title: granule cell-pilo-Dingledine-day 3-rat 4

status: Public on Jun 08 2013

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 150.

organism: Rattus norvegicus

source_name: granule cell, pilo, day 3

growth_protocol: Male Sprague-Dawley rats were used.   Individually housed animals were handled and allowed to acclimate for 1 week prior to experiments with food and water available ad libitum. All animals weighed 175-250g at the time of experimentation.

extract_protocol: LCM and RNA Isolation: Ten micron coronal sections were taken through the hippocampus and collected onto uncoated microscope slides, refrozen on dry ice, and stored in a -80°C freezer until staining for LCM.  For staining, sections were fixed in ice-cold 70% ethanol for 2 min, rinsed in water, dipped in cresyl violet stain, then rinsed and dehydrated to xylene.  Sections were dried in a fume hood and LCM was performed within 1 hour.  LCM was performed using an Arcturus Pixcell IIe system with transmission illumination (Arcturus, CA) and the following parameters: spot size = 25-30μm; power = 50-65mW; and duration = 1700-2500μs per hit.  The dentate gyrus was harvested from 10-16 sections per subject in order to get at least 10ng total RNA for amplification.  LCM HS Caps (Arcturus) were used to collect dentate granule cells with 2-5 sections per cap, resulting in 2-8 LCM Caps used per subject.  Total RNA was immediately extracted from each LCM cap using the PicoPure Isolation Kit protocol (Arcturus) with DNase digestion (Quiagen Rnase-free DNase Set), and stored at -80°C until RNA quality verification and quantification using Agilent RNA 6000 PicoChips.   Pico Kit instructions were followed to analyze the RNA isolations from each subject, and the PicoChip was run on the Agilent 2100 Bioanalyzer.  The results of the PicoChip determined whether the RNA was of high enough quality to keep for amplification and later hybridization.  Only total RNA with a RNA Integrity Number (RIN) > 7.0 was kept to include in a pool of total RNA from each LCM cap per subject in order to obtain one sample with a minimum of 10ng total RNA.  Once a total RNA pool was complete for each subject, the sample was run through the BioAnalyzer, quantity and quality recorded, and samples were frozen at -80°C until shipment to TGEN (Phoenix, AZ, USA) for RNA amplification and microarray hybridization.

treatment_protocol:
Pilocarpine Model of Epilepsy (Dingledine and Coulter):  Sprague-Dawley rats (180-200g) were purchased from Charles-River (Raleigh, NC).  All animals were given an injection of methylscopolamine (1mg/kg, i.p., Sigma) to minimize cholinergic peripheral effects of pilocarpine.  After 30 minutes, animals received pilocarpine hydrochloride (300-350 mg/kg, s.c., Sigma) or saline.  Seizures were classified according to Racine (1972) and Schauwecker and Steward (1997) with slight modifications (Borges et al., 2003). SE was defined by continuous seizure activity consisting of at least stage 3 seizures and one stage 5 or 6 seizure or several stage 4 seizures.  SE was terminated with pentobarbital (25 mg/kg, i.p., Sigma) after 90 min of SE activity.  Animals were monitored daily and given dextrose in lactate Ringer solution (~1mL, i.p.) when needed.  Animals were euthanized by decapitation.  The brains were rapidly removed, bisected down the midline.  One half of the brain was placed in 4% paraformaldehyde and stored at 5°C until shipped. The other half was frozen on dry ice and stored at -70°C to -80°C until shipped.
Kainate Model of Epilepsy (Wadman and Nadler):  Sprague Dawley rats (175-250g) were purchased from Charles-River, Raleigh (Nadler group) or Harlan, Netherlands (Wadman group).  All animals were injected with kainic acid (5mg/kg, i.p.) or saline hourly until status epilepticus was achieved.  The Wadman group used an initial intraperitoneal injection of 7.5 mg/kg, followed by hourly 5mg/kg until SE induction.  All animals were given 5-6 injections before SE onset.  The Nadler group allowed SE to self-terminate after 6-8 hours, while the Wadman group stopped seizure activity with pentobarbital 90 min after SE onset.  SE onset was defined by continuous stage 4 and stage 5 seizure activity for 3 hours.   Animals were euthanized by decapitation.  The brains were rapidly removed and bisected down the midline.  One half of the brain was placed in 4% paraformaldehyde and stored at 5°C until shipped. The other half was frozen on dry ice and stored at -70°C to -80°C until shipped.
Self-Sustained Status Epilepticus Model of Epilepsy (Wasterlain): Male Sprague-Dawley rats were purchased from Charles River, Raleigh at 280-300g.  The animals were implanted with a stimulating electrode in the angular bundle in reference to lambda (AP +0.5mm, ML +4.5mm--left side, DV -4.0mm from surface of brain).  Electrodes were positioned under isoflurane anesthesia (4% in O2), and animals were treated for post-operative pain with buprenorphine for three days following surgery.  They were allowed to recover for 14 days before initiating SE.  EEG was recorded from skull screws located over the dorsal hippocampi.  SE was initiated by 30 minutes of perforant path stimulation.  The stimulation wave form consisted of 10 second trains of 20hz biphasic square waves delivered at 1 train per minute superimposed on continuous 2 hz monophasic square waves.  All square waves were 1 millisecond in duration.   Animals received no treatment following stimulation of the perforant path and were included in the study only if they remained in SE for at least 10 minutes after the end of perforant path stimulation.  Control animals were implanted but not stimulated. The experimental animals were euthanized at 1 day, 3 days, and 10 days after initiating SE.  Animals were euthanized by isoflurane anesthesia followed by decapitation.  The brains were rapidly removed, bisected down the midline.  One half of the brain was placed in 4% paraformaldehyde and stored at 5°C until shipped. The other half was frozen on dry ice and stored at -70°C until shipped.
All samples were shipped to the Dingledine laboratory. The fixed hemispheres were sent to Robert Slovitor for Nissl histology, and the frozen hemispheres of the pilocarpine and kainate models were sent to Duke University (Pate Skene) for laser capture microscopy of dentate granule cells. Granule cells from the SSSE model were captured at Emory University.

tag: laboratory

value: Ray Dingledine

tag: harvest time

value: day 3

tag: epilepsy model

value: pilocarpine

value: granule cell

tag: genetic background

value: Sprague-Dawley


title: 838T, rep1

status: Public on Jun 09 2013

type: RNA

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: 838T replicate 1

hyb_protocol: A total hybridisation volume of 15ul is prepared for each sample and 15ul loaded into a single array on the Sentrix Human-HT12v4 BeadChip. The chip is hybridised at 58C for 16 hours in an oven with a rocking platform. After hybridisation, the chip is washed using the appropriate protocols as outlined in the Illumina manual. Upon completion of the washing, the chips are then coupled with Cy3 and scanned in the illumina BeadArray Reader.

scan_protocol: Arrays were scanned in the Illumina BeadArray Reader.

data_processing: The GenomeStudio software (version 1.9.0) was used to convert the signal on the array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was carried out in R (version 2.15.2) using the limma package (version 4.15.9).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: xenograft tumor

label_protocol: Human total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 500ng was labelled using the Ambion Total Prep RNA amplification kit (Cat. No. IL1791). The quantity of labelled product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 750ng of labelled cRNA was then prepared for hybridisation to the Sentrix Human- HT12v4 BeadChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the BeadChip).

extract_protocol: RNA was extracted using Invitrogen Trizol Reagent in accordance with the prescribed protocol provided with the kit. DNase treatment was performed using the QIAGEN RNase-free DNase Set prior to RNA purification using the QIAGEN RNAeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: breast tumor xenograft

tag: tumor id


title: granule cell-pilo-Dingledine-day 3-rat 1

country: USA

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

tag: cell type


title: granule cell-pilo-Dingledine-day 3-rat 2


title: granule cell-pilo-Dingledine-day 1-rat 4

source_name: granule cell, pilo, day 1

value: day 1


title: granule cell-pilo-Dingledine-day 3-rat 6


title: granule cell-pilo-Dingledine-day 1-rat 5


title: granule cell-pilo-Dingledine-day 1-rat 1


title: granule cell-pilo-Dingledine-day 3-rat 5


title: granule cell-pilo-Dingledine-day 3-rat 3


title: granule cell-pilo-Dingledine-day 1-rat 2


title: granule cell-pilo-Dingledine-day 10-rat 5

source_name: granule cell, pilo, day 10

value: day 10


title: granule cell-pilo-Dingledine-day 1-rat 6


title: granule cell-pilo-Dingledine-day 10-rat 3


title: granule cell-pilo-Dingledine-day 10-rat 6


title: granule cell-pilo-Coulter-day 3-rat 5

value: Douglas Coulter


title: granule cell-pilo-Dingledine-day 1-rat 3


title: granule cell-pilo-Coulter-day 3-rat 3


title: granule cell-pilo-Coulter-day 3-rat 6


title: granule cell-pilo-Coulter-day 1-rat 5


title: granule cell-pilo-Dingledine-day 10-rat 2


title: granule cell-pilo-Dingledine-day 10-rat 4


title: granule cell-pilo-Dingledine-day 10-rat 1


title: granule cell-pilo-Coulter-day 1-rat 6


title: granule cell-pilo-Coulter-day 1-rat 2


title: granule cell-pilo-Coulter-day 1-rat 1


title: granule cell-pilo-Coulter-day 3-rat 4


title: granule cell-pilo-Coulter-day 3-rat 1


title: granule cell-pilo-Coulter-day 10-rat 4


title: granule cell-pilo-Coulter-day 10-rat 6


title: granule cell-pilo-Coulter-day 10-rat 1


title: granule cell-kainate-Wadman-day 3-rat 1

source_name: granule cell, kainate, day 3

value: Wytse Wadman

value: kainate


title: granule cell-kainate-Wadman-day 3-rat 4


title: granule cell-pilo-Coulter-day 1-rat 4


title: granule cell-pilo-Coulter-day 10-rat 5


title: granule cell-kainate-Wadman-day 3-rat 3


title: granule cell-kainate-Wadman-day 3-rat 5


title: granule cell-pilo-Coulter-day 10-rat 2


title: granule cell-kainate-Wadman-day 3-rat 2


title: granule cell-pilo-Coulter-day 10-rat 3


title: granule cell-pilo-Coulter-day 1-rat 3


title: granule cell-kainate-Wadman-day 3-rat 6


title: granule cell-kainate-Wadman-day 1-rat 4

source_name: granule cell, kainate, day 1


title: granule cell-kainate-Wadman-day 1-rat 6


title: granule cell-kainate-Wadman-day 10-rat 2

source_name: granule cell, kainate, day 10


title: granule cell-kainate-Wadman-day 1-rat 1


title: granule cell-kainate-Wadman-day 1-rat 2


title: granule cell-kainate-Wadman-day 10-rat 1


title: granule cell-kainate-Wadman-day 10-rat 6


title: granule cell-kainate-Wadman-control-rat 4

source_name: granule cell, kainate, control

value: control


title: granule cell-kainate-Wadman-day 10-rat 3


title: granule cell-kainate-Wadman-day 10-rat 5


title: granule cell-kainate-Wadman-day 1-rat 5


title: granule cell-kainate-Wadman-day 1-rat 3


title: granule cell-kainate-Wadman-control-rat 5


title: granule cell-kainate-Wadman-control-rat 6


title: granule cell-kainate-Wadman-day 10-rat 4


title: granule cell-kainate-Wadman-control-rat 2


title: granule cell-kainate-Wadman-control-rat 1


title: granule cell-pilo-Dingledine-control-rat 4

source_name: granule cell, pilo, control


title: granule cell-pilo-Dingledine-control-rat 1


title: granule cell-kainate-Wadman-control-rat 3


title: granule cell-pilo-Dingledine-control-rat 3


title: granule cell-pilo-Dingledine-control-rat 2


title: granule cell-pilo-Dingledine-control-rat 6


title: granule cell-pilo-Dingledine-control-rat 5a


title: granule cell-pilo-Dingledine-control-rat 2a


title: granule cell-pilo-Dingledine-control-rat 4a


title: granule cell-pilo-Dingledine-control-rat 5


title: granule cell-pilo-Coulter-control-rat 3


title: granule cell-pilo-Coulter-control-rat 6


title: granule cell-SSSE-Wasterlain-day 1-rat 3

source_name: granule cell, SSSE, control

value: Claude Wasterlain

value: SSSE


title: granule cell-kindling-McNamara-control-rat 3

source_name: granule cell, kindling, control

value: James McNamara

value: kindling


title: granule cell-SSSE-Wasterlain-day 1-rat 2

source_name: granule cell, SSSE, day 1


title: granule cell-kindling-Rogawski-stage 5-rat 2

source_name: granule cell, kindling, stage 5

value: Michael Rogawski

value: stage 5


title: granule cell-kindling-Rogawski-control-rat 3


title: granule cell-kindling-McNamara-stage 5-rat 2


title: granule cell-pilo-Coulter-control-rat 2


title: granule cell-pilo-Dingledine-control-rat 3a

value: Ray Dingledine


title: granule cell-kainate-Nadler-control-rat 3

value: Victor Nadler


title: granule cell-kainate-Nadler-day 10-rat 2

value: granule cell


title: granule cell-kindling-Rogawski-stage 4-rat 2

source_name: granule cell, kindling, stage 4

value: stage 4

value: Sprague-Dawley


title: granule cell-kindling-McNamara-stage 4-rat 2


title: granule cell-kindling-Rogawski-control-rat 2


title: granule cell-kindling-McNamara-stage 2-rat 2

source_name: granule cell, kindling, stage 2

value: stage 2


title: granule cell-pilo-Coulter-control-rat 4

value: pilocarpine


title: granule cell-kainate-Nadler-day 1-rat 2

value: day 1


title: granule cell-kainate-Nadler-control-rat 2


title: granule cell-kindling-McNamara-control-rat 2


title: granule cell-kainate-Nadler-day 3-rat 2

value: day 3


title: granule cell-SSSE-Wasterlain-control-rat 5


title: granule cell-pilo-Coulter-control-rat 1

value: Douglas Coulter


title: granule cell-kindling-Rogawaski-stage 5-rat 1


title: granule cell-pilo-Coulter-control-rat 5

value: control


title: granule cell-kindling-McNamara-stage 5-rat 1


title: granule cell-SSSE-Wasterlain-day 1-rat 1

value: Claude Wasterlain


title: granule cell-pilo-Coulter-day 3-rat 2


title: granule cell-kindling-Rogawski-stage 2-rat 2


title: granule cell-kindling-Rogawski-stage 5-rat 6


title: granule cell-SSSE-Wasterlain-control-rat 4

value: SSSE


title: granule cell-kindling-Rogawski-stage 4-rat 1


title: granule cell-kindling-McNamara-stage 4-rat 1

value: James McNamara


title: granule cell-kainate-Nadler-day 10-rat 1

value: day 10

value: kainate


title: granule cell-kainate-Nadler-day 3-rat 1


title: granule cell-kindling-Rogawski-stage 4-rat 6

value: Michael Rogawski

value: kindling


title: granule cell-kindling-Rogawski-control-rat 6


title: granule cell-kainate-Nadler-day 10-rat 6

value: Victor Nadler


title: granule cell-kindling-Rogawski-stage 5-rat 5

value: stage 5

value: granule cell


title: granule cell-kindling-McNamara-stage 5-rat 6

value: Sprague-Dawley


title: granule cell-kindling-McNamara-control-rat 6


title: granule cell-kindling-McNamara-stage 4-rat 6a

value: stage 4


title: granule cell-kindling-McNamara-stage 4-rat 6


title: granule cell-SSSE-Wasterlain-day 10-rat 6

source_name: granule cell, SSSE, day 10


title: granule cell-kainate-Nadler-day10-rat 5


title: granule cell-SSSE-Wasterlain-day 10-rat 3


title: granule cell-SSSE-Wasterlain-control-rat 3


title: granule cell-kainate-Nadler-control-rat 6


title: granule cell-kindling-McNamara-stage 5-rat 5


title: granule cell-kainate-Nadler-day 3-rat 6


title: granule cell-kindling-McNamara-stage 2-rat 1

value: stage 2


title: granule cell-kindling-Rogawski-stage 2-rat 6


title: granule cell-kindling-Rogawski-stage 2-rat 1


title: granule cell-kindling-McNamara-stage 2-rat 6


title: granule cell-kainate-Nadler-day 1-rat 6

value: day 1


title: granule cell-kainate-Nadler-day 1-rat 1


title: granule cell-pilo-Dingledine-control-rat 1a

value: Ray Dingledine

value: pilocarpine


title: granule cell-SSSE-Wasterlain-control-rat 2

value: control


title: granule cell-kindling-Rogawski-control-rat 5


title: granule cell-kindling-Rogawski-stage 5-rat 4


title: granule cell-SSSE-Wasterlain-day 3-rat 4

source_name: granule cell, SSSE, day 3

value: Claude Wasterlain

value: day 3


title: granule cell-kainate-Nadler-control-rat 5


title: granule cell-kindling-Rogawski-stage 4-rat 5


title: granule cell-SSSE-Wasterlain-day 10-rat 1

value: SSSE


title: granule cell-SSSE-Wasterlain-day 3-rat 6


title: granule cell-kindling-McNamara-stage 4-rat 5

value: James McNamara

value: state 4


title: granule cell-kindling-McNamara-control-rat 5


title: granule cell-kainate-Nadler-day 10-rat 4

value: day 10

value: kainate


title: granule cell-kainate-Nadler-day 1-rat 5

value: Victor Nadler


title: granule cell-kainate-Nadler-day 3-rat 5 rehyb


title: granule cell-kainate-Nadler-day 3-rat 5


title: granule cell-SSSE-Wasterlain-day 10-rat 2


title: granule cell-SSSE-Wasterlain-day 3-rat 3


title: granule cell-kindling-McNamara-stage 2-rat 5

value: kindling


title: granule cell-kindling-Rogawski-stage 2-rat 5

value: Michael Rogawski

value: granule cell


title: granule cell-kindling-McNamara-stage 5-rat 4

value: stage 5

value: Sprague-Dawley


title: granule cell-kainate-Nadler-day 3-rat 4


title: granule cell-SSSE-Wasterlain-day 3-rat 5


title: granule cell-kindling-Rogawski-stage 2-rat 4

value: stage 2


title: granule cell-kindling-Rogawski-stage 4-rat 4

value: stage 4


title: granule cell-kainate-Nadler-day 1-rat 4

value: day 1


title: granule cell-kainate-McNamara-stage 2-rat 4

source_name: granule cell, kainate, stage 2


title: granule cell-kindling-McNamara-stage 4-rat 4


title: granule cell-SSSE-Wasterlain-day 3-rat 2


title: granule cell-kainate-Nadler-control-rat 4

value: control


title: granule cell-kindling-McNamara-control-rat 4


title: granule cell-SSSE-Wasterlain-day 1-rat 6

value: Claude Wasterlain


title: granule cell-kindling-Rogawski-control-rat 4


title: granule cell-SSSE-Wasterlain-day 1-rat 5


title: granule cell-kainate-Nadler-day 1-rat 3


title: granule cell-kindling-Rogawski-stage 4-rat 3


title: granule cell-kindling-McNamara-stage 4-rat 3


title: granule cell-SSSE-Wasterlain-control-rat 1


title: granule cell-kindling-McNamara stage 5-rat 3


title: granule cell-kainate-Nadler-day 10-rat 3


title: granule cell-SSSE-Wasterlain-day 1-rat 4


title: granule cell-SSSE-Wasterlain-day 1-rat 6 rehyb


title: granule cell-kainate-Nadler-control-rat 1


title: granule cell-kindling-Rogawski-stage 5-rat 3


title: granule cell-kindling-Rogawski-control-rat 1


title: granule cell-kindling-Rogawski-stage 2-rat 3


title: granule cell-kindling-McNamara-control-rat 1


title: granule cell-kindling-McNamara-stage 2-rat 3


title: granule cell-kainate-Nadler-day 3 -rat 3

value: day 3


title: Bone marrow derived macrophage, LPS-stimulated, biological rep3

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics and Deep-Sequencing Unit

country: Germany

institute: Max-Planck-Institute for Immunobiology and Epigenetics

description:
Gene expression data from macrophages
newly synthesized RNA
S1730_L15_BMM_LPS3

hyb_protocol: Hybridization, Wash and Stain Kit Affymetrix. cRNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays.

scan_protocol: Hybridization, Wash and Stain Kit Affymetrix. Affymetrix scanner 3000 7g.

data_processing: RMA normalization (Bioconductor (expresso from affy package)).

organism: Mus musculus

source_name: Bone marrow derived, M-CSF induced ex vivo differentiated macrophages

label_protocol: Newly synthesized RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol:
in vitro grown cells in DMEM containing 10% FCS and M-CSF
Bone marrow derived macrophages grown in DMEM medium containing 10% fetal calf serum and M-CSF and MPI cells in RPMI containing 10% FCS and GM-CSF

extract_protocol: Cells were lysed in Trifast (PeqLab, Germany) and total RNA was extracted according to the suggestions of the manufacturer. Biotinylation of 4sU labeled RNA and the purification of biotinylated RNA was performed as described (Dolken et al., 2008).

treatment_protocol: Cells were stimulated with 0.1 mg/ml R-LPS. Metabolic labelling and purification of nascent RNA were performed as described (Dolken et al., 2008) with 250 mM 4-thiouridine labeling for 60 minutes starting 30 minutes after LPS stimulation

value: macrophage (M-CSF induced ex vivo differentiated)

tag: cell type derived from

value: Bone marrow

tag: agent

value: LPS

tag: strain


title: MPI-2 cell line, unstimulated,  biological rep2

description:
Gene expression data from MPI cells
newly synthesized RNA
S2097_C3labeled RNA_Rep3

source_name: Fetal liver derived, GM-CSF induced macrophages

growth_protocol:
in vitro grown cells in RPMI medium containing 10% fetal calf serum and GM-CSF
Bone marrow derived macrophages grown in DMEM medium containing 10% fetal calf serum and M-CSF and MPI cells in RPMI containing 10% FCS and GM-CSF

treatment_protocol: Metabolic labelling and purification of nascent RNA were performed as described (Dolken et al., 2008) with 250 mM 4-thiouridine labeling for 60 minutes

tag: cell line

value: macrophage (GM-CSF induced)

value: Fetal liver

value: mock


title: MPI-2 cell line, LPS-stimulated, biological rep2

description:
Gene expression data from MPI cells
newly synthesized RNA
S2100_Z2_LPS labeled_Rep2


title: MPI-2 cell line, unstimulated,  biological rep1

description:
Gene expression data from MPI cells
newly synthesized RNA
S2096_C2labeled RNA_Rep2


title: MPI-2 cell line, LPS-stimulated, biological rep1

description:
Gene expression data from MPI cells
newly synthesized RNA
S2099_Z1_LPS_labeled RNA_Rep1


title: Bone marrow derived macrophage, unstimulated, biological rep1

description:
Gene expression data from macrophages
newly synthesized RNA
S1725_L9_BMM_Mock1


title: MPI-2 cell line, unstimulated,  biological rep3

description:
Gene expression data from MPI cells
newly synthesized RNA
S2098_C4labeled RNA_Rep4


title: MPI-2 cell line, LPS-stimulated, biological rep3

description:
Gene expression data from MPI cells
newly synthesized RNA
S2101_Z3_LPS_labeled RNA_Rep 3


title: Bone marrow derived macrophage, LPS-stimulated, biological rep2

description:
Gene expression data from macrophages
newly synthesized RNA
S1729_L14_BMM_LPS2


title: MPI-3 cell line  biological rep2

description:
Gene expression data from MPI cells
S931_8_MPI_3_4

data_processing: RMA normalization (Affymetrix Expression Console 1.1).

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: in vitro grown cells in RPMI medium containing 10% fetal calf serum and GM-CSF

extract_protocol: Cells were lysed in Trifast (PeqLab, Germany) and total RNA was extracted according to the suggestions of the manufacturer.


title: Bone marrow derived macrophage, unstimulated, biological rep2

description:
Gene expression data from macrophages
newly synthesized RNA
S1726_BMM_Mock2


title: MPI-3 cell line  biological rep3

description:
Gene expression data from MPI cells
S932_9_MPI_3_4


title: Bone marrow derived macrophage, unstimulated, biological rep3

description:
Gene expression data from macrophages
newly synthesized RNA
S1727_BMM_Mock3


title: SP37A3 cell line biological rep2

description:
Gene expression data from dendritic cells
S928_5_SPG

source_name: Spleen derived, M-CSF and GM-CSF induced immature dendritic cells

value: immature dendritic cell (M-CSF and GM-CSF induced)

value: Spleen


title: Bone marrow derived macrophage, LPS-stimulated, biological rep1

description:
Gene expression data from macrophages
newly synthesized RNA
S1728_L13_BMM_LPS1


title: MPI-3 cell line  biological rep1

description:
Gene expression data from MPI cells
S930_7_MPI_3_4


title: MPI-2 cell line biological rep1

description:
Gene expression data from MPI cells
S924_1_MPI_2


title: MPI-2 cell line biological rep2

description:
Gene expression data from MPI cells
S925_2_MPI_2


title: SP37A3 cell line biological rep1

description:
Gene expression data from dendritic cells
S927_4_SPG


title: SP37A3 cell line biological rep3

description:
Gene expression data from dendritic cells
S929_6_SPG


title: miR-106a-5p inhibitor for 24 hours 106I

city: Changzhou

first: Yilin

last: Yang

state: Jiangsu

address: 185#, Juqian Road

department: Modern Medical Research Center

country: China

institute: Third Affiliated Hospital of Soochow University

description: The total RNA of this sample was extracted from the cultured U251 cells transfected with miR-106a-5p inhibitor for 24 hours.

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

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

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

source_name: Human Neuronal Astrocytoma cell line

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

growth_protocol: The human astrocytoma U251 cancer cells were cultured in Dulbecco's Modified Eagle’s Medium (Invitrogen, USA) supplemented with 10 % fetal bovine serum (Hyclone, USA) in a humidified 37 °C incubator that was maintained at 5 % CO2.

extract_protocol: Total RNA was extracted from cultured cells or clinical samples using TRIzol Reagent (Invitrogen) according to the manufacturer’s protocols. The RNA molecules were then treated with RNase-free DNase (TaKaRa, Dalian, China) using a standardized protocol.

treatment_protocol: U251 cells were transfected with microRNA inhibitor negative control, miR-106a-5p inhibitor, microRNA negative mimics control or miR-106a-5p mimics using Lipofectamine 2000. The cells were harvested at 24 h after transfection, and total RNA was extracted from the cultured cells using TRIzol Reagent.

tag: treatment

value: miR-106a-5p inhibitor for 24 hours


title: miR-106a-5p mimics for 24 hours 106M

description: The total RNA of this sample was extracted from the cultured U251 cells transfected with miR-106a-5p mimics for 24 hours.

value: miR-106a-5p mimics for 24 hours


title: Bone marrow derived macrophage biological rep3

description:
Gene expression data from macrophages
S521_3A3T

growth_protocol:
in vitro grown cells
bone marrow derived cells differentiated and grown in DMEM medium containing 10% fetal calf serum and M-CSF


title: Bone marrow derived macrophage biological rep2

description:
Gene expression data from macrophages
S513_3A2T


title: MPI-2 cell line biological rep3

description:
Gene expression data from MPI cells
S926_3_MPI_2


title: microRNA negative mimics control for 24 hours M-C

description: The total RNA of this sample was extracted from the cultured U251 cells transfected with microRNA negative mimics control for 24 hours.


title: liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with acetaminophen (APAP)_2

city: Bozeman

first: Ed

last: Schmidt

state: MT

department: M&I Dept

institute: Montana State University

description:
Gene expression data mus musculus liver tissue
APAP_2_null

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

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner

data_processing: The data were imported into FlexArray using RMA preprocessing for analysis.

source_name: Mus musculus liver - txnrd1 null

label_protocol: One cycle biotinyllated cRNA generated from 1 µg total RNA with Ambion Message Amp-II Biotin Enhanced system.

growth_protocol: Experimental livers from male mice with a conditional-null allele of txnrd1 disrupted by albCre.

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

treatment_protocol: Mice were treated with either saline or 100mg/kg APAP by IP injection, liver samples harvested eight hours later.

tag: genotype/variation

value: txnrd1 null

tag: age

tag: developmental stage

value: adult

tag: gender

value: male

value: acetaminophen (APAP)

value: liver


title: liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with vehicle (saline)_4

description:
Gene expression data mus musculus liver tissue
PBS_4_null

value: vehicle (saline)


title: liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with acetaminophen (APAP)_17

description:
Gene expression data mus musculus liver tissue
APAP_17_null


title: liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with vehicle (saline)_16

description:
Gene expression data mus musculus liver tissue
PBS_16_null


title: Bone marrow derived macrophage biological rep1

description:
Gene expression data from macrophages
S310_3A1T_3huninfiziert


title: liver cells from wildtype 8wk male mouse 8 challenged with acetaminophen (APAP)_13

description:
Gene expression data mus musculus liver tissue
APAP_13_++

source_name: Mus musculus liver - wildtype

value: wildtype


title: Ovary-Tg-Foxo3-/-rep3

city: Paris

first: Chris

last: Ottolenghi

address: rue des Saint-Peres

country: France

institute: Inserm/Univ.Paris Descartes

description: Ovary  tissue from 14 dpn female

hyb_protocol: Standard Illumina protocol. In short, a total of 1.5ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Mouse WG-6 v2.0 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~25,600 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.

data_processing: normalization using loess module in R

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: Animals were euthanized and the ovary dissected for total RNA isolation. Total RNA was prepared using the Total RNA Extraction Mini Kit (Real Biotech Corporation) CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.

value: FVB/N

value: Female

value: ovary

value: 14 dpn


title: liver cells from wildtype 8wk male mouse 8 challenged with acetaminophen (APAP)_14

description:
Gene expression data mus musculus liver tissue
APAP_14_++


title: Ovary-NoTg-Foxo3-/-rep2

description: Ovary  tissue from 14 dpn female


title: Ovary-Tg-Foxo3+/-rep1

description: Ovary  tissue from 14 dpn female


title: HDAC1/2 KO mice colon rep.1

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

description: gene expression data in colon epitelial cells from HDAC1/2 KO mice

hyb_protocol: Hybridized target cRNA is stained with streptavidin phycoerythrin

scan_protocol: arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.

data_processing: Data analysis, normalization average difference and expression measurements were subsequently completed with Flexarray software version 1.6.1.  Background correction and normalization were assessed with a multi-array average (RMA) algorithm. Significant statistical differences were calculated with the Student’s t test, with the cut-off for statistical significance set to a p value of 0.05 or below.

source_name: epithelium from colon of HDAC1/2 KO mouse no.1

label_protocol: Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization

growth_protocol: HDAC1 and HDAC2 conditionally mutated mice were provided by Dr EN Olson (University of Texas Southwestern Medical Center, Dallas, TX) (Montgomery et al., 2007). Floxed HDAC1 and HDAC2 mice were crossed with villin-Cre transgenic mice to insure specific intestinal epithelial cell gene deletion (Madison et al., 2002). Genomic DNA was recovered with the Spin Doctor genomic DNA kit (Gerard Biotech, Oxford, OH). Mouse genotypes were determined with already published RT-PCR protocols (Montgomery et al., 2007). Mice were fed a normal diet in a transgenic mouse facility.

extract_protocol: Total RNAs from the colon of three control and three HDAC1/2 IEC-specific knockout mice were isolated with the Rneasy kit (Qiagen, Mississauga, ON, Canada). cDNA preparation and microarray assay were performed at the Microarray platform of the McGill University and Génome Quebec Innovation Centre

treatment_protocol: no treatment was given to mice

value: colon

value: HDAC1/2 KO


title: Ovary-NoTg-Foxo3-/-rep3

description: Ovary  tissue from 14 dpn female


title: liver cells from wildtype 8wk male mouse 8 challenged with vehicle (saline)_10

description:
Gene expression data mus musculus liver tissue
PBS_10_++


title: Ovary-Tg-Foxo3+/-rep3

description: Ovary  tissue from 14 dpn female


title: Ovary-NoTg-Foxo3-/-rep1

description: Ovary  tissue from 14 dpn female


title: Ovary-NoTg-Foxo3+/-rep3

description: Ovary  tissue from 14 dpn female


title: control mice colon rep.3

description: gene expression data in colon epitelial cells from normal mice

source_name: epithelium from colon of control mouse no.3

value: wild type


title: HDAC1/2 KO mice colon rep.3

source_name: epithelium from colon of HDAC1/2 KO mouse no.3


title: Ovary-Tg-Foxo3-/-rep2

description: Ovary  tissue from 14 dpn female


title: liver cells from wildtype 8wk male mouse 8 challenged with acetaminophen (APAP)_12

description:
Gene expression data mus musculus liver tissue
APAP_12_++


title: HDAC1/2 KO mice colon rep.2

source_name: epithelium from colon of HDAC1/2 KO mouse no.2


title: liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with acetaminophen (APAP)_3

description:
Gene expression data mus musculus liver tissue
APAP_3_null


title: liver cells from wildtype 8wk male mouse 8 challenged with vehicle (saline)_8

description:
Gene expression data mus musculus liver tissue
PBS_8_++


title: liver cells from txnrd1 liver-null 8wk male mouse 8 challenged with vehicle (saline)_5

description:
Gene expression data mus musculus liver tissue
PBS_5_null


title: Ovary-NoTg-Foxo3+/-rep1

description: Ovary  tissue from 14 dpn female


title: control mice colon rep.2

source_name: epithelium from colon of control mouse no.2


title: microRNA negative inhibitor control for 24 hours I-C

description: The total RNA of this sample was extracted from the cultured U251 cells transfected with microRNA negative inhibitor control for 24 hours.


title: PA14 PA2444 LB 7h 37C biofilm cell

city: College Station

first: Mingming

last: Pu

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from biofilm cells of PA14 PA2444 mutant after 7 hours of growth in LB with glasswool at 37ºC

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

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa PA14

source_name: P. aeruginosa PA14 PA2444 mutant

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104)

tag: strains

value: P. aeruginosa PA14 PA2444 mutant

tag: time

value: 7 hours

tag: medium

value: LB

value: biofilm cells on glasswool

tag: temp


title: PA14 wt LB 7h 37C biofilm cell

description: RNA extracted from biofilm cells of PA14 wild type after 7 hours of growth in LB with glasswool at 37ºC

source_name: P. aeruginosa PA14 wild type

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

value: P. aeruginosa PA14 wild type


title: liver cells from wildtype 8wk male mouse 8 challenged with vehicle (saline)_9

description:
Gene expression data mus musculus liver tissue
PBS_9_++

value: adult

value: male


title: control mice colon rep.1

source_name: epithelium from colon of control mouse no.1


title: Ovary-NoTg-Foxo3+/-rep2

description: Ovary  tissue from 14 dpn female


title: siRNA LMG2 treated HeLa cells 2

status: Public on Jun 07 2013

city: Berlin

first: Bruno

last: Stuhlmueller

state: Berlin

address: Charitéplatz 1

department: Rheumatology and Clinical Immunology

institute: Charité Universitiy Hospital

description: siRNA = silencing RNA

hyb_protocol: Hybridisation to Affymetrix™ GeneChip Human Genome U133 Plus 2.0 microarrays was perforemd with Biotin labelled cRNAs according to the manufacturer (Affymetrix).

scan_protocol: The microarray chips were washed and scanned at 560 nm in a Affymetrix GeneChip Scanner according to the insturctions of the manufacturer (Affymetrix).

data_processing: The data were analyzed by the Affymetrix GCOS software with default analysis settings. BioRetis database was used for the statistical analyses (www.bioretis.com).

label: Biotin

source_name: HeLa, epithelial cells, adenocarcinoma (CCL-2; American Tissue Culture Collection ATCC, Manassas, VA, USA)

label_protocol: After extraction RNA was converted to cDNA, amplified to cRNA and labelled with Biotin according to the manufacturer instruction manual (Affymetrix).

growth_protocol: HeLa cells cultured at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 10% fetal calf serum and 1% streptomycin/penicillin (Biochrome; Berlin; Germany).

extract_protocol: RNA was isolated after 48 h post transfection using the RNeasy 96 BioRobot® 8000 (Qiagen). Knockdown rates were independently measured three times by quantitative PCR using the Quantitec SYBR Green RT-PCR Kit according to Qiagen protocol. Total RNA was treated with DNAse-I (Quiagen). Quality of RNA samples was assessed by micro fluidic technology using the Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany) and the RNA 6000 Nano Assay Kit (Agilent Technologies). RNA quantity and 260/280 ratios were measured in a NanoDrop 1000 (NanoDrop Technologies, Wilmington, USA). Only RNA samples which fulfilled the criteria of RNA quality required for microarray analysis (28S/18S RNA ratio >2.2; RIN value >7) were used for labelling.

treatment_protocol: 2e4 HeLa cells/well were seeded in a 96-well plate for 20 h prior to transfection with siRNAs LMG2 and LMG4. Cells were transfected in triplicates with 1 µl of siRNA (50 nM/well).

value: siRNA LMG2


title: siRNA LMG4 treated HeLa cells 1

description: siRNA = silencing RNA

value: siRNA LMG4


title: siRNA LMG4 treated HeLa cells 2

description: siRNA = silencing RNA


title: Untreated native HeLa cells 2

description: Med = Medium

value: Untreated


title: siRNA LMG2 treated HeLa cells 1

description: siRNA = silencing RNA


title: Early Endoderm

city: Kobe

first: Cantas

last: Alev

state: Chuo-ku

address: 2-2-3 Minatojima Minamimachi

country: Japan

institute: RIKEN CDB

description: Pooled samples collected at every 4 hours over 1 day

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Gallus gallus

source_name: Early Endoderm

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix)

growth_protocol: Fertilized hens’ eggs were incubated at 38°C in a humid incubator to the desired stages.

extract_protocol: Total RNA from endodermal tissues were isolated with using Invitrogen TRIzol reagent and purified using Qiagen RNAeasy Mini-Kit. RNA concentrations were measured and equalized, and RNA quality was checked on gel. 5 ug of total RNA were used for each array.

treatment_protocol: The endoderm layer from embryos at stages HH4-5 was dissected from underlying mesenchymal cells by the use of a 27-gauge medical needle. Endodermal cells were collected from 500 embryos. The foregut endoderm (endoderm anterior to the anterior intestinal portal) samples from embryos at stages HH10-11 and the mid/hindgut endoderm (gut endoderm posterior to the presumptive small intestinal area according to the fate mapping of Matsushita, 1996) tissue samples from embryos at stages HH8-10 were isolated together with surrounding mesenchymal tissues. After treatment with 0.03 % collagenase type I in Pannett-Compton saline for 30 minutes at room temperature, endoderm tissues were separated from the surrounding mesenchyme and used for further experiments. Collected tissues were stored at -70 ˚C.

value: Early Endoderm

value: Embryonic Stage HH4-5


title: Foregut Endoderm

source_name: Foregut Endoderm

value: Foregut Endoderm

value: Embryonic Stage HH10-11


title: Sicd2-ISCL4 biol rep 2 [exon-level]

city: Los Angeles

first: Paula

middle: Elyse

last: Schauwecker

state: California

address: 1333 San Pablo Street, BMT 403

department: Cell and Neurobiology

institute: University of Southern California

hyb_protocol: Samples were hybridized with Mouse Exon 1.0 ST arrays (Affymetrix) according to standard protocols at the University of Tennessee DNA and Microarray Core Facility.

scan_protocol: Array scanning was performed according to the Affymetrix standard protocol at the University of Tennessee DNA and Microarray Core Facility.

data_processing:
Normalized microarray data were imported using the RMA algorithm.  Data analysis and statistical evaluations were performed using Partek Genomics Suite 6.6 (Missouri, USA).  We defined a probeset as present when it had a p-value <0.05 and a fold change cut-off of ±1.2.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.rs.dt1.mm9.core.mps

source_name: Sicd2-ISCL4 biol rep 2

label_protocol: Affymetrix standard protocol, University of Tennessee DNA and Microarray Core Facility

growth_protocol: Hippocampi dissected from 6-8 week old male mice

extract_protocol: Total RNA was isolated from combined hippocampi from each individual mouse using the RiboPure Kit (Ambion) according to the manufacturer's instructions.

value: 6-8 week old

value: hippocampus


title: FVB-like littermate biol rep 5 [exon-level]

source_name: FVB-like littermate biol rep 5


title: Sicd2-ISCL4 biol rep 4 [exon-level]

source_name: Sicd2-ISCL4 biol rep 4


title: Untreated native HeLa cells 1

description: Med = Medium


title: Sicd2-ISCL4 biol rep 5 [exon-level]

source_name: Sicd2-ISCL4 biol rep 5


title: Sicd2-ISCL4 biol rep 7 [exon-level]

source_name: Sicd2-ISCL4 biol rep 7


title: Control - #1731 - hippocampus CA3 - Female - 74yr

city: Seattle

first: Jeremy

last: Miller

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with normalize.quantiles() in R

source_name: hippocampus - CA3

label_protocol: Biotinylated cRNA were prepared by the Southern California Genotyping Consortium (www.semel.ucla.edu/core/scgc), using their standard procedure.

extract_protocol: Using a scalpel CA1 and CA3 subfields were dissected from sectioned but unlabeled tissue on dry ice and immediately placed into elution buffer for RNA extraction.  Total RNA from each sample was isolated using the RNeasy Micro Kit with DNase I treatment (QIAGEN; Valencia, CA), then tested for quality on the Agilent 2100 Bioanalyzer using RNA 6000 Nano Chips (Agilent Technologies; Palo Alto, CA).  This extraction followed the protocols provided by the manufacturers.

tag: subjectnumber

tag: regioninhippocampus

value: Female

tag: age(years)

tag: postmorteminterval(hours)

tag: apoegenotype(alleles)

tag: diseaseduration(years)

tag: brainbank

value: OHSU

tag: chipnumber(batch)

tag: locationonchip

value: K


title: FVB-like littermate biol rep 4 [exon-level]

source_name: FVB-like littermate biol rep 4

tag: tissue


title: FVB-like littermate biol rep 8 [exon-level]

source_name: FVB-like littermate biol rep 8

tag: age


title: FVB-like littermate biol rep 6 [exon-level]

source_name: FVB-like littermate biol rep 6


title: Sicd2-ISCL4 biol rep 1 [exon-level]

source_name: Sicd2-ISCL4 biol rep 1


title: AD - #4098 - hippocampus CA1 - Female - 68yr

source_name: hippocampus - CA1

value: VA

value: L


title: Sicd2-ISCL4 biol rep 3 [exon-level]

source_name: Sicd2-ISCL4 biol rep 3


title: AD - #4125 - hippocampus CA3 - Female - 61yr

value: I


title: FVB-like littermate biol rep 7 [exon-level]

source_name: FVB-like littermate biol rep 7


title: Sicd2-ISCL4 biol rep 6 [exon-level]

source_name: Sicd2-ISCL4 biol rep 6


title: FVB-like littermate biol rep 3 [exon-level]

source_name: FVB-like littermate biol rep 3


title: Sicd2-ISCL4 biol rep 8 [exon-level]

source_name: Sicd2-ISCL4 biol rep 8


title: FVB-like littermate biol rep 2 [exon-level]

source_name: FVB-like littermate biol rep 2


title: FVB-like littermate biol rep 1 [exon-level]

source_name: FVB-like littermate biol rep 1


title: Control - #3777 - hippocampus CA3 - Male - 84yr

value: Male

value: J


title: Control - #3740 - hippocampus CA3 - Female - 88yr

value: A


title: AD - #4152 - hippocampus CA3 - Female - 74yr

value: G


title: Control - #1064 - hippocampus CA3 - Female - 83yr

value: F


title: AD - #4098 - hippocampus CA3 - Female - 68yr

value: H


title: AD - #1380 - hippocampus CA3 - Female - 84yr


title: AD - #1440 - hippocampus CA1 - Male - 72yr

value: C


title: AD - #4152 - hippocampus CA1 - Female - 74yr


title: Control - #3912 - hippocampus CA3 - Male - 80yr

value: B


title: Control - #1716 - hippocampus CA1 - Male - 90yr

value: E


title: Control - #1385 - hippocampus CA1 - Male - 81yr


title: Control - #1761 - hippocampus CA3 - Male - 86yr


title: Control - #588 - hippocampus CA3 - Male - 85yr


title: AD - #926 - hippocampus CA1 - Female - 79yr

value: D


title: Control - #1376 - hippocampus CA3 - Male - 85yr


title: AD - #827 - hippocampus CA3 - Male - 90yr


title: AD - #926 - hippocampus CA3 - Female - 79yr


title: AD - #4155 - hippocampus CA1 - Female - 79yr


title: AD - #1388 - hippocampus CA3 - Male - 67yr


title: Ovary-Tg-Foxo3+/-rep2

description: Ovary  tissue from 14 dpn female

tag: strain

value: FVB/N

value: ovary

tag: developmental stage

value: 14 dpn


title: Ovary-Tg-Foxo3-/-rep1

description: Ovary  tissue from 14 dpn female

tag: gender

value: Female


title: Control - #862 - hippocampus CA1 - Male - 75yr

value: OHSU


title: AD - #1167 - hippocampus CA1 - Male - 68yr


title: AD - #827 - hippocampus CA1 - Male - 90yr


title: AD - #704 - hippocampus CA3 - Male - 81yr


title: Control - #3912 - hippocampus CA1 - Male - 80yr

value: VA


title: the gacA mutant_cell_28℃_rep3

city: Shanghai

first: xianqing

last: Huang

address: 800 Dong chuan RD

institute: Shanghai Jiao Tong University

description: gene expression of the gacA mutant

hyb_protocol: Each Slide was hybridized with 875 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US)Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit( Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent technologies, Santa Clara, CA, US) using default parameters.

organism: Pseudomonas aeruginosa M18

source_name: the gacA mutant, Cells, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the  Low RNA Input Linear Amplification  kit (Agilent technologies, Santa Clara, CA, US) according to the manufacturer's instructions,and purified by RNeasy mini kit ( QIAGEN, GmBH, Germany).

growth_protocol: For microarray analysis, the fresh overnight cultures of P. aeruginosa M18 and its gacA mutant were inoculated, at a final concentration with an OD600 of 0.05, into the 500-ml Erlenmeyer flasks containing 100 ml KMB, and then grown at 28°C with shaking at 200 rpm. After 22 hours of incubation, cells were harvested in the early stationary phase with an OD600 of 5.08 for M18 and 5.29 for the gacA mutant.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen,Carlsbad, CA, USA).

tag: genotype

value: the gacA mutation


title: the gacA mutant_cell_28℃_rep2

description: gene expression of the gacA mutant

source_name: the gacA mutant, Cells, replicate 2


title: 8 wk CD-1 mice estrus uterus /8 wk CD-1 mice proestrus uterus /Replicates#1 and #2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Estrus/Proestrus_reps1and2
dyeswap
12-02-2010_252665510407_S01_GE2_107_Sep09_1_4.txt: Alexa647_estrus; Alexa555_proestrus
12-02-2010_252665510408_S01_GE2_107_Sep09_1_4.txt: Alexa647_proestrus; Alexa555_estrus
Each RNA sample was a pool of RNA extracted from uterine horns of 4-6 individual mice.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 10.7.1.1, protocol GE2_107_Sep09).

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)

label: Alexa 555, Alexa 647

source_name: CD-1 mouse uterus in estrus

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA

value: 8 wk

tag: estrus cycle stage

value: estrus

value: uterine horns

source_name: CD-1 mouse uterus in proestrus

value: proestrus


title: Mouse uterus lumenal epithelial cells at estrus/Mouse uterus lumenal epithelial cells at proestrus

description:
Each RNA sample was a pool of RNA extracted from lumenal epithelium of uterine horns of 4-5 individual mice.
This Sample represents 2 replicates.
252665512551_201204250724_S01_GE2_1100_Jul11_1_1.txt: Alexa 555=estrus, Alexa 647=proestrus.
252665512551_201204250724_S01_GE2_1100_Jul11_1_2.txt: Alexa 555=proestrus, Alexa 647=estrus.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent's SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent's SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent's Feature Extraction software (version 10.7.1.1, protocol GE2_107_Sep09).

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1).

source_name: CD-1 mouse uterine lumenal epithelial cells at estrus

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor's protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA.

tag: strain/background

tag: Sex

value: female

value: lumenal epithelium of uterine horn

label: Alexa 647, Alexa 555

source_name: CD-1 mouse uterine lumenal epithelial cells at proestrus


title: the gacA mutant_cell_28℃_rep1

description: gene expression of the gacA mutant

source_name: the gacA mutant, Cells, replicate 1


title: Control - #1013 - hippocampus CA1 - Male - 90yr

tag: subjectnumber

tag: regioninhippocampus

value: Male

value: C


title: WT_cell_rep1

description: gene expression of WT

source_name: Wild-type, Cells,replicate 1

value: wild-type


title: WT_cell_rep2

description: gene expression of WT

source_name: Wild-type, Cells,replicate 2


title: Control - #3777 - hippocampus CA1 - Male - 84yr

source_name: hippocampus - CA1

tag: age(years)

tag: postmorteminterval(hours)

value: G


title: Mid/hindgut Endoderm

source_name: Mid/hindgut Endoderm

value: Mid/hindgut Endoderm

value: Embryonic Stage HH8-10


title: AD - #1673 - hippocampus CA3 - Male - 81yr

source_name: hippocampus - CA3

tag: apoegenotype(alleles)

tag: diseaseduration(years)

value: L


title: Control - #962 - hippocampus CA1 - Female - 70yr

value: Female

tag: brainbank

tag: chipnumber(batch)

value: B


title: AD - #1673 - hippocampus CA1 - Male - 81yr

value: OHSU

tag: locationonchip

value: A


title: Control - #3795 - hippocampus CA3 - Female - 72yr

value: VA

value: K


title: Control - #881 - hippocampus CA3 - Male - 90yr

value: J


title: med15/16, rep 2

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

description: Gene expression data from med5/16 degron strain

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on Affymetrix Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with robust multi-array average (RMA) algorithm using default settings.

organism: Saccharomyces cerevisiae

source_name: Med15/16 double degron

label_protocol: One-Cycle Target Labeling kit (Affymetrix)

growth_protocol: All strains were grown in YPRCu at 24C to approximately 1x10 7 cells/ml. The media was switched to YPGalactose and growth was continued at 24C for 35 minutes. The cells were transferred to pre-warmed YPGalactose (37C) and growth was continued at 37C for 45 minutes before harvesting

extract_protocol: RNeasy Mini kit (Qiagen), with on-column Dnase digestion

value: Med15/16 double degron


title: med5/15, rep 2

description: Gene expression data from med5/15 degron strain

source_name: Med5/15 double degron

value: Med5/15 double degron


title: Spinal cord, affected individuals vs. control individuals, rep2

city: Viterbo

first: Alessio

last: Valentini

address: via San Camillo de Lellis

department: IBAF

country: Italy

institute: University of Tuscia

description: Sample a2b2

hyb_protocol: Pooled cDNA probes of 4 control and 4 affected animals were hybridised onto bovine cDNA slides according to Genisphere’s instructions. Hybridization was performed at 60°C for 16 hours in a hybridization oven with shaking. Upon hybridization, microarrays were washed and dried according to Genisphere's instructions.

scan_protocol: Images and fluorescence measurements were obtained using a ScanArray Lite (Perkin Elmer) laser scanner and Spotfinder software (TIGR).

data_processing:
cDNA spots were automatically segmented, total foreground and background intensities of the two dyes were calculated for each spot. The spots were flagged by the software when they exhibited poor hybridization signals or when they were saturated. Spots with signal to background ratio below 1.5 were filtered, together with flagged spots. Systematic bias in the data was removed by applying the dye-swap normalization (Fang et al. 2003) that makes use of the reverse labelling in the two microarray replicates and the lowess normalization (Yang et al. 2001). For one half of the slides the local spot background signal was not subtracted from the foreground signal, since the correlation between the log-ratio calculated for the foreground intensities (M) and the log-ratio calculated for the background intensities (Mb) was very low (below 0.3), as recently suggested by Scharpf and coauthors (Scharpf et al. 2006); for the other half, the local spot background signal was subtracted from the foreground signal. To establish the significance of observed regulation for each gene, t-test, correcting p.values for multiple tests (Benjamini and Hochberg 1995), was used. Finally, only genes with a satisfactory effect (absolute value of the fold change at least 2.0 and a P value < 0.05) were considered. Lowess normalization was performed using a built-in script in R.

GSM621137_a2.mev.gz: Control sample labeled with Cy5, affected sample labeled with Cy3.
GSM621137_b2.mev.gz: Control sample labeled with Cy3, affected sample labeled with Cy5.

organism: Bos taurus

source_name: Spinal cord, affected individuals

label_protocol: Fluorescently-labeled cRNA was prepared using the 3DNA Array 900 MPX Cy3/Cy5 Kit (Genisphere) according to the manufacturer's protocol. In short, 2 μg of total RNA was reverse transcribed using T7 tagged oligo-dT primer and labeled with Cy3 or Cy5.

extract_protocol: Total RNA was extracted from 250 µg spinal cord tissue samples by homogenization in QIAzol Lysis Reagent (Qiagen) and mixed with chloroform. The lysate was centrifuged at 12000 × g for 15 minutes at 4°C, and the aqueous phase was transferred to be mixed with isopropanol, which precipitates total RNA. After centrifugation (10 minutes, 12000 xg at 4°C), the pellet was washed with 75% ethanol and resuspended in RNase free water. Upon extraction, the RNA was purified according to the RNeasy Lipid kit (Qiagen) protocol.

treatment_protocol: Samples of spinal cord from 4 affected and 4 control individuals of the Romagnola breed were collected immediately after slaughtering and later stored in RNA (Sigma-Aldrich). The experimental work was approved by the Animal Ethics Committee of CRA, Italy, in accordance with local ethical requirements.

tag: breed

value: Romagnola

tag: tissue

value: spinal cord

tag: disease state

value: bovine spastic paresis

source_name: Spinal cord, control individuals

value: control


title: med15/16, rep 1

tag: strain


title: Spinal cord, affected individuals vs. control individuals, rep1

description: Sample ab

data_processing:
cDNA spots were automatically segmented, total foreground and background intensities of the two dyes were calculated for each spot. The spots were flagged by the software when they exhibited poor hybridization signals or when they were saturated. Spots with signal to background ratio below 1.5 were filtered, together with flagged spots. Systematic bias in the data was removed by applying the dye-swap normalization (Fang et al. 2003) that makes use of the reverse labelling in the two microarray replicates and the lowess normalization (Yang et al. 2001). For one half of the slides the local spot background signal was not subtracted from the foreground signal, since the correlation between the log-ratio calculated for the foreground intensities (M) and the log-ratio calculated for the background intensities (Mb) was very low (below 0.3), as recently suggested by Scharpf and coauthors (Scharpf et al. 2006); for the other half, the local spot background signal was subtracted from the foreground signal. To establish the significance of observed regulation for each gene, t-test, correcting p.values for multiple tests (Benjamini and Hochberg 1995), was used. Finally, only genes with a satisfactory effect (absolute value of the fold change at least 2.0 and a P value < 0.05) were considered. Lowess normalization was performed using a built-in script in R.

GSM621136_a.mev.gz: Control sample labeled with Cy5, affected sample labeled with Cy3.
GSM621136_b.mev.gz: Control sample labeled with Cy3, affected sample labeled with Cy5.


title: med5/15, rep 1


title: AD - #1380 - hippocampus CA1 - Female - 84yr

tag: gender

value: I


title: med15, rep 2

description: Gene expression data from med15 degron strain

source_name: Med15 degron

value: Med15 degron


title: AD - #1294 - hippocampus CA1 - Female - 90yr

value: C


title: WT_cell_rep3

description: gene expression of WT

source_name: Wild-type, Cells,replicate 3

tag: genotype

value: wild-type


title: AD - #4159 - hippocampus CA1 - Female - 80yr

value: Female

value: E


title: med16, rep 1

description: Gene expression data from med16 degron strain

source_name: Med16 degron

value: Med16 degron


title: med15, rep 1


title: med5, rep 2

description: Gene expression data from med5 degron strain

source_name: Med5 degron

value: Med5 degron


title: Control - #1720 - hippocampus CA3 - Male - 73yr

value: Male

value: OHSU


title: IPS_MR90C2_P6_Rep3

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

institute: University of Queensland

hyb_protocol: llumina Human 6 BeadChips (V3) were hybridized, washed, stained and scanned according to Illuminas protocol

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were first extracted with Illumina BeadStudio software without normalisation.  Data was then uploaded into R, where RMA background adjustment and Quantile normalisation was performed using the BeadExplorer package

source_name: Induced Pluripotent Cells

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: RNA samples were prepared using Qiagen RNeasy Micro Kit (Qiagen) and then assayed using the Agilent Systems Bioanalyzer 2100 to ensure that high-quality RNA was used for the array experiments.

tag: cell type

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 med CD9 med (P6)


title: med16, rep 2


title: IPS_MR90C2_P4_Rep3

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 neg CD9 neg (P4)


title: AD - #4155 - hippocampus CA3 - Female - 79yr

value: VA

value: B


title: Control - #588 - hippocampus CA1 - Male - 85yr

value: A


title: med5, rep 1


title: IPS_MR90C2_P5_Rep3

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 low CD9 low (P5)


title: Control - #862 - hippocampus CA3 - Male - 75yr

value: G


title: AD - #993 - hippocampus CA1 - Male - 83yr

value: H


title: KYN2-HSF1 KD1

city: Sapporo

first: Makoto

last: Chuma

address: Kita 15, Nishi 7, Kita-ku,

department: Gastroenterology and Hepatology

institute: Hokkaido University

description: SAMPLE 2

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

source_name: HSF1 KD-HCC

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: A HSF1 small hairpin RNA (shRNA) plasmid were purchased from SABiosciences (QIAGEN, Valencia CA). The shRNA sequences targeting HSF1 were from position 5'-CAGGTTGTTCATAGTCAGAAT-3' as in the nucleotide sequence of HSF1. Transfection was achieved using Oligofectamine reagent (Invitrogen) according to the instructions from the manufacturer. To establish stable knockdown cell lines, shRNA plasmids were transfected into KYN2 cells, and cultured in the presence of puromycin (Sigma-Aldrich, St. Louis, MO).

value: liver

tag: cell line

value: hepatocellular carcinoma (HCC) cells

tag: genotype/variation

value: HSF1 knockdown


title: Control - #1720 - hippocampus CA1 - Male - 73yr

tag: subjectnumber

tag: regioninhippocampus

value: I


title: KYN2-HSF1 control1

description: SAMPLE 1

value: control


title: IPS_MR90C2_P7_Rep3

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 high CD9 high (P7)


title: Control - #962 - hippocampus CA3 - Female - 70yr

value: Female

tag: age(years)

tag: postmorteminterval(hours)

value: L


title: Wild-type, rep 1

description: Gene expression data from wild-type yeast strain

source_name: Wild-type

value: Wild-type


title: Wild-type, rep 2


title: AD - #1294 - hippocampus CA3 - Female - 90yr

tag: apoegenotype(alleles)

tag: diseaseduration(years)

value: OHSU

value: E


title: Control - #1731 - hippocampus CA1 - Female - 74yr

tag: brainbank

tag: chipnumber(batch)

value: F


title: IPS_MR90C2_P6_Rep2

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 med CD9 med (P6)


title: Control - #1064 - hippocampus CA1 - Female - 83yr

tag: locationonchip


title: IPS_MR90C2_P4_Rep1

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 neg CD9 neg (P4)


title: MC3T3-E1 LIPUS-6 h 2

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: MC3T3-E1 LIPUS + 6h culture at 37˚C-2

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite. RMA normalized.

source_name: Mouse preosteoblast MC3T3-E1cells

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: LIPUS treatment was applied by a sonic accelerated gracture-healing system (SAFHS) apparatus (SAFHS 4000J, Teijin Pharma Ltd., Tokyo, Japan). The signal had the SATA (spatial average, temporal average) intensity of 30 mW/cm2, with a frequency of 1.5 MHz in a pulsed-wave mode (0.2 s-burst sine waves repeated at 1.0 kHz). The cells were cultivated in MEMα supplemented with 10% FBS, 0.3 mM L-ascorbic acid and 10 mM β-glycerophosphate at 37˚C for 14 days. After trypsinization, the cells (5 x 105 cells) were seeded on 35-mm plastic culture dish (ASAHI GLASS Co., Ltd., Tokyo, Japan) and cultured at 37˚C for 24 h. LIPUS was transmitted through the bottom of the culture dish with standard ultrasound coupling gel (Teijin Pharma Ltd.). Attached cells in the dish with 2 ml of culture medium were sonicated for 20 min at 37˚C in a CO2 incubator. After sonication, cells were incubated at 37˚C in a CO2 incubator for 6 and 24 h. Mock-treated cells were served as control.

tag: age

value: 0-day-old newborn

tag: tissue

value: calvaria

tag: treatment

value: LIPUS + 6h culture at 37˚C

value: fibroblast-like

tag: time

value: 6 h


title: IPS_MR90C2_P5_Rep2

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 low CD9 low (P5)


title: IPS_MR90C2_P6_Rep1


title: IPS_MR90C2_P7_Rep2


title: MC3T3-E1 LIPUS-6 h 3

description: MC3T3-E1 LIPUS + 6h culture at 37˚C-3

tag: strain


title: AD - #1167 - hippocampus CA3 - Male - 68yr

tag: gender

value: Male

value: C


title: IPS_MR90C2_P4_Rep2

tag: cell type


title: IPS_MR90C2_P5_Rep1


title: Control - #881 - hippocampus CA1 - Male - 90yr

value: D


title: IPS_MR90C2_P7_Rep1

value: IPS_iMR90_C2 (derived from lung Fibroblast) IPS cells GCTM-2 high CD9 high (P7)


title: Bo3

city: Baltimore

first: Scott

last: Kominsky

state: MD

address: 720 Rutland Ave, Ross 209

institute: Johns Hopkins University School of Medicine

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Data in the matrix table below were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method.  The nonparametric hypothesis-based analysis of microarrays approach of Kowalski et al., Bioinformatics, 2004 was applied, designed to address analyses of several groups based on as few as a single sample per group. This approach was applied to (quantile) normalized, within each sample type, log2 transformed expression data using the RMA approach of Irizarry et al., Biostatistics, 2003 to obtain candidate overexpressed genes.  The complete set of log2 RMA normalized data were not supplied by the submitter.

source_name: NT2.5 bone sub-line, 3rd passage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

extract_protocol: RNeasy RNA purification kit  (Qiagen) was used according to the manufacturer's instructions.

value: NT2.5 bone sub-line, 3rd passage

tag: metastatic site preference

value: bone


title: Li3

source_name: NT2.5 liver sub-line, 3rd passage

value: NT2.5 liver sub-line, 3rd passage

value: liver


title: MC3T3-E1 LIPUS-6 h 1

description: MC3T3-E1 LIPUS + 6h culture at 37˚C-1

tag: cell line


title: AD - #1580 - hippocampus CA3 - Male - 90yr

tag: subjectnumber

tag: regioninhippocampus

value: OHSU

value: B


title: AD - #1440 - hippocampus CA3 - Male - 72yr

tag: age(years)

tag: postmorteminterval(hours)

value: K


title: AD - #1388 - hippocampus CA1 - Male - 67yr

source_name: hippocampus - CA1

tag: apoegenotype(alleles)

tag: diseaseduration(years)

value: A


title: WT

source_name: Wild type NT2.5

value: Wild type NT2.5

value: bone, liver, lung


title: Li1

source_name: NT2.5 liver sub-line, 1st passage

value: NT2.5 liver sub-line, 1st passage


title: Control - #1376 - hippocampus CA1 - Male - 85yr

tag: brainbank

tag: chipnumber(batch)

value: F


title: IPS_ES4CL1_P6_rep3

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 med CD9 med (P6)


title: AD - #4125 - hippocampus CA1 - Female - 61yr

value: Female

value: VA

tag: locationonchip

value: J


title: IPS_ES4CL1_P5_rep3

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 low CD9 low (P5)


title: AD - #4147 - hippocampus CA1 - Male - 66yr

value: Male

value: L


title: Atria, Control, biological replicate 2

city: Houston

first: San-pin

last: Wu

address: 1 Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Hybridization cocktails containing Affymetrix spike-in controls and 15.0ug of each fragmented, labeled cRNA were loaded onto Affymetrix GeneChip® Mouse 430 2.0 arrays.  The arrays were hybridized for 16 hours at 45°C with rotation at 60 rpm in the Affymetrix GeneChip® Hybridization Oven 640. The arrays were washed and stained with a streptavidin, R-phycoerythrin conjugate stain using the Affymetrix GeneChip® Fluidics Station 450 using fluidics protocol FS450_0001. Signal amplification was done using biotinylated antistreptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with GeneSpring 12.5 GX using default analysis settings with RMA as the summerization algorithm.

source_name: Control right atria

label_protocol: Samples were labeled using the standard Affymetrix linear amplification protocol using the 3’ IVT Express Kit.  250 ng of total RNA was reverse transcribed to produce double-stranded cDNA.  The cDNA product was used as a template for the vitro transcription reaction, producing biotin-labeled cRNA. The labeled cRNA was tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDrop® ND-1000 spectrophotometer.  15.0 µg of the labeled cRNA was fragmented and re-checked for concentration and size.

extract_protocol: Trizol extraction followed by Qiagen RNeasy purification

tag: tissue

value: atria

tag: genotype

value: COUP-TFIIflox/flox

tag: age

value: 2 months

tag: genetic background


title: Control - #1013 - hippocampus CA3 - Male - 90yr

source_name: hippocampus - CA3

tag: gender

value: OHSU

value: G


title: IPS_ES4CL1_P7_rep3

tag: cell type

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 high CD9 high (P7)


title: Bo6

source_name: NT2.5 bone sub-line, 6th passage

value: NT2.5 bone sub-line, 6th passage

tag: metastatic site preference

value: bone


title: Ventricles, Control, biological replicate 2

source_name: Control ventricles

value: ventricles


title: IPS_ES4CL1_P7_rep2


title: Ventricles, Control, biological replicate 3


title: IPS_ES4CL1_P4_rep2

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 neg CD9 neg (P4)


title: IPS_ES4CL1_P6_rep1

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 med CD9 med (P6)


title: Sicd2-ISCL4 biol rep 7 [gene-level]

source_name: Sicd2-ISCL4 biol rep 7

value: male

value: 6-8 week old

value: hippocampus


title: Sicd2-ISCL4 biol rep 8 [gene-level]

source_name: Sicd2-ISCL4 biol rep 8


title: Control - #1385 - hippocampus CA3 - Male - 81yr

value: B


title: IPS_ES4CL1_P5_rep2

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 low CD9 low (P5)


title: IPS_ES4CL1_P6_rep2


title: Atria, Mutant, biological replicate 1

source_name: Mutant right atria

value: Myh6-cre; COUP-TFIIflox/flox


title: IPS_ES4CL1_P5_rep1


title: AD - #4147 - hippocampus CA3 - Male - 66yr

value: Male

value: VA

value: A


title: Atria, Mutant, biological replicate 3

value: atria

value: 2 months


title: IPS_ES4CL1_P4_rep3


title: Control - #1716 - hippocampus CA3 - Male - 90yr

value: OHSU

value: I


title: Ventricles, Control, biological replicate 1

value: COUP-TFIIflox/flox


title: Atria, Control, biological replicate 1


title: IPS_ES4CL1_P7_rep1

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 high CD9 high (P7)


title: IPS_ES4CL1_P4_rep1

value: IPS_foreskin_CL1 (derived from foreskin) IPS cells GCTM-2 neg CD9 neg (P4)


title: Control - #3795 - hippocampus CA1 - Female - 72yr

value: Female

value: C


title: Atria, Mutant, biological replicate 2


title: Andrey_FL_E10_d(8-13)d(a-S3)_K27m3

type: genomic

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

description: Chromatin immuno-precipitated with antibody against H3K27me3

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
We used input gDNA for ChIP hybridisation to quantile normalized as in (Montavon et al., 2011). We scaled it to medial feature of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of PM-MM pairs within a sliding window of 250 bp. The average ratios were plotted along the genomic DNA sequence in UCSC. Raw files are in mm8.
bedGraph files of normalized signals (ploted in mm9)

molecule: genomic DNA

source_name: Early forelimb buds E10.5

label_protocol: standard Affymetrix protocol

treatment_protocol: Early forelimb buds, presumptive digits and proximal segments of E12.5 forelimbs were micro-dissected from mouse embryos, fixed in 1% formaldehyde for 15 minutes at room temperature, washed three times with 4°C PBS and stored at -80°C. Pools of 40 early forelimbs (E9.5), 10 limb buds (10.5), 10 autopods or 10 Proximal forelimbs were used for each experiment. ChIP was performed according to (Lee et al., 2006), using 2 μg of anti-H3K4me3 (07-436, Millipore), H3K27me3 (17-622, Millipore) and EZview Red protein G/A Affinity Gel (Sigma). Immuno-precipitated and whole cell extract DNA (input) were de-crosslinked at 65°C overnight, treated with RNAseA, proteinase K and purified by phenol/chloroform extraction. ChIP and input DNA were amplified using ligation-mediated PCR (Lee et al., 2006), fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) and hybridized to custom tiling arrays (Affymetrix). For each sample, two independent ChIP-chip experiments were performed, with all antibodies.

tag: strain

value: Forelimb buds

tag: Stage

tag: chip antibody

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #

source_name: control

value: input


title: Andrey_FL_E10_d(8-13)_K27m3

extract_protocol: Immuno-precipitated and whole cell extract DNA (input) were de-crosslinked at 65°C overnight, treated with RNAseA, proteinase K and purified by phenol/chloroform extraction.


title: Control - #3740 - hippocampus CA1 - Female - 88yr

tag: subjectnumber

tag: regioninhippocampus

tag: age(years)

tag: postmorteminterval(hours)

tag: apoegenotype(alleles)

value: H


title: Control - #1761 - hippocampus CA1 - Male - 86yr

tag: diseaseduration(years)

tag: brainbank

tag: chipnumber(batch)

tag: locationonchip

value: E


title: Andrey_DFL_E12_WT_K27m3

source_name: Digits E12.5

tag: tissue

value: Digits

tag: genotype

value: wild type


title: Sicd2-ISCL4 biol rep 5 [gene-level]

source_name: Sicd2-ISCL4 biol rep 5

tag: gender

value: male

tag: age

value: 6-8 week old

value: hippocampus


title: Andrey_DFL_E12_del(Nsi-Atf2)hom_K27m3

tag: strain

tag: Stage


title: Sicd2-ISCL4 biol rep 6 [gene-level]

source_name: Sicd2-ISCL4 biol rep 6


title: Sicd2-ISCL4 biol rep 3 [gene-level]

source_name: Sicd2-ISCL4 biol rep 3


title: Andrey_FL_E10_WT_K4m3

description: Chromatin immuno-precipitated with antibody against H3K4me3

tag: chip antibody

tag: chip antibody manufacturer


title: Sicd2-ISCL4 biol rep 4 [gene-level]

source_name: Sicd2-ISCL4 biol rep 4


title: Andrey_FL_E9_WT_K4m3

source_name: Early forelimb buds E9.5

tag: chip antibody catalog #


title: Andrey_PFL_E12_WT_K27m3

source_name: Proximal Forelimbs E12.5

value: Proximal Forelimbs


title: Andrey_FL_E10_WT_K27m3


title: Andrey_FL_E9_WT_K27m3


title: Atria, Control, biological replicate 3

value: atria

value: 2 months

tag: genetic background


title: AD - #704 - hippocampus CA1 - Male - 81yr

source_name: hippocampus - CA1

tag: subjectnumber

tag: regioninhippocampus

value: Male

tag: age(years)

value: OHSU

value: F


title: Andrey_PFL_E12_WT_K4m3


title: Sicd2-ISCL4 biol rep 2 [gene-level]

source_name: Sicd2-ISCL4 biol rep 2


title: Sicd2-ISCL4 biol rep 1 [gene-level]

source_name: Sicd2-ISCL4 biol rep 1


title: FVB-like littermate biol rep 7 [gene-level]

source_name: FVB-like littermate biol rep 7


title: FVB-like littermate biol rep 4 [gene-level]

source_name: FVB-like littermate biol rep 4


title: FVB-like littermate biol rep 3 [gene-level]

source_name: FVB-like littermate biol rep 3


title: FVB-like littermate biol rep 8 [gene-level]

source_name: FVB-like littermate biol rep 8


title: FVB-like littermate biol rep 1 [gene-level]

source_name: FVB-like littermate biol rep 1


title: FVB-like littermate biol rep 6 [gene-level]

source_name: FVB-like littermate biol rep 6


title: FVB-like littermate biol rep 5 [gene-level]

source_name: FVB-like littermate biol rep 5


title: control early stationary vs. iron limiting early stationary Ratio 4-DF0_STAT_block3 and 4-DF30_STAT_block3

status: Public on Jun 06 2013

city: Nijmegen

first: Hester

last: Bootsma

address: Kapittelweg 29

department: Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

hyb_protocol: 2 µg of labeled cDNA was applied in duplicate to 4x72K custom design NimbleGen GAF arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

scan_protocol: Array images were acquired with a NimbleGen MS200 scanner following their standard operation protocol, using the autogain function per subarray.

data_processing: ANAIS (Simon and Biot, 2010, Bioinformatics 26;2468-2469) was used for intra-array (background adjustment) and inter-array (quantile) normalization to obtain normalized probe signal intensities (SI), three replicate spots per array (designated block1-3). Normalized probe SI were corrected for a threshold of five times the median SI of the negative-control probes. Statistical analysis was performed on the ratio between the SI of the control and challenge (iron-limiting) conditions using the CyberT implementation of Student’s t-test (cybert.microarray.ics.uci.edu). The false discovery rate (FDR) was calculated from the Bayesian p-value as described in (van Hijum et al., 2005, BMC Genomics 6; 77).

organism: Moraxella catarrhalis BBH18

source_name: Control DF0, early-stationary phase, biological replicate 4, replicate spot 3

label_protocol: Chromosomal DNA was digested with AluI restriction enzyme and purified using the MinElute reaction clean-up kit (Qiagen). 2 µg digested DNA served as a template for a T7 RNA polymerase reaction (MegaScript, Ambion) using the outward-facing T7 sites of the transposon element. The template DNA was degraded with DNase I and the T7 RNA was purified using the RNeasy Minelute kit (Qiagen). 2 µg T7 RNA was reverse transcribed into cDNA in the presence of 16.7 ng µl-1 actinomycin D (Sigma Aldrich) using 1 µg Cy3-labeled random nonamers (Nimblegen) for priming.

growth_protocol: Mutant library was pre-culture to mid-log, washed, and resuspended in PBS-gelatin

extract_protocol: Mutants were recovered at the mid-log and early-stationary phase. The recovered mutants were expanded for chromosomal DNA isolation using Genomic-tip 20/G columns.

treatment_protocol: Growth of the mutant library under control condition (DF0), sample taken at early-stationary phase

tag: transposon element

value: marinerT7 mutant library

tag: antibiotic resistance

value: spectinomycin resistance

tag: genbank

tag: treatment

value: control

tag: growth phase

value: early stationary

source_name: iron limiting DF30, early-stationary phase, biological replicate 4, replicate spot 3

treatment_protocol: Growth of the mutant library under iron limiting (DF30), sample taken at early-stationary phase

value: iron limiting


title: control early stationary vs. iron limiting early stationary Ratio 4-DF0_STAT_block2 and 4-DF30_STAT_block2

source_name: Control DF0, early-stationary phase, biological replicate 4, replicate spot 2

source_name: iron limiting DF30, early-stationary phase, biological replicate 4, replicate spot 2


title: control early stationary vs. iron limiting early stationary Ratio 4-DF0_STAT_block1 and 4-DF30_STAT_block1

source_name: Control DF0, early-stationary phase, biological replicate 4, replicate spot 1

source_name: iron limiting DF30, early-stationary phase, biological replicate 4, replicate spot 1


title: control early stationary vs. iron limiting early stationary Ratio 1-DF0_STAT_block3 and 1-DF30_STAT_block3

source_name: Control DF0, early-stationary phase, biological replicate 1, replicate spot 3

source_name: iron limiting DF30, early-stationary phase, biological replicate 1, replicate spot 3


title: control early stationary vs. iron limiting early stationary Ratio 1-DF0_STAT_block2 and 1-DF30_STAT_block2

source_name: Control DF0, early-stationary phase, biological replicate 1, replicate spot 2

source_name: iron limiting DF30, early-stationary phase, biological replicate 1, replicate spot 2


title: control exponential vs. iron limiting exponential Ratio 4-DF0_EXP_block1 and 4-DF30_EXP_block1

source_name: Control DF0, exponential phase, biological replicate 4, replicate spot 1

treatment_protocol: Growth of the mutant library under control condition (DF0), sample taken at exponential phase

value: exponential

source_name: iron limiting DF30, exponential phase, biological replicate 4, replicate spot 1

treatment_protocol: Growth of the mutant library under iron limiting (DF30), sample taken at exponential phase


title: control early stationary vs. iron limiting early stationary Ratio 2-DF0_STAT_block2 and 2-DF30_STAT_block2

source_name: Control DF0, early-stationary phase, biological replicate 2, replicate spot 2

source_name: iron limiting DF30, early-stationary phase, biological replicate 2, replicate spot 2


title: control early stationary vs. iron limiting early stationary Ratio 3-DF0_STAT_block1 and 3-DF30_STAT_block1

source_name: Control DF0, early-stationary phase, biological replicate 3, replicate spot 1

source_name: iron limiting DF30, early-stationary phase, biological replicate 3, replicate spot 1


title: control early stationary vs. iron limiting early stationary Ratio 3-DF0_STAT_block3 and 3-DF30_STAT_block3

source_name: Control DF0, early-stationary phase, biological replicate 3, replicate spot 3

source_name: iron limiting DF30, early-stationary phase, biological replicate 3, replicate spot 3


title: FVB-like littermate biol rep 2 [gene-level]

source_name: FVB-like littermate biol rep 2

tag: tissue


title: control exponential vs. iron limiting exponential Ratio 4-DF0_EXP_block2 and 4-DF30_EXP_block2

source_name: Control DF0, exponential phase, biological replicate 4, replicate spot 2

source_name: iron limiting DF30, exponential phase, biological replicate 4, replicate spot 2


title: control early stationary vs. iron limiting early stationary Ratio 2-DF0_STAT_block1 and 2-DF30_STAT_block1

source_name: Control DF0, early-stationary phase, biological replicate 2, replicate spot 1

source_name: iron limiting DF30, early-stationary phase, biological replicate 2, replicate spot 1


title: control early stationary vs. iron limiting early stationary Ratio 1-DF0_STAT_block1 and 1-DF30_STAT_block1

source_name: Control DF0, early-stationary phase, biological replicate 1, replicate spot 1

source_name: iron limiting DF30, early-stationary phase, biological replicate 1, replicate spot 1


title: control early stationary vs. iron limiting early stationary Ratio 2-DF0_STAT_block3 and 2-DF30_STAT_block3

source_name: Control DF0, early-stationary phase, biological replicate 2, replicate spot 3

source_name: iron limiting DF30, early-stationary phase, biological replicate 2, replicate spot 3


title: control exponential vs. iron limiting exponential Ratio 3-DF0_EXP_block2 and 3-DF30_EXP_block2

source_name: Control DF0, exponential phase, biological replicate 3, replicate spot 2

source_name: iron limiting DF30, exponential phase, biological replicate 3, replicate spot 2


title: control early stationary vs. iron limiting early stationary Ratio 3-DF0_STAT_block2 and 3-DF30_STAT_block2

source_name: Control DF0, early-stationary phase, biological replicate 3, replicate spot 2

source_name: iron limiting DF30, early-stationary phase, biological replicate 3, replicate spot 2


title: control exponential vs. iron limiting exponential Ratio 4-DF0_EXP_block3 and 4-DF30_EXP_block3

source_name: Control DF0, exponential phase, biological replicate 4, replicate spot 3

source_name: iron limiting DF30, exponential phase, biological replicate 4, replicate spot 3


title: control exponential vs. iron limiting exponential Ratio 3-DF0_EXP_block1 and 3-DF30_EXP_block1

source_name: Control DF0, exponential phase, biological replicate 3, replicate spot 1

source_name: iron limiting DF30, exponential phase, biological replicate 3, replicate spot 1


title: control exponential vs. iron limiting exponential Ratio 2-DF0_EXP_block2 and 2-DF30_EXP_block2

source_name: Control DF0, exponential phase, biological replicate 2, replicate spot 2

source_name: iron limiting DF30, exponential phase, biological replicate 2, replicate spot 2


title: control exponential vs. iron limiting exponential Ratio 2-DF0_EXP_block3 and 2-DF30_EXP_block3

source_name: Control DF0, exponential phase, biological replicate 2, replicate spot 3

source_name: iron limiting DF30, exponential phase, biological replicate 2, replicate spot 3


title: ΔMCR 0457 biological repl 3 repl spot 4

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 3, replicate spot 4

hyb_protocol: 2 µg of labeled cDNA was applied to 4x72K custom design NimbleGen arrays. Overnight hybridization at 42°C and subsequent washing of arrays was performed according to the manufacturer’s instructions (available from www.nimblegen.com).

data_processing: ANAIS (Simon and Biot, 2010, Bioinformatics 26;2468-2469) was used for intra-array (background adjustment) and inter-array (quantile) normalization to obtain normalized probe signal intensities (SI), three replicate spots per array (designated block1-3). Normalized probe SI were corrected for a threshold of seven times the median SI of the negative-control probes. Statistical analysis was performed on the SI (median of eight probes per gene) of the directed mutant strain and the parental wild-type strain using the CyberT implementation of Student’s t-test (cybert.microarray.ics.uci.edu). The false discovery rate (FDR) was calculated from the Bayesian p-value as described in (van Hijum et al., 2005, BMC Genomics 6; 77).

label: 5'Cy3-labeled random nonamers

label_protocol: Total RNA (5 µg) was labeled according to standard Nimblegen gene expression array protocols.

growth_protocol: M. catarrhalis BBH18 directed mutants (n = 3) and wild-type BBH18 strain (n = 4) were expanded to mid-log phase (OD620nm, 1.2 to 1.4) in brain heart infusion (BHI) medium (iron-rich) at 37°C 250 rpm.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by DNase digestion with the DNA-free kit (Ambion).

treatment_protocol: Bacteria were treated with 2 volumes of RNAprotect bacteria reagent (Qiagen).

tag: genotype

value: MCR_0457 deletion mutant

value: Exponential phase


title: ΔMCR 0457 biological repl 3 repl spot 3

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 3, replicate spot 3


title: control exponential vs. iron limiting exponential Ratio 1-DF0_EXP_block3 and 1-DF30_EXP_block3

source_name: Control DF0, exponential phase, biological replicate 1, replicate spot 3

source_name: iron limiting DF30, exponential phase, biological replicate 1, replicate spot 3


title: ΔMCR 0457 biological repl 1 repl spot 3

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 1, replicate spot 3


title: ΔMCR 0457 biological repl 2 repl spot 2

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 2, replicate spot 2


title: control exponential vs. iron limiting exponential Ratio 1-DF0_EXP_block1 and 1-DF30_EXP_block1

source_name: Control DF0, exponential phase, biological replicate 1, replicate spot 1

source_name: iron limiting DF30, exponential phase, biological replicate 1, replicate spot 1


title: ΔMCR 0457 biological repl 3 repl spot 2

description: Moraxella catarrhalis BBH18 ΔMCR_0457, exponential growth phase, biological replicate 3, replicate spot 2


title: control exponential vs. iron limiting exponential Ratio 3-DF0_EXP_block3 and 3-DF30_EXP_block3

source_name: Control DF0, exponential phase, biological replicate 3, replicate spot 3

source_name: iron limiting DF30, exponential phase, biological replicate 3, replicate spot 3