title: YH8

hyb_protocol: Biotinylated RNA was fragmented and hybridised to Affymetrix Human Genome U133Plus2 Arrays according to the Affymetrix protocol.

scan_protocol: All arrays were washed and stained on an Affymetrix FS450 fluidics station then scanned using an Affymetrix GeneChip 3000 7G scanner as per Affymetrix procedures.

data_processing: Expression array data were analysed with GCOS using the default settings except that the target signal was set to 100.

label_protocol: The eluted RNA was collected by ethanol precipitation in the presence of 1 µl P-carrier (AmpTec), washed twice with 80% ethanol and subjected to three rounds of amplification followed by biotin labelling using an ExpressArt TR Nano amplification kit (AmpTec) and an Affymetrix IVT labelling kit.

extract_protocol: 8 micron cryosections were transferred onto PALM membrane slides (P.A.L.M. Microlaser Technologies) and air dried on ice for about 1 minute. Slides were immersed for 2 minutes in cold 75% ethanol, tapped dry and stained for 30 seconds in cold haematoxylin and eosin (9:1) containing 1% NucleoGuard (AmpTec, Hamburg). Excess stain was tapped off and slides were washed in cold nuclease-free water for 30 seconds, cold 75% ethanol for 1 minute, cold 100% ethanol for 1 minute then air dried. Tumour cells for analysis were excised by laser microdissection and pressure catapulting using a PALM MicroBeam instrument and caught on PALM Adhesive Caps. A minimum of 200,000 µm2 of tissue was collected for each DNA or RNA extraction. RNA was extracted by adding 100µl of RLT buffer (Qiagen) supplemented with 1µl of N-carrier (AmpTec) and 1 µl of NucleoGuard followed by incubation at room temperature for 15 minutes. Extracted RNA was cleaned up using a Qiagen RNeasy mini kit, including the on-column DNase step as per the manufacturer’s instructions.


title: IMGUS_5

status: Public on Dec 10 2012

type: RNA

city: Heidelberg

first: Julia

last: Starmann

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center (DKFZ) and National Center for Tumor Diseases Heidelberg (NCT)

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes. After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using a Beadstation array scanner, setting adjusted to a scaling factor of 1 and PMT settings at 430.

data_processing: Data processing was done using open source statistical tool lumi package from Bioconductor. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated. Finally data was transformed using quantile normalization.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Total RNA was prepared for hybridization on Illumina  human-6 v3 BeadChip arrays (Illumina) according to manufacturer’s recommendations. In brief, 300 ng/µl total RNA was used for cDNA synthesis, followed by the generation of biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion).

growth_protocol: 44 human liver tissue surgical samples (normal n=13; steatosis n=19; steatohepatitis n=12, 8/2 cirrhotic/non-cirrhotic) obtained from patients undergoing liver surgery for HCC, other malignancy/metastatic disease, benign tumors of the liver and organ dedicated to transplantation. Virtually normal control samples in this cohort were taken from patients undergoing surgical resection of liver metastasis, but the surrounding liver tissue used for the molecular analyses was normal, non-tumorous liver tissue without detectable pathological changes. The samples were provided by the Biobank at the Medical University of Graz.

extract_protocol: Total RNA was isolated from the samples using TRI Reagent® (Molecular Research Center, Cincinnati, OH, USA) according to the manufacturer´s protocols. The RNA quality was analyzed using microcapillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies, Böblingen, Germany). Only samples with RIN (RNA integrity number) of 5.0 or higher were subjected to gene expression array analysis.

treatment_protocol: No treatment

tag: tissue

value: liver

tag: diagnosis

value: steatohepatitis


title: blastocyst [B87]

city: Nantes

first: Raluca

last: TEUSAN

address: 1, rue gaston veil

country: France

institute: INSERM U915

description:
Sample name: B87
Raw data file: 22_1.txt

hyb_protocol: RNA  samples  were hybridised  on  Whole  Human  Genome  Oligo  Microarray 4x44K  (Agilent Technologies: Two-Color  Microarray-162 Based  Gene  Expression  Analysis)

scan_protocol: Hybridized arrays were scanned using Agilent fluorescence scanner.

data_processing: Hybridization and background signals were measured using GenePix Pro 5.0 image analysis software (Axon Instruments).  For each microarray, Cy3 and Cy5 signal intensities were individually normalized to the median profile of all Cy3 or Cy5 signal intensities by Lowess

source_name: Cumulus cells

label_protocol: RNA  samples  were  prepared  according  to  the  Agilent  protocol  (Two-Color  Microarray-162 Based  Gene  Expression  Analysis)  and  hybridised  on  Whole  Human  Genome  Oligo  Microarray 4x44K  (Agilent Technologies).

extract_protocol: Total RNA  extraction  was  carried  out  using  the  Rneasy Micro Kit (Qiagen).  A DNase  step  was included  in  the  extraction  protocol  to  remove  residual  genomic  DNA  contamination.

tag: cell type

value: Cumulus cells

tag: oocyte developmental competence

value: B


title: IMGUS_3


title: IMGUS_12


title: C666

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

source_name: NPC cell line

label_protocol: The RNA was subjected to three rounds of amplification followed by biotin labelling using an ExpressArt TR Nano amplification kit (AmpTec) and an Affymetrix IVT labelling kit.

extract_protocol: RNA was extracted from biopsy samples using TRIzol Reagent (Invitrogen, USA) and purified by the RNeasy Mini Kit (Qiagen, UK).

tag: disease state

value: nasopharyngeal carcinoma


title: IMGUS_37

value: steatosis


title: embryo of poor quality [E70]

description:
Sample name: E70
Raw data file: 29_4.txt

value: E


title: blastocyst [B13a]

description:
Sample name: B13a
Raw data file: 29_4.txt


title: IMGUS_7


title: embryo of poor quality [E95]

description:
Sample name: E95
Raw data file: 29_3.txt


title: YH7

source_name: NPC biopsy


title: embryo of poor quality [E38a]

description:
Sample name: E38a
Raw data file: 29_2.txt


title: MOUZ


title: MDIG


title: IMGUS_33


title: embryo of poor quality [E39a]

description:
Sample name: E39a
Raw data file: 29_3.txt


title: MKAV


title: IMGUS_34


title: blastocyst [B96]

description:
Sample name: B96
Raw data file: 29_2.txt


title: MKEC


title: IMGUS_35


title: MMAH


title: IMGUS_32


title: HK6


title: IMGUS_36


title: HK4


title: XY23


title: XY6


title: blastocyst [B39_30]

description:
Sample name: B39_30
Raw data file: 92_3.txt


title: HKD1


title: embryo of poor quality [E48_32]

description:
Sample name: E48_32
Raw data file: 92_4.txt


title: embryo of poor quality [E71]

description:
Sample name: E71
Raw data file: 29_1.txt


title: immature oocytes [VG15_27]

description:
Sample name: VG15_27
Raw data file: 92_2.txt

value: VG


title: embryo of poor quality [E39_31]

description:
Sample name: E39_31
Raw data file: 92_4.txt


title: T3

source_name: tonsil

extract_protocol: 8 micron cryosections were transferred onto PALM membrane slides (P.A.L.M. Microlaser Technologies) and air dried on ice for about 1 minute. Slides were immersed for 2 minutes in cold 75% ethanol, tapped dry and stained for 30 seconds in cold haematoxylin and eosin (9:1) containing 1% NucleoGuard (AmpTec, Hamburg). Excess stain was tapped off and slides were washed in cold nuclease-free water for 30 seconds, cold 75% ethanol for 1 minute, cold 100% ethanol for 1 minute then air dried. Epithelial cells for analysis were excised by laser microdissection and pressure catapulting using a PALM MicroBeam instrument and caught on PALM Adhesive Caps. A minimum of 200,000 µm2 of tissue was collected for each DNA or RNA extraction. RNA was extracted by adding 100µl of RLT buffer (Qiagen) supplemented with 1µl of N-carrier (AmpTec) and 1 µl of NucleoGuard followed by incubation at room temperature for 15 minutes. Extracted RNA was cleaned up using a Qiagen RNeasy mini kit, including the on-column DNase step as per the manufacturer’s instructions.

value: normal control


title: immature oocytes [VG12_28]

description:
Sample name: VG12_28
Raw data file: 92_2.txt


title: HKC1


title: XY5


title: XY8


title: embryo of poor quality [E83]

description:
Sample name: E83
Raw data file: 29_1.txt


title: immature oocytes [VG2_24]

description:
Sample name: VG2_24
Raw data file: 91_4.txt


title: embryo of poor quality [E13_26]

description:
Sample name: E13_26
Raw data file: 92_1.txt


title: MHAU

source_name: normal nasopharyngeal biopsy

extract_protocol: 8 micron cryosections were transferred onto PALM membrane slides (P.A.L.M. Microlaser Technologies) and air dried on ice for about 1 minute. Slides were immersed for 2 minutes in cold 75% ethanol, tapped dry and stained for 30 seconds in cold haematoxylin and eosin (9:1) containing 1% NucleoGuard (AmpTec, Hamburg). Excess stain was tapped off and slides were washed in cold nuclease-free water for 30 seconds, cold 75% ethanol for 1 minute, cold 100% ethanol for 1 minute then air dried.  Cells for analysis were excised by laser microdissection and pressure catapulting using a PALM MicroBeam instrument and caught on PALM Adhesive Caps. A minimum of 200,000 µm2 of tissue was collected for each DNA or RNA extraction. RNA was extracted by adding 100µl of RLT buffer (Qiagen) supplemented with 1µl of N-carrier (AmpTec) and 1 µl of NucleoGuard followed by incubation at room temperature for 15 minutes. Extracted RNA was cleaned up using a Qiagen RNeasy mini kit, including the on-column DNase step as per the manufacturer’s instructions.


title: MSTA


title: IMGUS_24


title: embryo of poor quality [E23_25]

description:
Sample name: E23_25
Raw data file: 92_1.txt


title: hMSC_normal_4

status: Public on Dec 09 2012

city: Moscow

first: Denis

middle: Olegovich

last: Omelchenko

address: Moskvorechie, 1

department: Scientific Department

country: Russia

institute: FSBI "Research Center for Medical Genetics" RAMS

description: isolated cell culture

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were RSN normalised and VST transformed using lumi in R

source_name: human adipose tissue MSCs

label_protocol: Standard Illumina label protocol

growth_protocol: Grown in DMEM (PanEco, Russia) supplemented with 5% fetal bovine serum

extract_protocol: Qiagen RNEasy RNA isolation kit according to manufacturer's instructions

treatment_protocol: No additional treatment

tag: sample type

value: Normal

tag: cell line

value: hMSC normal


title: hMSC_normal_1

description: isolated cell culture


title: blastocyst [B23_29]

description:
Sample name: B23_29
Raw data file: 92_3.txt


title: hMSC_normal_6

description: isolated cell culture


title: hMSC_normal_5

description: isolated cell culture


title: hMSC_transformed_6

description: isolated cell culture

value: Transformed

value: hMSC transformed


title: MBEZ


title: hMSC_normal_3

description: isolated cell culture


title: hMSC_normal_2

description: isolated cell culture


title: anx/anx neocortex replicate 3

status: Public on Dec 08 2012

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
anx/anx neocortex, biological replicate 3 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)

hyb_protocol: Labeled RNA (8µl) was combined with 22 µl hybridization buffer (final concentrations: 4X SSC, 0.1% SDS, 38% formamide, 0.5 µg/µl herring sperm DNA), denatured and hybridized to the microarray for 16-20 hours at 65°C. Post hybridization washes were in 4X SSC at 60°C to remove the coverslip, followed by three times in 2X SSC, 0.025% SDS for 5 min each, three times in 0.8X SSC for 2 min each and two times in 0.4X SSC for 3 min each. Three biological replicates were analyzed for each of the two classes to be compared: three for the anx/anx and three for wild type phenotype (Bak et al. 2008, Rna 14(3):432-444).

scan_protocol: Microarray slides were scanned using an ArrayWorx Biochip Reader (Applied Precision) and scanning images were analyzed using GridGrinder (http://gridgrinder.sourceforge.net/) (Bak et al. 2008, Rna 14(3):432-444).

data_processing: Data were normalised using VSN (Huber et al. 2002, Bioinformatics 18:S96). Values are an average of four replica spots. The A and B in the flag-colomns indicate that data from one or more spots have been removed prior to calculation of the average due to a large coefficient of variation of the replica spots. Data are natural logs. Target genes were considered as differentially expressed when above 5% false discovery rate (FDR), using significant analysis of microarrays (SAM), setting the two class paired t-test option implemented in R (Tusher et al. 2001, Proc Natl Acad Sci U S A  98(9):5116-5121).

organism: Mus musculus

source_name: neocortex

label_protocol: Total RNA (4 µg) was 3’end-labeled using T4 RNA ligase and a Cy3-labeled RNA linker (Bak et al. 2008, RNA 14(3):432-444; Cole K et al. 2004 , Nucleic Acids Res, 32(11):e86; Wienholds et al. 2005, Science 309(5732):310-311.

growth_protocol: Homozygous anorexia mice were produced from heterozygous breeder pairs (B6C3Fe a/a-anx/J) obtained from the Jackson Laboratory. Postnatal day 16 weanling mice housed with their parents were separated into two groups: anx/anx and control mice. anx/anx mice were identified by their reduced body weight, body tremor, and mild hyperactivity. Because homozygous and heterozygous mice cannot be phenotypically distinguished from wild types, control groups probably contained both genotypes (wt/wt or wt/anx). anx/anx and control mice were allowed ad libitum access to the mother, food, and water. Three anx/anx and three control mice animals were anesthetized with isofluorane, decapitated and hypothalamus was dissected. Tissues were immediately frozen with liquid nitrogen and stored until the experiments were performed. Sex was determined by a simplex PCR assay as described (Clapcote and Roder 2005).

extract_protocol: RNA was extracted from the tissue using Trizol (Invitrogen), following manufracturer’s recommendations. RNA quantification was performed through a Nanodrop spectrophotometer, and their quality was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE).

value: neocortex tissue from individual postnatal day 16 weanling anx/anx mouse littermate (B6C3Fe a/a-anx/J strain)

tag: genotype

value: anx/anx

value: neocortex

tag: genetic background

value: B6C3Fe a/a-anx/J strain


title: anx/anx hypothalamus replicate 2

description:
anx/anx hypothalamus, biological replicate 2 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)

source_name: hypothalamus

value: Hypothalamus tissue from individual postnatal day 16 weanling anx/anx mouse littermate (B6C3Fe a/a-anx/J strain)

value: hypothalamus


title: wild type neocortex replicate 2

description:
wild type neocortex, biological replicate 2 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)

value: neocortex tissue from individual postnatal day 16 weanling wild type mouse littermate (B6C3Fe a/a-anx/J strain)

value: wild type


title: anx/anx hypothalamus replicate 3

description:
anx/anx hypothalamus, biological replicate 3 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: anx/anx hypothalamus replicate 1

description:
anx/anx hypothalamus, biological replicate 1 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: wild type hypothalamus replicate 3

description:
wild type hypothalamus, biological replicate 3 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)

value: Hypothalamus tissue from individual postnatal day 16 weanling wild type mouse littermate (B6C3Fe a/a-anx/J strain)


title: wild type hypothalamus replicate 2

description:
wild type hypothalamus, biological replicate 2 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: wild type neocortex replicate 1

description:
wild type neocortex, biological replicate 1 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: anx/anx neocortex replicate 2

description:
anx/anx neocortex, biological replicate 2 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: anx/anx neocortex replicate 1

description:
anx/anx neocortex, biological replicate 1 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: wild type hypothalamus replicate 1

description:
wild type hypothalamus, biological replicate 1 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: wild type neocortex replicate 3

description:
wild type neocortex, biological replicate 3 of 3.
raw data uses GPL6485 (but since normalized data are provided as average of 4 replicate spots we provide a new platform entry)


title: hMSC_transformed_4

description: isolated cell culture


title: XRQ_Control_2 with array type SUNFLOWER from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.

hyb_protocol: labelled extract quantity: 5.5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: aerial - Seeds are surface-sterilized and place 2 days in soaked filter paper at 28°C. Plantlets are then transferred in 20 litre boxes (48 plantlets per box) filled with a complete hydroponic medium and grown during 12 days until treatment and harvesting. Growth chamber 14h day light at 23°C and 70% humidity, 10h night at 20°C and 70% humidity Detailed element concentration as follow: Element Concentration (mM) N 60.0209286 P 1.2491733 K 20.0474472 Mg 1.5011360 Mn 0.0999718 Cu 0.0001002 B 0.1002701 Mn 0.0999718 Mo 0.0010333 Zn 0.0299089 S 1.7311132 Ca 3.4113816 Cl 6.8230627

treatment_protocol: no treatment

tag: age

value: 12 days

tag: developmental stage (boyes et al. plant cell 2001)

value: vegetative

value: leaves


title: XRQ_Control_6 with array type SUNFLOWER from Affymetrix


title: hMSC_transformed_2

description: isolated cell culture


title: hMSC_transformed_5

description: isolated cell culture


title: hMSC_transformed_3

description: isolated cell culture


title: p53-/- MEF, siIrf3, 6 hr ISD stimulation, biological rep2

city: Cambridge

first: Mark

last: Lee

state: MA

address: 7 Cambridge Center

department: MIT

country: USA

institute: Broad Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 1.0 ST Array in an Affymetrix oven (HO640), while rotating at 60rpm. GeneChips were washed and stained in the Affymetrix Fluidic 450 according to manufacturing protocols (using Affymetrix Script FS_0001).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS300.

data_processing: The data were analyzed with RMA quantile normalization using GenePattern software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (IVT Express Kit, Affymetrix).

growth_protocol: Cells were cultured in plates at 37C

extract_protocol: Qiagen RNeasy extraction of total RNA was performed according to the manufacturer's protocols.

treatment_protocol: Cells were treated with siRNAs and then transfected with dsDNA for 6 hrs (or left stimulated), and then lysed in Qiagen RLT buffer.

value: embryonic fibroblasts

tag: sirna


title: XRQ_ABA_9 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:ABA - compound based treatment - compound addition,aba:quantity 10uM time 6hour . ABA was prepared in methanol at a concentration of 400 mM. 500 µl were added to 20 litres of hydroponic medium (ref Massoneau 2001 Planta). 500 µl methanol were added to controls. Leaves of 4 plantlets per box were harvested after 6 hours and pooled together as one sample.


title: XRQ_ABA_5 with array type SUNFLOWER from Affymetrix


title: XRQ_ABA_7 with array type SUNFLOWER from Affymetrix


title: hMSC_transformed_1

description: isolated cell culture


title: p53-/- MEF, siIrf3, 6 hr ISD stimulation, biological rep1


title: XRQ_Control_4 with array type SUNFLOWER from Affymetrix


title: anx/anx versus wild type neocortex replicate 2

description: Neocortex biological replicate 2 of 3. Technical replicate 1 of 2. anx/anx versus wild type littermate comparison.

hyb_protocol: Three biological replicate experiments were performed, each comparing anx/anx verus wild type neocortex. For two of the three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects, whereas the third was only hybridized once. Thus, five microarray hybridizations were processed in total.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Target genes were considered as differentially expressed when above 0.001 false discovery rate (FDR), using significant analysis of microarrays (SAM) test implemented in the samr library in R (Tusher et al 2001). All quantitative and statistical analyses were performed using using Limma package in the R. environment (Smyth 2004).

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

extract_protocol: RNA was extracted from the tissue using Trizol (Invitrogen), following manufacturer’s recommendations. RNA quantification was performed through a Nanodrop spectrophotometer, and their quality was assessed using the Bioanalyzer 2100 nanoelectrophoresis Lab-on-a–chip system (Agilent, Wilmington, DE).


title: anx/anx versus wild type neocortex replicate 2 dye swap

description: Neocortex biological replicate 2 of 3. Technical replicate 2 of 2, with dye reversal. anx/anx versus wild type littermate comparison.


title: anx/anx versus wild type neocortex replicate 3

description: Neocortex biological replicate 3 of 3. Has no technical replicates. anx/anx versus wild type littermate comparison.


title: anx/anx versus wild type neocortex replicate 1 dye swap

description: Neocortex biological replicate 1 of 3. Technical replicate 2 of 2, with dye reversal. anx/anx versus wild type littermate comparison.


title: p53-/- MEF, siIrf3, No stim, biological rep2

source_name: p53-/- MEF, siIrf3, No stim


title: anx/anx versus wild type neocortex replicate 1

description: Neocortex biological replicate 1 of 3. Technical replicate 1 of 2. anx/anx versus wild type littermate comparison.


title: Day 6_S1.15

city: Chicago

first: and

last: PhD

state: Illinois

address: 5841 South Maryland Avenue, MC 5032 Room AB540

department: Department of Surgery

institute: University of Chicago

description: repeat 3

hyb_protocol: Standard Illumina hybridization protocol. Samples were randomly hybrized to BeadChips.

data_processing: The data were transformed using the variance stabilization transformation method (Lin et al. 2008) and normalized by robust spline normalization (Du et al. 2008) using R 2.15.2 and the lumi 2.8.0 package from Bioconductor.

source_name: Murine follicle after 6 days in 0.5% alginate

label_protocol: mRNA samples were in vitro labeled using the TargetAmp 1-Round Aminoallyl-aRNA Kit with biotin  (Epicentre, Madison, WI).

growth_protocol: Alginate-encapsulated follicles were placed in individual wells of a 96-well plate containing 100 ul of growth media (alpha minimum essential medium (alphaMEM) supplemented with 10 mIU/ml recombinant FSH (Organon, Roseland, NJ), 3 mg/ml bovine serum albumin (MP Biomedicals, Irvine, CA), 1 mg/ml bovine fetuin (Sigma, St. Louis, MO), 5 ug/ml insulin, 5 ug/ml transferrin and 5 ng/ml selenium) and cultured for 2, 4, 5, 6 or 8 days in a 5% CO2:21% O2 atmosphere. Half of the culture media (50 ul) was exchanged every 2 days and conditioned media stored at -80ºC. To collect follicles at each time point, alginate-encapsulated follicles were removed from growth media, pooled (20-40 follicles per group, n = 3 independent experiments) and transferred into 1 ml of Liebovitz L-15 media containing 10 U/ml alginate lyase (Sigma) for 20 min at 37ºC. Follicles were aspirated, then transferred into microcentrifuge tubes, flash frozen in liquid nitrogen and stored at -80ºC until subsequent RNA isolation was performed.

extract_protocol: RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).

tag: strain

value: 16 days

value: ovarian follicle

tag: chip batch


title: p53-/- MEF, siAbcf1(si-1), No stim, biological rep1

source_name: p53-/- MEF, siAbcf1(si-1), No stim


title: Day 0_REF.0.5

description: repeat 5

source_name: Murine follicle isolated and no encapsulated


title: p53-/- MEF, siAbcf1(si-1), 6 hr ISD stimulation, biological rep1


title: p53-/- MEF, siAbcf1(si-1), 6 hr ISD stimulation, biological rep2


title: Day 2_S1.6

description: repeat 3

source_name: Murine follicle after 2 days in 0.5% alginate


title: p53-/- MEF, siAbcf1(si-1), No stim, biological rep2


title: p53-/- MEF, siIrf3 No stim, biological rep1

source_name: p53-/- MEF, siIrf3 No stim


title: p53-/- MEF, siCtrl, 6 hr ISD stimulation, biological rep2

value: siCtrl


title: Day 4_S1.9

description: repeat 3

source_name: Murine follicle after 4 days in 0.5% alginate


title: Day 8_S1.18

description: repeat 3

source_name: Murine follicle after 8 days in 0.5% alginate


title: p53-/- MEF, siCtrl, No stim, biological rep4

source_name: p53-/- MEF, siCtrl, No stim


title: Day 0_REF0.4

description: repeat 4


title: Day 0_REF0.3

description: repeat 3


title: Day 8_S1.17

description: repeat 2


title: Day 4_S1.8

description: repeat 2


title: p53-/- MEF, siCtrl, 6 hr ISD stimulation, biological rep3


title: p53-/- MEF, siCtrl, No stim, biological rep3


title: p53-/- MEF, siCtrl, 6 hr ISD stimulation, biological rep1


title: p53-/- MEF, siCtrl, No stim, biological rep2


title: p53-/- MEF, siCtrl, 6 hr ISD stimulation, biological rep4


title: p53-/- MEF, siCtrl, No stim, biological rep1


title: Day 4_S1.7

description: repeat 1


title: Day 5_S1.11

description: repeat 2

source_name: Murine follicle after 5 days in 0.5% alginate


title: Day 5_S1.12

description: repeat 3


title: Day 2_S1.5

description: repeat 2


title: 293T_IFNbeta_12hr

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array in an Affymetrix oven (HO640), while rotating at 60rpm. GeneChips were washed and stained in the Affymetrix Fluidic 450 according to manufacturing protocols (using Affymetrix Script FS_0001).

source_name: 293T, IFNbeta, 12hr

treatment_protocol: Cells were stimulated with recombinant IFNbeta for 12 hours and then lysed in Qiagen RLT buffer.

value: embryonic kidney cells

tag: treatment

value: IFNbeta, 12hr


title: Day 5_S1.10

description: repeat 1


title: Day 0_REF0.2

description: repeat 2


title: Day 2_S1.4

description: repeat 1


title: Day 0_REF0.1

description: repeat 1


title: Human iDC stimulated with IL-8, replicate 2

city: Milwaukee

first: Michael

middle: Andrew

last: Kron

state: Wisconsin

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

description: IL8 KRON7124

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/)  to determine signal log ratios. The mean fold change was calculated from the 2 independent biological replicates for each of the 3 experimental conditions (6 arrays total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in BioConductor (RankProd, www.bioconductor.org/).

source_name: Human iDC_IL-8

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Human immature dendritic cells (iDCs) were generated from CD14+ cells isolated from human peripheral blood mononuclear cells, cultured in 6 well plates for 5 days with 50 ng/ml of IL-4 and GM-CSF (1000 IU/ml).

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: On day 7 iDCs were either left without stimulation (2 control samples) or stimulated with 1 mg/l human recombinant IL-8 (2 IL-8 samples) or with recombinant Brugia malayi AsnRS (2 samples rBmAsnRS). After 48 hours, cells were harvested, pelleted and frozen at -86*C (in TRIzol) for RNA extraction.

tag: tissue source

value: peripheral blood mononuclear cells

tag: responder cells

value: immature dendritic cells (iDCs)

tag: stimulated with

value: 1 mg/l human recombinant IL-8


title: 293T_unstim

source_name: 293T, unstim

tag: tissue

value: unztim


title: Day 8_S1.16

description: repeat 1


title: H460 cells cultured under normoxia and incubated for 16 h with 100 nM BAY 87-2243

city: Wuppertal

first: Peter

last: Ellinghaus

address: Aprather Weg 18a

department: GDD-CS-GBM

institute: Bayer Pharma AG

hyb_protocol: Following fragmentation, 5,5 µg of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Scanner 3000

data_processing: The data was analyzed with Genedata Expressionist package software. Condensation and normalization was done with Genedata Expressionist Refiner and further analysis was done with Genedatas Expressionist Analyst. RMA algorithm (compatible to Bioconductor) was used for condensing including quantile normalization and median polish. Antigenomic background probes were used for background substraction .

source_name: H460 cell normoxia + 100 nM BAY 87-2243

label_protocol: Biotinylated cDNAs for hybridization were prepared according to the standard Ambion WT Expression Kit for Affymetrix gene Chip Arrays and Affymetrix fragmentation and labeling kit from 200 ng of total RNA.

growth_protocol: H460 cells were seeded in 6-well plates at cultured to appr. 80 confluency in medium containg 10 % FCS

extract_protocol: Total RNA from H460 cells was isolated using Rneasy (Qiagen)

treatment_protocol: H460 cells were incubated under normoxic or hypoxic conditions for 16 h with the indicated concentration of BAY 87-2243 in medium containing 0,5 % FCS. Cells not traeted with BAY 87-2243 were incubated with medium containg 0,1 % DMSO


title: Human iDC control no stimulation, replicate 2

description: Ctrl KRON1862

source_name: Human iDC control_no stimulation


title: Human iDC stimulated with IL-8, replicate 1

description: IL8 KRON15


title: H460 cells cultured under normoxia

source_name: H460 cell normoxia

value: cultured under normoxia


title: Human iDC stimulated with AsnRS, replicate 1

description: AsnRS KRON16

source_name: Human iDC_AsnRS

value: recombinant Brugia malayi AsnRS


title: Day 6_S1.13

description: repeat 1


title: Human iDC stimulated with AsnRS, replicate 2

description: AsnRS KRON7139


title: H460 cells cultured under hypoxia (16 h 1 % pO2) and incubated with 10 nM BAY 87-2243

source_name: H460 cells hypoxia + 1 nM BAY 87-2243


title: H460 cells cultured under hypoxia (16 h 1 % pO2)

source_name: H460 cells hypoxia

value: cultured under hypoxia (16 h 1 % pO2)


title: H460 cells cultured under hypoxia (16 h 1 % pO2) and incubated with 1 nM BAY 87-2243

source_name: H460 cells hypoxia + 10 nM BAY 87-2243


title: Human iDC control no stimulation, replicate 1

description: Ctrl KRON14


title: shFUT8-2 vs. Control Replicates 4

status: Public on Dec 07 2012

city: Taipei

first: Chi-Huey

last: Wong

address: 128, Academia Road, Section 2,

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Biological replicate 4 of 4, CL1-5/shFU8-2 vs CL1-5/Control.

hyb_protocol: The fluorochrome-labeled cDNAs were hybridized on Agilent human GE array 8x60K using Agilent Gene Expression Hybridization Kit. After hybridization, sildes were wased sequential.

scan_protocol: Scanned on an Agilent G2565CA Microarray Scanner. Images were then quantified using Agilent Feature Extraction Software (version A.10.5.1.1, protocol GE2_105_Dec08)

data_processing:
Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.
Normalized log2 ratio (Alexa Fluor 647/Alexa Fluor 555) representing knockdown/control calculated using Gene spring v. 12.1.

source_name: FUT8 knockdown

label_protocol: The cDNAs of CL1-5/Control and CL1-5/shFUT8 cells were reverse transcribed from 10 microgram of total RNAs and labeled with Alexa Fluor 555 and Alexa Flour 647, respectively, by SuperScript® Indirect cDNA Labeling System (Life Technologies) following manufacturer's instructions.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% FBS at 37oC under 5% CO2.

extract_protocol: Total RNAs of CL1-5/Control and CL1-5/shFUT8 cells were extracted by RNeasy Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: CL1-5 cells were transfected with contorl or shFUT8 vectors using lentiviral infection and under the seletion of purimycin.

tag: clone

tag: genotype/variation

value: FUT8 knockdown

source_name: vector control

value: control


title: shFUT8-2 vs. Control Replicates 1

description: Biological replicate 1 of 4, CL1-5/shFU8-2 vs CL1-5/Control.


title: Day 6_S1.14

description: repeat 2

source_name: Murine follicle after 6 days in 0.5% alginate


title: shFUT8-1 vs. Control Replicates 4

description: Biological replicate 4 of 4, CL1-5/shFU8-1 vs CL1-5/Control.


title: delta atmA 0 h starvation x delta atmA 24 h starvation, replicate 2

city: Ribeirão Preto

first: Nadia

middle: Graciele

last: Krohn

state: São Paulo

address: Av do Cafe

department: Pharmacy

country: Brazil

institute: University of São Paulo

description: Biological replicate 2 of 3.

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent's instructions.

scan_protocol: Scanned using a GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After, data were processed using the TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

source_name: delta atmA after 0h starvation

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for non-starved samples) or Cyanine-5 (for starved samples) for 2 hours at 40 oC.

growth_protocol: A. nidulans strains (WT, delta xprG, delta atmA) were grown on minimal medium for 24 h (0 h starvation reference), then exposed to 12 and 24 h starvation. The experiment was carried out at 37°C and 180 rpm.

extract_protocol: Total RNA was extracted with the RNeasy® Plant Mini Kit (Qiagen) following manufacturer's instructions, followed by DNase treatment and purification using the RNeasy® Mini Kit (Qiagen).

tag: strain/background

value: delta atmA

value: glucose 1% during 24h followed by 0h starvation

source_name: delta atmA after 24h of starvation

value: glucose 1% during 24h followed by 24h of starvation


title: shFUT8-1 vs. Control Replicates 2

description: Biological replicate 2 of 4, CL1-5/shFU8-1 vs CL1-5/Control.


title: shFUT8-2 vs. Control Replicates 3

description: Biological replicate 3 of 4, CL1-5/shFU8-2 vs CL1-5/Control.


title: shFUT8-2 vs. Control Replicates 2

description: Biological replicate 2 of 4, CL1-5/shFU8-2 vs CL1-5/Control.


title: delta atmA 0 h starvation x delta atmA 12 h starvation, replicate 3

description: Biological replicate 3 of 3.

source_name: delta atmA after 12h of starvation

value: glucose 1% during 24h followed by 12h of starvation


title: shFUT8-1 vs. Control Replicates 3

description: Biological replicate 3 of 4, CL1-5/shFU8-1 vs CL1-5/Control.


title: delta xprG 0 h starvation x delta xprG 12 h starvation, replicate 3

description: Biological replicate 3 of 3.

source_name: delta xprG after 0h starvation

value: delta xprG

source_name: delta xprG after 12h of starvation


title: delta atmA 0 h starvation x delta atmA 12 h starvation, replicate 1

description: Biological replicate 1 of 3.


title: delta atmA 0 h starvation x delta atmA 12 h starvation, replicate 2

description: Biological replicate 2 of 3.


title: delta xprG 0 h starvation x delta xprG 24 h starvation, replicate 2

description: Biological replicate 2 of 3.

source_name: delta xprG after 24h of starvation


title: delta atmA 0 h starvation x delta atmA 24 h starvation, replicate 1

description: Biological replicate 1 of 3.


title: delta xprG 0 h starvation x delta xprG 24 h starvation, replicate 3

description: Biological replicate 3 of 3.


title: delta xprG 0 h starvation x delta xprG 24 h starvation, replicate 1

description: Biological replicate 1 of 3.


title: delta atmA 0 h starvation x delta atmA 24 h starvation, replicate 3

description: Biological replicate 3 of 3.


title: WT 0 h starvation x WT 24 h starvation, replicate 3

description:
Biological replicate 3 of 3.
Strain R21: Fantes, P. A., and C. F. Roberts. 1973. Beta-galactosidase activity and lactose utilization in Aspergillus nidulans. J. Gen. Microbiol. 77:417-486 (PMID 4584063).

source_name: WT after 0h starvation

value: wild-type

source_name: WT after 24h of starvation


title: shFUT8-1 vs. Control Replicates 1

description: Biological replicate 1 of 4, CL1-5/shFU8-1 vs CL1-5/Control.


title: delta xprG 0 h starvation x delta xprG 12 h starvation, replicate 2

description: Biological replicate 2 of 3.


title: WT 0 h starvation x WT 24 h starvation, replicate 2

description:
Biological replicate 2 of 3.
Strain R21: Fantes, P. A., and C. F. Roberts. 1973. Beta-galactosidase activity and lactose utilization in Aspergillus nidulans. J. Gen. Microbiol. 77:417-486 (PMID 4584063).


title: delta xprG 0 h starvation x delta xprG 12 h starvation, replicate 1

description: Biological replicate 1 of 3.


title: WT 0 h starvation x WT 24 h starvation, replicate 1

description:
Biological replicate 1 of 3.
Strain R21: Fantes, P. A., and C. F. Roberts. 1973. Beta-galactosidase activity and lactose utilization in Aspergillus nidulans. J. Gen. Microbiol. 77:417-486 (PMID 4584063).


title: WT 0 h starvation x WT 12 h starvation, replicate 2

source_name: WT after 12h of starvation


title: S11

city: Barcelona

first: Erika

last: Lorenzo Vivas

address: Doctor Aiguader 88

institute: CMRB

description: Gene expression data from WT fibroblast

hyb_protocol: Sample was hybridized to Human Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: Data normalization and analyses were performed in R (v 2.15) using the RMA algorithm.

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: miRNeasy Kit QIAGEN

tag: cell type

value: wild type fibroblasts


title: WT 0 h starvation x WT 12 h starvation, replicate 1


title: S1

description: Gene expression data from WT fibroblast


title: F8

description: Gene expression data from FiPS

tag: cell source

value: induced pluripotent stem cells derived from fibroblasts (FiPSc)


title: WT 0 h starvation x WT 12 h starvation, replicate 3

tag: genotype


title: Fibros

description: Gene expression data from Gaucher disease patient fibroblast

source_name: Fibros

value: Gaucher Disease (GD) fibroblasts


title: A8

description: Gene expression data from Gaucher disease iPSc clon A8

value: Gaucher Disease type 2 fibroblasts


title: 6_cells_5mM Creatine monohydrate 3hr_rep1

city: Oxford

first: Sevasti

last: Zervou

address: Roosevelt Drive

institute: University of Oxford

description:
SAMPLE 2
Replicate1.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was background corrected, filtered and normalized using the vsn package in R.

source_name: Mouse 3T3 fibroblasts stably overexpressing CrT, creatine monohydrate

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

growth_protocol: DMEM high glucose, 10% FBS, P/S, L-glutamine, G418, Puromycin. Adherent culture, 70% confluent, grown on 6-well plates.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit.

treatment_protocol: Treated with 5mM creatine monohydrate in growth media for 3hr. Controls remained untreated.

tag: cell line

value: stably overexpressing creatine transporter (CrT)

value: creatine monohydrate

tag: culture type

value: adherent


title: 1_cells_untreated control_rep2

description:
SAMPLE 3
Replicate2.

source_name: Mouse 3T3 fibroblasts stably overexpressing CrT, untreated


title: 21C

description: Gene expression data from Gaucher disease iPSc clon 21C


title: Day 5 from the day length shift, at 8:00

city: Tsukuba

first: Takeshi

last: Izawa

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: 825ng of labeled cRNA were used for hybridization according to manufacturer's protocol. Open-lab in rgrc in NIAS was used.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1). Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

source_name: rice,leaf,in the field

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy3 CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a growth chamber under long- or short-day conditions with daily cycles of 14.5 to 10 hours of light and 9.5 to 14 hours of dark. Day length was shifted from long-day to short-day condition.

extract_protocol: Total RNA extracted using QIAGEN RNeasy Plant Mini Kit following manufacturer's instructions

treatment_protocol: 14-day-old seedlings were sampled in the growth chamber. Samples were frozen using liquid N imediately.

tag: cultivar

value: Norin 8

tag: sampling time


title: 2_cells_untreated control_rep3

description:
SAMPLE 5
Replicate3.


title: 4_cells_5mM Creatine monohydrate 3hr_rep2

description:
SAMPLE 4
Replicate2.


title: 3_ES4_p15

description: Gene expression data from human embryonic stem cell line ES4

value: human embryonic stem cells


title: 5_cells_5mM Creatine monohydrate 3hr_rep3

description:
SAMPLE 6
Replicate3.


title: 3_cells_untreated control_rep1

description:
SAMPLE 1
Replicate1.


title: Day 5 from the day length shift, at 6:00


title: Day 5 from the day length shift, at 2:00


title: Day 5 from the day length shift, at 0:00


title: Day 5 from the day length shift, at 4:00


title: Day 1 from the day length shift, at 12:00


title: Day 5 from the day length shift, at 20:00


title: Day 1 from the day length shift, at 10:00


title: Day 5 from the day length shift, at 12:00


title: Day 5 from the day length shift, at 10:00


title: Day 5 from the day length shift, at 18:00


title: Day 5 from the day length shift, at 22:00


title: Day 1 from the day length shift, at 18:00


title: Day 1 from the day length shift, at 4:00


title: Day 1 from the day length shift, at 8:00


title: Day 1 from the day length shift, at 2:00


title: Day 1 from the day length shift, at 20:00


title: Day 1 from the day length shift, at 22:00


title: Day 1 from the day length shift, at 0:00


title: Day 1 from the day length shift, at 6:00


title: Day 0 from the day length shift, at 8:00


title: Day 0 from the day length shift, at 6:00


title: Day 0 from the day length shift, at 12:00


title: H460 cells cultured under hypoxia (16 h 1 % pO2) and incubated with 100 nM BAY 87-2243

source_name: H460 cells hypoxia + 100 nM BAY 87-2243


title: Day 0 from the day length shift, at 2:00


title: Day 0 from the day length shift, at 0:00


title: Day 0 from the day length shift, at 4:00


title: Day 0 from the day length shift, at 10:00


title: Day 0 from the day length shift, at 22:30


title: Aug_24_2009_at_13:00_transplanted_on_May_19_rep2

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1).
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy5 (or Cy3) CTP at 40 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a paddy field in Tsukuba, Japan on 2009 using a typical cultivation method. Transplanting dates were May 19, June 19, July 16 and July 31 to obtain RNA from plants at different developmental stage on the sampling date.

treatment_protocol: Rice leaves were sampled at the paddy field. Cut leaves were frozen using liquid N imeditately after sampling.

value: osgi

tag: developmental stage

value: transplanted on May 19


title: Aug_24_2009_at_13:00_transplanted_on_June_19_rep2

value: transplanted on June 19


title: Aug_24_2009_at_13:00_transplanted_on_July_16_rep1

value: transplanted on July 16


title: Aug_24_2009_at_13:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_11:00_transplanted_on_June_19_rep2


title: Aug_24_2009_at_13:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_13:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_9:00_transplanted_on_July_16_rep1


title: Aug_24_2009_at_11:00_transplanted_on_May_19_rep2


title: Aug_24_2009_at_9:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_11:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_9:00_transplanted_on_June_19_rep2


title: Aug_24_2009_at_9:00_transplanted_on_May_19_rep2


title: Aug_24_2009_at_9:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_9:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_11:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_11:00_transplanted_on_July_16_rep1


title: Aug_24_2009_at_7:00_transplanted_on_May_19_rep2


title: Aug_24_2009_at_7:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_7:00_transplanted_on_June_19_rep2


title: Aug_24_2009_at_17:00_transplanted_on_July_16_rep1


title: Aug_24_2009_at_17:00_transplanted_on_May_19_rep2


title: Aug_24_2009_at_7:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_7:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_17:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_17:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_15:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_17:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_15:00_transplanted_on_July_16_rep1


title: Oct_8_2009_at_11:00_transplanted_on_July_31_rep3

value: transplanted on July 31


title: Aug_24_2009_at_15:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_15:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_15:00_transplanted_on_May_19_rep2


title: Aug_24_2009_at_17:00_transplanted_on_June_19_rep2


title: Oct_8_2009_at_11:00_transplanted_on_July_31_rep2


title: Oct_9_2009_at_11:00_transplanted_on_July_31_rep4


title: Aug_24_2009_at_15:00_transplanted_on_June_19_rep2


title: Oct_9_2009_at_11:00_transplanted_on_July_31_rep3


title: Aug_12_2009_at_12:00_transplanted_on_June_19_rep2


title: Aug_12_2009_at_12:00_transplanted_on_June_19_rep1


title: Oct_9_2009_at_11:00_transplanted_on_July_31_rep1


title: Oct_9_2009_at_11:00_transplanted_on_July_31_rep2


title: Aug_12_2009_at_6:00_transplanted_on_June_19_rep2


title: Aug_11_2009_at_24:00_transplanted_on_June_19_rep1


title: Oct_8_2009_at_11:00_transplanted_on_July_31_rep1


title: Aug_11_2009_at_24:00_transplanted_on_June_19_rep2


title: Aug_11_2009_at_18:00_transplanted_on_June_19_rep2


title: Aug_12_2009_at_6:00_transplanted_on_June_19_rep1


title: Aug_11_2009_at_12:00_transplanted_on_June_19_rep1


title: Aug_11_2009_at_12:00_transplanted_on_June_19_rep2


title: Aug_11_2009_at_6:00_transplanted_on_June_19_rep2


title: Aug_11_2009_at_6:00_transplanted_on_June_19_rep1


title: Aug_10_2009_at_24:00_transplanted_on_June_19_rep1


title: Aug_10_2009_at_24:00_transplanted_on_June_19_rep2


title: Aug_10_2009_at_18:00_transplanted_on_June_19_rep1


title: Aug_10_2009_at_12:00_transplanted_on_June_19_rep1


title: Aug_10_2009_at_18:00_transplanted_on_June_19_rep2


title: Aug_25_2009_at_7:00_transplanted_on_July_16_rep1


title: Aug_25_2009_at_7:00_transplanted_on_June_19_rep2


title: Aug_25_2009_at_7:00_transplanted_on_July_16_rep2


title: Aug_25_2009_at_7:00_transplanted_on_June_19_rep1


title: Aug_25_2009_at_7:00_transplanted_on_May_19_rep2


title: Aug_11_2009_at_18:00_transplanted_on_June_19_rep1


title: Aug_10_2009_at_12:00_transplanted_on_June_19_rep2


title: Aug_25_2009_at_7:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_7:00_transplanted_on_July_16_rep1


title: Aug_25_2009_at_5:00_transplanted_on_June_19_rep2


title: Aug_25_2009_at_3:00_transplanted_on_June_19_rep1


title: Aug_25_2009_at_3:00_transplanted_on_July_16_rep2


title: Aug_25_2009_at_3:00_transplanted_on_June_19_rep2


title: Aug_25_2009_at_5:00_transplanted_on_June_19_rep1


title: Aug_25_2009_at_5:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_11:00_transplanted_on_June_19_rep1


title: Aug_25_2009_at_5:00_transplanted_on_July_16_rep1


title: Aug_25_2009_at_1:00_transplanted_on_July_16_rep2


title: Aug_25_2009_at_3:00_transplanted_on_July_16_rep1


title: Aug_25_2009_at_3:00_transplanted_on_May_19_rep2


title: Aug_25_2009_at_3:00_transplanted_on_May_19_rep1


title: Aug_25_2009_at_1:00_transplanted_on_June_19_rep1


title: Aug_25_2009_at_1:00_transplanted_on_May_19_rep2


title: Aug_25_2009_at_1:00_transplanted_on_June_19_rep2


title: Aug_25_2009_at_1:00_transplanted_on_July_16_rep1


title: Aug_24_2009_at_23:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_21:00_transplanted_on_July_16_rep1


title: Aug_24_2009_at_23:00_transplanted_on_May_19_rep2


title: Aug_24_2009_at_23:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_23:00_transplanted_on_July_16_rep1


title: Aug_25_2009_at_1:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_21:00_transplanted_on_June_19_rep2


title: Aug_24_2009_at_23:00_transplanted_on_June_19_rep2


title: Aug_24_2009_at_21:00_transplanted_on_July_16_rep2


title: Aug_24_2009_at_23:00_transplanted_on_July_16_rep2


title: Aug_25_2009_at_5:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_21:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_21:00_transplanted_on_May_19_rep1


title: Aug_24_2009_at_19:00_transplanted_on_June_19_rep2


title: Aug_24_2009_at_19:00_transplanted_on_June_19_rep1


title: Aug_24_2009_at_19:00_transplanted_on_July_16_rep2


title: Day 6 from the temperature shift, at 2:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113716_S01_GE2-v5_95_Feb07_1_3.txt

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.9.5.3.1). LOWESS normalization.
Experiments were performed technically as dual channel (e.g., Cy3 and Cy5-labeled samples hybridized to the same array) but were processed as though they were single channel (i.e., Cy3 and Cy5 signals are treated independently; Cy3/Cy5 ratios are not calculated).

source_name: rice,leaf,in a growth chamber

label_protocol: 400 ng of total RNA were primed with 0.6 µl of 100 µM T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 0.5ul of MMLV-RT, and 500 µM dNTP, then labelled by T7 RNA polymerase using NTP and 400 µM Cy5 (or Cy3) CTP at 40°C for 2h. Labelled cRNA were purifed by columns in the Quiagen RNeasy mini kit.

growth_protocol: Rice plants were grown in a growth chamber using a typical cultivation method for 27 days before the temperature shift.

treatment_protocol: Rice leaves were sampled in the growth chamber. Cut leaves were frozen using liquid N imeditately after sampling.

tag: replicate


title: Aug_24_2009_at_21:00_transplanted_on_May_19_rep2


title: Aug_31_2009_at_12:00_transplanted_on_June_19_rep2


title: Day 6 from the temperature shift, at 14:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113716_S01_GE2-v5_95_Feb07_1_4.txt


title: Aug_31_2009_at_18:00_transplanted_on_June_19_rep2


title: Day -1 from the temperature shift, at 14:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113715_S01_GE2-v5_95_Feb07_1_2.txt


title: Aug_24_2009_at_19:00_transplanted_on_May_19_rep1


title: Aug_31_2009_at_18:00_transplanted_on_June_19_rep1


title: Day 2 from the temperature shift, at 2:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113715_S01_GE2-v5_95_Feb07_1_3.txt


title: Day 6 from the temperature shift, at 2:00_Cy5


title: Day 4 from the temperature shift, at 2:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113716_S01_GE2-v5_95_Feb07_1_1.txt


title: Day 4 from the temperature shift, at 14:00_Cy5

description:
Agilent Feature Extraction file:
US22502560_251524113716_S01_GE2-v5_95_Feb07_1_2.txt


title: Aug_24_2009_at_19:00_transplanted_on_July_16_rep1


title: Aug_31_2009_at_12:00_transplanted_on_June_19_rep1


title: Day 2 from the temperature shift, at 14:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113715_S01_GE2-v5_95_Feb07_1_4.txt


title: Day -1 from the temperature shift, at 2:00_Cy3

description:
Agilent Feature Extraction file:
US22502560_251524113715_S01_GE2-v5_95_Feb07_1_1.txt


title: Aug_24_2009_at_19:00_transplanted_on_May_19_rep2


title: Day 4 from the temperature shift, at 14:00_Cy3


title: Day 6 from the temperature shift, at 14:00_Cy5


title: Day 2 from the temperature shift, at 2:00_Cy5


title: Day 4 from the temperature shift, at 2:00_Cy5


title: Day -1 from the temperature shift, at 2:00_Cy5


title: Day 2 from the temperature shift, at 14:00_Cy5


title: Day -1 from the temperature shift, at 14:00_Cy5


title: #19_CD44+

city: Chuo-ku

first: Hirokazu

last: Ohata

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

description: Gene expression in CD44+ cells.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried immediately.

scan_protocol: Slides were scanned, immediately after washing, on the Agilent DNA Microarray Scanner using the one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_105_Jan09 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: #19, colonospheres, CD44+

label_protocol: Cy3-labeled cRNA was prepared from 0.2 ug RNA using the Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by the RNeasy mini kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Colonospheres were grown in serum-free STEMPRO hESC SFM supplemented with FGF2 and Y27632.

extract_protocol: Total RNAs from CD44+ or CD44- cells were extracted using the miRNeasy mini kit (QIAGEN) according to the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Colonospheres were sorted into CD44+ and CD44- cells using FACS.

value: colon cancer

value: colonosphere CD44+ cells

tag: patient identifier


title: #17_CD44+

description: Gene expression in CD44+ cells.

source_name: #17, colonospheres, CD44+


title: #20_CD44+

description: Gene expression in CD44+ cells.

source_name: #20, colonospheres, CD44+


title: #20_CD44-

description: Gene expression in CD44- cells.

source_name: #20, colonospheres, CD44-

value: colonosphere CD44- cells


title: #17_CD44-

description: Gene expression in CD44- cells.

source_name: #17, colonospheres, CD44-


title: NOD CRE natural Treg_MLB 024

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: wild type Treg

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: The data were analyzed using Partek Genomics Suite 6.5 and summarized by the RMA method

source_name: NOD CRE natural Treg

label_protocol: Biotinylated cRNA were prepared according to the  Affymetrix 3' IVT Express protocol

growth_protocol: Cells were lysed directly after sorting

extract_protocol: Spleens were dissociated with frosted glass slides into complete RPMI media supplemented with 10% fetal calf serum. T cells were sorted on CD3+CD4+GFP- and mRNA isolated using TRIZOL

treatment_protocol: Spleens were isolated from 6 week old Tg(Foxp3-EGFP/cre)1aJbs (WT) and Foxp3tm2Ayr NOD/LtJ mice (KI) (No other treatment given)

value: Spleen

tag: strain

value: NOD/LtJ

value: Treg


title: NOD KI natural Treg_MLB 019

description: Foxp3gfp Treg

source_name: NOD KI natural Treg

value: Foxp3tm2Ayr NOD/LtJ


title: NOD KI Tconv_MLB 027

description: Foxp3gfp Tconv

source_name: NOD KI Tconv

value: Tconv


title: NOD CRE Tconv_MLB 025

description: wild type Tconv

source_name: NOD CRE Tconv


title: epidermal_cells_uninfected_rep4

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

institute: URMITE

description: Sample name: C4

hyb_protocol: Performed according to Agilent's protocol

scan_protocol: Scan performed by DNA microarray scanner (Agilent Technologies)

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters.
Background subtracted (with half algorithm) and quantile normalization on mean signal, using R and Bioconductor softwares

label_protocol: RNA was amplified and labeled with Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Total RNA was extracted  using RNeasy Mini kit and DNase digestion

treatment_protocol: Patients included in this study were recruited at the Infectious Diseases Department of Oran, Algeria or at the Infectious Diseases Division of the Ibn Rochd Casablanca Teaching Hospital and at the Dermatology Department of Militar Hospital Mohamed V of Rabat, Morocco. All patients presented with clinical characteristics of MSF were diagnosed using serology as described elsewhere (4) and/or confirmed by positive PCR assay with specific primers for R. conorii subsp. conorii of the blood or the skin biopsy of the eschar (4). Severe cases were defined as having multiple organ deficiency systems syndrome (MODS) or death as previously described (4).

tag: infection

value: uninfected

value: epidermis


title: epidermal_cells_uninfected_rep5

description: Sample name: C5


title: #6_CD44+

description: Gene expression in CD44+ cells.

source_name: #6, colonospheres, CD44+


title: NOD KI Tconv_MLB 023

description: Foxp3gfp Tconv


title: NOD KI natural Treg_MLB 013

description: Foxp3gfp Treg


title: epidermal_cells_uninfected_rep6

description: Sample name: C6


title: NOD KI natural Treg_MLB 026

description: Foxp3gfp Treg


title: NOD KI natural Treg_MLB 015

description: Foxp3gfp Treg


title: #6_CD44-

description: Gene expression in CD44- cells.

source_name: #6, colonospheres, CD44-


title: NOD KI Tconv_MLB 022

description: Foxp3gfp Tconv


title: NOD KI Tconv_MLB 016

description: Foxp3gfp Tconv


title: #19_CD44-

description: Gene expression in CD44- cells.

source_name: #19, colonospheres, CD44-


title: epidermal_cells_uninfected_rep3

description: Sample name: C3


title: epidermal_cells_uninfected_rep1

description: Sample name: C1


title: epidermal_cells_infected_rep19

description: Sample name: A7

value: R. conorii subsp. conorii

tag: origin

value: Algeria


title: NOD CRE Tconv_MLB 008

description: wild type Tconv

tag: tissue


title: NOD CRE natural Treg_MLB 005

description: wild type Treg


title: epidermal_cells_infected_rep17

description: Sample name: A5


title: epidermal_cells_infected_rep13

description: Sample name: A1


title: NOD CRE natural Treg_MLB 006

description: wild type Treg


title: NOD CRE Tconv_MLB 009

description: wild type Tconv


title: epidermal_cells_infected_rep14

description: Sample name: A2


title: epidermal_cells_infected_rep15

description: Sample name: A3


title: epidermal_cells_infected_rep16

description: Sample name: A4


title: epidermal_cells_uninfected_rep2

description: Sample name: C2


title: epidermal_cells_infected_rep12

description: Sample name: M12

value: Morocco


title: NOD CRE Tconv_MLB 007

description: wild type Tconv


title: MDM_Control_2

description: control

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters.

source_name: control

growth_protocol: Human monocytes were isolated from blood of healthy donors (buffy coat obtained from Etablissement Français du Sang) as previously described (ref ) with slight modifications. Monocytes were isolated using CD14 MACS (Miltenyl Biotec , Auburn, CA) according to the manufacturer’s protocol. More than 95% of recovered cells expressed CD14 and were considered as monocytes

extract_protocol: RNA was extracted using RNeasy kit according to the manufacturer’s recommendations, which included a DNase step and the RNAs were eluted in 30 µL of water and stored at -20°C The quality and quantity of isolated RNAs were assessed using the Nanodrop (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies),

treatment_protocol: Monocytes were seeded (2 x 106 cells per well in 6-well plates and 2 x 105 cells per well in 24-well plates) in complete medium  To obtain MGCs, 100 U/ml recombinant human IFN-g (Roche Biochemicals, Basel, Switzerland) and 5 ug/ml ConA (Sigma-Aldrich, St Louis, MO, USA) were added after 24 hours and cells were cultivated for 10 days as described in Verollet et al. Monocytes were cultivated for 10 days in complete medium and the obtention of monocyte-derived macrophages (MDMs) was checked using CD68 expression. To compare the transcriptional programs of MGCs with that of MDMs or stimulated MDMs, MDMs were or not  stimulated with IFN-g  (100 U/ml) or ConA (5 ug/ml) 18 h before RNA extraction.

value: monocytes

tag: treatment


title: epidermal_cells_infected_rep11

description: Sample name: M11


title: MGC_3

description: multinucleated giant cells

source_name: multinucleated giant cells

value: multinucleated giant cells


title: epidermal_cells_infected_rep10

description: Sample name: M10


title: epidermal_cells_infected_rep18

description: Sample name: A6


title: epidermal_cells_infected_rep9

description: Sample name: M9


title: NOD CRE natural Treg_MLB 004

description: wild type Treg


title: MDM_ConA_1

description: monocytes treated by concanavalin

source_name: monocytes, concanavalin

value: concanavalin


title: MDM_IFNg_3

description: monocytes treated by IFN-g

source_name: monocytes, IFNg

value: IFNg


title: MDM_Control_3

description: control


title: epidermal_cells_infected_rep8

description: Sample name: M8


title: epidermal_cells_infected_rep5

description: Sample name: M5


title: epidermal_cells_infected_rep7

description: Sample name: M7


title: MGC_2

description: multinucleated giant cells


title: MDM_IFNg_2

description: monocytes treated by IFN-g


title: MDM_IFNg_1

description: monocytes treated by IFN-g


title: MDM_ConA_4

description: monocytes treated by concanavalin


title: epidermal_cells_infected_rep1

description: Sample name: M1


title: epidermal_cells_infected_rep3

description: Sample name: M3


title: MDM_ConA_3

description: monocytes treated by concanavalin


title: MDM_Control_1

description: control


title: epidermal_cells_infected_rep6

description: Sample name: M6


title: epidermal_cells_infected_rep2

description: Sample name: M2


title: epidermal_cells_infected_rep4

description: Sample name: M4


title: MGC_1

description: multinucleated giant cells


title: 4862_4_NS_1

hyb_protocol: Performed according to Agilent's protocol (17 hours at 65°C and 10 rpm)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10,5.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Microarray data analysis was performed using the software GeneSpring 10.01 with inter-array normalization and inter-replicate corrections using the default settings. To identify genes that were differentially expressed, we used a Student’s t test unpaired with P <0.01 with multiple testing correction by Benjamini-Hochberg test and an absolute fold change (FC) greater than 2.0. An analysis of Gene Ontology (GO) terms was performed, which identifies the modulated biological processes

growth_protocol: JEG cell line ATCC  HTB-36 were cultured according ATCC recommandations

treatment_protocol: unstimulated cells were kept in DMEM-F12 medium, infected cells were stimulated for 6 hours with 200 bacteria per cells

value: JEG trophoblastic cell line (ATCC  HTB-36)

value: control


title: 4866_2_Cb_3

source_name: infected by Coxiella

value: Coxiella


title: 4865_1_NS_3


title: 4771_4_Cb_1


title: 4863_2_Cb_2


title: 4863_3_NS_2


title: MDMs 2

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters. Date were background subtracted (with half algorithm) and quantile normalization on mean signal, using R and Bioconductor software.

source_name: macrophages derived from monocytes

growth_protocol: cells were cultured in DMEM-F12 media complemented with 10 % FCS and supplemented by 100 U/ml penicillin and 100 µg/ml streptomycin

treatment_protocol: maintain in culture for placental cells. For monocytes an incubation step for 3 days using RPMI1640 media with 10% human serum AB and 100 IU/mL penicillin and 100 µg/mL streptomycin

value: macrophages derived from monocytes


title: Monocytes 1

source_name: CD14+ cells isolated from PBMC which are extracted from the whole human blood of healthy donors


title: MDMs 1


title: MGCs 3

source_name: placental macrophages after 9 days in culture


title: Monocytes 3

value: CD14+ cells isolated from PBMC which are extracted from the whole human blood of healthy donors


title: Monocytes 2


title: MDMs 3


title: MGCs 2

value: placental macrophages after 9 days in culture


title: CD14+ macrophages 2

source_name: placental macrophages just after isolation


title: buffyCoat_3043

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression data were obtained from guthrie card blood spots, along with matched buffy coat samples and reference brain RNA.

hyb_protocol: Agilent hybridization protocol 65C 10rpm 17 h.

scan_protocol: Agilent arrays were scanned using the Agilent Scanner G2565BA.

data_processing: Agilent using Feature Extraction software v.9.5.3.1.  The data was first processed by background correction and then quantile normalization.

label: Buffy coat and Brain samples: Agilent  part #5190-0442 Quick-Amp Labeling kit 1-color. , Blood spot samples:  Invitrogen  part # 18097-012 BioPrime total genomic labeling system.

source_name: Homo Sapiens

label_protocol: Buffy coat and Brain samples: 300 ng of Qiagen-purified total RNA , Blood spot samples: 3 ug of Zymo Research purified cDNA

extract_protocol: Buffy coat and Brain samples: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Blood spot samples: illustra mini spin kit (GE Whatman) was performed according to the manufacturer's instructions with slight modification.

tag: sample type

value: buffyCoat


title: buffyCoat_3054


title: buffyCoat_3069


title: buffyCoat_3064


title: brain_tissue_control_a

value: brain


title: buffyCoat_4022


title: CD14+ macrophages 3

value: placental macrophages just after isolation


title: buffyCoat_3044


title: buffyCoat_4034


title: CD14+ macrophages 1


title: bloodSpot_4022

value: bloodSpot


title: buffyCoat_3045


title: MGCs 1


title: brain_tissue_control_b


title: buffyCoat_3056


title: bloodSpot_4034


title: bloodSpot_3044


title: bloodSpot_3069


title: bloodSpot_3056


title: bloodSpot_3054


title: bloodSpot_3064


title: bloodSpot_3045


title: bloodSpot_3043


title: UpSET_Ovary_expression_rep2

city: Seattle

first: Hector

last: Rincon-Arano

state: Washington

address: 1100 Fairview Ave N

department: Basic Science Division

institute: Fred Hutchinson Cancer Research Center

description:
SAMPLE 5
This sample is of upSET mutant ovaries. It is the second of first upSET mutant biological replicates used in this experiment.

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

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

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

organism: Drosophila melanogaster

source_name: upSET mutant ovary

label_protocol: 1 mg of total RNA was labeled with Cy3 and hybridized to the array following the manufacturer’s recommendations.  Arrays were scanned on a GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) and data was extracted using NimbleScan v2.4 software (Roche NimbleGen, Inc. Madison, WI, USA)

growth_protocol: Flies were fattened for 2-Day old wildtype after eclosion

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

treatment_protocol: Ovaries from wildtype and mutant flies were dissected in in CCM3 media and wash twice in PBS.

tag: genotype/variation

value: upSET mutant

tag: gender

value: female

tag: age

value: 2-day old

value: ovary


title: UpSET_Ovary_expression_rep1

description:
SAMPLE 4
This sample is of upSET mutant ovaries. It is the first of first upSET mutant biological replicates used in this experiment.


title: upSET_Ovary_expression_rep3

description:
SAMPLE 6
This sample is of upSET mutant ovaries. It is the third of first upSET mutant biological replicates used in this experiment.


title: WT_Ovary_expression_rep2

description:
SAMPLE 2
This sample is of wild-type ovaries. It is the second of three wild-type biological replicates used in this experiment.

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

source_name: Wildtype ovary

value: OregonG

value: wild type


title: untreated Normal astrocytic culture 1

city: Cordoba

first: Pablo

last: Helguera

state: Cordoba

address: Friuli 2434

country: Argentina

institute: INIMEC-CONICET

description:
NL astrocytic culture 1
1888849021_F
NL1
SAMPLE 14

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Quantile normalization, probe detection, fold-change comparison in R and Matlab

source_name: NL astrocytic culture 1

label_protocol: Standard Illumina labeling protocol

growth_protocol: Astrocytes were maintained in DMEM supplemented with 10% calf bovine serum (Invitrogen).

extract_protocol: Total mRNA was collected from all samples using QIAshredder (Qiagen) for cell homogenization and RNeasy Mini Kit (Qiagen) for RNA extraction, according to manufacturer's protocols.

treatment_protocol: NL and DS astrocytes were grown on basal conditions or treated with 50 mM H2O2 for 24 hs, and then total RNA samples were extracted. Treated with H2O2: T. Non Treated: NT

value: untreated

tag: cell type

value: astrocyte

tag: disease state

value: normal


title: untreated Normal astrocytic culture 3

description:
NL astrocytic culture 3
1888849021_H
NL3
SAMPLE 16

source_name: NL astrocytic culture 3


title: untreated Normal astrocytic culture 2

description:
NL astrocytic culture 2
1888849021_G
NL2
SAMPLE 15

source_name: NL astrocytic culture 2


title: H2O2 Normal astrocytic culture 2

description:
NL astrocytic culture 2
1888849008_G
NL2
SAMPLE 7


title: untreated Down's Syndrome astrocytic culture 4

description:
DS astrocytic culture 4
1888849021_D
DS4
SAMPLE 12

source_name: DS astrocytic culture 4

value: Down's Syndrome


title: untreated Down's Syndrome astrocytic culture 5

description:
DS astrocytic culture 5
1888849021_E
DS5
SAMPLE 13

source_name: DS astrocytic culture 5


title: untreated Down's Syndrome astrocytic culture 3

description:
DS astrocytic culture 3
1888849021_C
DS3
SAMPLE 11

source_name: DS astrocytic culture 3


title: WT_Ovary_expression_rep3

description:
SAMPLE 3
This sample is of wild-type ovaries. It is the third of three wild-type biological replicates used in this experiment.


title: untreated Down's Syndrome astrocytic culture 2

description:
DS astrocytic culture 2
1888849021_B
DS2
SAMPLE 10

source_name: DS astrocytic culture 2


title: H2O2 Normal astrocytic culture 3

description:
NL astrocytic culture 3
1888849008_H
NL3
SAMPLE 8


title: H2O2 Down's Syndrome astrocytic culture 3

description:
DS astrocytic culture 3
1888849008_C
DS3
SAMPLE 3


title: WT_Ovary_expression_rep1

description:
SAMPLE 1
This sample is of wild-type ovaries. It is the first of three wild-type biological replicates used in this experiment.


title: H2O2 Down's Syndrome astrocytic culture 2

description:
DS astrocytic culture 2
1888849008_B
DS2
SAMPLE 2


title: untreated Down's Syndrome astrocytic culture 1

description:
DS astrocytic culture 1
1888849021_A
DS1
SAMPLE 9

source_name: DS astrocytic culture 1


title: H2O2 Down's Syndrome astrocytic culture 1

description:
DS astrocytic culture 1
1888849008_A
DS1
SAMPLE 1


title: H2O2 Normal astrocytic culture 1

description:
NL astrocytic culture 1
1888849008_F
NL1
SAMPLE 6


title: H2O2 Down's Syndrome astrocytic culture 5

description:
DS astrocytic culture 5
1888849008_E
DS5
SAMPLE 5


title: H2O2 Down's Syndrome astrocytic culture 4

description:
DS astrocytic culture 4
1888849008_D
DS4
SAMPLE 4


title: Liver-GBE-HCC-6

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Liver, GBE treated

hyb_protocol: 15 μg of amplified biotin-cRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

source_name: Liver, GBE treated

label_protocol: One μg of total RNA was amplified as directed in the Affymetrix One-Cycle cDNA Synthesis protocol.

growth_protocol: N/A; tumors and tissue collected from B6C3F1 mice on 2-year Natinal Toxicology Program Bioassay.

extract_protocol: Affymetrix Mouse Genome 430 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA) were used to assess gene expression. Amplification of 1ug total RNA was performed as instructed in the Affymetrix One-Cycle cDNA Synthesis protocol. For each array, 15 μg of amplified biotin-cRNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization protocol. Array slides were double stained with streptavidin/phycoerythrin and washed using the EukGE-WS2v5 protocol from the Affymetrix Fluidics Station FS450 for antibody amplification. Arrays were scanned in an Affymetrix Scanner 3000 and GeneChip® Command Console Software (AGCC; Version 1.1) was used to obtain the data. Fluorescent pixel intensity measurements were processed using the MAS5 algorithm {Hubbell, 2002 #1177}, and signals were background subtracted and averaged across probes within a probeset using a mean Tukey biweight function.  Control probes on the array were removed and then the gene expression data from the remaining probsets were normalized across the groups of samples using the Robust Multi-array Analysis (RMA) methodology {Irizarry, 2003 #324} in the R statistical software.

treatment_protocol: Treatment group (GBE) was treated with 2000mg/kg ginkgo biloba extract (GBE761) by gavage for two years.

value: Liver


title: Liver-GBE-HCC-5

description: Liver, GBE treated


title: Liver-GBE-HCC-3

description: Liver, GBE treated


title: Liver-GBE-HCC-2

description: Liver, GBE treated


title: Liver-GBE-HCC-4

description: Liver, GBE treated


title: d11.5 placenta control 13

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: pooled from two placentas

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K Whole Mouse Genome microarrays (Design ID 026655, Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: d11.5 placenta, mom 120

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

extract_protocol: Placentas were halved and frozen in Trireagent (Sigma).  After phase separation, the aqueous phase was applied to RNEasy columns (Qiagen) according to manufacturer's protocol.  Total RNA from two placentas per mother were pooled.

treatment_protocol: Mice were mated, and on pregnancy day 1.5, randomized to (1) ad libitum fed (control); (2) restricted to 50% of previous food consumption (restricted); (3) restricted to 50% and injected once daily with 1 mg/kg recombinant mouse leptin. Mice were sacrificed on d11.5 and placentas were collected.

value: ad libitum fed

value: placenta

tag: maternal treatment group

value: control

tag: pregnancy stage

tag: genetic background

value: Swiss Webster


title: d11.5 placenta leptin 29

description: pooled from two placentas

source_name: d11.5 placenta, mom 151

value: 50% food restriction w/ leptin replacement

value: leptin


title: Chromatin accesibility_rep1

type: genomic

description: Differential chromatin accesibility in UpSET knock down cells

data_processing: For chromatin profiling, raw signals of corresponding experimental replicates were loess normalized within arrays and quantile normalized between arrays. Enrichment statistics (test versus control signals) were computed using the 'sam' algorithm within Bioconductor . Fdr values of the sam statistic were determined using ‘locfdr’ . Region summarization was performed using the HMM algorithm of TileMap . Probes were considered to be bound significantly if the posterior probability of the HMM was greater than 0.9 and if the enriched region was larger than 4Kb. Chromatin accesibility datasets were loess normalized and end analysis were performed as described  (Henikoff, S., et al., 2009 Genome research, 19(3), 460–469.) (Deal, R. B., et al., Science (New York, NY), 328(5982), 1161–1164). [Average Log 2 ratio (Dam_Epic vs Dam or Knock down vs mock) data is available as a Series Supplementary data]

molecule: genomic DNA

source_name: UpSET Knock down in Kc cells

label_protocol: 3 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers ( DNA isolated from DamEpic transfected cells or Epic Knock down cells) or with Cy3 nonamers (DNA isolated from Dam transfected cells or mock cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were grown for 7 days at 25C

extract_protocol: For DamID experiments, genomic DNA from DamEpic- or Dam-transfected cells was recovered, DpnI digested and fractionated according to Orian A. Methods in molecular biology (2009), 567, 155–169. For chromatin accesibility assays, Nuclei from Epic knock down and mock cells were treated with MNaseI and hypersentivity nucleosomes were extracted in 80mM low salt buffer (Henikoff, S.,(2009). Genome research, 19(3), 460–469.)

treatment_protocol: Cells were treated with Cupper to induce Epic knock down

tag: cell line

value: Kc cell

source_name: mock-treated Kc cells

treatment_protocol: Mock cells were treated with Cupper


title: UpSET chromatin profiling_rep3

description: DamID-based UpSET chromatin profiling

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

data_processing: For chromatin profiling, raw signals of corresponding experimental replicates were loess normalized within arrays and quantile normalized between arrays. Enrichment statistics (test versus control signals) were computed using the 'sam' algorithm within Bioconductor . Fdr values of the sam statistic were determined using ‘locfdr’ . Region summarization was performed using the HMM algorithm of TileMap . Probes were considered to be bound significantly if the posterior probability of the HMM was greater than 0.9 and if the enriched region was larger than 4Kb. Chromatin accesibility datasets were loess normalized and end analysis were performed as described  (Henikoff, S., et al., 2009 Genome research, 19(3), 460–469.) (Deal, R. B., et al., Science (New York, NY), 328(5982), 1161–1164). [Average Log 2 ratio (Dam_UpSET vs Dam or Knock down vs mock) data is available as a Series Supplementary data]

source_name: Dam_UpSET expressed in Kc cells

label_protocol: 3 µg DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers ( DNA isolated from DamUpSET transfected cells or UpSET Knock down cells) or with Cy3 nonamers (DNA isolated from Dam transfected cells or mock cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Dam_UpSET transfected cells were incubated for 72h at 25C

extract_protocol: For DamID experiments, genomic DNA from DamUpSET- or Dam-transfected cells was recovered, DpnI digested and fractionated according to Orian A. Methods in molecular biology (2009), 567, 155–169. For chromatin accesibility assays, Nuclei from UpSET knock down and mock cells were treated with MNaseI and hypersentivity nucleosomes were extracted in 80mM low salt buffer (Henikoff, S.,(2009). Genome research, 19(3), 460–469.)

treatment_protocol: 16 ug of DamUpSET plasmid was electroporated in Kc cells

tag: transfected with

value: 16 ug of DamUpSET plasmid

source_name: Dam expression in Kc cells

growth_protocol: Dam transfected cells cells were incubated for 72h at 25C

treatment_protocol: 16 ug of Dam plasmid was electroporated in Kc cells

value: 16 ug of Dam plasmid


title: d11.5 placenta leptin 27

description: pooled from two placentas

source_name: d11.5 placenta, mom 149


title: Liver-GBE-HCC-1

description: Liver, GBE treated


title: d11.5 placenta control 15

description: pooled from two placentas

source_name: d11.5 placenta, mom 132


title: d11.5 placenta control 17

description: pooled from two placentas

source_name: d11.5 placenta, mom 136


title: Chromatin accesibility_rep2


title: d11.5 placenta restricted 5

description: pooled from two placentas

source_name: d11.5 placenta, mom 131

value: 50% food restriction

value: restricted


title: d11.5 placenta restricted 3

description: pooled from two placentas

source_name: d11.5 placenta, mom 130


title: d11.5 placenta restricted 1

description: pooled from two placentas

source_name: d11.5 placenta,  mom 116


title: d11.5 placenta leptin 25

description: pooled from two placentas

source_name: d11.5 placenta, mom 126


title: d11.5 placenta restricted 7

description: pooled from two placentas

source_name: d11.5 placenta, mom 147


title: upSET chromatin profiling_rep1

description: DamID-based UpSET chromatin profiling

source_name: Dam_upSET expressed in Kc cells

value: 16 ug of DamupSET plasmid


title: Rotem Number Rip Chip 3 4-10-09

city: Bethesda

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

hyb_protocol: Tilling array chips on which the complete Escherichia coli MG1655 genome sequence is represented were used (E. coli_Tab520346F; Affymetrix, Santa Clara, CA). The RNA samples were hybridized directly to the oligonucleotide arrays with no prior labelling or cDNA synthesis. The RNA samples were added to the hybridization solution [1x MES (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20, pH 6.6), 0.1 mg ml-1 herring sperm DNA, 0.5 mg ml-1 BSA and 50 pM of the control Biotinoligonucleotide B2 (GeneChip® Expression Analysis Technical Manual)], heated to 99oC for 5 minutes and then incubated at 45oC for an additional 5 minutes before being placed in the microarray cartridge. Hybridization was carried out at 45oC for 16 hours on a rotary mixer at 60 r.p.m. Following hybridization, the sample solution was removed and the array was washed as recommended in the technical manual (Affymetrix).

scan_protocol: Arrays were scanned on an GeneChip© Scanner 3000 per manufacturer’s protocol.

data_processing:
The program used to generate the bed/bar files is Affymetrix Tiling Analysis Software.
pvalue.bar files also provided
.bar files are generated using Affymetrix Tiling Analysis Software.
The TAS software provides analysis capabilities specifically for the GeneChip Tiling Arrays. TAS analyzes feature intensity data stored in GCOS output .CEL files and produces:
Signal and p-values for each genomic position interrogated.
Computation of genomic intervals based on computed signal and p-values
Computation of summary statistics
Visualizations for assessing the quality of the array data

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707224/suppl/GSM707224_Rotem Number Rip Chip 3 4-10-09 minus_pvalue.bar.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707224/suppl/GSM707224_Rotem Number Rip Chip 3 4-10-09 plus_pvalue.bar.gz

organism: Escherichia coli

source_name: Negative control (No Antibody)

label_protocol: Hybridization was assayed using antibodies specific to the RNA:DNA hybrid and the Digene HC ExpressArray™ Kit (Digene, Gaithersburg, MD). This antibody is not a commercially available since it was developed for experimental research purposes. 25 ml of an RNA:DNA polyclonal antibody (1.3 mg ml-1) was resuspended in 475 ml of matrix solution, loaded on the array and incubated at 25oC for 20 minutes. After removal of the first antibody stain and 10 wash cycles, the array was incubated with the second antibody stain, containing 0.036 mg ml-1 biotin rabbit anti-goat IgG and 0.4 mg ml-1 rabbit IgG in 1x MES. Then, the RNA:DNA hybrids then were fluorescently labelled by incubating with 10 mg ml-1 streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and 2 mg ml-1 BSA in 1x MES. Hybridized, washed and stained tilling arrays were scanned using a Genechip Scanner 3000 (Affymetrix).

growth_protocol: Cells of E .coli MG1655 derivative with eight myc tags fused to Hub were grown in M63 medium supplemented with 0.2% glucose, 0.1% casaminoacids and 0.002% vitamin B1 at 37oC to exponential phase (OD600 = 0.4).

extract_protocol: Immunoprecipitation reaction consisted of 20 ml anti-myc antibody, 15 mg of protein-A-sepharose (Amersham Biosciences, Piscataway, NJ) and 400 ml of cell extract. RNA was isolated from immunoprecipitated pellets by RNaeasy kit (Qiagen). The RNA pellet was dissolved in DEPC H2O.


title: d11.5 placenta leptin 23

description: pooled from two placentas

source_name: d11.5 placenta, mom 125


title: d11.5 placenta restricted 9

description: pooled from two placentas

source_name: d11.5 placenta, mom 148


title: UpSET chromatin profiling_rep2

description: DamID-based UpSET chromatin profiling


title: d11.5 placenta leptin 21

description: pooled from two placentas

source_name: d11.5 placenta, mom 122


title: Rotem Number Rip Chip 2 4-10-09

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707223/suppl/GSM707223_Rotem Number Rip Chip 2 4-10-09 minus_pvalue.bar.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM707nnn/GSM707223/suppl/GSM707223_Rotem Number Rip Chip 2 4-10-09 plus_pvalue.bar.gz

source_name: IP RNA

value: MG1655 derivative with eight myc tags fused to Hub


title: d11.5 placenta control 11

description: pooled from two placentas

source_name: d11.5 placenta, mom 119


title: AR0757_06 NPC2B

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: Murasakicho 1-1

institute: Biohistory Research Hall

description: Gene expression in NPC2

hyb_protocol: 0.6 ug of Cy3-labeled cRNA was hybridized a 65°C for 17 hr using Gene Expression Hybridization Kit (Agilent) and washied using Gene Expression Wash Buffers Pack Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565A).

data_processing: The scanned images were analyzed with an Agilent Feature Extraction Software to obtain background subtracted and spatially detrented Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using Low Input Quick Amp Labeling kit, one color (Agilent) with fragmentation at 60°C for 30 min, according to the manufacturer's instruction.

growth_protocol: Epiblast stem cells (EpiSCs) were placed in the epiblastic cell maintenance condition (EpiSC) or in a neural plate developmental condition (Iwafuchi-Doi et al. Dev Biol 352, 354-366, 2011) for one (NPC1) or two (NPC2) days.

extract_protocol: Total RNAs were extracted using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions.

value: EpiSCs

tag: culture condition

value: EpiSC under NPC condition 2 days


title: d11.5 placenta control 19

description: pooled from two placentas

source_name: d11.5 placenta, mom 143