMU

institute: Texas A&M University

hyb_protocol: Following the Affymetrix protocol.

scan_protocol: After washing and staining, the probe array was scanned using the Affymetrix GeneChip scanner GCS3000 7G system and the software GeneChip Operating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

label_protocol: cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using the Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: Overnight cultures of cobB/pCA24N were cultured to a turbidity of 0.05 at 600 nm, grown 2h and then 0.1 mM IPTG was added for another 4 h, then the cells were exposed to 20 mM H2O2 for 10 min. Cell pellets were collected and resuspended in RNAlater.

tag: background strain

tag: genotype

tag: treatment


title: H1N1 O+ CA BAL 14171 d14

source_name: Ilhem H1N1 O+ CA BAL 14171 d14


title: H1N1 A- CA BAL 22203 d14

source_name: Ilhem H1N1 A- CA BAL 22203 d14


title: H1N1 A- CA BAL 22203 d10

source_name: Ilhem H1N1 A- CA BAL 22203 d10

value: day 10


title: BW25113 cobB/pCA24N-cobB under stress conditions

extract_protocol: Overnight cultures of cobB/pCA24N_cobB were cultured to a turbidity of 0.05 at 600 nm, grown 2h and then 0.1 mM IPTG was added for another 4 h, then the cells were exposed to 20 mM H2O2 for 10 min. Cell pellets were collected and resuspended in RNAlater.


title: H1N1 A- CA BAL 26303 d7

source_name: Ilhem H1N1 A- CA BAL 26303 d7

value: A/California/04/2009 H1N1


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipJ


title: HFF cells residing in G1 phase, biological replicate 3

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. HFF cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle.

hyb_protocol: nONCOchip 1.0 arrays were proceed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and an commercial Hyb-Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 100%, PMT: 300/400, resolution: 5µm, Focus: 0µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Expression levels were normalized (quantile normalization) and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

label_protocol: 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protokoll).

tag: cell cycle


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipJ


title: High density associated fibroblasts #5

first: RosaAnna

last: DeFilippis

address: 513 Parnassus Ave

department: Pathology

institute: University of California San Francisco

description: gene expression data

hyb_protocol: Following fragmentation, 10ug of cRNA was hybridized to Affymetrix HU133 plus 2 chips following manufactorer's instructions in GeneChip Expression Analysis Technical Manual 701021 Rev. 3.

scan_protocol: Gene chips were scanned using the affymetrix Gene Chip Scanner 3000 (GCS3000).

data_processing: The dataset was processed using Affymetrix GCOS 1.4 software.

source_name: mammary fibroblast from woman with high MD

label_protocol: 1 ug of total RNA was used make to amplified and biotinylated cRNA using Ambion's Message Amp II kit according to the manufacturer's instructions.

growth_protocol: Fibroblasts were cultured in RPMI-1640 with L-glutamine, 25 mM Hepes and 10% FBS.

extract_protocol: Total RNA was isolated from cell pellets using Qiagen's Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Fibroblasts were trypsinized, counted on a hemacytometer and 7.4x10^5 - 1x10^6 cells pelleted down. Cell pellets were washed 1x in cold 1x PBS, repelleted in microcentrifugre tubes and snap frozen.

tag: source tissue

value: mammary gland

value: fibroblast

tag: phenotype

value: high mammographic density


title: Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipJ


title: High density associated fibroblasts #7

description: gene expression data

tag: cell type


title: HFF cells residing in G1 phase, biological replicate 2


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipG


title: H1N1 O- CA BAL 14623 d10

source_name: Ilhem H1N1 O- CA BAL 14623 d10

tag: infection

value: bronchial lavage


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipJ


title: HFF cells residing in G0 phase, biological replicate 2

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. HFF cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle.


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipG


title: High density associated fibroblasts #2

description: gene expression data


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G1_chipI


title: HFF cells residing in G1 phase, biological replicate 1


title: High density associated fibroblasts #1

description: gene expression data


title: Low density associated fibroblasts #6

description: gene expression data

source_name: mammary fibroblast from woman with low MD

value: low mammographic density


title: High density associated fibroblasts #3

description: gene expression data


title: HFF cells residing in G0 phase, biological replicate 3


title: High density associated fibroblasts #4

description: gene expression data


title: HFF cells using TAS (G1 phase) ChipI


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipG


title: HFF cells using TAS (G1 phase) ChipJ


title: Whole transcriptome diff. expression analysis of HFF cells using TileShuffle variant B (G0 vs. G1)_chipH


title: HFF cells using TAS (G0 phase) ChipJ


title: High density associated fibroblasts #6

description: gene expression data


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)_chipG


title: Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipJ


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)_chipH


title: Whole transcriptome differential expression analysis of HFF cells using MAT_G0_chipJ