title: Colorectal Adenocarinoma 14837

source_name: genomic DNA from colorectal adenocarcinoma 14837

value: Female


title: Adjacent non-tumor colorectal tissue 17781

status: Public on Jun 03 2011

type: RNA

city: Los Angeles

first: Toshinori

last: Hinoue

state: CA

address: 1450 Biggy Street, NRT G511

country: USA

institute: USC Epigenome Center

description: Paired with tumor 17755

hyb_protocol: The biotinylated cRNA was hybridized to the BeadChips per standard Illumina hybridization protocol.

scan_protocol: The hybridized chips were stained and scanned using the Illumina HD BeadArray following the standard Illumina protocol.

data_processing: Scanned image and bead-level data processing were performed using the Illumina BeadStudio software v3.2. The summarized data for each bead type were then processed, log2 transformed and normalized using Robust Spline Normalization (RSN) as implemented in the R-based lumi package.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: total RNA from adjacent non-tumor colorectal tissue 17781

label_protocol: Biotinylated, amplified cRNA was prepared from total RNA using the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was isolated using the Trizol reagent according to the manufacturer’s protocol. The quality of the RNA samples was assessed using the Bio-Rad Experion RNA StdSens analysis kit.

tag: sample type

value: Fresh Frozen Tissue

tag: disease state

value: Normal adjacent to colorectal adenocarcinoma

tag: gender

value: Male

tag: tissue pair

value: tumor 17755


title: ∆idr1∆idr2 double mutant 40 minutes after addition of iron, replicate 1

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

description:
raw data file 13116.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13117.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing:
AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.
VERA/SAM normalized log10 ratio (test/reference); see also: Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. 2006. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics. 7:286.
Each Sample is based on two arrrays (one with dye-swap).

label: cy3, cy5

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium salinarum, iron

label_protocol: 5 ug quality-checked total RNA was direct-labeled with Cy3 and Cy5 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).

growth_protocol: The Δura3 parent, Δidr2 and Δidr1, and Δ idr1Δidr2 mutant strains were grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CDM (Schmid et al., 2009, Mol Sys Biol, 5:282) with all trace metals except iron.

extract_protocol: RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was measured using an Agilent Bioanalyzer as described (Schmid et al., 2009). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.

treatment_protocol: Cultures were split in half and FeSO4 was added to one half, while the other was continued under iron limitation. 8-mL samples were collected from each culture every 20 minutes for 60 minutes (see also experimental design, Supplementary Figure 1). The zero time point was harvested immediately before the addition of iron. At each time point, samples were removed from the culture, pelleted for 30 seconds at 15 krpm in a microcentrifuge and snap frozen in liquid nitrogen. Pellets were stored at -80°C overnight

tag: strain

tag: iron concentration (um)

tag: time (min)

label: cy5, cy3

source_name: Halobacterium standard reference sample

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: E2 (feeder)-1

city: Sydney

first: Henry

last: Chung

state: NSW

address: High St

department: Clinical Sciences Bld

country: Australia

institute: Prince of Wales Hospital

hyb_protocol: Following fragmentation, cRNA was processed through second-cycle single stranded cDNA. Fragmented and labelled cDNA was then hybridized onto Affymetrix Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual).

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

data_processing: Gene array data is processed by Partek GenomeSuite software in which mean probeset signals for all probesets were analysed. A receiver operating curve (ROC) is generated by thresholding the computed value for the probesets. PLIER signals that pass this QC control is used for subsequent analysis.

source_name: hESC maintained under feeder conditions

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual).

extract_protocol: Total RNA was extracted from cell cultures using TRIZOL (Invitrogen) as per manufacturer instructions.

tag: cell type

value: hESC

tag: culture condition

value: feeder


title: Colorectal Adenocarinoma 14836

type: genomic

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27k Beadchip using standard Illumina protocol.

scan_protocol: Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Mean non-background corrected signal intensities of the methylated (M) and unmethylated (U) for each CpG locus were extracted using the Illumina BeadStudio software v3.2. We masked data point as “NA” for the following conditions; 1) Probes containing single-nucleotide polymorphisms (SNPs), 2) those that overlap with a repetitive element that covers the targeted CpG dinucleotide, 3) those that overlap with regions of insertions and deletions in the human genome. Beta values with detection P value greater than 0.05 were also replaced as "NA". Furthermore, probes containing at least one “NA” across the tumor sample set were masked as “NA”. Beta values were normalized to eliminate the batch effects. Briefly, the batch means of beta values were brought closer to the overall mean while retaining the original range of DNA methylation data (0 to 1). We used only the tumor samples to calculate the batch means and overall mean in estimating the scaling factor for each batch.
Beta value was calculated as M/(M+U). Detection P values were obtained using the Z-score formula as previously described (Noushmehr et al., 2010, Cancer Cell). Detection P values that are less than 1.11e-16 are represented as 0.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from colorectal adenocarcinoma 14836

label_protocol: standard Illumina label protocol

extract_protocol: Genomic DNA was extracted using Trizol reagent according to the manufacturer’s protocol.

value: Fresh Frozen tissue

value: Adenocarcinoma

tag: tumor subsite

value: Proximal

tag: tissue source site

value: The ontario tumor bank network,Canada

tag: batch

value: Batch 1


title: Colorectal Adenocarinoma 14840

source_name: genomic DNA from colorectal adenocarcinoma 14840


title: Colorectal Adenocarinoma 17778

description: Paired with normal adjacent tissue17804

source_name: total RNA from colorectal adenocarcinoma 17778

value: normal adjacent tissue 17804


title: ∆idr1∆idr2 double mutant 20 minutes after addition of iron, replicate 2

description:
raw data file 13112.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13113.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

treatment_protocol: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: ∆idr1∆idr2 double mutant 20 minutes after addition of iron, replicate 1

description:
raw data file 13078.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13079.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: 293T_MeTA_exp1

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Gene expression in 293T cells transfected with pcDNA6-3xFLAG-NFkB (AD)-MBD

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul 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), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 293T, MeTA, experiment 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A human embryonic kidney cell line 293T was grown in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% fetal bovine serum (Invitrogen).

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 293T cells were seeded on 6-well tissue culture dishes and transfected with an aliquot of 4 ug of pcDNA6-3xFLAG-NFkB (AD)-MBD. Transfection was performed using lipofectamine reagents (Invitrogen) according to supplier’s recommendations. The cells were harvested 48 h after transfection.

tag: transfection

value: MeTA

tag: cell line

value: embryonic kidney cell line 293T

tag: age

value: fetus


title: Colorectal Adenocarinoma 14835

source_name: genomic DNA from colorectal adenocarcinoma 14835


title: ∆idr1∆idr2 60 minute treatment control, no iron replicate 2

description:
raw data file 13122.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13123.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14839

source_name: genomic DNA from colorectal adenocarcinoma 14839


title: ∆idr1∆idr2 60 minute treatment control, no iron replicate 1

description:
raw data file 13120.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13121.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14834

source_name: genomic DNA from colorectal adenocarcinoma 14834


title: Colorectal Adenocarinoma 14833

source_name: genomic DNA from colorectal adenocarcinoma 14833

value: Distal


title: ∆idr1∆idr2 40 minute treatment control, no iron replicate 1

description:
raw data file 13114.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13115.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Adjacent non-tumor colorectal tissue 17780

description: Paired with tumor 17754

source_name: total RNA from adjacent non-tumor colorectal tissue 17780

value: Female

value: tumor 17754


title: Adjacent non-tumor colorectal tissue 17793

description: Paired with tumor 17767

source_name: total RNA from adjacent non-tumor colorectal tissue 17793

value: Fresh Frozen Tissue

value: Normal adjacent to colorectal adenocarcinoma

value: tumor 17767


title: ∆idr1∆idr2 20 minute treatment control, no iron replicate 2

description:
raw data file 13076.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13077.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: E2 (feeder)-2

value: hESC


title: Colorectal Adenocarinoma 14831

source_name: genomic DNA from colorectal adenocarcinoma 14831


title: ∆idr1∆idr2 20 minute treatment control, no iron replicate 1

description:
raw data file 13074.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13075.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17774

description: Paired with normal adjacent tissue17800

source_name: total RNA from colorectal adenocarcinoma 17774

value: normal adjacent tissue 17800


title: Colorectal Adenocarinoma 17775

description: Paired with normal adjacent tissue17801

source_name: total RNA from colorectal adenocarcinoma 17775

value: normal adjacent tissue 17801


title: Adjacent non-tumor colorectal tissue 17779

description: Paired with tumor 17753

source_name: total RNA from adjacent non-tumor colorectal tissue 17779

value: tumor 17753


title: Colorectal Adenocarinoma 17773

description: Paired with normal adjacent tissue17799

source_name: total RNA from colorectal adenocarcinoma 17773

value: Adenocarcinoma

value: Proximal

value: normal adjacent tissue 17799


title: Colorectal Adenocarinoma 14832

source_name: genomic DNA from colorectal adenocarcinoma 14832

value: Fresh Frozen tissue

value: Male

value: The ontario tumor bank network,Canada

value: Batch 1


title: Colorectal Adenocarinoma 17776

description: Paired with normal adjacent tissue17802

source_name: total RNA from colorectal adenocarcinoma 17776

value: Distal

value: normal adjacent tissue 17802


title: Colorectal Adenocarinoma 14829

source_name: genomic DNA from colorectal adenocarcinoma 14829

value: Female


title: Colorectal Adenocarinoma 17777

description: Paired with normal adjacent tissue17803

source_name: total RNA from colorectal adenocarcinoma 17777

value: Fresh Frozen Tissue

value: normal adjacent tissue 17803


title: Colorectal Adenocarinoma 14828

source_name: genomic DNA from colorectal adenocarcinoma 14828


title: Colorectal Adenocarinoma 14827

source_name: genomic DNA from colorectal adenocarcinoma 14827


title: Colorectal Adenocarinoma 17771

description: Paired with normal adjacent tissue17797

source_name: total RNA from colorectal adenocarcinoma 17771

value: normal adjacent tissue 17797


title: ∆idr1∆idr2 double mutant immediately prior to addition of iron, replicate 2

description:
raw data file 13068.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13069.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

source_name: Halobacterium salinarum, iron

source_name: Halobacterium standard reference sample

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample. Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: ∆idr1∆idr2 double mutant immediately prior to addition of iron, replicate 1

description:
raw data file 13070.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13071.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17772

description: Paired with normal adjacent tissue17798

source_name: total RNA from colorectal adenocarcinoma 17772

value: normal adjacent tissue 17798


title: ∆idr1∆idr2 double mutant immediately prior to addition of iron, replicate 3

description:
raw data file 13072.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13073.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17769

description: Paired with normal adjacent tissue17795

source_name: total RNA from colorectal adenocarcinoma 17769

value: normal adjacent tissue 17795


title: Colorectal Adenocarinoma 17770

description: Paired with normal adjacent tissue17796

source_name: total RNA from colorectal adenocarcinoma 17770

value: Rectum

value: normal adjacent tissue 17796


title: Colorectal Adenocarinoma 14822

source_name: genomic DNA from colorectal adenocarcinoma 14822

value: Adenocarcinoma


title: ∆idr2 mutant, 40 minutes after addition of iron, replicate 2

description:
raw data file 13032.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13033.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr2 mutant, 60 minutes after addition of iron, replicate 1

description:
raw data file 12106.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12107.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14820

source_name: genomic DNA from colorectal adenocarcinoma 14820


title: Colorectal Adenocarinoma 14825

source_name: genomic DNA from colorectal adenocarcinoma 14825

value: Transverse


title: ∆idr2 mutant, 60 minutes after addition of iron, replicate 2

description:
raw data file 13034.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13035.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14821

source_name: genomic DNA from colorectal adenocarcinoma 14821


title: ∆idr2 mutant, 40 minutes after addition of iron, replicate 1

description:
raw data file 12056.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12057.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr2 mutant, 20 minutes after addition of iron, replicate 2

description:
raw data file 13030.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13031.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17768

description: Paired with normal adjacent tissue17794

source_name: total RNA from colorectal adenocarcinoma 17768

value: normal adjacent tissue 17794


title: Colorectal Adenocarinoma 14819

source_name: genomic DNA from colorectal adenocarcinoma 14819

value: Fresh Frozen tissue


title: ∆idr2 mutant, 20 minutes after addition of iron, replicate 1

description:
raw data file 12047.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12053.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr2 mutant 60 minute treatment control, no iron, replicate 2

description:
raw data file 13022.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13023.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17766

description: Paired with normal adjacent tissue17792

source_name: total RNA from colorectal adenocarcinoma 17766

value: Proximal

value: normal adjacent tissue 17792


title: Colorectal Adenocarinoma 17767

description: Paired with normal adjacent tissue17793

source_name: total RNA from colorectal adenocarcinoma 17767

value: normal adjacent tissue 17793


title: ∆idr2 mutant 60 minute treatment control, no iron, replicate 1

description:
raw data file 12108.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12109.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17765

description: Paired with normal adjacent tissue17791

source_name: total RNA from colorectal adenocarcinoma 17765

value: Male

value: Distal

value: normal adjacent tissue 17791


title: Colorectal Adenocarinoma 14815

source_name: genomic DNA from colorectal adenocarcinoma 14815

value: Female

value: The ontario tumor bank network,Canada

value: Batch 1


title: Colorectal Adenocarinoma 14817

source_name: genomic DNA from colorectal adenocarcinoma 14817


title: Colorectal Adenocarinoma 14816

source_name: genomic DNA from colorectal adenocarcinoma 14816


title: Colorectal Adenocarinoma 14814

source_name: genomic DNA from colorectal adenocarcinoma 14814


title: ∆idr2 mutant 40 minute treatment control, no iron, replicate 2

description:
raw data file 13045.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13005.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

source_name: Halobacterium salinarum, iron

source_name: Halobacterium standard reference sample


title: Colorectal Adenocarinoma 14824

source_name: genomic DNA from colorectal adenocarcinoma 14824


title: Colorectal Adenocarinoma 17764

description: Paired with normal adjacent tissue17790

source_name: total RNA from colorectal adenocarcinoma 17764

value: Fresh Frozen Tissue

value: normal adjacent tissue 17790


title: ∆idr2 mutant 40 minute treatment control, no iron, replicate 1

description:
raw data file 12058.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12059.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr2 mutant 20 minute treatment control, no iron, replicate 2

description:
raw data file 13044.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13003.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr2 mutant 20 minute treatment control, no iron, replicate 1

description:
raw data file 12054.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12055.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14818

source_name: genomic DNA from colorectal adenocarcinoma 14818


title: Colorectal Adenocarinoma 17762

description: Paired with normal adjacent tissue17788

source_name: total RNA from colorectal adenocarcinoma 17762

value: normal adjacent tissue 17788


title: Colorectal Adenocarinoma 14813

source_name: genomic DNA from colorectal adenocarcinoma 14813


title: Colorectal Adenocarinoma 17763

description: Paired with normal adjacent tissue17789

source_name: total RNA from colorectal adenocarcinoma 17763

value: normal adjacent tissue 17789


title: Colorectal Adenocarinoma 17758

description: Paired with normal adjacent tissue17784

source_name: total RNA from colorectal adenocarcinoma 17758

value: Adenocarcinoma

value: normal adjacent tissue 17784


title: Colorectal Adenocarinoma 17760

description: Paired with normal adjacent tissue17786

source_name: total RNA from colorectal adenocarcinoma 17760

value: normal adjacent tissue 17786


title: ∆idr2 mutant immediately prior to addition of iron, replicate 3

description:
raw data file 13028.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13029.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14810

source_name: genomic DNA from colorectal adenocarcinoma 14810

value: Fresh Frozen tissue

value: Transverse


title: ∆idr2 mutant immediately prior to addition of iron, replicate 1

description:
raw data file 12051.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12052.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17761

description: Paired with normal adjacent tissue17787

source_name: total RNA from colorectal adenocarcinoma 17761

value: Proximal

value: normal adjacent tissue 17787


title: Colorectal Adenocarinoma 14809

description: Paired with normal adjacent 17807

source_name: genomic DNA from colorectal adenocarcinoma 14809

value: Male


title: Colorectal Adenocarinoma 14811

source_name: genomic DNA from colorectal adenocarcinoma 14811

value: Distal


title: ∆idr2 mutant immediately prior to addition of iron, replicate 2

description:
raw data file 13000.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13001.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14812

source_name: genomic DNA from colorectal adenocarcinoma 14812

value: Rectum


title: Colorectal Adenocarinoma 17757

description: Paired with normal adjacent tissue17783

source_name: total RNA from colorectal adenocarcinoma 17757

value: normal adjacent tissue 17783


title: Colorectal Adenocarinoma 17756

description: Paired with normal adjacent tissue17782

source_name: total RNA from colorectal adenocarcinoma 17756

value: Female

value: normal adjacent tissue 17782


title: Colorectal Adenocarinoma 17759

description: Paired with normal adjacent tissue17785

source_name: total RNA from colorectal adenocarcinoma 17759

value: Fresh Frozen Tissue

value: normal adjacent tissue 17785


title: ∆idr1 mutant, 60 minutes after addition of iron, replicate 1

description:
raw data file 12046.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12048.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

source_name: Halobacterium salinarum, iron

source_name: Halobacterium standard reference sample


title: Colorectal Adenocarinoma 17755

description: Paired with normal adjacent tissue17781

source_name: total RNA from colorectal adenocarcinoma 17755

value: normal adjacent tissue 17781


title: Colorectal Adenocarinoma 14807

description: Paired with normal adjacent 17806

source_name: genomic DNA from colorectal adenocarcinoma 14807

value: The ontario tumor bank network,Canada

value: Batch 1


title: Colorectal Adenocarinoma 14806

source_name: genomic DNA from colorectal adenocarcinoma 14806

value: Adenocarcinoma


title: ∆idr1 mutant, 20 minutes after addition of iron, replicate 1

description:
raw data file 10222.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 10223.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14808

source_name: genomic DNA from colorectal adenocarcinoma 14808


title: Colorectal Adenocarinoma 14805

description: Paired with normal adjacent 17805

source_name: genomic DNA from colorectal adenocarcinoma 14805


title: Colorectal Adenocarinoma 17753

description: Paired with normal adjacent tissue17779

source_name: total RNA from colorectal adenocarcinoma 17753

value: normal adjacent tissue 17779


title: ∆idr1 mutant 60 minute treatment control, no iron, replicate 1

description:
raw data file 12049.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12050.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr1 mutant 40 minute treatment control, no iron, replicate 1

description:
raw data file 12044.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12045.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr1 mutant, 40 minutes after addition of iron, replicate 1

description:
raw data file 12042.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12043.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 17754

description: Paired with normal adjacent tissue17780

source_name: total RNA from colorectal adenocarcinoma 17754

value: normal adjacent tissue 17780


title: ∆idr1 mutant 20 minute treatment control, no iron, replicate 1

description:
raw data file 10226.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 10227.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆idr1 mutant immediately prior to addition of iron, replicate 1

description:
raw data file 10213.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 10214.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆ura3 isogenic parent control strain, 60 minutes after addition of iron, replicate 1

description:
raw data file 11062.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 11063.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14804

source_name: genomic DNA from colorectal adenocarcinoma 14804

value: Fresh Frozen tissue

value: Transverse


description:
Idr1 ChIP-chip at 100 uM iron, replicate 4
raw data file 12800.csv:  Halobacterium salinarum NRC-1 idr1 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12801.csv: Halobacterium salinarum NRC-1 Idr1 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3

hyb_protocol: see Facciotti, MT, Reiss, DJ, Pan, M, Kaur, A, Vuthoori, M, Bonneau, R, Shannon, P, Srivastava, A, Donohoe, SM, Hood, LE and Baliga, NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007;104: 4630-4635.

data_processing:
AnalyzerDG software for spotfinding. For more details, see Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286
Processed (VERA and SAM normalized) log10 enrichment ratio IP:WCE (see also Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T. (2006) SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics 7:286)
Each Sample is based on two arrrays (one with dye-swap).

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Halobacterium salinarum NRC-1 Idr1 or Idr2 cmyc-tagged strain was grown in rich media (CM) with 20 ug/mL mevinolin to mid-log phase (0.47-0.58 for Idr1, 0.5-0.8 for Idr2, 50mL culture in 125mL flask). Cultures were grown in the presence or absence of exogenously added 100 uM iron sulfate as indicated in the sample name and title.

extract_protocol: Chromatin immunoprecipitation (IP) was conducted as described in Facciotti, MT, Reiss, DJ, Pan, M, Kaur, A, Vuthoori, M, Bonneau, R, Shannon, P, Srivastava, A, Donohoe, SM, Hood, LE and Baliga, NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007;104: 4630-4635. Optimizations of the ChIP protocol are described in Schmid AK, Pan M, Sharma K, Baliga NS.2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon.Nucleic Acids Res.39(7):2519-33. Primary antibody is the Covance 9E10 monoclonal antibody (anti-c-myc) from mouse, cat #MMS-150P, and secondary antibody is ECL mouse IgG HRP-linked whole antibody from sheep, Amersham cat #NA931.

value: Halobacterium sailnarum NRC-1 idr1::cmyc

tag: iron concentration (µm)

tag: iron concentration  (µm)


title: rosette at 27 day_PBZ_biological replica 1

city: Potsdam

first: Jos

last: Schippers

address: Am Muehlenberg 1

department: Plant Signaling

country: Germany

institute: MPIMP-golm

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: CEL files from the Affymetrix Chips were processed by use of the Robin program (Lohse et al., 2010). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding Robin function. Present, Marginal or Absent (P/M/A) calls were computed with the affy package.

organism: Arabidopsis thaliana

source_name: Rosette_Long Day 16/8_Soil_25 day

label_protocol: RNA was labelled with the MessageAMP II biotin enhanced (Ambion) kit according to the manufactures protocol

growth_protocol: Arabidopsis thaliana (L.) Heynh. Col-0 transgenic lines expressing the 35S:HF-RPL18B seeds (kindly provided by J. Bailey-Serres, University of California, Riverside, CA, USA) were sown on standard greenhouse soil (Stender AG; Schermbeck, Germany) in plastic pots with 0.1 L capacity. After 3 days of vernilization at 4 degrees the trays containing the pots were placed under a 16/8 h day/night  (22/16 oC) regime with 60/75% relative humidity and 180 μmol m-2 s-1 light intensity.

extract_protocol: All mRNA extraction procedures were performed at 4 °C or on ice (Mustroph et al., 2009). Frozen pulverized tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA), 36 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene(23) lauryl ether (Brig® 35), 1% (v/v) Triton X-100, 1% (v/v) Tween-20, 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 1 mM dithiothreitol (DTT), 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol, 0.5 mg mL-1 heparin) using 2.5 mL PEB per mL tissue. A typical extraction was 1 to 2 ml packed volume of frozen pulverised rosette tissue. Homogenates were clarified by centrifugation at 16,000 g for 15 min and filtrated with miracloth. Six-hundred µL of the supernatant was reserved for isolation of total RNA. To the remaining supernatant 150 µL of anti-FLAG agarose beads (Sigma) were added and incubated at 4°C for 2 h with gentle shaking. The beads were recovered by centrifugation at 3,500 g, and washed four times for 5 min each with 6 mL of wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 36 mM MgCl2, 5 mM DTT, 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol). Polysomes were eluted by resuspension of the washed beads in 300 µL of wash buffer per 100 µl beads that additionally contained 200 µg mL-1 of [FLAG]3 peptide (Sigma) at 4°C for 30 min. RNA extraction was performed by addition of two volumes of 8 M guanidine-HCl and three volumes of ethanol to the cleared eluate, incubation overnight at –20 °C and pelleting by centrifugation at 15,000 g for 45 min. RNA samples were further purified using RNeasy columns (Qiagen) as described previously (Branco-Price et al., 2008). Total RNA was extracted from the same cell lysate of p35S:HF-RPL18 that was used for polysome immunoprecipitation. For this, an aliquot of the homogenized sample was without further modifications precipitated by adding two volumes of 8 M guanidine-HCl and three volumes of ethanol, incubation overnight at –20 °C, pelleting by centrifugation at 15,000 g for 45 min and purification by use of RNeasy columns (Qiagen). Quality of RNA was checked with an Agilent 2100 Bioanalyzer (Atlas, Biolabs service)

treatment_protocol: Plants were grown untill 27 days on soil after which whole rosettes were collected. Fourteen days after sowing, plants were watered with 10 mL PBZ solution   (50 mg L-1, 0.5 mg pot-1). For gibberellin treatment, each plant was sprayed every second day with 1 mL of 50 µM GA3. Rosettes were harvested and directly frozen in liquid nitrogen.

tag: treatment

value: PBZ

tag: ecotype

tag: tissue

value: Rosette


title: ∆ura3 isogenic parent control strain, 60 minute treatment control, no iron, replicate 2

description:
raw data file 13042.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12979.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: Colorectal Adenocarinoma 14801

source_name: genomic DNA from colorectal adenocarcinoma 14801

tag: sample type

tag: disease state

tag: gender

value: Proximal


description:
Idr1 ChIP-chip at 0 uM iron, replicate 1
raw data file 11828.csv:  Halobacterium salinarum NRC-1 idr1 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 11829.csv: Halobacterium salinarum NRC-1 Idr1 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3

tag: strain


title: Colorectal Adenocarinoma 14802

source_name: genomic DNA from colorectal adenocarcinoma 14802

value: Male


description:
Idr2 ChIP-chip at 100 uM iron, replicate 5
raw data file 12792.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12793.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3

value: Halobacterium sailnarum NRC-1 idr2::cmyc


title: ∆ura3 isogenic parent control strain,40 minutes after addition of iron, replicate 1

description:
raw data file 12040.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12041.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3

tag: iron concentration (um)

tag: time (min)


title: ∆ura3 isogenic parent control strain,20 minutes after addition of iron, replicate 2

description:
raw data file 12986.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12987.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆ura3 isogenic parent control strain,20 minutes after addition of iron, replicate 1

description:
raw data file 10215.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 10221.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆ura3 isogenic parent control strain,40 minutes after addition of iron, replicate 2

description:
raw data file 12992.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12993.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


description:
Idr1 ChIP-chip at 100 uM iron, replicate 1
raw data file 12794.csv:  Halobacterium salinarum NRC-1 idr1 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12795.csv: Halobacterium salinarum NRC-1 Idr1 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


title: ∆ura3 isogenic parent control strain, immediately before addition of iron, replicate 2

description:
raw data file 12984.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12985.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆ura3 isogenic parent control strain, immediately before addition of iron, replicate 1

description:
raw data file 13040.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 13041.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: rosette at 27 day_PBZ_biological replica 2


description:
Idr1 ChIP-chip at 100 uM iron, replicate 3
raw data file 12798.csv:  Halobacterium salinarum NRC-1 idr1 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12799.csv: Halobacterium salinarum NRC-1 Idr1 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


title: ∆ura3 isogenic parent control strain, 20 minute treatment control, no iron, replicate 1

description:
raw data file 10224.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 10225.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆ura3 isogenic parent control strain, 40 minute treatment control, no iron, replicate 2

description:
raw data file 12976.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12977.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: ∆ura3 isogenic parent control strain, 20 minute treatment control, no iron, replicate 2

description:
raw data file 12974.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 12975.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


title: rosette at 27 day_GA_biological replica 2

value: GA


title: ∆ura3 isogenic parent control strain, 60 minute treatment control, no iron, replicate 1

description:
raw data file 11060.csv: Halobacterium salinarum, iron (ch1) Sample is labeled with Cy3
raw data file 11061.csv: Halobacterium standard reference sample (ch1) Sample is labeled with Cy3


description:
Idr2 ChIP-chip at 0 uM iron, replicate 3
raw data file 11836.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 11837.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


description:
Idr2 ChIP-chip at 100 uM iron, replicate 1
raw data file 12786.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12787.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


title: Colorectal Adenocarinoma 14803

source_name: genomic DNA from colorectal adenocarcinoma 14803

tag: tumor subsite

value: Distal


description:
Idr1 ChIP-chip at 100 uM iron, replicate 2
raw data file 12796.csv:  Halobacterium salinarum NRC-1 idr1 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12797.csv: Halobacterium salinarum NRC-1 Idr1 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


title: rosette at 27 day_no treatment_biological replica 1


description:
Idr2 ChIP-chip at 0 uM iron, replicate 1
raw data file 11830.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 11831.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


title: rosette at 27 day_no treatment_biological replica 2


description:
Idr2 ChIP-chip at 0 uM iron, replicate 2
raw data file 12790.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 12791.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


description:
Idr2 ChIP-chip at 100 uM iron, replicate 2
raw data file 11838.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 11839.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


description:
Idr2 ChIP-chip at 100 uM iron, replicate 4
raw data file 11846.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 11847.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


description:
Idr2 ChIP-chip at 100 uM iron, replicate 3
raw data file 11844.csv:  Halobacterium salinarum NRC-1 idr2 cmyc-tagged strain IP fraction. is labeled with Cy3
raw data file 11845.csv: Halobacterium salinarum NRC-1 Idr2 cmyc-tagged strain whole cell extract (WCE) faction. is labeled with Cy3


title: KO stromal cells

city: Urbana

first: Quanxi

last: Li

state: IL

address: 2001 S lincoln Avenue

department: Comparative Bioscience

institute: Universit of Illinois at Urbana-Champaign

hyb_protocol: 10 micrograms of labeled aRNA were hybridized to a Mouse Genome 430 2.0 Affymetrix 3' Expression Analysis Array.  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

organism: Mus musculus

source_name: uterine stromal cells from KO mice on day4 of pregnancy

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. Hand2 floxed mice obtained from Dr. Deepak Srivastava (University of California) were crossed with PRcre mice (provided by Dr. Francceso DeMayo, (Baylor College of Medicine) to conditionally ablate Hand2 in the uterus.

extract_protocol: Total RNA was extracted from uterine stromal cells (n=4 for each genotype) using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Hand2-null mice (n=5) and the corresponding controls (n=5) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day1 of pregnancy. On day4 of pregnancy, uterine horns were excised and cut into  3-5 mm pieces, then placed in HBSS containing 6g/L dispase (Gibico BRL), 25g/L pancreatin (Sigma), and 100 U/L penicillin, 0.1 g/L streptomycin, 1.25 mg/L fungizone (Gibico BRL) for 1h on ice followed by 1h at room temperature and then 10 min at 37⁰C. The tubes were gently mixed and the supernatant was discarded to remove the emdometrial epithelial clumps. The partially digested tissues were then washed twice in HBSS and placed in HBSS containing 0.5g/L collagenase (Sigma). After incubation for 45 min at 37⁰C, the tubes were mixed for 10-12 seconds by vortexing until the supernatant became turbid with dispersed endometrial stromal cells. The content of the tube was then passed through a 70 m gauze filter (Millipore). After washing with HBSS, cells were suspended in Dulbecco’s modified Eagle’s Medium-F12 medium containing 2% heat-inactivated fetal calf serum and then allowed to attch to the culture plates for 1 h at 37⁰C.  Unattached Cells were removed prior to RNA extraction.

value: uterus, D4 of pregnancy, implantation, stromal-epithelial communication, FGFs

tag: genotype

tag: cell type

value: uterine stromal cell

value: day 4 of pregnancy

tag: genetic background

value: Prcre, C57BL/6, SV129 mixed background


title: rosette at 27 day_GA_biological replica 1


title: Testes of rat 6 day after birth

status: Public on Jun 02 2011

city: Hohhot

first: taodi

last: liu

address: xinhua street

country: China

institute: Inner Mongolia Medical College

hyb_protocol: Hybridization was performed by NimbleGen Systems4 (Nimblegen, 05223679001). NimbleGen Hybridization Kit (Nimblegen, 05223474001).

scan_protocol: Slides were scanned with the Axon GenePix 4000B microarray scanner following their standard operating protocol.

data_processing: Raw data were extracted as pair files by NimbleScan software (version 2.5). NimbleScan software’s implementation of RMA offers quantile normalization and background correction. The Probe level (*_norm_RMA.pair) files and Gene summary (*_RMA.calls) files were produced. The 2 gene summary files were imported into Agilent GeneSpring Software (version11.0) for further analysis. The positive effect of normalization is illustrated in Box-plot . Genes that have values greater than or equal to lower cut-off: 50.0 in all samples (“All Targets Value”) were chosen for data analysis. Differentially expressed genes were identified through Fold-change screening.

organism: Rattus norvegicus

source_name: testes of rat 6 day after birth

label_protocol: The samples were amplified and labeled using  NimbleGen One-Color DNA Labeling Kit

growth_protocol: Testes were individually collected from the rat postnatal day 6,8 and 10.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA quality and concentration was determined by analysis with the Nanodrop ND-1000.

treatment_protocol: Male and female Wistar-Imamichi rat (aged 3 months) were maintained in a temperature and humidity controlled room on a 12 hr light/12 hr darkness photoperiod. The rats had free access to food and water. Male and female mice mated naturally. The date of birth was designated as day 1. The testes were removed immediately after the animals were killed by cervical dislocation.

tag: sample collection time

value: 6 day after birth


title: Islets_wt_3

city: Uppsala

first: Margareta

middle: H

last: Lejonklou

address: Entrance 70, UAS

department: Medical Sciences

country: Sweden

institute: Uppsala University Hospital

hyb_protocol: GeneChip Mouse Genome 430 2.0 Array were hybridized for 16 hours in a 45C incubator, rotated at 60 rpm. The arrays were then washed and stained using the Fluidics Station 450.

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

data_processing: The gene expression data was carried out in the publicly available statistical computing language R (http://www.r-project.org) using packages available from the Bioconductor project (www.bioconductor.org). The raw data was normalized using the GCRMA method.

source_name: Five-week-old islets from wt mouse

label_protocol: Biotinylated cRNA was prepared from 100 ng of RNA, using a two-cycle amplification step.

growth_protocol: Animals were kept under normal conditions and sacrificed when reaching five weeks of age.

extract_protocol: Isolated islets (~100) were pooled from each animal and RNA was isolated with the QIAGEN RNeasy micro kit. Quality was assessed using the Agilent Bioanalyzer and the Agilent RNA 6000 nano kit.

value: female

tag: age

value: 5 weeks

value: C57 on a 129 background

value: pancreatic endocrine islets


title: Islets_hz_2

source_name: Five-week-old islets from hz mouse


title: Islets_hz_5


title: Islets_hz_1


title: heart, female wt, rep2

city: Boulder

first: Leslie

last: Leinwand

state: CO

address: 3415 Colorado Ave

department: MCD Biology and BioFrontiers Institute

institute: University of Colorado at Boulder

description: Gene expression data from wild-type female hearts

hyb_protocol: cRNA were hybridized 16 hours at 45 degrees Celsius on the Affymetrix Mouse Genome 430 2.0 GeneChip.  Chips were washed and stained in a Gene Chip Fluidics Station 450.

scan_protocol: Arrays were scanned using the Gene Chip Scanner 3000 6G.

data_processing: The data were analyzed with the Robust Multiarray Averaging (RMA) method in Affymetrix Expression Console using default settings.

source_name: left ventricle, female, wild-type

label_protocol: Biotinylated cRNA were amplified and labeled according to the Affymetrix instructions using 6 μg total RNA.

growth_protocol: Mice were housed until 2 months of age under standard conditions and fed ad libitum a casein-based diet supplemented with the phytoestrogens genistein and daidzein.

extract_protocol: Total RNA was extracted with TRI reagent according to the manufacturer's instructions. RNA was further purified with a Qiagen RNeasy kit.  For each sample, equal amounts of RNA from two or three animals was pooled.

treatment_protocol: At 2 months old, mice were anesthetized with inhaled isoflurane, sacrificed by cervical dislocation, and hearts were rapidly excised.  Hearts were exsanguinated in ice-cold, sterile PBS and left ventricles were flash frozen in liquid nitrogen.

value: left ventricle

value: wild-type

tag: Sex

tag: diet

value: phytoestrogen-supplemented casein-based


title: Islets_wt_4


title: Islets_wt_1


title: heart, female HCM, rep1

description: Gene expression data from HCM female hearts

source_name: left ventricle, female, HCM

value: HCM


title: heart, female HCM, rep2


title: Islets_hz_3


title: Control stromal cells

source_name: uterine stromal cells from Floxed control mice on day4 of pregnancy

value: Hand2 Floxed


title: Testes of rat 10 day after birth

source_name: testes of rat 10 day after birth

value: 10 day after birth


title: Islets_wt_5


title: Islets_wt_2


title: Islets_hz_4


title: Testes of rat 8 day after birth

source_name: testes of rat 8 day after birth

value: 8 day after birth


title: heart, male HCM, rep2

description: Gene expression data from HCM male hearts

source_name: left ventricle, male, HCM

value: male


title: Bcl6+/+ CXCR5hi PD-1hi cells_2

city: Yokohama

first: Takaharu

last: Okada

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Research Center for Allergy and Immunology

institute: RIKEN

description: freshly isolated T cells from immunized mice (Day 10)

hyb_protocol: The labeled cDNA was hybridized with Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Expression values for each probe set were calculated with gcrma method in a GeneSpring GX 7.3 software package (Agilent).

source_name: Sorted cells from immunized mice

label_protocol: RNA was subjected to biotinilated cDNA synthesis by using Ovation RNA Amplification System V2 (Nugen) and FL-Ovation cDNA Biotin Module V2 (Nugen).

growth_protocol: Mice were transferred with OT-II Bcl6yfp/+ cells, and immunized with NP-OVA in CFA subcutaneously.

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) or Rneasy Mini Kit (QIAGEN).

treatment_protocol: Seven or ten days after immunization, draining lymph nodes were collected, and cells were sorted by the expression of CXCR5, PD-1 and YFP on FACSAria.

value: lymph nodes

value: Bcl6yfp-wt CXCR5hi PD-1hi cells

tag: immunization status

value: immunized mice (Day 10)


title: Naive CD4+ T cells_2

description: freshly isolated T cells from naïve mouse

source_name: Sorted cells from unimmunized mice

value: spleen

value: Naïve CD4+ T cells

value: naïve mouse


title: heart, female wt, rep1

value: female


title: heart, male wt, rep1

description: Gene expression data from wild-type male hearts

source_name: left ventricle, male, wild-type


title: heart, male wt, rep3


title: heart, male HCM, rep1


title: Bcl6+/+ CXCR5hi PD-1hi cells_3

description: freshly isolated T cells from immunized mice (Day 7)

value: immunized mice (Day 7)


title: heart, male HCM, rep3


title: heart, male wt, rep2


title: Bcl6yfp/+ CXCR5hi PD-1hi cells_3

value: Bcl6yfp-hetero CXCR5hi PD-1hi


title: Bcl6+/+ CXCR5hi PD-1hi cells_1


title: Bcl6yfp/+ CXCR5hi PD-1hi cells_1


title: Bcl6yfp/+ CXCR5hi PD-1hi cells_2


title: CXCR5hi PD-1hi YFP-BCL6- cells_3

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen).

value: CXCR5hi PD-1hi YFP-BCL6- cells


title: CXCR5hi PD-1hi YFP-BCL6+ cells_4

value: CXCR5hi PD-1hi YFP-BCL6+ cells


title: CXCR5lo PD-1lo cells_1

value: CXCR5lo PD-1lo cells


title: CXCR5lo PD-1lo cells_3


title: CXCR5lo PD-1lo cells_2


title: CXCR5hi PD-1hi YFP-BCL6- cells_4


title: Yeast-only fermentation, day3, biological rep1

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Following fragmentation, 5 ug of labelled fragmented amplified RNA was hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChips were scanned using the Affymetrix GeneChip® 3000 Scanner 7G. AGCC is used for image acquisition.

data_processing: The cell intensity data was analyzed in Affymetrix Expression Console using the RMA algorithm. The RMA workflow is quantile normalisation with general background correction.

organism: Saccharomyces cerevisiae Vin13

source_name: Yeast Vin13 from a pure culture fermentation at day 3 of fermentation

label_protocol: Following second strand cDNA synthesis (starting material 100ng of total RNA), biotinylated cRNA was prepared in accordance with the Affymetrix 3' Expression protocol .  The expected profile of amplified RNA should be in the range of 250 -5500nt with most of the amplified RNA appearing in the 600-12--nt range. 7.5ug of amplified RNA is required for hybridisation to an array.

growth_protocol: Yeast were inoculated at an OD600 of 0.1 in synthetic wine must in microaerobic fermentation vials. In the mixed fermentations, Oeni. Were inoculated at a cell density of 5X106 cells/ml.  Fermentation was carried out at room temperature.

extract_protocol: RNA was extracted as described using a modified hot-phenol method as described by Abbott et al (2007).

treatment_protocol: Cells were harvested by brief centrifugation and washed prior to extraction.

tag: time point

tag: replicate


title: CXCR5hi PD-1hi YFP-BCL6- cells_2

tag: tissue


title: CXCR5hi PD-1hi YFP-BCL6+ cells_1


title: Yeast-only fermentation, day7, biological rep2

source_name: Yeast Vin13 from a pure culture fermentation at day 7 of fermentation


title: Yeast-only fermentation, day3, biological rep2


title: Yeast-only fermentation, day7, biological rep3


title: Yeast-only fermentation, day7, biological rep1


title: Mixed fermentation (yeast and Oenococcus oeni), day7, biological rep3

organism:
Oenococcus oeni
Saccharomyces cerevisiae Vin13

source_name: Yeast Vin13 from a mixed fermentation including Oenococcus oeni (strain S6) at day 7 of fermentation


title: CXCR5hi PD-1hi YFP-BCL6- cells_1


title: CXCR5hi PD-1hi YFP-BCL6+ cells_2


title: CXCR5hi PD-1hi YFP-BCL6+ cells_3


title: Mixed fermentation (yeast and Oenococcus oeni), day3, biological rep2

source_name: Yeast Vin13 from a mixed fermentation including Oenococcus oeni (strain S6) at day 3 of fermentation


title: Mixed fermentation (yeast and Oenococcus oeni), day7, biological rep2


title: Mixed fermentation (yeast and Oenococcus oeni), day3, biological rep1


title: Mixed fermentation (yeast and Oenococcus oeni), day3, biological rep3


title: Mixed fermentation (yeast and Oenococcus oeni), day7, biological rep1


title: Naive CD4+ T cells

value: Naive CD4+ T cells


title: Yeast-only fermentation, day3, biological rep3


title: Ball milled pine rep3 35100902_532

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

hyb_protocol: Hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C.

scan_protocol: Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4.

data_processing: Quantile normalization and robust multi-array averaging (RMA) were applied using the DNASTAR Arraystar module (version 4).

organism: Rhodonia placenta

source_name: mycelium, ball-milled pine

label_protocol: One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C.

growth_protocol: Six days growth in shaking flasks at room temperature.

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the Postia placenta MAD-698 whole genome expression array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

value: mycelium

tag: condition

value: ball-milled pine


title: wild-type strain_1

city: Sayo-gun

first: Kenji

last: Fukui

state: Hyogo

address: 1-1-1, Kouto, Sayo-cho

department: SPring-8 Center

hyb_protocol: Two micro g of 3’-terminal-labeled cDNA was hybridized to a TTHB8401a520105F GeneChip (Affymetrix). The array was incubated for 16 h at 50oC in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin, the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix).  Then the array was automatically washed and stained with streptavidin, biotin anti-streptavidin, and streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.4 (Affymetrix).

organism: Thermus thermophilus HB8

source_name: wild-type strain at early log phase

label_protocol: Ten micro g of total RNA was mixed with 750 ng of random primers (Invitrogen), incubated at 70°C for 10 min, and 25°C for 10 min.  The RNA/primer solution was reacted with SuperScript II (Invitrogen) reverse transcriptase to synthesize cDNA.  The reaction was performed in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen).  The synthesized DNA was purified by ethanol precipitation, and 3 micro g of cDNA was fragmented with 35 units of DNase I (GE Healthcare, Uppsala, Sweden) at 37°C for 10 min.  The reaction was stopped by incubation of the reaction solution at 98°C for 10 min.  Three micro g of fragmented cDNA was labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions (Affymetrix).  Gel-shift assay using NeutrAvidin (Invitrogne) as a probe confirmed that the majority of cDNA was successfully labeled with biotin.

growth_protocol: The T. thermophilus HB8 mutL deletion mutant strain was pre-cultured at 70°C in 3 mL of TR medium containing 0.4% polypeptone, 0.2% yeast extract, 0.1% NaCl, which was adjusted to pH 7.2 with NaOH.  One ml of pre-culture was inoculated into 1000 mL of TR medium. The cells were cultured at 70°C for 300 min.

extract_protocol: Collected cells were mixed with 1.4 ml of 5 mM Tris-HCl (pH 7.5) containing 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C.  Aqueous phase (0.2 ml) was collected and mixed with 0.75 ml of TRIZOL LS (Invitrogen, Carlsbad, CA), and incubated at room temperature for 5 min.  Then, 0.2 ml of chloroform was added, and the mixture was vortexed for 10 sec.  After centrifugation, aqueous phase was collected, mixed with 0.5 ml of chloroform, and vortexed for 10 min.   The aqueous phase was collected and mixed with 0.5 ml of isopropanol to precipitate RNA.  After incubation at -20°C for 60 min and centrifugation, aqueous phase was removed.  The pellet was dissolved in 0.2 ml of nuclease-free water, and further purified through the ethanol precipitation, and then resuspended in 0.2 ml of water.  The obtained RNA solution was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: The 50 ml of culture was harvested by centrifugation at 7000 rpm at 4°C for 10 minutes.  After the removal of supernatant, pellet was frozen by liquid nitrogen.

value: wild type


title: Ball milled pine rep2 35093502_532


title: mutS deletion mutant strain_3

source_name: mutS-deletion strain at early log phase

growth_protocol: The T. thermophilus HB8 mutS deletion mutant strain was pre-cultured at 70°C in 3 mL of TR medium containing 0.4% polypeptone, 0.2% yeast extract, 0.1% NaCl, which was adjusted to pH 7.2 with NaOH.  One ml of pre-culture was inoculated into 1000 mL of TR medium. The cells were cultured at 70°C for 300 min.

value: mutS deletion


title: mutL deletion mutant strain_3

source_name: mutL-deletion strain at early log phase

value: mutL deletion


title: wild-type strain_2


title: mutS2 deletion mutant strain_2

source_name: mutS2-deletion strain at early log phase

growth_protocol: The T. thermophilus HB8 mutS2 deletion mutant strain was pre-cultured at 70°C in 3 mL of TR medium containing 0.4% polypeptone, 0.2% yeast extract, 0.1% NaCl, which was adjusted to pH 7.2 with NaOH.  One ml of pre-culture was inoculated into 1000 mL of TR medium. The cells were cultured at 70°C for 300 min.

value: mutS2 deletion


title: mutS2 deletion mutant strain_1


title: wild-type strain_3


title: Control Vs DMBA+ellagic acid replicate 2

city: Tamil Nadu

first: Nagini

last: Siddavaram

address: Annamalainagar

department: Department of Biochemistry & Biotechnology

country: India

institute: Annamalai Universuty

description: Biological replicate 2 of 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Mesocricetus auratus

source_name: Buccal pouch

label_protocol: 200 ng of isolated RNA from each sample was used. Labeling was done using the Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, CA) as per the manufacturer’s protocol. Briefly, using affinity script-RT oligo dT promoter primer, cDNA was generated and from the cDNA, labeled cRNA was generated via an in vitro transcription reaction using T7 RNA polymerase and Cy5 (DMBA, DMBA+chlorophyllin, DMBA+ellagic acid) or Cy3 (control) CTP. Labeled cRNA (825 ng) from each sample was used for hybridization in the following combinations- DMBA (Cy5) and control (Cy3), DMBA+chlorophyllin (Cy5) and control (Cy3) and DMBA+ellagic acid (Cy5) and control (Cy3).

growth_protocol: The experiment was carried out with male Syrian hamsters aged 8-10 weeks weighing 100-110g. The animals housed four to a polypropylene cage were provided with standard pellet diet and water ad libitum and maintained under controlled conditions of temperature and humidity with an alternating light/dark cycle in accordance with the guidelines of the Indian Council of Medical Research, and approved by the ethical committee, Annamalai University

extract_protocol: Total RNA was extracted from each sample with Trizol and purified using RNAeasy columns (Qiagen GmbH, Hilden, Germany). RNA was quantitated by NanoDrop ND-1000 (Thermo Scientific, Wilmington DE) and the quantity and integrity was established by resolving on 0.8% formaldehyde agarose gels

treatment_protocol: The animals were randomized into experimental and control groups and divided into 4 groups of eight animals each. In group 1, the right buccal pouches of hamsters were painted with a 0.5 per cent solution of DMBA in liquid paraffin using a No.4 sable brush, three times per week for 14 weeks as described earlier (20). Group 2 and 3 animals painted with DMBA as in group 1, received 4 mg/kg bw of chlorophyllin and 0.4% of ellagic acid respectively in the diet for 14 weeks. Group 4 animals received basal diet and served as control

tag: breed

value: syrian

tag: gender

value: male

tag: disease state

value: healthy

tag: agent

value: Chemoprevention

value: tumor


title: mutS2 deletion mutant strain_3

tag: strain


title: Ball milled pine rep1 34959902_532


title: Control Vs DMBA+chlorophyllin replicate 2

description: Biological replicate 2 of 2


title: mutS deletion mutant strain_2


title: mutL deletion mutant strain_2


title: mutL deletion mutant strain_1


title: Control Vs DMBA+chlorophyllin replicate 1

description: Biological replicate 1 of 2


title: Control Vs DMBA replicate 1

description: Biological replicate 1 of 2


title: Control Vs DMBA+ellagic acid replicate 1

description: Biological replicate 1 of 2


title: Ball milled aspen rep3 34960102_532

source_name: mycelium, ball-milled aspen

value: ball-milled aspen


title: Ball milled aspen rep2 35082502_532


title: mutS deletion mutant strain_1


title: Ball milled aspen rep1 34954202_532


title: A549 MALAT-1 knockdown replication 2-1

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Mammalian non-coding transcript

hyb_protocol: hybridization_Kit: in situ hybridization plus hybridization_Manufacturer: Agilent Technologies hybridization_Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scaner Manufacturer: Agilent Technologies Software: Scanner Control software Manufacturer: Agilent Technologies Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

source_name: A549 MALAT-1 knockdown

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Cells were grown at 37°C, 5% CO2 in Dulbecco’s Modified Eagle's Medium supplemented with 10% fetal calf serum and penicillin/streptomycin

extract_protocol:
separation: scrapping from surface
extraction source: frozen
extraction source: pooled cells
kit: Invitrogen Trizol reagent

treatment_protocol: To carry out RNA interference, siRNA duplexes, synthesized by Invitrogen (stealth MALAT483:CACAGGGAAAGCGAGTGGTTGGTAA) were transfected into cells using Lipofectamine RNAi MAX (Invitrogen) according to the manufacturer's guidelines

tag: cell line

source_name: A549 Control

treatment_protocol: control


title: Control Vs DMBA replicate 2

description: Biological replicate 2 of 2


title: 14162189 - col_3dap_2 vs ros/dme_3dap_2

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Genes regulated by ros/dme?

hyb_protocol: ros/dme_3dap_2 Cy5 / col_3dap_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

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

growth_protocol: seed - media: soil (Minitray/comp:Balster)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype

value: mutant (ros/dme in col)

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

tag: hygrometry

tag: temperature

tag: light


title: 14162185 - ros/dme_3dap_1 vs col_3dap_1

description: Genes regulated by ros/dme?

hyb_protocol: col_3dap_1 Cy5 / ros/dme_3dap_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: A549 MALAT-1 knockdown replication 2

description: Mammalian non-coding transcript


title: 14162184 - col_3dap_1 vs ros/dme_3dap_1

description: Genes regulated by ros/dme?

hyb_protocol: ros/dme_3dap_1 Cy5 / col_3dap_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: A549 MALAT-1 knockdown replication 1-1

description: Mammalian non-coding transcript

treatment_protocol: To carry out RNA interference, siRNA duplexes, synthesized by SIGMA (SiMALAT2:GATCCATAATCGGTTTCAA) were transfected into cells using Lipofectamine RNAi MAX (Invitrogen) according to the manufacturer's guidelines


title: 14162190 - ros/dme_3dap_2 vs col_3dap_2

description: Genes regulated by ros/dme?

hyb_protocol: col_3dap_2 Cy5 / ros/dme_3dap_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Bone met sample 30

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

institute: Umeå University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio software, version 2009.1) and probes with all signals lower than two-times the mean background were excluded.

source_name: Patient 30

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays. Quality control was performed with Agilent Bioanalyser.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: disease stage

value: Castration-resistant prostate cancer

value: Bone metastases

tag: ar-v expression level

value: high (AR-V high)


title: Ball milled pine rep3 34960202_532

organism: Phanerodontia chrysosporium

growth_protocol: 5 days growth in shake flasks at 37C.

extract_protocol: RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.

value: mycelium


title: 14162186 - col_6dap_1 vs ros/dme_6dap_1

description: Genes regulated by ros/dme?

hyb_protocol: ros/dme_6dap_1 Cy5 / col_6dap_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162188 - ros/dme_6dap_1 vs col_6dap_1

description: Genes regulated by ros/dme?

hyb_protocol: col_6dap_1 Cy5 / ros/dme_6dap_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ball milled pine rep2 34969902_532

value: ball-milled pine


title: 14162194 - ros/dme_6dap_2 vs col_6dap_2

description: Genes regulated by ros/dme?

hyb_protocol: col_6dap_2 Cy5 / ros/dme_6dap_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ball milled pine rep1 34969402_532


title: A549 MALAT-1 knockdown replication 1

description: Mammalian non-coding transcript

extract_protocol:
separation: scrapping from surface
extraction source: frozen
extraction source: pooled cells
kit: Invitrogen Trizol reagent
manual: Invitrogen


title: Prdm1-/-_9

city: Oxford

first: Arne

middle: Wyndham

last: Mould

state: Oxfordshire

address: Warneford Hospital

department: Psychiatry

country: United Kingdom

institute: Oxford University

description: Villin-Cre, Prdm1CA/BEH biological replicate 9

data_processing: Rank invariant normalisation with background subtraction using the Gene Expression Module V1.6.0 of Illumina GenomeStudio V2009.2

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

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Mixed

tag: developmental stage

value: embryonic (E18.5)

tag: prdm1 genotype

value: Villin-Cre, Prdm1CA/BEH

value: small intestine


title: Bone met sample 29

source_name: Patient 29

tag: tissue


title: Bone met sample 27

source_name: Patient 27


title: Prdm1-/-_10

description: Villin-Cre, Prdm1CA/BEH biological replicate 10


title: Prdm1-/-_6

description: Villin-Cre, Prdm1CA/BEH biological replicate 6


title: Prdm1-/-_8

description: Villin-Cre, Prdm1CA/BEH biological replicate 8


title: 14162191 - col_6dap_2 vs ros/dme_6dap_2

description: Genes regulated by ros/dme?

hyb_protocol: ros/dme_6dap_2 Cy5 / col_6dap_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Ball milled aspen rep2 34965202_532

tag: condition


title: Ball milled aspen rep1 34960002_532


title: Bone met sample 25

source_name: Patient 25


title: Prdm1-/-_4

description: Villin-Cre, Prdm1CA/BEH biological replicate 4


title: Prdm1-/-_3

description: Villin-Cre, Prdm1CA/BEH biological replicate 3


title: Prdm1-/-_7

description: Villin-Cre, Prdm1CA/BEH biological replicate 7


title: Prdm1-/-_5

description: Villin-Cre, Prdm1CA/BEH biological replicate 5


title: Prdm1-/-_2

description: Villin-Cre, Prdm1CA/BEH biological replicate 2


title: Ball milled aspen rep3 34969102_532


title: Bone met sample 24

source_name: Patient 24


title: Bone met sample 23

source_name: Patient 23


title: Bone met sample 21

source_name: Patient 21


title: Bone met sample 20

source_name: Patient 20

value: low (others)


title: Bone met sample 26

source_name: Patient 26


title: Bone met sample 22

source_name: Patient 22


title: Bone met sample 28

source_name: Patient 28


title: NE-ZF-4d-3

city: Bowling Green

first: Michael

middle: E.

last: Smith

state: KY

address: 1906 College Heights Blvd.

department: Department of Biology

institute: Western Kentucky University

description: Gene expression 4 days after sound exposure

hyb_protocol: 1.65 µg of each labeled cRNA sample was fragmented at 60 °C for 30 min (Agilent Gene Expression Hybridication kit) and then hybridized to Agilent Zebrafish (Danio rerio) oligonucleotide arrays (Agilent Unrestricted AMADID Release GE 4x44K, 60-mer oligonucleotides; G2519F; V1: 015064) at 65 °C for 17 hours.  This microarray has 21,000 D. rerio probes, replicated twice. Three technical replicates were hybridized for each of the three time points (control, Day 2, and Day 4), with one replicate of each time point on each of the three 4-array plates processed. After hybridization, the microarray slides were washed with Agilent gene expression wash buffers.

scan_protocol: The slides were scanned with the aid of an Agilent microarray scanner (G2565BA) with a setting for one-color using the green channel and 5 µm resolution.

data_processing:
The one-color microarray images (.tif) were extracted with the aid of Feature Extraction software (v 9.5.1, Agilent).
The raw data were normalized and then filtered by flag using GeneSpring software. Normalization:  1. log2 transformation  2. Per chip: normalized to 50% quantile 3. Per gene: Normalized to median. Filtered on the Flag:  Entities (genes) were filtered based on their flag values.  Flag values were selected that an entity must satisfy to pass the filter by defining the acceptable flags (Present or Marginally Present).  We retained entities in which at least 3 out of 9 samples had acceptable values.

organism: Danio rerio

source_name: Inner ear, 4 days after sound exposure, replicate 3

label_protocol: 300 ng total RNA was used to generate fluorescent cRNA with the aid of Low RNA Input Linear Amplification kit with one-color (Agilent, Wilmington, DE).  Briefly, this kit uses a T7 promoter primer to synthesize cDNA and T7 RNA polymerase to synthesize cRNA, which simultaneously amplifies the target material and incorporates cyanine 3-labeled CTP (Cy3). The labeled cRNA was purified by using the RNeasy Mini Elute kit (Qiagen, Valencia, CA). The yield and incorporation efficiency were measured on a spectrophotometer (NanoDrop Technologies). The yield for this project was greater than 1.5 ug, and the specific activity was greater than 9.0 pmol Cy3 per ug cRNA.

extract_protocol: Fish were sacrificed one at a time with an overdose of MS-222, their heads were removed, and both whole ears (saccule, lagena, utricle and semi-circular canals) were immediately dissected out while being completely submerged in RNAlater (Ambion, Austin, TX), as preliminary work indicated that either the small size of the saccule, or the length of time needed to separate it from the inner ear, resulted in low RNA yield.  Ears were then placed in sterile Eppendorf tubes and flash frozen in liquid nitrogen.  Three to four hours were required to dissect all the fish in one group.  Once all the ears for a sample were collected, the tissue was pooled and homogenized with a Kontes Pellet Pestle Microgrinder and sterile disposable pestles (Kontes, Vineland, NJ), then processed for RNA isolation using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA).  RNA quality was checked with the aid of an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE).  For this project, sharp ribosomal RNA bands were evident with an RNA integrity number greater than 7.0.

treatment_protocol: RNA samples were obtained from the inner ears of the three groups of 18 to 20 fish each (controls, 2 dpse, 4 dpse).  One group served as non-sound exposed controls, and the remaining two groups were exposed to the acoustic stimulus and allowed to recover for 2 or 4 days. The day 2 time point was selected in order to investigate gene expression during proliferation, which had been shown to peak at 2 dpse, and 4 dpse was chosen since it represented a post-proliferative phase

value: Inner ear

tag: treatment

value: 4 days after sound exposure


title: Prdm1+/+_10

description: Prdm1CA/+ biological replicate 10


title: Prdm1-/-_1

description: Villin-Cre, Prdm1CA/BEH biological replicate 1


title: Prdm1+/+_8

description: Prdm1CA/+ biological replicate 8


title: NE-ZF-4d-1

source_name: Inner ear, 4 days after sound exposure, replicate 1


title: NE-ZF-2d-3

description: Gene expression 2 days after sound exposure

source_name: Inner ear, 2 days after sound exposure, replicate 3

value: 2 days after sound exposure


title: Prdm1+/+_6

description: Prdm1CA/+ biological replicate 6


title: NE-ZF-4d-2

source_name: Inner ear, 4 days after sound exposure, replicate 2


title: Prdm1+/+_11

description: Prdm1CA/+ biological replicate 11


title: Bone met sample 18

source_name: Patient 18


title: Bone met sample 16

source_name: Patient 16


title: Bone met sample 19

source_name: Patient 19


title: Bone met sample 17

source_name: Patient 17


title: Prdm1+/+_5

description: Prdm1CA/+ biological replicate 5


title: Prdm1+/+_4

description: Prdm1CA/+ biological replicate 4


title: Prdm1+/+_2

description: Prdm1CA/+ biological replicate 2


title: Prdm1+/+_3

description: Prdm1CA/+ biological replicate 3


title: NE-ZF-2d-2

source_name: Inner ear, 2 days after sound exposure, replicate 2


title: C-ZF-3

description: Gene expression without sound exposure

source_name: Inner ear, no sound exposure, replicate 3

value: no sound exposure


title: C-ZF-2

description: Gene expression without sound exposure

source_name: Inner ear, no sound exposure, replicate 2


title: Bone met sample 14

source_name: Patient 14


title: Bone met sample 13

source_name: Patient 13


title: heart from JMJD2A-tg mice after TAC surgery 2

city: Dallas

first: Qingjun

last: Zhang

address: 5323 Harry Hines Blvd,NB11.110

institute: UT Southwestern

description: replicate 6

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: mouse heart

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina® TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

tag: genetic bacground

value: FvB

tag: age

value: 8 week

tag: surgery

value: thoracic aortic constriction

value: JMJD2a transgenic

value: heart


title: Prdm1+/+_1

description: Prdm1CA/+ biological replicate 1

tag: strain


title: heart from JMJD2A-tg mice after TAC surgery 1

description: replicate 5


title: Prdm1+/+_7

description: Prdm1CA/+ biological replicate 7


title: genotype: GmMPK4-silenced Williams 82 - rep4

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

hyb_protocol: Soybean probe hybridization protocol

scan_protocol: Affy soybean scanning protocol

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Glycine max

source_name: The top fully expanded trifoliolate leaves, petioles and stem segments. (genotype: GmMPK4-silenced Williams 82)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: Affy soybean extraction protocol

tag: williams 82 (germplasm name); ud

value: 0000075 The top fully expanded trifoliolate leaves, petioles and stem segments., (Organism Part); UD:0000076 35 day old plant (Development Stage); field soil (Growth Media).


title: genotype: GmMPK4-silenced Williams 82 - rep3


title: C-ZF-1

description: Gene expression without sound exposure

source_name: Inner ear, no sound exposure, replicate 1


title: heart from JMJD2A-tg mice after sham surgery

description: replicate 4

value: sham

tag: genotype


title: NE-ZF-2d-1

source_name: Inner ear, 2 days after sound exposure, replicate 1


title: heart from wt mice after TAC surgery 2

description: replicate 3

value: wild type


title: genotype: GmMPK4-silenced Williams 82 - rep1


title: genotype: GmMPK4-silenced Williams 82 - rep2


title: Bone met sample 11

source_name: Patient 11

value: Castration-resistant prostate cancer

value: Bone metastases


title: heart from wt mice after TAC surgery 1

description: replicate 2


title: Bone met sample 9

source_name: Patient 9


title: Bone met sample 4

source_name: Patient 4


title: Bone met sample 6

source_name: Patient 6


title: Bone met sample 5

source_name: Patient 5


title: genotype: Williams 82 - rep3

description: BPMV vector control 3

source_name: The top fully expanded trifoliolate leaves, petioles and stem segments. (genotype: Williams 82)


title: Bone met sample 12

source_name: Patient 12