title: Control_rep3

hyb_protocol: As per Affymetyrix instructions

scan_protocol: As per Affymetyrix instructions

data_processing:
Data were imported into Partek Genomic Suite and prenormalized using RMA.  Enriched regions were determined using the MAT algorithm tool in this software.
additional results files: Low Glucose vs Control promoter arrays for tranposed for GEO submission.txt;Low Oxygen vs Control promoter arrays transposed for GEO submission.txt
results file descriptions: These are .txt files of the RMA prenormalized data for Low Oxygen OR Low Glucose vs Control.  Please note that the Control samples are the same for both comparisons.

source_name: HCT116 Cell line, no treatment

label_protocol: As per Affymetyrix instructions

growth_protocol: HCT116 cells were grown in DMEM + 10% FBS+50 μg/ml gentamicin + 1 mM sodium pyruvate at 37 deg in 5% CO2  None

extract_protocol: genomic DNA was isolated from cells using the Qiagen Blood and Tissue genomic DNA preparation kit

tag: treatment


title: Low_Glucose_rep3

status: Public on Jul 07 2014

type: RNA

city: Guelph

first: Brenda

last: Coomber

state: Ontario

address: 50 Stone Road

department: Department of Biomedical Sciences

country: Canada

institute: University of Guelph

hyb_protocol: As per Affymetrix Instructions

scan_protocol: As per Affymetrix Instructions

data_processing: Cel Files imported into Partek Genomics Suite, RMA prenormalization.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HCCT116 cell line, Low glucose

label_protocol: As per Affymetrix Instructions

growth_protocol: Human colorectal cancer cells, HCT116  were cultured in DMEM + 10% fetal bovine serum + 50 μg/ml gentamicin+ 1mM sodium pyruvate at 37°C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA was isolated using TRIPure according to manufacturer’s instructions.

treatment_protocol: Control:  No treatment.  Low Oxygen:  As above, except with 5% CO2, 95% N2.  Low Glucose: As above, except with Glucose/pyruvate free media.

tag: cell line

tag: condition

value: low glucose


title: Control_rep2

source_name: HCCT116 cell line, Control

value: untreated


title: Low_Glucose_rep3

type: genomic

label: biotin

molecule: genomic DNA

source_name: HCT116 Cell line, Low Glucose

value: Low Glucose


title: Low_Glucose_rep1

source_name: HCCT116 cell line, Low Glucose


title: Control_rep1

source_name: HCCT116 cell line, Untreated


title: NN insect treated, biological rep2

city: Nanjing

first: Yongli

last: Wang

address: Weigang No.1

department: Agricultural college

country: China

institute: Nanjing Agricultural University

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

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

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

organism: Glycine max

source_name: NN soybean leaves from insect induced plants

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

growth_protocol: Seeds of Wanxianbaidongdou and Nannong99-10 soybean lines were sown in 15 cm plastic pots that contained a sterile soil mixture (top soil:sand:vermiculite, 3:2:1). The seedlings were grown in a greenhouse maintained at 30 ± 5°C, 70 ± 10% RH, and a 14 h/10 h (day/night) photoperiod with supplementary metal-halide illumination.

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

treatment_protocol: Treatments of cotton worm (obtained from a colony maintained on an artificial diet) feeding and untreated (control) plants were applied to soybean plants at the V4 (vegetative stage with four nodes) stage of growth. Defoliation (about 20–30%) was induced by placing three third or four instar cotton worm larvaes on the first and second trifoliate leaf for 48 hours, after which the larvae were removed.

tag: tissue

value: trifoliate leaf

tag: genotype

tag: age

value: vegetative stage with four nodes


title: Low_Oxygen_rep1

source_name: HCCT116 cell line, Low Oxygen

value: low oxygen


title: NN insect treated, biological rep1


title: WX control, biological rep3

source_name: WX soybean leaves from insect non-induced plants

value: Wanxianbaidongdou


title: WX control, biological rep1


title: Low_Glucose_rep2


title: WX control, biological rep2


title: Low_Oxygen_rep2

source_name: HCT116 Cell line, Low Oxygen

value: Low Oxygen


title: Control_rep1


title: HCT116_rep1

data_processing:
Data from chips was compared to the HAPMAP 270 sample database.  Data were prenormalized using RMA.  All analyses were performed using Partek Genomic Suite.
primary_data_description: SNP/CNV probe info provided in an accompanying file (SNP 6 transposed for GEO submission.txt), as it is too large a file for EXCEL)

source_name: HCT116 cell line

extract_protocol: genomic DNA was isolated from cells using the Qiagen Blood and Tissuew genomic DNA preparation kit


title: Control_rep2


title: Low_Glucose_rep2


title: HCT116_rep2

data_processing:
Data from chips was compared to the HAPMAP 270 sample database.  Data were prenormalized using RMA.  All analyses were performed using Partek Genomic Suite.
primary_data_description: SNP/CNV probe info provided in an accompanying file (SNP 6 transposed for GEO submission.txt) that is linked to the Series record.


title: Low_Glucose_rep1


title: Low_Oxygen_rep3


title: Low_Oxygen_rep1


title: Low_Oxygen_rep3


title: WX insect treated, biological rep3

source_name: WX soybean leaves from insect induced plants


title: WX insect treated, biological rep2


title: WX insect treated, biological rep1


title: R1 vs. bphPR deletion

city: Jeongeup

first: Im

last: Seong Hun

address: Jeongeup 580-185, Republic of KoreaInstitute

country: South Korea

institute: Korea Atomic Energy Research Institute

hyb_protocol: The hybridizations were conducted at 57°C for 17 hours in an Agilent Hybridization oven and washed following the manufacturer’s protocol (Agilent Technologies, Inc.).

scan_protocol: The scans were performed with an Agilent DNA microarray Scanner (Agilent Technologies, Inc.) using Agilent Feature Extraction software 10.7 (Agilent Technologies, Inc.). The signal intensities were quantified using GeneSpringGX 7.3.1 software (Agilent Technologies, Inc.).

data_processing:
The normalization of gene expression by a LOWESS regression was applied for 3 data obtained from 3 biological replicates. The genes were considered to be differentially expressed when the logarithmic gene expression ratios had more than a 2-fold difference in the expression level.
The statistical significance of the data was determined by Student’s t test. P-values of less than 0.05 were taken to be statistically significant.

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

label_protocol: 50 µg of total RNA were primed with 2 µl of 3 µg/µl random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 2 µl of 50X aminoallyl-dNTP mix, 25 µM Cy3-labeling dye and Cy5-labeling dye.

growth_protocol: R1 and bphPR deletion mutant cells were cultured O.D 1.0 at the 37 °C shaking incubator

extract_protocol: Total RNA extracted using RiboEX (GeneAll biotechnology, Korea) following manufacturer's instructions

treatment_protocol: Non treatment

tag: genotype/variation

value: control

source_name: ∆bphPR

value: bphPR deletion mutant


title: Wnt3a treated DRG culture rep2

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

description: replicate 2

hyb_protocol: Microarrays were hybridized following Illumina's standard hybridization protocol on MouseRef-8 v2.0 expression BeadChips.

scan_protocol: Processed arrays were scanned on Illumina iScan System array reader according to the manufacturer's instructions.

data_processing: Raw array data were processed with Illumina BeadStudio software (v3.2) using background subtraction and cubic-spline normalisation.

organism: Mus musculus

source_name: mouse DRG tissue

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrep kit for Illumina arrays.

growth_protocol: DRGs from 6-8 weeks old mice were collected in cold PBS after removing axons and meningeal tissue, and digested for 30 min at 37°C in trypsin, collagenase and DNAse. Neurons were than separated from non-neuronal cells using a discontinuous Percoll gradient, plated on poly-L-lysine coated coverslips and cultured in F12 medium plus 10% serum in presence of a mixture of growth factors (BDNF 10 ng/ml, NGF 10 ng/ml, GDNF 5 ng/ml, NT3 5ng/ml, all from SIGMA) and mitotic inhibitor AraC 5 µM (SIGMA) for 3 days before treatment.

extract_protocol: Total RNA was extracted with Trizol (Life Technologies) followed by clean-up and DNase I treatment with Qiagen RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA quality control was performed with Agilent Bioanalyzer.

treatment_protocol: The DRG cultures were serum-starved for 1h and then treated with Wnt3a (200 ng/ml) or vehicle (PBS) for 6h.

tag: strain

value: 4-6 weeks

value: neuronal-enriched DRG culture


title: Wnt3a treated DRG culture rep1

description: replicate 1


title: R1 MMC vs. bphPR deletion MMC

source_name: R1 MMC

treatment_protocol: A 10 ml culture grown to the early log phase (OD600 ≈ 1.0) was treated with MMC (5 μg/ml) and incubated for 1 h.

tag: stress treatment

value: 5ug/ml MMC for 1hr

source_name: ∆bphPR MMC


title: CorticalProgenitors_Fezf2_48hr_rep2

status: Public on Jul 06 2014

city: Cambridge

first: Paola

last: Arlotta

state: Massachusetts

address: 7 Divinity Ave SF301-7

department: Stem Cell and Regenerative Biology

country: USA

institute: Harvard University

hyb_protocol: Hybridization was performed according to Affymetrix protocols.

scan_protocol: Scanning was performed according to Affymetrix protocols.

data_processing: Data from individual microarrays normalized by GC-RMA. Fold changes were calculated in Rosetta Resolver

source_name: in utero electorporated cortex, dissociated and FACS sorted

label_protocol: RNA was amplified per Affymetrix small sample protocol, using two consecutive rounds of linear in vitro transcription to obtain 15–20 μg of amplified and labeled cRNA for each hybridization

growth_protocol: N/A, cells were FACS purified from in vivo sources

extract_protocol: Fezf2GFP and CtrlGFP electroporated cells were purified by FACS directly into RNAlater7 and RNA was extracted with the StrataPrep Total RNA Micro Kit (Stratagene), and RNA quality was assessed using a bioanalyzer (Agilent Technologies).

treatment_protocol: 800 nl of purified DNA (2 μg/μl,  Fezf2GFP and CtrlGFP construct) were mixed with 0.005% Fast Green in sterile PBS and were injected in utero into the lateral ventricle of CD1 embryos at E14.5 under ultrasound guidance (Vevo 770, VisualSonics). Five 40 volt pulses of 50 ms were delivered at 1 second intervals in an appropriate orientation across the embryonic head using 1 cm-diameter platinum electrodes placed outside the uterus, using a CUY21EDIT square wave electroporator (Nepa Gene). Injected embryos were collected for FACS purification either 24 hours or 48 hours after electroporation.

tag: expression vector

tag: time of purification


title: control (vehicle-treated) DRG culture rep2

description: replicate 2

value: vehicle treated


title: WT Duct at 4 weeks, biological rep2

city: Irvine

first: Michael

middle: L

last: Salmans

state: CA

address: 250 Sprague Hall

institute: University of California Irvine

description: Gene expression data from laser capture microdissected WT mammary gland ducts of 4 week old mouse

hyb_protocol: cRNA was hybridized on MouseGene 1.0ST array according to Affymetrix protocol in Affymetrix GeneChip Hybridization Oven 640 and washed and stained in GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G

data_processing: The data were analyzed with the PLIER algorithm using Affymetrix default analysis settings.

source_name: Mouse mammary gland at early puberty

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: Mice were grown according to regulatory guidelines approved by the International Animal Care and Use Committee of the University of California Irvine

extract_protocol: For laser capture microdissected samples: Qiagen RNeasy Mini; for sorted cells: Direct-zol RNA MiniPrep (Zymo Research)

treatment_protocol: For laser capture microdissection, mammary glands were frozen embedded in OCT, sectioned at 8 microns, and H&E stained prior to microdissection. For sorted cells, single cell isolations of mammary glands were generated and labeled with CD24, C29, and lineage markers (CD31, CD45, and TER119) prior to sorting.

value: Mammary gland duct

value: Wild type

value: 4 weeks

tag: genetic background


title: CorticalProgenitors_Fezf2_48hr_rep4


title: control (vehicle-treated) DRG culture rep1

description: replicate 1


title: CorticalProgenitors_Fezf2_24hr_rep2


title: CorticalProgenitors_Fezf2_48hr_rep1


title: CorticalProgenitors_Fezf2_24hr_rep3


title: CorticalProgenitors_GFP_48hr_rep3

value: CtrlGFP


title: CorticalProgenitors_Fezf2_48hr_rep3


title: Normal.mouse.control.lung.2 (mouse)

status: Public on Jul 04 2014

city: Philadelphia

first: Robert

last: Bowman

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania School of Medicine

description: SAMPLE 35

hyb_protocol: 15 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G using the GeneChip Command Console version 3.2 as CEL files.

data_processing: Raw CEL files were imported into R using the 'affy' package. Two separate Affybatch objects were created: one mouse/stroma affybatch, and one human/tumor affybatch. Microarrays on RNA isolated from control cells in vitro were not included in the mouse/stroma affybatch. Likewise, microarrays on RNA isolated from control, non-tumor-burdened tissue were not included in the human affybatch. The robust multi-array average (RMA) method was used to generate expression values which were then quantile normalized in the 'affy' package. The RMA analysis was restricted to species specific and control probes as defined by GPL3385. For publication, expression values were aggregated by the gene symbol and mean values of all probes for a given gene are reported. Non-aggregated, probe-level intensities are reported here.

source_name: Non-tumor-burdened lung from 6 week old NOD.SCID mouse

label_protocol: 75 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: All animal studies were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center.

extract_protocol: Tissue was homogenized and RNA was isolated with TriZOL.

value: NOD/SCID

value: lung

tag: metastasis stage

value: normal tissue

tag: rna source

value: mouse


title: CorticalProgenitors_Fezf2_24hr_rep1


title: CorticalProgenitors_GFP_48hr_rep1


title: Normal.mouse.control.lung.1 (mouse)

description: SAMPLE 34


title: CorticalProgenitors_GFP_48hr_rep2


title: CorticalProgenitors_GFP_48hr_rep4


title: CorticalProgenitors_GFP_24hr_rep2


title: CorticalProgenitors_GFP_24hr_rep3


title: Late.lung.3 (mouse)

description: SAMPLE 33

source_name: Late-stage lung metastasis formed by I.V. injection of MDA-MB-231 Lu-M cells

value: late metastasis

value: human and mouse


title: Normal.mouse.control.lung.3 (mouse)

description: SAMPLE 36


title: CorticalProgenitors_GFP_24hr_rep1


title: Late.brain.3 (mouse)

description: SAMPLE 24

source_name: Late-stage brain metastasis formed by intra-cardiac injection of MDA-MB-231 Br-M cells

value: athymic nude

value: brain


title: Early.lung.3 (mouse)

description: SAMPLE 30

source_name: Early-stage lung metastasis formed by I.V. injection of MDA-MB-231 Lu-M cells

value: early metastasis


title: Late.lung.1 (mouse)

description: SAMPLE 31


title: Early.brain.1 (mouse)

description: SAMPLE 19

source_name: Early-stage brain metastasis formed by intra-cardiac injection of MDA-MB-231 Br-M cells


title: Early.lung.1 (mouse)

description: SAMPLE 28


title: Normal.mouse.control.brain.1 (mouse)

description: SAMPLE 13

source_name: Non-tumor-burdened brain from 6 week old Athymic Nude mouse


title: Early.lung.2 (mouse)

description: SAMPLE 29


title: Late.bone.1 (mouse)

description: SAMPLE 10

source_name: Late-stage bone metastasis formed by I.V. injection of MDA-MB-231 Bo-M cells

value: bone


title: Late.brain.2 (mouse)

description: SAMPLE 23


title: Early.brain.3 (mouse)

description: SAMPLE 21


title: Late.brain.1 (mouse)

description: SAMPLE 22


title: Normal.mouse.control.brain.2 (mouse)

description: SAMPLE 14


title: Normal.mouse.control.brain.3 (mouse)

description: SAMPLE 15


title: Late.bone.3 (mouse)

description: SAMPLE 12


title: Normal.mouse.control.bone.2 (mouse)

description: SAMPLE 2

source_name: Non-tumor-burdened bone from 6 week old Athymic Nude mouse


title: Early.bone.2 (mouse)

description: SAMPLE 8

source_name: Early-stage bone metastasis formed by I.V. injection of MDA-MB-231 Bo-M cells


title: Early.bone.1 (mouse)

description: SAMPLE 7


title: Normal.mouse.control.bone.3 (mouse)

description: SAMPLE 3


title: Early.bone.3 (mouse)

description: SAMPLE 9


title: Early.lung.1 (human)

description: SAMPLE 28


title: Late.lung.2 (mouse)

description: SAMPLE 32


title: Early.brain.2 (mouse)

description: SAMPLE 20


title: stromal compartment of non-responding patient A15

city: Manchester

first: Narges

last: Azadbakht

address: Wilmslow Road

department: The University of Manchester

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description:
A15 s
S_NR_02.CEL

hyb_protocol: The hybridisation cocktail was prepared using the fragmented and biotin-labelled amplified cDNA and according to the “NuGEN Exon Hybridisation Cocktail PICR v1.0” protocol (Oct 2008, available from http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_COCKTAIL_PROTOCOLS/), which was derived from the NuGEN WT-Ovation™ Exon Module Version 1.0 user guide (NuGEN Technologies, Inc., 2007). Hybridisation of the labelled DNA to the array was carried out according to the “NuGEN Exon Hybridisation PICR v1.0” protocol (“Hybridisation, Washing, Staining and Scanning of NuGEN exon labelled targets to Genomic Arrays of feature size 11 μM. Version 1.0” (Oct 2008, available from http://bioinformatics.picr.man.ac.uk/mbcf/downloads/_HYBRIDISATION_PROTOCOLS/)), which was derived from the NuGEN WT-Ovation™ Exon Module Version 1.0 user guide (NuGEN Technologies, Inc. 2007) and the Affymetrix GeneChip® Expression Analysis Technical Manual (Affymetrix, Inc., 1999-2004).

scan_protocol: Scanning was carried out using the Affymetrix GeneChip® Scanner 3000 system with Autoloader (Affymetrix, Inc.). Data collection and management were conducted using the Affymetrix GeneChip® Command Console® (AGCC) software (version 3.2.1, Affymetrix, Inc.). Probe cell intensity data was subsequently stored as .CEL files.

data_processing: The RMA algorithm was implemented using the “apt-probeset-summarize” program from APT, (version 1.14.2 Windows Installer – win32, Affymetrix, Inc.). To define the probesets the probe group file (.pgf) and the cel layout file (.clf) from the Affymetrix “Human Exon 1.0 ST Array Analysis” zip file, “HuEx-1_0-st-v2.r2.zip” (Affymetrix, Inc., Accessed on 31.08.2012; available from http://www.affymetrix.com/catalog/131452/AFFY/Human-Exon-ST-Array#1_3), were used in the analysis.

label_protocol:
Amplification protocol: Amplified cDNA was prepared from 100 ng of the extracted RNA using the Ovation® FFPE WTA System (Part No. 3403, NuGEN Technologies, Inc. 2011-2012) and according to the manufacturer’s protocol. The implemented amplification protocol was modified so that poly A controls were added to the total RNA.
ST-cDNA generation protocol: Sense transcript cDNA (ST-cDNA) was generated from 4 µg of the amplified cDNA using the WT-Ovation™ Exon Module Version 1.0 (Part No. 2000-12, 2000-60, NuGEN Technologies, Inc. 2009-2010) and according to the manufacturer’s protocol.
Fragmentation and labelling were carried out using the Encore® Biotin Module (Part No. 4200, NuGEN Technologies, Inc. 2009-2012) and according to the manufacturer’s protocol (NuGEN Technologies, Inc. 2009-2012).

extract_protocol: RNA extraction was performed using RNeasy® FFPE Kit (Catalog No. 74404, QIAGEN, 2006). RNA extraction was carried out according to the QIAGEN supplementary protocol for “Copurification of total RNA and miRNA from formalin-fixed, paraffin-embedded (FFPE) tissue sections using the RNeasy® FFPE Kit” (Catalog No. 74404, QIAGEN, 2006). Deparaffinisation steps of the extraction protocol were not carried out, as deparaffinisation was conducted prior to microdissection. The incubation with Proteinase K at 55°C was extended to 30 minutes. To elute the RNA, 2×15 µl of RNase-free water was added to the spin column membrane. Centrifugation was also carried out 4 minutes after the addition of each 15 µl volume of RNase-free water. Isolated material were stored at -80°C.

treatment_protocol:
Tissue preservation protocol: Breast cancer tumour biopsies were formalin-fixed paraffin-embedded (FFPE). The implemented protocol for this process is unavailable. (At the time of LCM, these samples had been preserved for more than 20 years.)
10 µm thick tissue sections from FFPE blocks were mounted on metal-framed polyethylene terephthalate (PET) membrane slides (membrane thickness 1.4 μm, steel frames, Order no. 11505151, Leica Microsystems) and underwent deparaffinisation, staining and dehydration prior to Laser Capture Microdissection (LCM). Staining was carried out using Hematoxylin (Shandon Gill 1, Thermo Scientific). Epithelial cells and stromal cells were isolated from each section by LCM which was conducted using Leica LMD6000 Laser Microdissection System (Leica Microsystems).

tag: patient id

tag: gender

value: female

tag: age of patient at diagnosis (years)

value: tamoxifen

tag: treatment duration (days)

tag: response

value: non-responding

value: breast cancer tumour

tag: carcinoma type

value: Ductal

tag: grade

tag: tissue preservation type

value: FFPE

tag: tissue compartment

value: Stromal

tag: array hybridisation batch number


title: stromal compartment of non-responding patient A19

description:
A19 s
S_NR_06.CEL

tag: treatment

tag: tissue


title: stromal compartment of responding patient B42

description:
B42 s
S_R_10.CEL

value: responding


title: Late.bone.2 (mouse)

description: SAMPLE 11

tag: genotype


title: epithelial compartment of non-responding patient B59

description:
B59 e
E_NR_03.CEL

value: Unknown

value: Epithelial


title: epithelial compartment of non-responding patient A19

description:
A19 e
E_NR_05.CEL


title: epithelial compartment of non-responding patient A15

description:
A15 e
E_NR_01.CEL


title: Late.lung.1 (human)

description: SAMPLE 31

value: NOD/SCID

value: lung


title: Normal.mouse.control.bone.1 (mouse)

description: SAMPLE 1

value: normal tissue

value: mouse


title: stromal compartment of responding patient A29

description:
A29 s
S_R_08.CEL


title: Normal.human.control.brain.1 (human)

description: SAMPLE 16

source_name: Brain homing metastatic cell line derived from MDA-MB-231

value: MDA-MB-231 Br-M

tag: cell line

value: MDA-MB-231 Br-M in vitro

value: cultured cells

value: human


title: Late.lung.3 (human)

description: SAMPLE 33

value: late metastasis

value: human and mouse


title: Early.brain.3 (human)

description: SAMPLE 21

value: athymic nude

value: brain

value: early metastasis


title: Normal.human.control.lung.3 (human)

description: SAMPLE 27

source_name: Lung homing metastatic cell line derived from MDA-MB-231

value: MDA-MB-231 Lu-M

value: MDA-MB-231 Lu-M in vitro


title: Early.brain.2 (human)

description: SAMPLE 20


title: Late.bone.3 (human)

description: SAMPLE 12

value: bone


title: Normal.human.control.lung.2 (human)

description: SAMPLE 26


title: Early.lung.2 (human)

description: SAMPLE 29


title: Normal.human.control.lung.1 (human)

description: SAMPLE 25


title: epithelial compartment of responding patient B42

description:
B42 e
E_R_09.CEL

value: female

value: tamoxifen

value: responding

value: breast cancer tumour

value: Ductal

value: FFPE

value: Epithelial


title: Late.bone.2 (human)

description: SAMPLE 11


title: Normal.human.control.brain.3 (human)

description: SAMPLE 18

value: MDA-MB-231 Br-M

value: MDA-MB-231 Br-M in vitro

value: cultured cells


title: Late.brain.2 (human)

description: SAMPLE 23

value: late metastasis

value: human and mouse


title: epithelial compartment of responding patient B61

description:
B61 e
E_R_11.CEL

value: Ductal/Lobular mixed

value: Unknown


title: epithelial compartment of responding patient A29

description:
A29 e
E_R_07.CEL


title: Normal.human.control.bone.2 (human)

description: SAMPLE 5

source_name: Bone homing metastatic cell line derived from MDA-MB-231

value: MDA-MB-231 Bo-M

value: MDA-MB-231 Bo-M in vitro

value: human


title: Late.bone.1 (human)

description: SAMPLE 10

value: athymic nude

value: bone


title: Late.brain.1 (human)

description: SAMPLE 22

value: brain


title: Early.brain.1 (human)

description: SAMPLE 19

value: early metastasis


title: Early.bone.2 (human)

description: SAMPLE 8


title: Late.lung.2 (human)

description: SAMPLE 32

value: NOD/SCID

value: lung


title: Normal.human.control.bone.3 (human)

description: SAMPLE 6


title: Early.bone.3 (human)

description: SAMPLE 9


title: TFOE_8468_3911

city: RENTON

first: Tige

last: Rustad

state: WASHINGTON

address: 1700 DAYTON AVE NE

institute: Seattle BioMed

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

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.

data_processing: Data was normalized using RMA normalization with the 'affy' package for R.

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: H37Rv was grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Transcription factor overexpression experiments done at 100 ng/ml of anhydrotetracycline after 18 hours of induction.

tag: experiment

tag: stress

value: Rv3911 overexpression

tag: time (hours)

tag: concentration (ng)


title: Early.lung.3 (human)

description: SAMPLE 30

tag: metastasis stage

tag: rna source


title: Early.bone.1 (human)

description: SAMPLE 7


title: Normal.human.control.bone.1 (human)

description: SAMPLE 4


title: TFOE_8127_3911


title: TFOE_7945_3862c_B

value: Rv3862c overexpression


title: TFOE_4985_3862c_A


title: TFOE_6830_3862c


title: TFOE_2656_3862c


title: Late.brain.3 (human)

description: SAMPLE 24


title: TFOE_3194_3855

value: Rv3855 overexpression


title: TFOE_3695_3849

value: Rv3849 overexpression


title: TFOE_1176_3855


title: TFOE_6704_3852

value: Rv3852 overexpression


title: TFOE_8192_3849


title: TFOE_4936_3849


title: TFOE_2894_3852


title: TFOE_8311_3852


title: TFOE_2756_3911


title: TFOE_4103_3833

value: Rv3833 overexpression


title: TFOE_4551_3840

value: Rv3840 overexpression


title: TFOE_4939_3833


title: TFOE_9032_3855


title: TFOE_7414_3840


title: TFOE_1539_3840


title: TFOE_1864_3830c

value: Rv3830c overexpression


title: TFOE_2975_3833


title: TFOE_1447_3765c

value: Rv3765c overexpression


title: TFOE_8264_3830c


title: TFOE_9040_3765c


title: TFOE_1156_3765c


title: TFOE_8731_3744

value: Rv3744 overexpression


title: TFOE_2107_3692

value: Rv3692 overexpression


title: TFOE_9939_3830c


title: TFOE_1935_3744


title: TFOE_1910_3736

value: Rv3736 overexpression


title: TFOE_8016_3736


title: Normal.human.control.brain.2 (human)

description: SAMPLE 17

value: MDA-MB-231 Br-M

value: MDA-MB-231 Br-M in vitro

value: cultured cells

value: human


title: TFOE_5037_3744


title: TFOE_4357_3736


title: TFOE_5851_3692


title: TFOE_4909_3597c

value: Rv3597c overexpression


title: TFOE_3847_3676

value: Rv3676 overexpression


title: TFOE_2092_3681c

value: Rv3681c overexpression


title: TFOE_3373_3597c


title: TFOE_9798_3681c


title: TFOE_5338_3597c


title: TFOE_7750_3597c


title: TFOE_9192_3681c


title: TFOE_6346_3676


title: TFOE_4182_3692


title: TFOE_4445_3676


title: TFOE_8131_3574_C_3000ng

value: Rv3574 overexpression


title: TFOE_7355_3574


title: TFOE_3529_3583c

value: Rv3583c overexpression


title: TFOE_4577_3583c


title: TFOE_2077_3583c


title: TFOE_3005_3574_A


title: TFOE_9860_3557c

value: Rv3557c overexpression


title: TFOE_3677_3574


title: TFOE_4186_3574_B


title: TFOE_8709_3557c


title: TFOE_3630_3488

value: Rv3488 overexpression


title: TFOE_9515_3488


title: TFOE_4902_3488


title: TFOE_8280_3417c

value: Rv3417c overexpression


title: TFOE_6435_3417c


title: TFOE_2895_3417c


title: TFOE_8067_3416

value: Rv3416 overexpression


title: TFOE_6695_3416


title: TFOE_1352_3414c

value: Rv3414c overexpression


title: TFOE_6644_3405c

value: Rv3405c overexpression


title: TFOE_6629_3334_B

value: Rv3334 overexpression


title: TFOE_4076_3557c


title: TFOE_4667_3328c

value: Rv3328c overexpression


title: TFOE_1113_3328c


title: TFOE_2203_3328c


title: TFOE_9162_3301c

value: Rv3301c overexpression


title: TFOE_5242_3334_C


title: TFOE_3290_3334


title: TFOE_3349_3334


title: TFOE_1949_3405c


title: TFOE_2558_3416


title: TFOE_9642_3334


title: TFOE_1523_3414c


title: TFOE_9539_3405c


title: TFOE_7743_3414c


title: TFOE_4398_3301c


title: TFOE_5343_3295

value: Rv3295 overexpression


title: TFOE_3866_3295


title: TFOE_3625_3295


title: TFOE_9544_3286c

value: Rv3286c overexpression


title: TFOE_9882_3295_C


title: TFOE_6107_3291c

value: Rv3291c overexpression


title: TFOE_5261_3291c


title: TFOE_6181_3286c


title: TFOE_6616_3301c


title: TFOE_3822_3260c

value: Rv3260c overexpression


title: TFOE_1382_3286c


title: TFOE_2104_3260c


title: TFOE_7368_3260c


title: TFOE_8518_3249c

value: Rv3249c overexpression


title: TFOE_9237_3249c_B


title: TFOE_8008_3249c


title: TFOE_7589_3249c


title: TFOE_5586_3249c


title: TFOE_4091_3219

value: Rv3219 overexpression


title: TFOE_5324_3291c


title: TFOE_8750_3219


title: TFOE_3369_3246c

value: Rv3246c overexpression


title: TFOE_6905_3246c


title: TFOE_1563_3197A

value: Rv3197 overexpression


title: TFOE_9004_3223c

value: Rv3223c overexpression


title: TFOE_3116_3223c


title: TFOE_6856_3208

value: Rv3208 overexpression


title: TFOE_6841_3183

value: Rv3183 overexpression


title: TFOE_5371_3246c


title: TFOE_4681_3219


title: TFOE_7201_3197A


title: TFOE_6758_3208


title: TFOE_2214_3183


title: TFOE_4521_3208


title: TFOE_2841_3223c


title: TFOE_8668_3173c

value: Rv3173c overexpression


title: TFOE_4545_3173c


title: TFOE_9265_3167c

value: Rv3167c overexpression


title: TFOE_5080_3197A


title: TFOE_3028_3183


title: TFOE_7273_3164c

value: Rv3164c overexpression


title: TFOE_7389_3173c


title: TFOE_5913_3167c


title: TFOE_6726_3164c


title: TFOE_2967_3164c


title: TFOE_7537_3160c

value: Rv3160c overexpression


title: TFOE_7163_3167c


title: TFOE_3603_3160c


title: TFOE_5289_3160c


title: TFOE_7016_3133c_C

value: Rv3133c overexpression


title: TFOE_9466_3143

value: Rv3143 overexpression


title: TFOE_7106_3095

value: Rv3095 overexpression


title: TFOE_6258_3095_B


title: TFOE_2737_3082c

value: Rv3082c overexpression


title: TFOE_4863_3124

value: Rv3124 overexpression


title: TFOE_1639_3095_A


title: TFOE_3883_3143


title: TFOE_9652_3133c_A


title: TFOE_3509_3143


title: TFOE_9549_3124


title: TFOE_7935_3095_C


title: TFOE_8886_3095


title: TFOE_7973_3082c


title: TFOE_1150_3124


title: TFOE_9956_3066_C_2


title: TFOE_7200_3060c

value: Rv3060c overexpression


title: TFOE_9956_3066_C_1

value: Rv3066 overexpression


title: TFOE_6169_3066


title: TFOE_7687_3066


title: TFOE_1615_3082c


title: TFOE_4265_3133c_B


title: TFOE_9515_3058c

value: Rv3058c overexpression


title: TFOE_5383_3060c


title: TFOE_3326_3066_B


title: TFOE_2404_3060c


title: TFOE_6654_3058c


title: TFOE_6030_3058c


title: TFOE_1720_3055

value: Rv3055 overexpression


title: TFOE_7735_3055


title: TFOE_8602_3050c

value: Rv3050c overexpression


title: TFOE_9036_2986c

value: Rv2986c overexpression


title: TFOE_1155_2989

value: Rv2989 overexpression


title: TFOE_2629_3066


title: TFOE_8073_2986c


title: TFOE_7826_3050c


title: TFOE_6862_2989


title: TFOE_2753_2986c


title: TFOE_1362_3050c


title: TFOE_7388_2912c

value: Rv2912c overexpression


title: TFOE_3550_2989


title: TFOE_2591_2887

value: Rv2887 overexpression


title: TFOE_9099_2884

value: Rv2884 overexpression


title: TFOE_1663_2884


title: TFOE_1147_2887


title: TFOE_9441_2827c

value: Rv2827c overexpression


title: TFOE_2177_2884


title: TFOE_1725_2887


title: TFOE_4976_2912c


title: TFOE_6566_2912c


title: TFOE_5952_2827c


title: TFOE_4460_2827c


title: TFOE_2915_2788

value: Rv2788 overexpression


title: TFOE_5811_2788


title: TFOE_8611_2779c

value: Rv2779c overexpression


title: TFOE_7703_2788


title: TFOE_9629_2745c

value: Rv2745c overexpression


title: TFOE_6773_2760c

value: Rv2760c overexpression


title: TFOE_4478_2779c


title: TFOE_1738_2760c


title: TFOE_3097_2760c


title: TFOE_7817_2745c


title: TFOE_6563_2745c_A


title: TFOE_8166_2720_A

value: Rv2720 overexpression


title: TFOE_4405_2720_C


title: TFOE_8203_2720


title: TFOE_1356_2745c_B


title: TFOE_1580_2711

value: Rv2711 overexpression


title: TFOE_2792_2720


title: TFOE_4740_2711


title: TFOE_6954_2779c


title: TFOE_3093_2710

value: Rv2710 overexpression


title: TFOE_9973_2703

value: Rv2703 overexpression


title: TFOE_3123_3295_B

value: Rv3295 overexpression


title: TFOE_6068_2710


title: TFOE_5281_2710


title: TFOE_0700_2711


title: TFOE_6112_2642

value: Rv2642 overexpression


title: TFOE_7260_2703


title: TFOE_1958_2720_B


title: TFOE_5523_2703


title: TFOE_5185_2642_B


title: TFOE_7229_2640c

value: Rv2640c overexpression


title: TFOE_5176_2642


title: TFOE_7096_2642


title: TFOE_3286_2640c


title: TFOE_6126_2642


title: TFOE_6902_2621c

value: Rv2621c overexpression


title: TFOE_1608_2640c


title: TFOE_3554_2621c


title: TFOE_4000_2506

value: Rv2506 overexpression


title: TFOE_5359_2595

value: Rv2595 overexpression


title: TFOE_1371_2621c


title: TFOE_7928_2595


title: TFOE_5527_2488c

value: Rv2488c overexpression


title: TFOE_8824_2478c

value: Rv2478c overexpression


title: TFOE_2550_2478c


title: TFOE_1875_2488c


title: TFOE_9916_2374c

value: Rv2374c overexpression


title: TFOE_6098_2478c


title: TFOE_8765_2506


title: TFOE_1446_2359

value: Rv2359 overexpression


title: TFOE_2009_2359_A


title: TFOE_8900_2359


title: TFOE_2370_2595


title: TFOE_8402_2506


title: TFOE_7839_2359_B


title: TFOE_3535_2640c


title: TFOE_2973_2374c


title: TFOE_4270_2359


title: TFOE_9292_2324

value: Rv2324 overexpression


title: TFOE_7609_2324


title: TFOE_7476_2324


title: TFOE_9655_2374c


title: TFOE_5002_2324


title: TFOE_5689_2282c

value: Rv2282c overexpression


title: TFOE_3598_2282c


title: TFOE_8575_2282c


title: TFOE_6543_2258c

value: Rv2258c overexpression


title: TFOE_1288_2250c

value: Rv2250c overexpression


title: TFOE_9789_2250c


title: TFOE_7587_2242

value: Rv2242 overexpression


title: TFOE_5119_2258c


title: TFOE_5144_2258c


title: TFOE_5114_2258c


title: TFOE_3837_2250c


title: TFOE_8331_2175c

value: Rv2175c overexpression


title: TFOE_1260_2242


title: TFOE_7452_2242


title: TFOE_7707_2160c

value: Rv2160c overexpression


title: TFOE_5513_2160c


title: TFOE_2741_2160c


title: TFOE_9954_2160A

value: Rv2160A overexpression


title: TFOE_1515_2175c


title: TFOE_6777_3055

value: Rv3055 overexpression


title: TFOE_8195_2034

value: Rv2034 overexpression


title: TFOE_2247_2175c


title: TFOE_9229_2069

value: Rv2069 overexpression


title: TFOE_3843_2069


title: TFOE_7000_2034


title: TFOE_6208_2069


title: TFOE_6378_2034


title: TFOE_2095_2160A


title: TFOE_3073_2160A


title: TFOE_9389_2021c_B

value: Rv2021c overexpression


title: TFOE_6958_2034


title: TFOE_9628_2021c_C


title: TFOE_2313_2034_B


title: TFOE_6553_2021c


title: TFOE_8382_2011c

value: Rv2011c overexpression


title: TFOE_6702_2017

value: Rv2017 overexpression


title: TFOE_6279_2011c


title: TFOE_5219_2017


title: TFOE_2739_2011c


title: TFOE_8385_2009

value: Rv2009 overexpression


title: TFOE_7141_2009


title: TFOE_2577_2009


title: TFOE_9383_1994c_A

value: Rv1994c overexpression


title: TFOE_3237_2021c


title: TFOE_6107_1994c_B


title: TFOE_9332_1994c


title: TFOE_9172_1985c

value: Rv1985c overexpression


title: TFOE_4221_1994c


title: TFOE_7345_1985c_B


title: TFOE_8072_1985c_A


title: TFOE_1201_1990c_a

value: Rv1990c overexpression


title: TFOE_5649_1990c


title: TFOE_0658_2021c


title: TFOE_8740_2017


title: TFOE_7918_1963c

value: Rv1963c overexpression


title: TFOE_7976_1985_a2


title: TFOE_9768_1990c


title: TFOE_9027_1960c

value: Rv1960c overexpression


title: TFOE_5735_1985c


title: TFOE_5108_1956_C

value: Rv1956 overexpression


title: TFOE_7357_1956


title: TFOE_3155_1931c

value: Rv1931c overexpression


title: TFOE_2686_1985b2


title: TFOE_8453_1963c


title: TFOE_2807_1994c


title: TFOE_2318_1956


title: TFOE_1030_1960c


title: TFOE_8406_1931c


title: TFOE_5846_1963c


title: TFOE_6104_1909c

value: Rv1909c overexpression


title: TFOE_2915_1956


title: TFOE_1091_1956_B


title: TFOE_5966_1909c_B


title: TFOE_3220_1960c


title: TFOE_5117_1846c

value: Rv1846c overexpression


title: TFOE_5192_1830

value: Rv1830 overexpression


title: TFOE_9738_1830


title: TFOE_9820_1830


title: TFOE_1579_1931c


title: TFOE_9243_1909c


title: TFOE_3612_1909c_C


title: TFOE_1378_1909c


title: TFOE_4908_1828

value: Rv1828 overexpression


title: TFOE_3531_1773c

value: Rv1773c overexpression


title: TFOE_5006_1773c


title: TFOE_5447_1776c

value: Rv1776c overexpression


title: TFOE_6269_1846c


title: TFOE_3844_1828


title: TFOE_6565_1846c


title: TFOE_2106_1828


title: TFOE_5284_1740

value: Rv1740 overexpression


title: TFOE_9132_1816

value: Rv1816 overexpression


title: TFOE_6347_1816


title: TFOE_4408_1776c


title: TFOE_3092_1725c

value: Rv1725c overexpression


title: TFOE_8915_1816


title: TFOE_3943_1776c


title: TFOE_2509_1740


title: TFOE_7465_1725c


title: TFOE_9311_1740


title: TFOE_6676_1725c


title: TFOE_3497_1719

value: Rv1719 overexpression


title: TFOE_8941_1719


title: TFOE_1959_1719


title: TFOE_7690_1675c

value: Rv1675c overexpression


title: TFOE_7984_1773c


title: TFOE_7826_1674c

value: Rv1674c overexpression


title: TFOE_8687_1675c


title: TFOE_3423_1675c


title: TFOE_8139_1674c


title: TFOE_6102_1657

value: Rv1657 overexpression


title: TFOE_5212_1674c


title: TFOE_2216_1657


title: TFOE_9978_1556

value: Rv1556 overexpression


title: TFOE_0383_1626

value: Rv1626 overexpression


title: TFOE_6215_1560

value: Rv1560 overexpression


title: TFOE_7581_1560


title: TFOE_1494_1626


title: TFOE_1016_1657


title: TFOE_8543_1626


title: TFOE_8839_1560


title: TFOE_5953_1474c_B

value: Rv1474c overexpression


title: TFOE_1798_1474c_A


title: TFOE_4971_1474c


title: TFOE_7691_1474c_C


title: TFOE_7293_1473A

value: Rv1473A overexpression


title: TFOE_8380_1474c


title: TFOE_7362_1556


title: TFOE_2914_1556


title: Hippocampus; Stress-13 days + 5 days of rest; Biol. Rep. 3, dye swap

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

description: Technical replicate of 5-31

hyb_protocol: cRNA was hybridized using Gene Expression Hybridization Kit (Agilent). Hybridized microarrays were washed using standard Washing Buffer kit (Agilent). All procedures were performed according to manufacturer's protokol

scan_protocol: Data were extracted using G2565CA Microarray Scanner (Agilent, USA) and Agilent Feature Extraction Software (Agilent, USA) on default settings.

data_processing: Background correction method normexp was used and followed by loess method for within array normalization. Between array normalization was performed with the Aquantile method. Mean values of channels intensities were taken as an input and a median of background signal for background correction calculations.

source_name: Hippocampus; Contol-13 days + 5 days of rest

label_protocol: RNA was labeled using Two-Color Quick Amp Labeling Kits (Agilent) according to manufacturer protocol

growth_protocol: Before experiment mice were kept in kept in cages with their brothers (3-6 in cage) at ambient temperature of 22±1°C and 52 ±2% humidity

extract_protocol: RNA extracted using column-based NucleoSpin RNA II kit (Machery-Nagel) according to manufacturer protocol

treatment_protocol: Mice were subjected to chronic social stress. Social stress was performed by placing the animal into the cage belonging to group housed (4-5) male Swiss Webster mice (4 months old).

value: control

tag: strain

value: Swiss Webster

tag: time point

value: 13 days + 5 days of rest

value: stress


title: TFOE_4661_1473A

value: Rv1473 overexpression


title: TFOE_4931_1473A


title: Hippocampus; Stress-13 days + 5 days of rest; Biol. Rep. 1, dye swap

description: Technical replicate of 5-11


title: Hippocampus; Stress-13 days + 5 days of rest; Biol. Rep. 3

description: Technical replicate of 5-32


title: Hippocampus; Stress-13 days + 5 days of rest; Biol. Rep. 2, dye swap

description: Technical replicate of 5-21


title: Hippocampus; Stress-13 days + 5 days of rest; Biol. Rep. 2

description: Technical replicate of 5-22


title: Hippocampus; Stress-13 days; Biol. Rep. 3

description: Technical replicate of 4-32

source_name: Hippocampus; Stress-13 days

value: 13 days

source_name: Hippocampus; Contol-13 days


title: TFOE_1294_1460

value: Rv1460 overexpression


title: TFOE_4497_1460


title: Hippocampus; Stress-13 days + 5 days of rest; Biol. Rep. 1

description: Technical replicate of 5-12


title: Hippocampus; Stress-13 days; Biol. Rep. 3, dye swap

description: Technical replicate of 4-31


title: TFOE_3490_1453

value: Rv1453 overexpression


title: Hippocampus; Stress-13 days; Biol. Rep. 2, dye swap

description: Technical replicate of 4-21


title: Hippocampus; Stress-13 days; Biol. Rep. 2

description: Technical replicate of 4-22


title: TFOE_6788_1423

value: Rv1423 overexpression


title: TFOE_7839_1453


title: Hippocampus; Stress-13 days; Biol. Rep. 1, dye swap

description: Technical replicate of 4-11


title: TFOE_1447_1453


title: TFOE_7748_1460


title: TFOE_1845_1404

value: Rv1404 overexpression


title: TFOE_3615_1423


title: TFOE_5292_1423


title: TFOE_1833_1404


title: TFOE_5670_1404


title: Hippocampus; Stress-8 days; Biol. Rep. 3, dye swap

description: Technical replicate of 3-21

source_name: Hippocampus; Contol-8 days

value: 8 days

source_name: Hippocampus; Stress-8 days


title: TFOE_9640_1395

value: Rv1395 overexpression


title: Hippocampus; Stress-8 days; Biol. Rep. 2

description: Technical replicate of 3-22


title: Hippocampus; Stress-8 days; Biol. Rep. 2, dye swap

description: Technical replicate of 3-21


title: Hippocampus; Stress-13 days; Biol. Rep. 1

description: Technical replicate of 4-12


title: Hippocampus; Stress-acute; Biol. Rep. 3

description: Technical replicate of 1-32

source_name: Hippocampus; Stress-acute

value: acute

source_name: Hippocampus; Contol-acute


title: TFOE_6650_1395


title: Hippocampus; Stress-8 days; Biol. Rep. 1, dye swap

description: Technical replicate of 3-11


title: Hippocampus; Stress-acute; Biol. Rep. 1, dye swap

description: Technical replicate of 1-11


title: Hippocampus; Stress-8 days; Biol. Rep. 3

description: Technical replicate of 3-32


title: Hippocampus; Stress-acute; Biol. Rep. 2

description: Technical replicate of 1-22


title: Hippocampus; Stress-8 days; Biol. Rep. 1

description: Technical replicate of 3-12


title: Hippocampus; Stress-acute; Biol. Rep. 2, dye swap

description: Technical replicate of 1-21


title: TFOE_4670_1359

value: Rv1359 overexpression


title: wheat caryopses, Xi_19, 200, Rothamsted, 2011,  biological rep3

city: Harpenden

first: Artem

last: Lysenko

state: Herts

address: Rothamsted Estate

department: Computational and Systems Biology Department

institute: Rothamsted Research

description: Gene expression data from wheat caryopses harvested at 21 days after anthesis

hyb_protocol: Standard one-cycle cDNA synthesis protocol and hybridization (as described in the GeneChip Expression Analysis Technical Manual).

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Data processing was done in R/Bioconductor, using RMA normalisation method with default settings

organism: Triticum aestivum

source_name: wheat caryopses, from var. Xi_19, 200kg/ha N, grown at Rothamsted, 2011

label_protocol: Standard labeling protocol for plants (as described in the GeneChip Expression Analysis Technical Manual).

extract_protocol: RNA was extracted using a method based on Chang et al. (1993).

value: caryopsys

tag: cultivar

tag: site

value: Rothamsted

tag: year


title: TFOE_3534_1395


title: wheat caryopses, Xi_19, 200, Rothamsted, 2011,  biological rep1


title: wheat caryopses, Xi_19, 200, Rothamsted, 2011,  biological rep2


title: TFOE_3603_1359


title: TFOE_2892_1358

value: Rv1358 overexpression


title: TFOE_9428_1358


title: TFOE_6487_1359


title: TFOE_9869_1379

value: Rv1379 overexpression


title: Hippocampus; Stress-acute; Biol. Rep. 3, dye swap

description: Technical replicate of 1-31

value: control

value: Swiss Webster


title: TFOE_8006_1358


title: wheat caryopses, Marksman, 200, Rothamsted, 2011,  biological rep3

source_name: wheat caryopses, from var. Marksman, 200kg/ha N, grown at Rothamsted, 2011

value: Marksman


title: TFOE_5958_1353c

value: Rv1353c overexpression


title: TFOE_3701_1379


title: TFOE_3352_1379


title: TFOE_7099_1332

value: Rv1332 overexpression


title: TFOE_5758_1353c


title: wheat caryopses, Istabraq, 200, Rothamsted, 2011,  biological rep2

source_name: wheat caryopses, from var. Istabraq, 200kg/ha N, grown at Rothamsted, 2011

value: Istabraq


title: wheat caryopses, Istabraq, 200, Rothamsted, 2011,  biological rep3


title: wheat caryopses, Malacca, 200, Rothamsted, 2011,  biological rep1

source_name: wheat caryopses, from var. Malacca, 200kg/ha N, grown at Rothamsted, 2011

value: Malacca


title: TFOE_1741_1287

value: Rv1287 overexpression


title: Hippocampus; Stress-acute; Biol. Rep. 1

description: Technical replicate of 1-12

value: stress


title: wheat caryopses, Malacca, 200, Rothamsted, 2011,  biological rep2


title: TFOE_4687_1267c

value: Rv1267c overexpression


title: TFOE_2386_1332


title: TFOE_1963_1332


title: wheat caryopses, Marksman, 200, Rothamsted, 2011,  biological rep1


title: wheat caryopses, Cordiale, 200, Rothamsted, 2011,  biological rep1

source_name: wheat caryopses, from var. Cordiale, 200kg/ha N, grown at Rothamsted, 2011

value: Cordiale


title: TFOE_6011_1267c


title: wheat caryopses, Malacca, 200, Rothamsted, 2011,  biological rep3


title: wheat caryopses, Marksman, 200, Rothamsted, 2011,  biological rep2


title: wheat caryopses, Istabraq, 200, Rothamsted, 2011,  biological rep1


title: TFOE_5216_1267c


title: wheat caryopses, Hereward, 200, Rothamsted, 2011,  biological rep3

source_name: wheat caryopses, from var. Hereward, 200kg/ha N, grown at Rothamsted, 2011

value: Hereward


title: wheat caryopses, Hereward, 200, Rothamsted, 2011,  biological rep2


title: TFOE_1701_1353c


title: TFOE_2884_1287


title: TFOE_7245_1287


title: TFOE_2815_1287


title: wheat caryopses, Cordiale, 200, Rothamsted, 2011,  biological rep3


title: wheat caryopses, Xi_19, 200, RAGT, 2011,  biological rep3

source_name: wheat caryopses, from var. Xi_19, 200kg/ha N, grown at RAGT, 2011

value: RAGT


title: TFOE_5936_1255c_B

value: Rv1255c overexpression


title: TFOE_8005_1255c


title: TFOE_4094_1255c


title: wheat caryopses, Hereward, 200, Rothamsted, 2011,  biological rep1

value: caryopsys

value: Rothamsted


title: TFOE_3722_1255c


title: TFOE_6677_1221

value: Rv1221 overexpression


title: wheat caryopses, Xi_19, 200, RAGT, 2011,  biological rep2


title: TFOE_6050_1255c_C


title: wheat caryopses, Marksman, 200, RAGT, 2011,  biological rep3

source_name: wheat caryopses, from var. Marksman, 200kg/ha N, grown at RAGT, 2011


title: wheat caryopses, Malacca, 200, RAGT, 2011,  biological rep1

source_name: wheat caryopses, from var. Malacca, 200kg/ha N, grown at RAGT, 2011


title: TFOE_5098_1219c

value: Rv1219c overexpression


title: wheat caryopses, Marksman, 200, RAGT, 2011,  biological rep2


title: TFOE_3680_1221


title: TFOE_5112_1189

value: Rv1189 overexpression


title: wheat caryopses, Malacca, 200, RAGT, 2011,  biological rep3


title: TFOE_6238_1189


title: TFOE_5462_1221


title: wheat caryopses, Marksman, 200, RAGT, 2011,  biological rep1

value: Marksman


title: TFOE_1808_1186c

value: Rv1186c overexpression


title: wheat caryopses, Malacca, 200, RAGT, 2011,  biological rep2


title: wheat caryopses, Hereward, 200, RAGT, 2011,  biological rep3

source_name: wheat caryopses, from var. Hereward, 200kg/ha N, grown at RAGT, 2011


title: wheat caryopses, Xi_19, 200, RAGT, 2011,  biological rep1


title: wheat caryopses, Istabraq, 200, RAGT, 2011,  biological rep2

source_name: wheat caryopses, from var. Istabraq, 200kg/ha N, grown at RAGT, 2011


title: wheat caryopses, Istabraq, 200, RAGT, 2011,  biological rep1


title: wheat caryopses, Hereward, 200, RAGT, 2011,  biological rep1


title: wheat caryopses, Istabraq, 200, RAGT, 2011,  biological rep3


title: TFOE_6617_1219c


title: TFOE_2229_1219c


title: TFOE_8421_1189


title: TFOE_1734_1186c


title: TFOE_4810_1186c


title: TFOE_4001_1176c

value: Rv1176c overexpression


title: TFOE_9109_1176c


title: TFOE_7962_1167c

value: Rv1167c overexpression


title: TFOE_8236_1176c


title: TFOE_4812_1167c


title: TFOE_8087_1152

value: Rv1152 overexpression


title: TFOE_6929_1167c


title: TFOE_6301_1152_B


title: wheat caryopses, Hereward, 200, RAGT, 2011,  biological rep2


title: TFOE_8017_1152


title: wheat caryopses, Cordiale, 200, RAGT, 2011,  biological rep2

source_name: wheat caryopses, from var. Cordiale, 200kg/ha N, grown at RAGT, 2011


title: TFOE_5850_1152_A


title: wheat caryopses, Xi_19, 350, Rothamsted, 2010,  biological rep2

source_name: wheat caryopses, from var. Xi_19, 350kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Xi_19, 350, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Xi_19, 200, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Xi_19, 200kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Xi_19, 200, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Xi_19, 100, Rothamsted, 2010,  biological rep1

source_name: wheat caryopses, from var. Xi_19, 100kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Marksman, 350, Rothamsted, 2010,  biological rep2

source_name: wheat caryopses, from var. Marksman, 350kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Xi_19, 350, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Cordiale, 200, RAGT, 2011,  biological rep3


title: wheat caryopses, Xi_19, 100, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Xi_19, 200, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Xi_19, 100, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Marksman, 350, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Marksman, 350, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Cordiale, 200, Rothamsted, 2011,  biological rep2


title: TFOE_4316_1151c

value: Rv1151c overexpression


title: TFOE_7811_1151c


title: TFOE_4839_1129c

value: Rv1129c overexpression


title: TFOE_1474_1152


title: TFOE_1203_1151c


title: TFOE_3936_1129c


title: TFOE_3901_1129c


title: TFOE_4036_1049

value: Rv1049 overexpression


title: TFOE_8681_1049


title: TFOE_2218_1049


title: wheat caryopses, Marksman, 200, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Marksman, 200kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Marksman, 200, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Marksman, 200, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Marksman, 100, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Marksman, 100kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Marksman, 100, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Marksman, 100, Rothamsted, 2010,  biological rep1


title: TFOE_3474_1033c

value: Rv1033c overexpression


title: TFOE_8738_1033c


title: TFOE_2910_1033c


title: TFOE_9385_1027c

value: Rv1027c overexpression


title: TFOE_5333_1027c


title: TFOE_3781_1027c_2


title: wheat caryopses, Malacca, 200, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Malacca, 200kg/ha N, grown at Rothamsted, 2010

value: Malacca


title: wheat caryopses, Malacca, 350, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Malacca, 350kg/ha N, grown at Rothamsted, 2010


title: TFOE_3774_1019

value: Rv1019 overexpression


title: wheat caryopses, Malacca, 350, Rothamsted, 2010,  biological rep1

value: caryopsys


title: wheat caryopses, Malacca, 350, Rothamsted, 2010,  biological rep2

value: Rothamsted


title: wheat caryopses, Malacca, 200, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Istabraq, 350, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Istabraq, 350kg/ha N, grown at Rothamsted, 2010

value: Istabraq


title: wheat caryopses, Malacca, 100, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Malacca, 100kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Malacca, 100, Rothamsted, 2010,  biological rep2


title: TFOE_6892_1019


title: TFOE_8486_0981_b

value: Rv0981 overexpression


title: TFOE_5714_1019


title: TFOE_3781_1027c_1


title: TFOE_7807_0981


title: TFOE_8794_0981


title: wheat caryopses, Malacca, 100, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Istabraq, 350, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Istabraq, 350, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Istabraq, 200, Rothamsted, 2010,  biological rep2

source_name: wheat caryopses, from var. Istabraq, 200kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Istabraq, 100, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Istabraq, 100kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Istabraq, 200, Rothamsted, 2010,  biological rep1


title: TFOE_4707_0981_c


title: TFOE_2230_0981


title: wheat caryopses, Istabraq, 100, Rothamsted, 2010,  biological rep1


title: TFOE_8426_0967

value: Rv0967 overexpression


title: wheat caryopses, Istabraq, 200, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Istabraq, 100, Rothamsted, 2010,  biological rep2


title: TFOE_4620_0903c

value: Rv0903c overexpression


title: TFOE_6973_0967


title: TFOE_4073_0894

value: Rv0894 overexpression


title: wheat caryopses, Hereward, 350, Rothamsted, 2010,  biological rep2

source_name: wheat caryopses, from var. Hereward, 350kg/ha N, grown at Rothamsted, 2010

value: Hereward


title: TFOE_5872_0894


title: TFOE_7140_0903c


title: TFOE_4831_0903c


title: wheat caryopses, Hereward, 350, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Cordiale, 200, RAGT, 2011,  biological rep1

value: Cordiale

value: RAGT


title: TFOE_1581_0894


title: TFOE_9861_0891c

value: Rv0891c overexpression


title: TFOE_3705_0891c


title: wheat caryopses, Hereward, 200, Rothamsted, 2010,  biological rep1

source_name: wheat caryopses, from var. Hereward, 200kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Hereward, 200, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Hereward, 350, Rothamsted, 2010,  biological rep1


title: TFOE_7144_0967


title: wheat caryopses, Hereward, 200, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Hereward, 100, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Hereward, 100kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Hereward, 100, Rothamsted, 2010,  biological rep2


title: wheat caryopses, Cordiale, 350, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Cordiale, 350kg/ha N, grown at Rothamsted, 2010


title: TFOE_3083_0891c


title: wheat caryopses, Cordiale, 350, Rothamsted, 2010,  biological rep1


title: TFOE_9569_0844c

value: Rv0844c overexpression


title: TFOE_9682_0880

value: Rv0880 overexpression


title: TFOE_8078_0880


title: TFOE_1190_0880


title: TFOE_6292_0844c


title: wheat caryopses, Cordiale, 350, Rothamsted, 2010,  biological rep2


title: TFOE_9932_0827c

value: Rv0827c overexpression


title: TFOE_7662_0827c_A


title: TFOE_9113_0827c_B


title: wheat caryopses, Hereward, 100, Rothamsted, 2010,  biological rep1


title: TFOE_9505_0827c


title: wheat caryopses, Cordiale, 200, Rothamsted, 2010,  biological rep2

source_name: wheat caryopses, from var. Cordiale, 200kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Cordiale, 200, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Cordiale, 200, Rothamsted, 2010,  biological rep3


title: wheat caryopses, Xi_19, 200, RAGT, 2010,  biological rep3

source_name: wheat caryopses, from var. Xi_19, 200kg/ha N, grown at RAGT, 2010


title: wheat caryopses, Cordiale, 100, Rothamsted, 2010,  biological rep3

source_name: wheat caryopses, from var. Cordiale, 100kg/ha N, grown at Rothamsted, 2010


title: wheat caryopses, Cordiale, 100, Rothamsted, 2010,  biological rep1


title: wheat caryopses, Cordiale, 100, Rothamsted, 2010,  biological rep2


title: TFOE_6386_0823c

value: Rv0823c overexpression


title: TFOE_7749_0823c


title: TFOE_8344_0844c


title: wheat caryopses, Marksman, 200, RAGT, 2010,  biological rep1

source_name: wheat caryopses, from var. Marksman, 200kg/ha N, grown at RAGT, 2010

value: Marksman


title: wheat caryopses, Marksman, 200, RAGT, 2010,  biological rep2


title: TFOE_9343_0821c

value: Rv0821c overexpression


title: TFOE_5531_0823c


title: TFOE_5436_0821c


title: TFOE_1363_0823c_B


title: TFOE_4668_0821c


title: TFOE_6079_0818

value: Rv0818 overexpression


title: wheat caryopses, Malacca, 200, RAGT, 2010,  biological rep3

source_name: wheat caryopses, from var. Malacca, 200kg/ha N, grown at RAGT, 2010

value: caryopsys

value: Malacca


title: wheat caryopses, Istabraq, 200, RAGT, 2010,  biological rep3

source_name: wheat caryopses, from var. Istabraq, 200kg/ha N, grown at RAGT, 2010

value: Istabraq


title: wheat caryopses, Malacca, 200, RAGT, 2010,  biological rep2


title: wheat caryopses, Malacca, 200, RAGT, 2010,  biological rep1


title: TFOE_8354_0792c_C

value: Rv0792c overexpression


title: TFOE_4612_0792c


title: TFOE_4698_0818


title: TFOE_6585_0792c


title: wheat caryopses, Xi_19, 200, RAGT, 2010,  biological rep1


title: wheat caryopses, Hereward, 200, RAGT, 2010,  biological rep3

source_name: wheat caryopses, from var. Hereward, 200kg/ha N, grown at RAGT, 2010


title: wheat caryopses, Istabraq, 200, RAGT, 2010,  biological rep2


title: wheat caryopses, Cordiale, 200, RAGT, 2010,  biological rep3

source_name: wheat caryopses, from var. Cordiale, 200kg/ha N, grown at RAGT, 2010


title: wheat caryopses, Istabraq, 200, RAGT, 2010,  biological rep1


title: wheat caryopses, Malacca, 200, Rothamsted, 2010,  biological rep2

source_name: wheat caryopses, from var. Malacca, 200kg/ha N, grown at Rothamsted, 2010

value: Rothamsted


title: TFOE_2591_0767c

value: Rv0767c overexpression


title: TFOE_6352_0792c


title: TFOE_3681_0792c


title: TFOE_8010_0767c


title: TFOE_2777_0757

value: Rv0757 overexpression


title: TFOE_1634_0757


title: TFOE_9126_0744c

value: Rv0744c overexpression


title: TFOE_1255_0757_b


title: TFOE_9178_0744c


title: TFOE_5762_0818


title: TFOE_6289_0737

value: Rv0737 overexpression


title: wheat caryopses, Hereward, 200, RAGT, 2010,  biological rep1

value: Hereward

value: RAGT


title: TFOE_3894_0744c


title: TFOE_4251_0767c


title: TFOE_2546_0757


title: wheat caryopses, Hereward, 200, RAGT, 2010,  biological rep2


title: TFOE_8624_0737


title: TFOE_1168_0737


title: TFOE_6283_0735

value: Rv0735 overexpression


title: TFOE_4696_0735


title: wheat caryopses, Xi_19, 200, RAGT, 2010,  biological rep2


title: wheat caryopses, Marksman, 200, RAGT, 2010,  biological rep3


title: wheat caryopses, Xi_19, 350, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Xi_19, 350kg/ha N, grown at Rothamsted, 2009


title: TFOE_8722_0691c

value: Rv0691c overexpression


title: TFOE_2966_0735


title: wheat caryopses, Cordiale, 200, RAGT, 2010,  biological rep2

value: Cordiale


title: TFOE_3131_0691c


title: TFOE_4945_0691c


title: wheat caryopses, Cordiale, 200, RAGT, 2010,  biological rep1


title: wheat caryopses, Marksman, 200, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Marksman, 200kg/ha N, grown at Rothamsted, 2009

value: Marksman


title: wheat caryopses, Marksman, 350, Rothamsted, 2009,  biological rep1

source_name: wheat caryopses, from var. Marksman, 350kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Xi_19, 100, Rothamsted, 2009,  biological rep2

source_name: wheat caryopses, from var. Xi_19, 100kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Xi_19, 200, Rothamsted, 2009,  biological rep2

source_name: wheat caryopses, from var. Xi_19, 200kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Marksman, 350, Rothamsted, 2009,  biological rep2


title: TFOE_8012_0681

value: Rv0681 overexpression


title: wheat caryopses, Marksman, 350, Rothamsted, 2009,  biological rep3


title: TFOE_8204_0681


title: wheat caryopses, Marksman, 100, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Marksman, 100kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Xi_19, 100, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Marksman, 200, Rothamsted, 2009,  biological rep2


title: TFOE_6427_0681


title: wheat caryopses, Malacca, 350, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Malacca, 350kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Xi_19, 350, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Marksman, 100, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Marksman, 100, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Xi_19, 100, Rothamsted, 2009,  biological rep3


title: TFOE_3679_0681


title: wheat caryopses, Xi_19, 350, Rothamsted, 2009,  biological rep1


title: TFOE_3146_0678_2

value: Rv0678 overexpression


title: wheat caryopses, Malacca, 350, Rothamsted, 2009,  biological rep2

value: caryopsys


title: TFOE_3146_0678_1


title: wheat caryopses, Xi_19, 200, Rothamsted, 2009,  biological rep3


title: wheat caryopses, Xi_19, 200, Rothamsted, 2009,  biological rep1


title: TFOE_9349_0674

value: Rv0674 overexpression


title: wheat caryopses, Malacca, 200, Rothamsted, 2009,  biological rep2

source_name: wheat caryopses, from var. Malacca, 200kg/ha N, grown at Rothamsted, 2009

value: Malacca


title: TFOE_9487_0678


title: TFOE_6482_0674


title: TFOE_8059_0674


title: wheat caryopses, Marksman, 200, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Malacca, 100, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Malacca, 100kg/ha N, grown at Rothamsted, 2009


title: TFOE_7951_0653c

value: Rv0653c overexpression


title: TFOE_3495_0653c


title: TFOE_2952_0653c_A


title: wheat caryopses, Malacca, 200, Rothamsted, 2009,  biological rep1

value: Rothamsted


title: wheat caryopses, Malacca, 350, Rothamsted, 2009,  biological rep1


title: TFOE_3642_0653c


title: wheat caryopses, Malacca, 100, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Istabraq, 350, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Istabraq, 350kg/ha N, grown at Rothamsted, 2009

value: Istabraq


title: TFOE_5155_0623

value: Rv0623 overexpression


title: TFOE_5381_0623


title: wheat caryopses, Istabraq, 200, Rothamsted, 2009,  biological rep1

source_name: wheat caryopses, from var. Istabraq, 200kg/ha N, grown at Rothamsted, 2009


title: TFOE_7909_0608

value: Rv0608 overexpression


title: wheat caryopses, Istabraq, 350, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Istabraq, 200, Rothamsted, 2009,  biological rep3


title: TFOE_2192_0653c_B


title: TFOE_4083_0623


title: TFOE_2238_0608


title: wheat caryopses, Istabraq, 100, Rothamsted, 2009,  biological rep2

source_name: wheat caryopses, from var. Istabraq, 100kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Istabraq, 350, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Istabraq, 100, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Istabraq, 100, Rothamsted, 2009,  biological rep3


title: wheat caryopses, Hereward, 350, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Hereward, 350kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Malacca, 100, Rothamsted, 2009,  biological rep1


title: TFOE_8883_0602c

value: Rv0602c overexpression


title: TFOE_6605_0608


title: TFOE_7656_0602c


title: wheat caryopses, Istabraq, 200, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Hereward, 350, Rothamsted, 2009,  biological rep1

value: Hereward


title: TFOE_9543_0602c


title: TFOE_4634_0599c

value: Rv0599c overexpression


title: TFOE_5228_0599c


title: wheat caryopses, Hereward, 100, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Hereward, 100kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Hereward, 100, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Hereward, 200, Rothamsted, 2009,  biological rep1

source_name: wheat caryopses, from var. Hereward, 200kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Hereward, 350, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Hereward, 100, Rothamsted, 2009,  biological rep2


title: TFOE_6778_0586

value: Rv0586 overexpression


title: TFOE_3450_0599c


title: TFOE_4503_0586_B


title: wheat caryopses, Hereward, 200, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Cordiale, 350, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Cordiale, 350kg/ha N, grown at Rothamsted, 2009


title: TFOE_3199_0586_C


title: TFOE_2275_0678


title: TFOE_7778_0576_C

value: Rv0576 overexpression


title: TFOE_3439_0560c

value: Rv0560c overexpression


title: wheat caryopses, Cordiale, 350, Rothamsted, 2009,  biological rep2

value: Cordiale


title: TFOE_9438_0494_B

value: Rv0494 overexpression


title: wheat caryopses, Cordiale, 200, Rothamsted, 2009,  biological rep3

source_name: wheat caryopses, from var. Cordiale, 200kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Cordiale, 350, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Cordiale, 200, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Cordiale, 200, Rothamsted, 2009,  biological rep2


title: wheat caryopses, Cordiale, 100, Rothamsted, 2009,  biological rep2

source_name: wheat caryopses, from var. Cordiale, 100kg/ha N, grown at Rothamsted, 2009


title: wheat caryopses, Cordiale, 100, Rothamsted, 2009,  biological rep1


title: wheat caryopses, Cordiale, 100, Rothamsted, 2009,  biological rep3


title: TFOE_6335_0576_B


title: TFOE_7387_0491_B

value: Rv0491 overexpression


title: TFOE_2722_0491


title: TFOE_1075_0494_A


title: TFOE_1660_0485_B

value: Rv0485 overexpression


title: Mutant testis, replicate 4

city: ITHACA

first: John

last: Schimenti

state: New York

department: Biomedical Sciences

institute: Cornell University

hyb_protocol: Hybridization was performed using Affymetrix MOE430 2.0 gene chips that represent more than 39000 uniquely expressed murine transcripts

scan_protocol: Washing and scanning were also done according to Affymetrix protocols.

data_processing: The signals from scanning were analyzed using Affymetrix GCOS software. The normalized signals were then analyzed using R software using a standard t-test and genes were considered up- or down-regulated if they showed > 2 fold difference in expression with a p value of < 0.01

source_name: Mutant testis

label_protocol: Extracted RNA was then converted to biotin labeled cRNA fragments according to the protocols described by Affymetrix.

growth_protocol: Mice were grown to 27 day age from birth

extract_protocol: RNA was prepared from whole testes of WT and mutant mice using Trizol and purified using RNeasy columns. Briefly, the testes from each mouse were homogenized in 700ul Trizol and total RNA was extracted using 140ul chloroform. The aqueous phase was then separated by centrifugation and 525ul of 100% ethanol was added to it. This phase was then directly loaded onto a Qiagen RNeasy mini column and purified according to the manufacturer’s instructions.

treatment_protocol: no treatment

tag: genotype/variation

tag: age

value: 27 days

value: testis


title: Mutant testis, replicate 3


title: TFOE_1488_0485


title: TFOE_5597_0485_C


title: TFOE_2838_0494_C


title: TFOE_9310_0491_C


title: Wild-type testis, replicate 4

source_name: Wild-type testis

value: wild type:Brwd1+/-


title: Wild-type testis, replicate 2


title: TFOE_6945_0474_A

value: Rv0474 overexpression


title: Mutant testis, replicate 1


title: Wild-type testis, replicate 3


title: D_DENCcl4Tlr4wt C3H/HeOuJ Abx_12

city: New York

last: Schwabe

address: 1150 St. Nicholas Ave

institute: Columbia University

description: Gene expression of livers 10-12 week old mice, sacrficed 2 hours after liver resection.

hyb_protocol: 10 μg of aRNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

source_name: Livers of wt C3H/HeOuJ mice

label_protocol: 100 ng RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix).

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by Trizol followed by column purification (Qiagen) and quantification by NanoDrop Spectrophotometer.

treatment_protocol: DEN (100 mg/kg) was administered by injection at 12 weeks. CCl4 (0.50 ml/kg) was administered by injection at 13 and 15 weeks. Antibotics (a combination of ampicillin (1 g/l), neomycin (1 g/l), metronidazole (1 g/l) and vancomycin (500 mg/l) were administered in drinking water for 2 weeks starting at 10 weeks. Mice were sacrificed 48 hours after the last CCl4 injection.

tag: gender

value: male

value: WT C3H/HeOuJ

value: 15 weeks

value: liver

tag: treatment

value: treated with antibiotics for 2 weeks starting at 10 weeks, DEN at 12 weeks, CCl4 (0.50 ml/kg) at 13 and 15 weeks and sacrificed at 15 weeks 48 hours after the last dose of CCl4.


title: D_DENCcl4Tlr4wt C3H/HeOuJ Abx_14

tag: genotype

tag: tissue


title: C_DENCcl4Tlr4mut C3H/HeJ (P712H)_11

source_name: Livers of mutant C3H/HeJ mice (Tlr4P712H)

value: TLR4 mutant C3H/HeJ (Tlr4P712H)

value: treated with DEN (100 mg/kg) at 12 weeks, CCl4 (0.50 ml/kg) at 13 and 15 weeks and sacrificed at 15 weeks 48 hours after the last dose of CCl4.


title: Mutant testis, replicate 2


title: D_DENCcl4Tlr4wt C3H/HeOuJ Abx_13


title: TFOE_2101_0494_B

tag: experiment


title: D_DENCcl4Tlr4wt C3H/HeOuJ Abx_15


title: TFOE_1632_0474_C

tag: stress


title: Wild-type testis, replicate 1


title: TFOE_1557_0474_B

tag: time (hours)


title: TFOE_9656_0474_B

tag: concentration (ng)


title: TFOE_8690_0472c

value: Rv0472c overexpression


title: TFOE_5648_0472c


title: C_DENCcl4Tlr4mut C3H/HeJ (P712H)_09


title: TFOE_9476_0465c_B

value: Rv0465c overexpression


title: C_DENCcl4Tlr4mut C3H/HeJ (P712H)_10


title: TFOE_8951_0465c_c


title: TFOE_3221_0472c


title: C_DENCcl4Tlr4mut C3H/HeJ (P712H)_08


title: B_DENCcl4Tlr4wt C3H/HeOuJ_07

source_name: Livers of WT C3H/HeOuJ mice


title: TFOE_6247_0576

value: Rv0576 overexpression


title: B_DENCcl4Tlr4wt C3H/HeOuJ_06


title: TFOE_4248_0452

value: Rv0452 overexpression


title: TFOE_7468_0452


title: TFOE_2670_0465c_a


title: TFOE_7861_0465c_b


title: B_DENCcl4Tlr4wt C3H/HeOuJ_05


title: B_DENCcl4Tlr4wt C3H/HeOuJ_04


title: A_Tlr4wtun3_H03

source_name: Livers of WT C3H/HeOuJ mice sacrificed at 15 weeks.


title: TFOE_5809_0465c_C


title: A_Tlr4wtun2_H02


title: TFOE_2006_0445c

value: Rv0445c overexpression


title: TFOE_2520_0452


title: TFOE_2579_0445c_B


title: A_Tlr4wtun1_H01


title: TFOE_6963_0377_B

value: Rv0377 overexpression


title: wheat caryopses, Hereward, 200, Rothamsted, 2009,  biological rep3

value: caryopsys

value: Hereward

value: Rothamsted


title: TFOE_7012_0445c_C


title: TFOE_6732_0353

value: Rv0353 overexpression


title: TFOE_9336_0353


title: TFOE_1124_0353


title: TFOE_7521_0377_C


title: TFOE_7445_0348_A

value: Rv0348 overexpression


title: TFOE_5061_0339c

value: Rv0339c overexpression


title: TFOE_5847_0339c_C


title: TFOE_3770_0348_B


title: TFOE_4348_0339c_B


title: TFOE_6557_0330c

value: Rv0330c overexpression


title: TFOE_4688_0330c


title: TFOE_7856_0348


title: TFOE_9653_0328

value: Rv0328 overexpression


title: TFOE_3448_0330c


title: TFOE_6994_0328_B


title: TFOE_8699_0324

value: Rv0324 overexpression


title: TFOE_3809_0324


title: TFOE_6147_0324


title: TFOE_4095_0324_B


title: TFOE_5627_0324_B


title: TFOE_9252_0330c


title: TFOE_6251_0328_C


title: TFOE_7585_0302_B

value: Rv0302 overexpression


title: TFOE_6324_0302


title: TFOE_5740_0275c

value: Rv0275c overexpression


title: TFOE_4853_0302_C


title: TFOE_7768_0324_C


title: TFOE_5653_0275c_B


title: TFOE_3143_0275c_C


title: TFOE_6782_0377


title: TFOE_5046_0273c

value: Rv0273c overexpression


title: TFOE_7974_0273c_C


title: TFOE_7867_0260c

value: Rv0260c overexpression


title: TFOE_7279_0238

value: Rv0238 overexpression


title: TFOE_2419_0273c_B


title: TFOE_7938_0260c


title: TFOE_1122_0260c


title: TFOE_1399_0238


title: TFOE_8581_0232_C

value: Rv0232 overexpression


title: TFOE_9029_0232_B


title: TFOE_1878_0238


title: TFOE_3113_0232


title: TFOE_7879_0232


title: TFOE_5687_0195

value: Rv0195 overexpression


title: TFOE_1079_0232_C


title: TFOE_8843_0144

value: Rv0144 overexpression


title: TFOE_9056_0195


title: TFOE_3264_0144_B


title: TFOE_6052_0212c_C

value: Rv0212c overexpression


title: TFOE_1872_0144_C


title: TFOE_9308_0212c


title: TFOE_5169_0195


title: TFOE_5458_0165c

value: Rv0165c overexpression


title: TFOE_2934_0165c


title: TFOE_6084_0182c

value: Rv0182c overexpression


title: TFOE_9147_0144


title: TFOE_4328_0158_C

value: Rv0158 overexpression


title: TFOE_4602_0165c


title: TFOE_3258_0182c


title: TFOE_1153_0212c_B


title: TFOE_2329_0158


title: TFOE_9582_0158


title: TFOE_2281_0182c


title: TFOE_4110_0135c

value: Rv0135c overexpression


title: TFOE_3998_0117

value: Rv0117 overexpression


title: TFOE_8531_0117


title: TFOE_3110_0135c


title: TFOE_5569_0135c


title: TFOE_4399_0117_C


title: TFOE_1280_0117


title: TFOE_7211_0081_2B

value: Rv0081 overexpression


title: TFOE_8710_0081


title: TFOE_4428_0081_100ng


title: TFOE_6738_0081


title: 843

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

institute: Mayo Clinic

hyb_protocol: Labeled samples were subsequently processed according to manufacturer’s instructions for the Affymetrix miRNA Array 1.0 (Santa Clara, CA).  After hybridization for 16 h at 48oC, the arrays were washed and stained in an Affymetrix Fluidics station 450

scan_protocol: scanned in an Affymetrix 3000 7G scanner using Command Console (AGCC)

data_processing: The data were processed using RMA in Partek

label_protocol: Samples were labeled using the Genisphere FlashTag Biotin HSR kit (Hatfield, PA).  One microgram of total RNA was incubated with ATP and Poly A polymerase to add a 3’ polyA tail. A ligation reaction was then performed to covalently attach to the miRNA population a multiple-biotin molecule containing a 3DNA dendrimer

extract_protocol: TRIzol with O/N precipitation in 100% isopropanol

value: R-Het


title: TFOE_8209_0078

value: Rv0078 overexpression


title: 791

value: WT


title: 825

value: A-KO R-Het


title: TFOE_2284_0081


title: TFOE_4177_0081_3B


title: 826

value: A-KO


title: 817


title: 844


title: 788


title: TFOE_4225_0078_2


title: 853


title: TFOE_4167_0067c

value: Rv0067c overexpression


title: TFOE_1393_0067c


title: 794


title: TFOE_2446_0078


title: 800


title: 579


title: TFOE_4225_0078_1


title: 585


title: 821


title: 556


title: TFOE_6711_0067c


title: 786


title: TFOE_3190_0054

value: Rv0054 overexpression


title: 590


title: TFOE_3938_0054


title: TFOE_2431_0054


title: TFOE_7135_0047c

value: Rv0047c overexpression


title: 4 hours dex C pool_2

city: Seattle

first: Nicholas

last: Burwick

state: WA

address: 1100 Fairview Ave N , D5/100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

description:
4C replicate 2
fractionated polysome pooled RNA

hyb_protocol: standard illumina hybridization protocol

scan_protocol: standard illumina scanning protocol

data_processing: Total RNA samples were quantile normalized  using the Bioconductor package 'lumi.'   Fractionated RNA samples were normalized using ERCC spike-in controls by employing the  loess.normalize function in the Bioconductor package 'affy.'

label_protocol: RNA samples were converted to  cDNA and biotin-labeled for microarray analysis using Ambion's Illumina total prep RNAamplification kit

growth_protocol: MM1.S cells were grown in log phase in 10% FBS/RPMI

extract_protocol: Total RNA samples were extracted in TriZol per standard protocol. Polysome pooled RNA was precipitated out of sucrose using isoproponal followed by phenol:chloroform purification

treatment_protocol: MM1.S cells were treated with 1uM dexamethasone for 0 or 4 hours

tag: cell line

tag: cell type

value: myeloma


title: 4 hours dex C pool_1

description:
4C replicate 1
fractionated polysome pooled RNA


title: TFOE_9257_0043c

value: Rv0043c overexpression


title: TFOE_2911_0047c


title: 4 hours dex B pool_1

description:
4B replicate 1
fractionated polysome pooled RNA


title: Sox4 in Ph+ ALL (Cre-2)

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: Total RNA from Ph+ ALL

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

tag: strain

value: 129SvEv x C57BL/6J

value: 5 weeks

value: BCR-ABL1 transformed pre-B cells

tag: disease state

value: BCR-ABL1-driven ALL

tag: transduction


title: Sox4 in Ph+ ALL (ERT2-3)

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)


title: Sox4 in Ph+ ALL (ERT2-1)


title: Sox4 in Ph+ ALL (Cre-1)


title: Sox4 in Ph+ ALL (Cre-3)


title: Body, 18mM, replicate 3

city: dijon

first: Stéphane

last: Fraichard

state: Please select...

address: 6 bd gabriel

country: France

institute: csga UMR 6265 CNRS INRA  Université de Bourgogne

description:
CT 3
Gene expression after 12hr in 18mM-caffeine treated drosophila thorax and abdomen

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%),

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters (protocol GE1_105_Jan09 and Grid: 018972_D_F_20100204 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Drosophila melanogaster

source_name: thorax and abdomen, 18mM replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input quick Amp Labelling kit, one color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Four-day-old adult males were starved during 12 hours with a filter paper impregnated with water at 25°C,

extract_protocol: RNA was prepared using Isol RNA lysis reagent (5Prime) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Starved male were transfered on caffeine-rich medium (18mM) or normal medium (control) during 12hours at 25°C,

value: thorax and abdomen

value: Male


title: Body, 18mM, replicate 2

description:
CT 2
Gene expression after 12hr in 18mM-caffeine treated drosophila thorax and abdomen

source_name: thorax and abdomen, 18mM replicate 2


title: Body, 0mM, replicate 3

description:
CC 3
Gene expression after 12hr in 0mM-caffeine treated drosophila thorax and abdomen

source_name: thorax and abdomen, 0mM replicate 3


title: 4 hours dex A pool_2

description:
4A replicate 2
fractionated polysome pooled RNA


title: 0 hours dex total RNA_2

description:
0T replicate 2
total RNA


title: 4 hours dex B pool_2

description:
4B replicate 2
fractionated polysome pooled RNA


title: TFOE_5167_0047c


title: Sox4 in Ph+ ALL (ERT2-2)


title: TFOE_8173_0038_1

value: Rv0038 overexpression


title: TFOE_8173_0038_2


title: TFOE_8850_0038


title: TFOE_2830_0042c

value: Rv0042c overexpression


title: TFOE_8864_0042c_B


title: Body, 18mM, replicate 1

description:
CT 1
Gene expression after 12hr in 18mM-caffeine treated drosophila thorax and abdomen

source_name: thorax and abdomen, 18mM replicate 1


title: 4 hours dex total RNA_1

description:
4T replicate 1
total RNA


title: TFOE_2455_0042c_C


title: 0 hours dex C pool_1

description:
0C replicate 1
fractionated polysome pooled RNA


title: 825

hyb_protocol: cRNA products were column purified and hybridized, per Illuminas protocol, onto Illumina Mouse Ref8 Beadchips for 16 hours at 58° C.  Following hybridization, the arrays were washed, stained with streptavidin-cy3 conjugate

scan_protocol: scanned in an Illumina BeadArray Reader

data_processing: The data were normalized using fastlo normalization in R

label_protocol: Labeling of high quality samples was performed according to manufacturer’s instructions for the Illumina Total Prep RNA Amplification Kit (Life Technologies, Grand Island, NY).   Briefly, 200 ng of total RNA was reverse transcribed with T7 Oligo d(T) to create second strand cDNA.  Subsequently, the products were column purified and then in vitro transcribed to generate biotin-labeled cRNA.

tag: Sex

value: M

tag: ChIP

tag: chip position

value: H


title: 0 hours dex C pool_2

description:
0C replicate 2
fractionated polysome pooled RNA


title: Body, 0mM, replicate 1

description:
CC 1
Gene expression after 12hr in 0mM-caffeine treated drosophila thorax and abdomen

source_name: thorax and abdomen, 0mM replicate 1


title: 4 hours dex A pool_1

description:
4A replicate 1
fractionated polysome pooled RNA


title: TFOE_5294_0038


title: 0 hours dex B pool_1

description:
0B replicate 1
fractionated polysome pooled RNA


title: TFOE_3297_0043c


title: TFOE_5695_0043c


title: TFOE_9276_0023_B

value: Rv0023 overexpression


title: 0 hours dex total RNA_1

description:
0T replicate 1
total RNA


title: 843

value: R-Het

tag: age

value: G


title: Body, 0mM, replicate 2

description:
CC 2
Gene expression after 12hr in 0mM-caffeine treated drosophila thorax and abdomen

source_name: thorax and abdomen, 0mM replicate 2

tag: gender


title: TFOE_8686_0023_C


title: TFOE_7607_0022c

value: Rv0022c overexpression


title: TFOE_4883_0023


title: 853

value: A-KO

value: F


title: 0 hours dex B pool_2

description:
0B replicate 2
fractionated polysome pooled RNA

value: myeloma


title: 844

value: WT

value: E


title: TFOE_6389_0022c_B


title: TFOE_1636_0022c_C


title: 0 hours dex A pool_2

description:
0A replicate 2
fractionated polysome pooled RNA


title: 4 hours dex total RNA_2

description:
4T replicate 2
total RNA


title: 0 hours dex A pool_1

description:
0A replicate 1
fractionated polysome pooled RNA


title: 826

value: C


title: 821

value: A-KO R-Het

value: D


title: 791

value: B


title: 590


title: 800


title: TFOE_9607_0020c_C

value: Rv0020c overexpression


title: 788

value: A


title: 585

value: M


title: NPC [D9_HDF51IPS1_Split2_153_2757_2_1]

city: San Diego

first: Ronald

last: Coleman

state: California

address: 3215 Merryfield Row

department: Chemical Physiology

institute: The Scripps Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: NPC

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

extract_protocol: RNA was extracte using the Life Technologies mirVana isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Differentiated


title: NPC [D9_WA09_Split2_87_2744_2_1]


title: TFOE_9153_0020c_B


title: 817

description: damaged during processing; did not scan well; excluded from analyses

value: H


title: NPC [D9_HDF69iPS502_Split2_690_2751_2_1]


title: 786

value: R-Het


title: Fibroblast [HDF417__703_2726_1_1TG]

source_name: Fibroblast

value: Primary


title: TFOE_8440_0019c_C

value: Rv0019c overexpression


title: WA09 ESC [WA09__87_2725_1_1TG]

source_name: WA09 ESC

value: ESC


title: 794

value: A-KO


title: TFOE_7590_0019c


title: TFOE_7264_0019c_A


title: TFOE_2323_0020c


title: WA09 ESC [WA09__87_2733_1_5]


title: NPC [D9_WA09__87_2705_1_1TG]


title: NPC [D9_87_1469_1_1]


title: Empty vector (line9)-rep2

status: Public on Jul 03 2014

city: Bellaterra (Cerdanyola del Vallés)

first: Sonia

last: Campo

state: Barcelona

address: Parc de Recerca UAB Edifici CRAG, Campus UAB

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

organism: Oryza sativa Japonica Group

source_name: Empty vector (line9)

label_protocol: 100ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the LowInputQuick Amp Labeling kit  (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

tag: genotype/variation

value: empty vector

tag: growth condition

value: hydroponic culture

tag: line

value: leaves

value: 15 days


title: 579

tag: genotype

value: C


title: 556

value: WT


title: HDF69 IPSC [HDF69iPS502__690_2640_1_2]

source_name: HDF69 IPSC

value: iPSC


title: Empty vector (line3)-rep3

source_name: Empty vector (line3)

tag: tissue


title: HDF51 IPSC [HDF51iPS509__662_2637_1_2]

source_name: HDF51 IPSC


title: Empty vector (line3)-rep2


title: LC-COPD.20

city: Seville

last: Molina-Pinelo

address: Avda. MAnuel Siurot s/n

institute: IBIS

description: test

data_processing: Relative quantification of gene expression was determined using the comparative cycle threshold method (2(-ddCt)) as previously described Ref : Livak, K. J., and T. D. Schmittgen. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408. .

label: FAM

source_name: bronchoalveolar cell fraction

label_protocol: FAM

extract_protocol: Total RNA, containing small RNA, was extracted from bronchoalveolar cell fraction by Trizol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

value: bronchoalveolar cell fraction

tag: disease

value: LC and COPD


title: LC-COPD.19

description: test


title: LC-COPD.21

description: test


title: Empty vector (line9)-rep1


title: OsCPK4-rice (line13)-rep3

source_name: OsCPK4-rice (line13)

value: OsCPK4 transgenic


title: LC-COPD.18

description: test


title: Empty vector (line9)-rep3


title: LC-COPD.17

description: test


title: OsCPK4-rice (line 1)-rep3

source_name: OsCPK4-rice (line 1)


title: LC-COPD.16

description: test


title: OsCPK4-rice (line13)-rep2


title: LC-COPD.12

description: test


title: LC-COPD.13

description: test


title: LC-COPD.14

description: test


title: LC-COPD.10

description: test


title: LC-COPD.15

description: test


title: LC-COPD.11

description: test


title: OsCPK4-rice (line 1)-rep2


title: Empty vector (line3)-rep1


title: OsCPK4-rice (line 1)-rep1


title: LC-COPD.9

description: test


title: LC-COPD.8

description: test


title: LC-COPD.7

description: test


title: LC-COPD.6

description: test


title: LC-COPD.5

description: test


title: LC-COPD.3

description: test


title: LC-COPD.4

description: test


title: LC-COPD.1

description: test


title: LC-COPD.2

description: test


title: LC.27

description: test

value: LC


title: LC.22

description: test


title: LC.26

description: test


title: LC.24

description: test


title: LC.23

description: test


title: LC.20

description: test


title: LC.17

description: test


title: LC.19

description: test


title: LC.8

description: test


title: LC.12

description: test


title: LC.13

description: test


title: LC.10

description: test


title: LC.15

description: test


title: LC.11

description: test


title: LC.14

description: test


title: LC.6

description: test


title: LC.25

description: test


title: LC.7

description: test


title: LC.9

description: test


title: LC.18

description: test


title: LC.5

description: test


title: LC.4

description: test


title: LC.3

description: test


title: LC.1

description: test


title: LC.16

description: test


title: OsCPK4-rice (line13)-rep1


title: COPD.22

description: test

value: COPD


title: COPD.23

description: test


title: COPD.21

description: test


title: COPD.20

description: test


title: LC.2

description: test


title: COPD.18

description: test


title: COPD.15

description: test


title: COPD.16

description: test


title: COPD.14

description: test


title: LC.21

description: test


title: COPD.5

description: test


title: COPD.2

description: test


title: COPD.4

description: test


title: COPD.11

description: test


title: COPD.13

description: test


title: COPD.7

description: test


title: COPD.12

description: test


title: COPD.3

description: test


title: COPD.6

description: test


title: COPD.8

description: test


title: COPD.10

description: test


title: COPD.17

description: test


title: COPD.19

description: test


title: CONTROL.13

description: test

value: Neither LC nor COPD


title: CONTROL.16

description: test


title: CONTROL.14

description: test


title: CONTROL.15

description: test


title: CONTROL.11

description: test


title: CONTROL.10

description: test


title: COPD.9

description: test


title: CONTROL.12

description: test


title: COPD.1

description: test


title: CONTROL.7

description: test


title: CONTROL.8

description: test


title: CONTROL.5

description: test


title: CONTROL.9

description: test


title: CONTROL.2

description: test


title: CONTROL.1

description: test


title: CONTROL.6

description: test


title: CONTROL.3

description: test


title: R14 P+9 cell(sepa)

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: miRNA expression of the separated cultured cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: Bone marrow mesenchymal cell line

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: The Bone marrow mesenchymal stem cells and adult fibroblast cells were cultured in a reduced-serum (2%) medium (MesenPRO RS, Invitrogen) or StemPro (Invitrogen) containing Glutamax (Invitrogen) and an antibiotic-antimycotic (Invitrogen) at 37°C in 5% CO2.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: After incubation of cells for 2–3 days, the medium was collected and centrifuged at 2,000 x g for 15 minutes at room temperature. To thoroughly remove the cellular debris, the supernatant was filtered using a 0.22-µm filter unit (Millipore). The CM was then ultracentrifuged at 110,000 x g for 70 minutes at 4°C. The pellets were washed with 11 ml PBS, ultracentrifuged, and resuspended in PBS.

value: male


title: CD44- cell 7/7

description: miRNA expression of the CD44- cells

source_name: breast cancer cell line

value: female


title: R14 exosome stem pro

description: miRNA expression of R14-derived exosomes cultured with StemPro

source_name: Exosomes derived from bone marrow mesenchymal cell line


title: R14 cell(sort)

description: miRNA expression of the sorted cells


title: R14 exosome messen pro

description: miRNA expression of R14-derived exosomes cultured with MesenPro


title: CONTROL.4

description: test


title: AFB 76582 exosome messen pro

description: miRNA expression of AFB76582-derived exosomes cultured with MesenPro

source_name: Exosomes derived from adult fibroblast cell line


title: CD44+ cell 7/7

description: miRNA expression of the CD44+ cells


title: AFB 76582 cell(sepa)

source_name: adult fibroblast cell line