title: genetic line: QxSM017 - treatment: Mock - rep1

description:
qxsm017 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM017 - treated or untreated: Mock)


title: genetic line: QxSM018 - treatment: Mock - rep1

status: Public on Nov 15 2010

type: RNA

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

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

department: Virtual Reality Application Center

country: USA

institute: Iowa State University

description:
qxsm018 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

hyb_protocol: Affymetrix standard protocol:  Eukaryotic Target Hybridization

scan_protocol: Affymetrix standard protocol:  Array Scanning

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

label: biotin

molecule: total RNA

organism: Hordeum vulgare

source_name: (genetic line: QxSM018 - treated or untreated: Mock)

label_protocol: Affymetrix standard protocol: Eukaryotic Target Preparation

growth_protocol: Growth Description:  Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated with stem rust isolate TTKS (Ug99), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.  Environmental Conditions:  St. Paul 2007, Cereal Disease Lab GH#1 & #10

extract_protocol: Trizol RNA extraction followed by RNeasy purification

tag: genetic line

tag: tissue

value: seedling


title: Candida_albicans_normoxia_vs_hypoxia_rep2

city: Dublin

first: Alessandro

last: Guida

address: belfield

country: Ireland

institute: University College Dublin

hyb_protocol: Purified cDNA was denatured at 95 degree celsius for 2 min, and then chilled on ice for 10 sec. Two cDNA samples were mixed. The hybridization was carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies) according to the manufacture's manual.

scan_protocol: Scanned with an Axon 4000B scanner at 10 µm resolution. Data was acquired using GenePix 5.0 software.

data_processing: LOWESS normalized, no background correction using the LIMMA package from Bioconductor.

organism: Candida albicans

source_name: Total RNA from Candida albicans DAY286, grown in YPD medium at 30 degree celsius and 21% oxygen (normoxia).

label_protocol: RNA was concentrated and readjusted to a concentration of 4 μg /μl with RNase free water. A mixture of 24 μg  RNA, 2 μl Candida albicans specific RT primers mix (0.1 pmol μl-1 (Eurogentec)) and RNase free water to a volume of 18.5 μl was incubated at 70 degrees Celsius for 10 min. Tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. The cDNA synthesis step was carried out in dim light conditions because of the photosensitive properties of the Cyanine-5 (Cy5) dye. A mixture of 8 μl 5X  First Strand buffer, 4 μl 0.1 M Dithiothreitol (DTT), 3 μl 20 mM dNTP mix - dCTP (consisting of 6.67 mM each dATP, dGTP, and dTTP), 1  μl 2 mM dCTP and 2 μl (400 U) of Superscript II Reverse Transcriptase was added to the tubes. 2 μl of 1 mM Cy5 (Cy5-dCTP from Amersham Biosciences, 25 nmol) was added to the relevant tubes. Tubes were lightly mixed and centrifuged briefly in order to collect the contents of the tube. After 2 hours incubation at 42 degrees Celsius, the tubes were given a quick spin and another 2 μl (400 U) Superscript II Reverse Transcriptase was added. The reaction was incubated for an additional 1 hour at 42 degrees Celsius. Again, tubes were then placed on ice briefly to stop the reaction and centrifuged briefly in order to collect the contents of the tube. Any remaining RNA was degraded by the addition of 1 μl NRase A (0.05 mg/ml) and 1 μl NRase H (0.05 units /ml) and incubated at 37 degrees Celsius for 30 min.

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to an A600 of 0.2 in 50 ml of YPD medium at 21% oxygen (normoxia), and culture was incubated at 200 rpm at 30 degrees celsius for 3.5 hours.

extract_protocol: RNA was isolated using a RiboPure Yeast kit (Ambion)

tag: age

tag: growth condition

tag: medium

value: YPD medium

tag: strain

tag: stress

value: normoxia

source_name: Total RNA from Candida albicans DAY286 cells, grown in YPD medium at 30 degree celsius and 1% oxygen (hypoxia)

growth_protocol: Overnight cultures of C. albicans DAY286 were diluted to an A600 of 0.2 in 50 ml of YPD medium at 1% oxygen (hypoxia), and culture was incubated at 200 rpm at 30 degree for 3.5 hours.

value: 30 degree Celsius and 1% oxygen (hypoxia).

value: hypoxia


title: Pt#8

type: genomic

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: patient's CD34+ cells DNA hybridized against its own T cells DNA

hyb_protocol: According to the manufactuer's recommendations.

scan_protocol: Human 105K arrays were scanned with Agilent G2505B Micro-Array Scanner System. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. All arrays were then treated by the WACA algorithm [Lepretre et al., NAR 2010]. This algorithm was used to remove all false aberrations, without modifying real aberrations, allowing efficient further analysis. CGH analytics software V3.4, the Human Genome built 17 and the database of Genomic Variants built 36 (March 2006) were at last used for copy number detection and analysis.

molecule: genomic DNA

organism: Homo sapiens

source_name: Pt#8, CD34+ cells

label_protocol: manufacturer's instructions

extract_protocol: For each patient, CD34+ and T-lymphocytes (CD3+) cell separation from bone marrow and peripheral blood samples respectively were performed by positive-selection magnetic beads sorting using a MiniMACS device (Miltenyi Biotec Auburn, CA) according to the manufacturer’s instructions. DNAs were obtained using the QIAmp mini kit system (QIAGEN, Hilden, Germany) and whole genome amplification (GenomePlex Complete Whole Genome Amplification Kit, Sigma-Aldrich, Saint Louis) was performed according to the manufactuer’s recommendations. WGA DNAs from T-cells were used as references for the CGH array experiment, which was achieved using Agilent Human Genome 105K CGH oligonucleotide arrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s recommendations.

tag: group

value: Imatinib resistant

tag: cell type

value: CD34+ cells

source_name: Pt#8, T cells

value: T cells


title: genetic line: QxSM017 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM017 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM018 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM018 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM016 - treatment: Mock - rep1

description:
qxsm016 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM016 - treated or untreated: Mock)


title: Pt#11

source_name: Pt#11, CD34+ cells

source_name: Pt#11, T cells


title: Pt#12

source_name: Pt#12, CD34+ cells

source_name: Pt#12, T cells


title: Pt#4

source_name: Pt#4, CD34+ cells

source_name: Pt#4, T cells


title: Pt#7

source_name: Pt#7, CD34+ cells

source_name: Pt#7, T cells


title: Pt#6

source_name: Pt#6, CD34+ cells

source_name: Pt#6, T cells


title: Pt#5

source_name: Pt#5, CD34+ cells

source_name: Pt#5, T cells


title: Pt#3

source_name: Pt#3, CD34+ cells

source_name: Pt#3, T cells


title: genetic line: QxSM015 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm015 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM015 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM014 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm014 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM014 - treated or untreated: Inoculated - Pgt TTKS)


title: Pt#2

source_name: Pt#2, CD34+ cells

source_name: Pt#2, T cells


title: genetic line: QxSM013 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm013 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM013 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM010 - treatment: Mock - rep1

description:
qxsm010 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM010 - treated or untreated: Mock)


title: genetic line: QxSM008 - treatment: Mock - rep1

description:
qxsm008 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM008 - treated or untreated: Mock)


title: genetic line: QxSM011 - treatment: Mock - rep1

description:
qxsm011 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM011 - treated or untreated: Mock)


title: genetic line: QxSM005 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm005 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM005 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM013 - treatment: Mock - rep1

source_name: (genetic line: QxSM013 - treated or untreated: Mock)


title: genetic line: QxSM001 - treatment: Mock - rep1

description:
qxsm001 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM001 - treated or untreated: Mock)


title: genetic line: QxSM008 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM008 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM003 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm003 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM003 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM010 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM010 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM014 - treatment: Mock - rep1

source_name: (genetic line: QxSM014 - treated or untreated: Mock)


title: genetic line: QxSM011 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM011 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM001 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM001 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: QxSM002 - treatment: Mock - rep1

description:
qxsm002 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM002 - treated or untreated: Mock)


title: genetic line: QxSM003 - treatment: Mock - rep1

source_name: (genetic line: QxSM003 - treated or untreated: Mock)


title: Pt#1

source_name: Pt#1, CD34+ cells

source_name: Pt#1, T cells


title: liver_Trim28+/+ _rep9

city: Herston

first: Suyinn

last: Chong

state: Queensland

address: 300 Herston Rd

department: Division of Genetics and Population Health

country: Australia

institute: Queensland Institute of Medical Research

description: replicate 9

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina GenomeStudio software was used according to the recommendations of the manufacturer. Data was grouped (wildtype versus heterozygotes), background corrected, and normalised (average normalisation). Significantly differentially expressed genes were identified using Illumina's differential expression analysis.

organism: Mus musculus

source_name: liver, Trim28+/+

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion).

extract_protocol: RNA was extracted using the QIAGEN Rneasy-Plus kit in accordance with the prescribed protocol. All RNA samples were checked on Agilent’s Bioanalyzer (Agilent RNA 6000 Nano) and had RNA Integrity Numbers (RINs) greater than 8.

tag: genetic background

value: FVB/NJ

tag: gender

value: male

value: 4 weeks

value: liver

tag: genotype


title: genetic line: QxSM015 - treatment: Mock - rep1

source_name: (genetic line: QxSM015 - treated or untreated: Mock)


title: genetic line: SM89010 - treatment: Mock - rep1

description:
sm89010 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: SM89010 - treated or untreated: Mock)


title: genetic line: QxSM005 - treatment: Mock - rep1

source_name: (genetic line: QxSM005 - treated or untreated: Mock)


title: genetic line: QxSM002 - treatment: Inoculated - Pgt TTKS - rep1

source_name: (genetic line: QxSM002 - treated or untreated: Inoculated - Pgt TTKS)


title: genetic line: SM89010 - treatment: Mock - rep4


title: genetic line: SM89010 - treatment: Mock - rep2


title: liver_Trim28+/+ _rep8

description: replicate 8


title: genetic line: SM89010 - treatment: Inoculated - Pgt TTKS - rep4

source_name: (genetic line: SM89010 - treated or untreated: Inoculated - Pgt TTKS)


title: liver_Trim28+/+ _rep7

description: replicate 7


title: genetic line: SM89010 - treatment: Inoculated - Pgt TTKS - rep3


title: genetic line: SM89010 - treatment: Inoculated - Pgt TTKS - rep1


title: genetic line: SM89010 - treatment: Mock - rep3


title: 5'Aza-treated LNCaP at 48 hr v2

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

description:
Replicate 2 of 2, @48hr with 5'Aza treatment
raw data file: 09282007_251485019555_S01_GE2-v5_95_Feb07_1_4.txt

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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

source_name: Human LNCaP Prostate Cancer Cell Line, control treatment

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: LNCaP cells are cultured in RPMI media containing 10% FBS

extract_protocol: At the indicated time points cells were lysed with Trizol reagent (Invitrogen) and total RNA isolated for array experiment according to manufacturer's instructions

treatment_protocol: LNCaP cells maintained in 100 mm dishes were serum starved for 24 hours.  After 24 hours the cells were treated with either 1uM 5'Aza-cytidine (Sigma) or the vehicle Di methyl Sulphoxide for control cells (Used to dissolve 5-Aza) for 24 and 48 hours.

tag: cell line

value: LNCAP

tag: treatment

value: DMSO control

tag: time point

value: 48 hour

source_name: Human LNCaP Prostate Cancer Cell Line, 5’Azacytidine-treated


title: 5'Aza-treated LNCaP at 48hr

description:
Replicate 1 of 2, @48hr with 5'Aza treatment
raw data file: 09282007_251485019555_S01_GE2-v5_95_Feb07_1_3.txt


title: 5'Aza-treated LNCaP at 24 hr

description:
Replicate 1 of 2, @24hr with 5'Aza treatment
raw data file: 09282007_251485019555_S01_GE2-v5_95_Feb07_1_1.txt

value: 24 hour


title: genetic line: Q21861 - treatment: Mock - rep4

description:
q21861 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: Q21861 - treated or untreated: Mock)


title: liver_Trim28+/+ _rep6

description: replicate 6


title: genetic line: SM89010 - treatment: Inoculated - Pgt TTKS - rep2


title: liver_Trim28+/+ _rep5

description: replicate 5


title: 5'Aza-treated LNCaP at 24 hr v2

description:
Replicate 2 of 2, @24hr with 5'Aza treatment
raw data file: 09282007_251485019555_S01_GE2-v5_95_Feb07_1_2.txt


title: liver_Trim28+/+ _rep2

description: replicate 2


title: genetic line: Q21861 - treatment: Mock - rep3


title: genetic line: Q21861 - treatment: Inoculated - Pgt TTKS - rep4

source_name: (genetic line: Q21861 - treated or untreated: Inoculated - Pgt TTKS)


title: liver_Trim28+/+ _rep4

description: replicate 4


title: WT+GH_Bio-2 replication-05-17-10

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Affimetrixs standard hyb protocol

scan_protocol: Affimetrixs standard scan protocol using GCOS 1.0

data_processing: Software Partek 6.10.0511 with by default RMA normalization

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

extract_protocol: Cells were harvested and mRNAs were extracted by using RNeasy Plus Mini Kit (QIAGEN).

treatment_protocol: Passage 13 Control and Stat5a/b-null embryonic fibroblasts (MEFs) cells were starved for 5 hours, then stimulated with 1 ug/ml of GH or not stimulated (control) for 2 hours.

value: embryonic fibroblasts (MEFs)

tag: cell passage

value: passage 13

tag: genotype/variation

value: wild type

tag: stimulation

value: +GH


title: genetic line: Q21861 - treatment: Mock - rep1

tag: genetic line

tag: tissue

value: seedling


title: liver_Trim28MommeD9/+ _rep7

description: replicate 7

source_name: liver, Trim28MommeD9/+

tag: age


title: KO+GH_Bio-3 replication-5-17-10


title: liver_Trim28+/+ _rep1

description: replicate 1


title: genetic line: Q21861 - treatment: Inoculated - Pgt TTKS - rep3


title: WT-_Bio-2 replication-05-17-10

value: -GH


title: liver_Trim28MommeD9/+ _rep4

description: replicate 4


title: liver_Trim28MommeD9/+ _rep6

description: replicate 6


title: WT+GH_Bio-3 replication-05-17-10


title: genetic line: Q21861 - treatment: Inoculated - Pgt TTKS - rep1


title: KO-_Bio-3 replication-05-17-10


title: CB258-CD44+/CD24- Rep 2

city: Bangalore

first: Anurag

middle: N

last: Paranjape

state: Karnataka

address: CVRaman road

department: MRDG

country: India

institute: Indian Institute of Science

hyb_protocol: T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis)

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Agilent Feature Extraction Software (10.5.1.1 ) was used for background subtraction and LOWESS normalization.

source_name: Sorted CD44+/CD24- fractions from primary breast cancer (CB258)-derived cells

label_protocol: Labeling was done using Agilent’s Quick-Amp labeling Kit (p/n5190-0442)

growth_protocol: NBLE cells were grown in low attachment condition in the absence of serum for 6 days to form mammospheres. The media was supplemented with B27, EGF, insulin, hydrocortisone and heparin along with pen/strep/fungizone. Primary cancer cells were sorted immidiately without growing.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini columns

treatment_protocol: Not Applicable- CD44+/CD24- and rest fractions were flow sorted and RNA was extracted

source_name: Sorted rest fractions from primary breast cancer (CB258)-derived cells


title: WT-_Bio-3 replication-05-17-10


title: CB258-CD44+/CD24- Rep 1

value: Sorted CD44+/CD24- fractions from primary breast cancer (CB258)-derived cells

value: Sorted rest fractions from primary breast cancer (CB258)-derived cells


title: genetic line: Q21861 - treatment: Inoculated - Pgt TTKS - rep2


title: genetic line: Q21861 - treatment: Mock - rep2


title: KO-_Bio-2 replication-05-17-10


title: KO+GH_Bio-2 replication-05-17-10

source_name: KO+GH


title: genetic line: QxSM016 - treatment: Inoculated - Pgt TTKS - rep1

description:
qxsm016 (germplasm name); po: 0009025 (Organism Part); PO:0007098 (Development Stage); 1st leaf; 10 das (Age); garden soil (Growth Media).
Seedlings were grown in the greenhouse for 9 days. Nine-day old seedlings were inoculated (INOC) with stem rust isolate TTKS (Ug99) in Soltrol oil (inoculum per plant weight of 0.25 mg) or just Soltrol oil (MOCK), placed in a mist chamber for 16 hours in the dark, then 5 hours of light in the mist chamber, then the greenhouse for 2 hours until harvesting of tissue.

source_name: (genetic line: QxSM016 - treated or untreated: Inoculated - Pgt TTKS)


title: liver_Trim28MommeD9/+ _rep1

description: replicate 1


title: NBLE-CD44+/CD24- Rep 1

source_name: Sorted CD44+/CD24- fractions from immortalized mammosphere-derived cells grown as spheres

source_name: Sorted rest fractions from immortalized mammosphere-derived cells grown as spheres


title: liver_Trim28MommeD9/+ _rep2

description: replicate 2


title: liver_Trim28MommeD9/+ _rep3

description: replicate 3


title: RNA_H99

city: Roma

first: ada

last: florio

state: Roma

address: Largo A. Gemelli 8

department: Microbiology

country: Italy

institute: Catholic University of Sacred Heart

description:
C. neoformans control.
Biological replicates 1-3.

hyb_protocol: Aliquots (600 ng) of Cy3-labeled cRNAs were fragmented and hybridized for 17 h at 65°C to each array using the Gene Expression Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Slides were washed and processed according to the Agilent 60-mer Oligo Microarray Processing protocol and scanned on a Agilent microarray scanner G2565BA (Agilent Technologies).

data_processing:
The gene expression values obtained from FE software were imported into GeneSpring 10.0.2 software (Agilent Technologies) for preprocessing and data analysis. For inter-array comparisons, a linear scaling of the data was performed using the 75th percentile signal value of all non-control probes on the microarray to normalize one-color signal values. Probe sets with a signal intensity value below the 20th percentile were considered as absent and discarded from subsequent analysis. The expression of each gene was normalized by its median expression across all samples. Genes were included in the final data set if their expression changed by at least twofold between strain H99 FLC-exposed or -not exposed (control sample) in at least two independent experiments, together with a P value cut-off of <0.05 (by one-way analysis of variance [ANOVA] corrected).

The VALUEs in the Sample table represent the average normalized values for the three biological replicates.

organism: Cryptococcus neoformans

source_name: RNA_H99, not exposed

label_protocol: Agilent's One-Color Quick Amp Labeling kit (Agilent Technologies) was used to generate fluorescently labeled cRNA probes according to the manufacturer’s instructions.

growth_protocol: C. neoformans var. grubii serotype A strain (H99), kept as a 20% glycerol stock at -80°C, was subcultured on YEPD (1% yeast extract, 2% peptone, 2% glucose) agar plates at 30°C.

extract_protocol: Cultures were centrifuged at 4°C and 5,500 x g, and total RNA was extracted as previously described in Sanguinetti et al. 2006 (PMID 16428784).

treatment_protocol: Independent sets of overnight cultures, each obtained from a single yeast colony in YEPD broth at 30°C under constant agitation, were diluted 1:100 in fresh YEPD and grown at 30°C with agitation for 3 h to reach a density of 3 x 10^7 cells per ml. At this point, cultures were equally divided into two aliquots to which either FLC at a concentration of 10 µg/ml or distilled water was added, followed by incubation at 30°C for 90 min.

value: distilled water (control)

tag: treatment time

value: 90 minutes


title: Mouse M60 hepatocellular carcinoma tumor liver tissue

status: Public on Nov 14 2010

city: Philadelphia

first: Hojun

last: Li

state: PA

address: 3501 Civic Center Boulevard

department: Hematology

institute: Children's Hospital of Philadelphia

description: gene expression data from liver cancer

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99&ordmC for 5 min and hybridized for 16 h at 45&ordmC to Mouse Gene 1.0ST microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau = 0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.

source_name: 18 months post- AAV-vector injection mouse M60 tumor tissue

label_protocol: 0.2ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Mice were injected with AAV-vector at 2-3 months of age and followed for 18 months under normal conditions with normal diet

extract_protocol: RNA extraction with Rneasy kit (Qiagen) was performed according to manufacturers instructions

treatment_protocol: At 18 months post-injection, mice were necropsied and liver (normal and tumor) samples snap frozen in liquid nitrogen

value: frozen liver

value: male

tag: strain


title: Mouse M48 hepatocellular carcinoma tumor liver tissue

description: gene expression data from liver cancer

source_name: 18 months post- AAV-vector injection mouse M48 tumor tissue


title: liver_Trim28MommeD9/+ _rep5

description: replicate 5

value: FVB/NJ

value: 4 weeks

value: liver


title: RNA_H99_FLC

description:
Response of C. neoformans to fluconazole.
Biological replicates 1-3.

source_name: RNA_H99, FLC-exposed, 90m

value: fluconazole


title: Mouse M50 adjacent normal liver tissue

description: gene expression data from normal liver

source_name: 18 months post- AAV-vector injection mouse M50 adjacent normal liver tissue


title: 76h+BGP+AEBSF rep3

status: Public on Nov 13 2010

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

description: UMR106-01 culture, 76 h after plating, mineralizing conditions plus 400 micromolar AEBSF protease inhibitor, 10% fetal bovine serum

hyb_protocol: Affymetrix 1-cycle std protocol

scan_protocol: Affymetrix 1-cycle std protocol

data_processing: MAS5 using GCOS

organism: Rattus norvegicus

label_protocol: Affymetrix 1-cycle std protocol

growth_protocol: UMR-106-01 cells are seeded at 100,000 cells per cm2 at 37 C and 5% carbon dioxide in Eagle's minimum essential medium supplemented with Earle's salts, 1% non-essential amino acids, 10 mM final concentration HEPES, and 10% fetal bovine serum.

extract_protocol: For RNA extraction, media was removed from one well at a time.  Stat-60 solution (Tel-Test) was added and the cells were lysed by scraping with a wide mouth tip.  The lysis was transferred to a pre-labeled 2 ml tube and placed directly on liquid nitrogen for quick freeze.

treatment_protocol: At 64 hours after plating the cells are re-fed with Growth Medium containing 6.5 mM beta-glycerol phosphate, with or without 400 micromolar AEBSF protease inhibitor.


title: CB272-CD44+/CD24- Rep1

source_name: Sorted CD44+/CD24- fractions from primary breast cancer (CB272)-derived cells

source_name: Sorted rest fractions from primary breast cancer (CB272)-derived cells


title: NBLE-CD44+/CD24- Rep 2

value: Sorted CD44+/CD24- fractions from immortalized mammosphere-derived cells grown as spheres

value: Sorted rest fractions from immortalized mammosphere-derived cells grown as spheres


title: Mouse M50 hepatocellular carcinoma tumor liver tissue

description: gene expression data from liver cancer

source_name: 18 months post- AAV-vector injection mouse M50 tumor tissue


title: Mouse M60 adjacent normal liver tissue

description: gene expression data from normal liver

source_name: 18 months post- AAV-vector injection mouse M60 adjacent normal liver tissue


title: Mouse M48 adjacent normal liver tissue

description: gene expression data from normal liver

source_name: 18 months post- AAV-vector injection mouse M48 adjacent normal liver tissue


title: Mouse M24 hepatocellular carcinoma tumor liver tissue

description: gene expression data from liver cancer

source_name: 18 months post- AAV-vector injection mouse M24 tumor tissue


title: Mouse M24 adjacent normal liver tissue

description: gene expression data from normal liver

source_name: 18 months post- AAV-vector injection mouse M24 adjacent normal liver tissue


title: 76h+BGP+AEBSF rep1

source_name: UMR106-01 culture, 76 h after plating, mineralizing conditions plus 400 micromolar AEBSF protease inhibitor, 10% fetal bovine serum


title: 76h+BGP rep3

description: UMR106-01 culture, 76 h after plating, mineralizing conditions 10% fetal bovine serum


title: 76h+BGP+AEBSF rep2


title: 76h+BGP rep2

source_name: UMR106-01 culture, 76 h after plating, mineralizing conditions 10% fetal bovine serum


title: 76h+BGP rep1


title: CNSlymphoma_rep1

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description: Gene expression

hyb_protocol: Cyanine 3-labled linearly amplified cRNA was mixed with 10X blocking agent, nuclease-free water, and 25X fragmentation buffer provided in the Agilent Gene Expression Hybridization Kit (Agilent Technologies), and incubated for 30 min at 60oC to fragment RNA. After adding 2X GEx hybridization buffer Hi-RPM, the amplified fragmented RNA was hybridized on a 4 x 44K Whole Human Genome Oligo Microarray Chip (Agilent Technologies) containing 44,000 cDNA clones using a SureHyb DNA Microarray Hybridization Chamber in a DNA Microarray Hybridization Oven (Agilent Technologies) at 10 rpm, 65oC for 17 hours.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies).

data_processing: Feature Extraction Software v9 (Agilent Technologies) was used to extract and analyze the signals. To validate the amplification process, amplified and unamplified RNAs were labeled, hybridized and compared.

source_name: CNS lymphoma

label_protocol: 0.5 ug of total RNA was amplified and labeled using Agilent Quick Amp Labeling Kit. After labeling, cRNA was purified with Qiagen’s RNeasy Mini-spin columns (QIAGEN, Germantown, MD) and quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer for cyanine 3 dye concentration, RNA absorbance ratio (260 nm/280 nm), and cRNA concentration.

extract_protocol: RNA was extracted from 14 fresh-frozen tumor samples using standard proteinase K/RNAse treatment and phenol-chloroform extraction method.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fresh-frozen samples were obtained from 14 patients including 7 primary central nervous system diffuse large B cell lymphoma and 7 normal lymph nodes.

value: Brain


title: PerpheralBlood_rep11

description: CGH

hyb_protocol: After probe denaturation and preannealing with Cot-1 DNA, hybridization was performed at 65oC with rotation for 40 hours.

scan_protocol: Scanned on an Agilent DNA microarray scanner.

data_processing: Data were obtained using Agilent Feature Extraction Software 9 and analyzed with Agilent CGH Analytics 4.0 Software.

source_name: Peripheral blood

label_protocol: 1.5 ug of test DNA and reference DNAs were digested with Alu I and Rsa I (Promega, Madison, WI) and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown,MD). Test sample DNA and reference DNA were labeled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit PLUS.

extract_protocol: Fresh-frozen samples were obtained from 12 patients with primary central nervous system diffuse large B cell lymphoma and 13 peripheral blood from healthy men.

value: Whole blood

source_name: Reference DNA

value: Human reference DNA


title: PerpheralBlood_rep12

description: CGH


title: NormalLymphNode_rep4

description: Gene expression

source_name: Normal Lymph Node

value: Lymph node


title: CNSlymphoma_rep4

description: Gene expression


title: NormalLymphNode_rep1

description: Gene expression


title: liver_Trim28+/+ _rep3

description: replicate 3

source_name: liver, Trim28+/+


title: CNSlymphoma_rep3

description: Gene expression


title: PerpheralBlood_rep10

description: CGH


title: NormalLymphNode_rep7

description: Gene expression


title: CNSlymphoma_rep5

description: Gene expression


title: NormalLymphNode_rep3

description: Gene expression


title: NormalLymphNode_rep5

description: Gene expression


title: CNSlymphoma_rep7

description: Gene expression


title: CNSlymphoma_rep6

description: Gene expression


title: NormalLymphNode_rep2

description: Gene expression


title: CNSlymphoma_rep2

description: Gene expression


title: PerpheralBlood_rep7

description: CGH


title: PerpheralBlood_rep13

description: CGH


title: NormalLymphNode_rep6

description: Gene expression


title: PerpheralBlood_rep4

description: CGH


title: PerpheralBlood_rep9

description: CGH


title: PerpheralBlood_rep8

description: CGH


title: PerpheralBlood_rep3

description: CGH


title: PCNSlymphoma_rep12

description: CGH

source_name: PCNSL tumor sample


title: PerpheralBlood_rep2

description: CGH


title: PerpheralBlood_rep6

description: CGH


title: PerpheralBlood_rep5

description: CGH


title: PCNSlymphoma_rep11

description: CGH


title: PCNSlymphoma_rep1

description: CGH


title: PCNSlymphoma_rep8

description: CGH


title: PCNSlymphoma_rep7

description: CGH


title: PCNSlymphoma_rep9

description: CGH


title: PCNSlymphoma_rep4

description: CGH


title: PCNSlymphoma_rep10

description: CGH


title: PCNSlymphoma_rep6

description: CGH


title: PCNSlymphoma_rep3

description: CGH


title: PCNSlymphoma_rep2

description: CGH


title: gp130-KO mouse 6h IL-6 stimulated rep5

city: Münster

first: Frank

last: Ruehle

address: Domagkstr. 3

country: Germany

institute: Leibniz - Institut für Arterioskleroseforschung

description: replicate 5

data_processing: The data were normalised using cubic spline normalization with Illumina GenomeStudio version 1.6.0.

source_name: Isolated hepatocytes from hepatocyte-specific gp130 knockout mouse

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit from Applied Biosystems.

growth_protocol: Hepatocytes from gp130– and gp130flox mice were isolated as described in J Exp Med. 2007 Aug;204(8):1935–1944.

extract_protocol: Total RNA was extracted with TriFast-Reagent (peqLAB) and quality was controlled with an Experion Automated Electrophoresis System and an Implen NanoPhotometer.

treatment_protocol: Cells were starved overnight and stimulated with 200 ng/mL IL-6 for 0-12 hours under serum-free conditions.

tag: gp130 genotype

value: hepatocytes

tag: duration of il-6 treatment

value: 6 h


title: gp130-KO mouse unstimulated rep5

description: replicate 5

value: 0 h


title: gp130-KO mouse 6h IL-6 stimulated rep1

description: replicate 1


title: gp130-KO mouse 6h IL-6 stimulated rep4

description: replicate 4


title: gp130-KO mouse 6h IL-6 stimulated rep3

description: replicate 3


title: PCNSlymphoma_rep5

description: CGH


title: PerpheralBlood_rep1

description: CGH


title: gp130-KO mouse 12h IL-6 stimulated rep4

description: replicate 4


title: gp130-KO mouse 6h IL-6 stimulated rep2

description: replicate 2


title: gp130-KO mouse unstimulated rep1

description: replicate 1


title: gp130-KO mouse 12h IL-6 stimulated rep2

description: replicate 2


title: gp130-KO mouse 12h IL-6 stimulated rep6

description: replicate 6


title: gp130-KO mouse 3h IL-6 stimulated rep5

description: replicate 5

value: 3 h


title: gp130-KO mouse unstimulated rep6

description: replicate 6


title: gp130-KO mouse unstimulated rep3

description: replicate 3


title: gp130-KO mouse 12h IL-6 stimulated rep3

description: replicate 3


title: gp130-KO mouse 3h IL-6 stimulated rep4

description: replicate 4


title: gp130-KO mouse 12h IL-6 stimulated rep5

description: replicate 5


title: gp130-KO mouse unstimulated rep2

description: replicate 2


title: gp130-KO mouse 3h IL-6 stimulated rep3

description: replicate 3


title: gp130-KO mouse unstimulated rep4

description: replicate 4


title: gp130-KO mouse 3h IL-6 stimulated rep1

description: replicate 1


title: gp130-KO mouse 3h IL-6 stimulated rep2

description: replicate 2


title: gp130-KO mouse 1h IL-6 stimulated rep6

description: replicate 6

value: 1 h


title: WT mouse 3h IL-6 stimulated rep2

description: replicate 2

source_name: Isolated hepatocytes from wildtype mouse

value: wild type


title: WT mouse 3h IL-6 stimulated rep6

description: replicate 6


title: gp130-KO mouse 1h IL-6 stimulated rep4

description: replicate 4


title: WT mouse 12h IL-6 stimulated rep7

description: replicate 7


title: gp130-KO mouse 1h IL-6 stimulated rep2

description: replicate 2


title: WT mouse 12h IL-6 stimulated rep2

description: replicate 2


title: WT mouse 3h IL-6 stimulated rep4

description: replicate 4


title: WT mouse 3h IL-6 stimulated rep5

description: replicate 5


title: gp130-KO mouse 1h IL-6 stimulated rep1

description: replicate 1


title: WT mouse 12h IL-6 stimulated rep4

description: replicate 4


title: WT mouse 6h IL-6 stimulated rep7

description: replicate 7


title: WT mouse 12h IL-6 stimulated rep3

description: replicate 3


title: WT mouse 12h IL-6 stimulated rep6

description: replicate 6


title: WT mouse 6h IL-6 stimulated rep5

description: replicate 5


title: WT mouse 12h IL-6 stimulated rep5

description: replicate 5


title: WT mouse 3h IL-6 stimulated rep1

description: replicate 1


title: WT mouse 3h IL-6 stimulated rep3

description: replicate 3


title: WT mouse 6h IL-6 stimulated rep6

description: replicate 6


title: WT mouse 12h IL-6 stimulated rep1

description: replicate 1


title: WT mouse 6h IL-6 stimulated rep4

description: replicate 4


title: gp130-KO mouse 1h IL-6 stimulated rep3

description: replicate 3


title: WT mouse 6h IL-6 stimulated rep3

description: replicate 3


title: WT mouse 6h IL-6 stimulated rep2

description: replicate 2


title: gp130-KO mouse 1h IL-6 stimulated rep5

description: replicate 5


title: WT mouse unstimulated rep5

description: replicate 5


title: WT mouse 1h IL-6 stimulated rep5

description: replicate 5


title: WT mouse 1h IL-6 stimulated rep2

description: replicate 2


title: WT mouse 1h IL-6 stimulated rep1

description: replicate 1


title: WT mouse 1h IL-6 stimulated rep4

description: replicate 4


title: WT mouse unstimulated rep7

description: replicate 7


title: WT mouse 1h IL-6 stimulated rep6

description: replicate 6


title: WT mouse unstimulated rep6

description: replicate 6


title: WT mouse 1h IL-6 stimulated rep3

description: replicate 3


title: WT mouse unstimulated rep3

description: replicate 3


title: WT mouse unstimulated rep2

description: replicate 2


title: Lung_Untreated-2_42d

city: Newark

first: Mi-Sun

last: Koo

state: NJ

address: 225 Warren Street, W250Q

department: Public Health Research Institute

institute: University of Medicine and Dentistry of New Jersey

hyb_protocol: Followng fragmentation, labeled single stranded DNA hybrized unto the Mouse Gene 1.0 ST array, and placed in 45°C hybridization oven, at 60 rpm, and incubated for 17± 1 hours

scan_protocol: Gene chips were scanned using an Affymetrix Genechip Scanner 3000 7G Plus

data_processing: GeneChip CEL files were analyzed using Partek Genomics Suite

source_name: mouse lung, Mtb-infected, 42d

label_protocol: 300 ng of total RNA was processed using the GeneChip WT labelling protocol, version 4 cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mouse lungs were collected after 14, 21, 28 and 42 days after Mtb CDC1551 infection (low aerosol exposure, 200 cfu) with or without CC-3052 treatment.

extract_protocol: Trizol extraction was performed to isolate total RNA according to manufacturer's instruction.

treatment_protocol: Mice were treated with CC-3052 (PDE4 inhibitor, 25mg/kg/day) suspended in 0.2% carboxymethylcellulose solution by Ad libitum 5 days a week.

value: lung

tag: disease state

value: infected

tag: diagnosis

value: untreated

tag: collection date


title: Lung_Untreated-4_42d


title: Lung_CC3052-2_42d

source_name: mouse lung, Mtb-infected with CC3052 trx 42d

value: treated with CC-3052


title: Lung_Uninfected-4_42d

source_name: mouse lung, Uninfected, 42d

value: uninfected


title: Lung_CC3052-4_42d


title: Lung_Untreated-3_42d


title: Lung_Uninfected-3_42d


title: Lung_CC3052-1_42d


title: Lung_Uninfected-1_42d


title: WT mouse unstimulated rep4

description: replicate 4


title: Lung_CC3052-3_42d


title: Lung_CC3052-4_28d

source_name: mouse lung, Mtb-infected with CC3052 trx 28d


title: Lung_Untreated-1_42d


title: Lung_CC3052-2_28d


title: Lung_CC3052-3_28d


title: Lung_CC3052-1_28d


title: BC010-187

city: Boston

first: Jennifer

middle: L

last: Bowen

state: MA

address: 100 Morrissey Blvd

department: Biology Department

institute: University of Massachusetts Boston

description: 200 ng nirS PCR product

hyb_protocol: hybridization at 65 oC using Clontech hybridization solution

scan_protocol: Arrays were scanned on an Agilent High-Resolution C Scanner

data_processing: Data were analyzed using GenePix Pro (Version 6.0)

organism: Bacteria

source_name: ~0.5 g surface muf from rooting zone of tall form Spartina alterniflora

label_protocol: Targets were linearly ampified using Klenow and the dNTP mix included dUaa. The amplified product was post labeled by conjugation of Cy3 to the dUaa

extract_protocol: sediments were extracted using the MoBio Power Soil DNA extraction kit

treatment_protocol: sediments collected using sterile 5 cc syringe corer and were immediately frozen at -80oC until extraction

tag: location

value: PIE West Marsh (September 2005)

molecule: other

organism: unidentified

source_name: 20-mer standard reference

label_protocol: Each 90mer probe listed below consisted of a 70-mer specific target linked to 20-mer internal standard. The 20-mer standard was labeled with Cy5.

tag: sample type

value: internal oligo reference


title: BC010-188

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (September 2005)


title: BC010-185

description: 200 ng nirS PCR product

value: PIE West Marsh (August 2005)


title: BC010-184

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (June 2005)


title: BC010-186

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (August 2005)


title: Lung_Untreated-3_28d

source_name: mouse lung, Mtb-infected, 28d


title: Lung_Untreated-2_28d


title: BC010-182

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (May 2005)


title: BC010-183

description: 200 ng nirS PCR product

value: PIE West Marsh (June 2005)


title: Lung_Untreated-1_28d


title: BC010-180

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (September 2005)


title: BC010-179

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (September 2005)


title: WT mouse unstimulated rep1

description: replicate 1

value: hepatocytes

value: 0 h


title: BC010-178

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (August 2005)


title: BC010-181

description: 200 ng nirS PCR product

value: PIE West Marsh (May 2005)


title: Lung_Uninfected-2_42d

value: lung

value: untreated


title: BC010-177

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (August 2005)


title: Lung_Untreated-4_28d

value: infected


title: Lung_Uninfected-3_28d

source_name: mouse lung, Uninfected, 28d

value: uninfected


title: Lung_Uninfected-4_28d


title: Lung_Uninfected-2_28d


title: gp130-KO mouse 12h IL-6 stimulated rep1

description: replicate 1


title: Lung_Uninfected-1_28d


title: BC010-175

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (June 2005)

value: internal oligo reference


title: BC010-176

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (June 2005)


title: BC010-174

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (May 2005)


title: BC010-173

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (May 2005)


title: BC010-172

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (September 2005)


title: BC010-167

description: 200 ng nirS PCR product

value: PIE West Marsh (June 2005)


title: BC010-166

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (May 2005)


title: BC010-169

description: 200 ng nirS PCR product

value: PIE West Marsh (August 2005)


title: BC010-168

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (June 2005)


title: BC010-165

description: 200 ng nirS PCR product


title: BC010-162

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (August 2005)


title: BC010-164

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (September 2005)


title: BC010-163

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (September 2005)


title: BC010-171

description: 200 ng nirS PCR product

value: PIE West Marsh (September 2005)


title: Lung_CC3052-4_21d

source_name: mouse lung, Mtb-infected with CC3052 trx 21d

value: lung

value: treated with CC-3052


title: Lung_CC3052-1_21d

value: infected


title: BC010-161

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (August 2005)


title: BC010-170

description: 200 ng nirS PCR product

value: PIE Sweeney Marsh (August 2005)

value: internal oligo reference


title: Lung_CC3052-3_21d


title: Lung_CC3052-2_21d


title: BC010-158

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (May 2005)


title: BC010-159

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (June 2005)


title: BC010-160

description: 200 ng nirS PCR product

value: PIE Nelson Marsh (June 2005)


title: BC010-140

description: 200 ng nirS PCR product

value: GSM plot XF2 (Sept 2008)


title: Lung_Untreated-3_21d

source_name: mouse lung, Mtb-infected, 21d

value: untreated


title: BC010-157

description: 200 ng nirS PCR product

value: PIE Clubhead Marsh (May 2005)


title: BC010-138

description: 200 ng nirS PCR product

value: GSM plot HF2 (Sept 2008)


title: WT mouse 6h IL-6 stimulated rep1

description: replicate 1

value: wild type

value: hepatocytes

value: 6 h


title: BC010-139

description: 200 ng nirS PCR product

value: GSM plot XF1 (Sept 2008)


title: Lung_Uninfected-3_21d

source_name: mouse lung, Uninfected, 21d

value: lung

value: uninfected


title: BC010-137

description: 200 ng nirS PCR product

value: GSM plot HF1 (Sept 2008)


title: Lung_Untreated-1_21d

value: infected


title: BC010-136

description: 200 ng nirS PCR product

value: GSM plot LF2 (Sept 2008)


title: Lung_Uninfected-2_21d


title: BC010-106

description: 200 ng nirS PCR product

value: internal oligo reference


title: BC010-108

description: 200 ng nirS PCR product


title: BC010-134

description: 200 ng nirS PCR product

value: GSM plot CF2 (Sept 2008)


title: BC010-133

description: 200 ng nirS PCR product

value: GSM plot CF1 (Sept 2008)


title: BC010-135

description: 200 ng nirS PCR product

value: GSM plot LF1 (Sept 2008)


title: BC010-105

description: 200 ng nirS PCR product


title: BC010-103

description: 200 ng nirS PCR product


title: Lung_Uninfected-1_21d


title: Lung_CC3052-2_14d

source_name: mouse lung, Mtb-infected with CC3052 trx 14d

value: treated with CC-3052


title: Lung_CC3052-1_14d


title: BC010-107

description: 200 ng nirS PCR product


title: BC010-102

description: 200 ng nirS PCR product


title: Lung_Untreated-2_21d

value: untreated


title: Lung_Untreated-4_14d

source_name: mouse lung, Mtb-infected, 14d


title: BC010-104

description: 200 ng nirS PCR product


title: Lung_Uninfected-4_21d


title: BC010-101

description: 200 ng nirS PCR product


title: Lung_CC3052-3_14d


title: Lung_Untreated-3_14d


title: Lung_Uninfected-3_14d

source_name: mouse lung, Uninfected, 14d


title: Lung_Uninfected-4_14d


title: Lung_Uninfected-1_14d


title: Lung_Untreated-1_14d


title: Lung_CC3052-4_14d


title: Lung_Untreated-2_14d


title: Lung_Uninfected-2_14d


title: IkkβF/F_replicate1

status: Public on Nov 12 2010

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

hyb_protocol: Biotin-labeled cRNA was hybridized to Illumina Mouse-Ref8 BeadChips (Illumina) following manufacturer's directions.

scan_protocol: Scan protocol was followed manufacturer's directions.

data_processing: The data were quantile normalized using BeadStudio v3.1 software. Data analysis and quality control were carried out using Partek® software.

label: Biotin, Cy3

source_name: mature Ly-6G+ thioglycollate-elicited peritoneal neutrophils

label_protocol: Biotinylated cRNA was synthesized using an RNA Amplification Kit (Ambion) following manufacturer's directions.

extract_protocol: Ly-6G+ neutrophils were collected and total RNA was extracted with TRIzol® (Invitrogen) and was purified by RNA micro cleanup Kit (Qiagen).

value: IkkβF/F


title: Expression of Ube3a-Snurf/Snrpn region (Liver from F1 hybrid mouse MSMxB6)

city: Tsukuba

first: Koji

last: Numata

address: 3-1-1 Koyadai

country: Japan

institute: RIKEN

description:
Cy3 and Cy5 labels distinguish B6/MSM allele of a single Sample. See Platform data table (GPL10330) to get which channel detects B6 allele.
Expression of Ube3a-Snurf/Snrpn region (F1 hybrid mouse MSMxB6)

hyb_protocol: Illumina GoldenGate Assay was used. See manufacturer's web site for more details.

data_processing:
Cy3 and Cy5 labels distinguish B6/MSM allele of a single Sample. See Platform data table (GPL10330) to get which channel detects B6 allele.
Signal intensity values of two channels (Cy3 and Cy5) were normalized by loess (limma package from R was used). Unsupervised thresholding based on the discriminant analysis method was conducted for each of Cy3 and Cy5 signal intensity distribution to discriminate expressed/non-expressed SNP sites. Given both Cy3 and Cy5 signals showed under threshold values, site was marked as non-expressed. Theta value (= (2/π)tan–1(SM/SB)), where SM and SB denote signals representing MSM and B6 allele, respectively.) was then calculated for each SNP sites to discriminate expressed allele-type, i.e. B6 (<0.15), MSM (0.82<), or bi-allelic (intermediates). Threshold values were determined by the same method as expressed/non-expressed thresholding. Value "-1" indicates non-expressed.

source_name: Liver RNA came from F1 hybrid mouse (MSM x B6)

extract_protocol: Total RNA (brain and liver came from 8 to 10 weeks old mouse of each strain) was isolated by using Trizol reagent (Invitrogen), and was reverse-transcribed by using random hexamers. Generated cDNA then subjected to Illumina GoldenGate Assay.

value: F1 hybrid mouse (MSM x B6)

value: liver


title: Expression of Ube3a-Snurf/Snrpn region (Liver from F1 hybrid mouse B6xMSM)

description:
Cy3 and Cy5 labels distinguish B6/MSM allele of a single Sample. See Platform data table (GPL10330) to get which channel detects B6 allele.
Expression of Ube3a-Snurf/Snrpn region (F1 hybrid mouse B6xMSM)

scan_protocol: Illumina GoldenGate Assay was used. See manufacturer's web site for more details.

source_name: Liver RNA came from F1 hybrid mouse (B6 x MSM)

value: F1 hybrid mouse (B6 x MSM)


title: Expression of Ube3a-Snurf/Snrpn region (Brain from F1 hybrid mouse B6xMSM)

source_name: Brain RNA came from F1 hybrid mouse (B6 x MSM)

label_protocol: Illumina GoldenGate Assay was used. See manufacturer's web site for more details.

value: brain


title: IkkβΔ_replicate1

value: IkkβΔ


title: IkkβΔ_replicate2


title: Expression of Ube3a-Snurf/Snrpn region (Brain from F1 hybrid mouse MSMxB6)

source_name: Brain RNA came from F1 hybrid mouse (MSM x B6)


title: ATH1_OXUPB1-2_elongation zone_first biological rep

city: Durham

first: HIRONAKA

last: TSUKAGOSHI

state: NC

address: 4128 FFSC Building

department: Biology

institute: Duke university

description: Gene expression data from root elongation zone of 35S::UPB1-3YFP #2/upb1-1 under standard conditions for 6 days

hyb_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

organism: Arabidopsis thaliana

source_name: root elongation zone

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized for 5 minutes in 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH and seeds were planted at 5 seeds/cm in two rows.

extract_protocol: Approximately 60 roots were collected per replicate.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Micro Kit (Qiagen).

treatment_protocol: Seedlings were grown for 6 days.  Roots were cut into the meristematic and elongation zone with a razor blade under microscope and collected into RNA extraction buffer.  Approximately 60 roots were collected per replicate, with two biological replicates being performed per sample.  Samples were briefly sonicated to disrupt the tissue.

tag: ecotype

value: Seedling root elongation zone

value: 6 days after germination

tag: growth media

value: Standard media (1xMS, 1% Sucrose, 1% agarose)


title: Transfection of HCT116 dicer- cell line with miR-124 G10.12/P, 24h timepoint

city: Seattle

first: Lee

last: Lim

state: WA

institute: Rosetta Inpharmatics

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45 deg C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver® system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin

source_name: HCT-116 dicer- cells

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.

extract_protocol: Qiagen RNAeasy

tag: cell line

value: HCT-116 dicer- cells

tag: conditions

value: transfection with 10nM miR-124 G10.12/P


title: ATH1_OXUPB1-2_meristematic zone_second biological rep

description: Gene expression data from root meristem zone of 35S::UPB1-3YFP #2/upb1-1 under standard conditions for 6 days

scan_protocol: Samples were submitted to Duke Microarray Facility (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

source_name: root meristem zone

value: Seedling root meristem zone


title: Control #1: mock transfection of HCT116 dicer- cell line, 24 h timepoint

value: mock transfection


title: OSKM induced pluripotent stem cell line repeat 3

city: Beijing

first: Tong

last: Wu

address: No. 7, Science Park Road, Zhongguancun Life Science Park, Beijing

country: China

institute: National Institute of Biological Sciences, Beijing

hyb_protocol: Hybridization, Wash and Stain Kit(Affymetrix, Inc.)

scan_protocol: GeneChip® Scanner 3000 7G3000 (Affymetrix, Inc.)

data_processing: GCOS 1.4 software provided by Affymetrix

source_name: Induced pluripotent stem cell line

label_protocol: WT Terminal Labeling Kit (Affymetrix, Inc.)

extract_protocol: By Trizol following manufacturer’s recommendation (Invitrogen)

value: 129 x Rosa26-rtTA

value: OSKM induced pluripotent stem cell line


title: ATH1_OXUPB1-2_meristematic zone_first biological rep


title: Oct4 induced pluripotent stem cell line repeat 1

value: Oct4 induced pluripotent stem cell line


title: Oct4 induced pluripotent stem cell line repeat 3


title: IkkβF/F_replicate2

tag: genotype/variation


title: OSKM induced pluripotent stem cell line repeat 2


title: Worm_wildtype_rep4

city: Saint Louis

first: Michael

last: Nonet

state: MO

address: 660 South Euclid Avenue

department: Anatomy and Neurobiology

institute: Washington University Medical School

description: Slide 129

hyb_protocol: Each sample pair (~5ul) is resuspended in Formamide-based  hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and Rnase/Dnase-free water (19ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 350 kit (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere)  (26ul), and Rnase/Dnase-free water (21ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min.  Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 3 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence.  Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence.

data_processing: Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

organism: Caenorhabditis elegans

source_name: wild type, N2

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 350 kit (Genisphere).  Modified oligo-dT primers are utilized in which a fluorophore/dendrimer specific oligo sequence is attached to the 5’ end of the dT primer.  For cDNA synthesis, 1ul of fluorophore specific oligo-dT primer is added to 5ug of total RNA and the solution is incubated at 80C for 10 minutes then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul).  For RNA expression level comparison, samples are paired and concentrated using Microcon YM30 microconcentrators (Millipore) according to the manufacturer’s protocol.

growth_protocol: Worm egg prep  (by bleaching) were hatched overnight at 20C.  L1 animals were then fed on OP50 for 2 hours at room temperature before harvesting.

extract_protocol: RNA was isolated using a standard Trizol protocol (invitrogen)

value: wild type, N2

value: whole worm, first larva stage

source_name: mutant, sam-10

value: mutant, sam-10


title: ATH1_Col-0_elongation zone_first biological rep

description: Gene expression data from root elongation zone of Col-0 under standard conditions for 6 days


title: Oct4 induced pluripotent stem cell line repeat 2


title: Worm_wildtype_swap_rep3

description: Slide 128


title: Trophoblast Stem Cell 129R3 repeat 3

source_name: Trophoblast Stem Cell line

value: Trophoblast Stem Cell 129R3


title: Transfection of HCT116 dicer- cell line with miR-124 G/P, 24h timepoint

value: transfection with 10nM miR-124 G/P


title: Worm_wildtype_swap_rep1

description: Slide 124


title: OSKM induced pluripotent stem cell line repeat 1


title: ATH1_OXUPB1-2_elongation zone_second biological rep


title: Worm_wildtype_rep3

description: Slide 127


title: root_UPB1_2_2

first: Wolfgang

last: Busch

address: 124 Science Drive

institute: Duke University

description: Wildtype control (no GFP) ChIP sample v ProUPB1:UPB1:GFP transcription factor ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis

hyb_protocol: Hybridization was performed according to the  Agilent Mammalian ChIP-on-chip Kit protocol

scan_protocol: Scanner G2565BA with protocoll CGH-v4_95_Feb07

data_processing: Signal extraction and initial data processing were done using the Agilent feature extraction software. Additional analysis as described in Tsukagoshi et. al. 2010

label_protocol: DNA from the upb1-1 / ProUPB1:UPB1:GFP and wildtype ChIPs were blunted using T4 DNA polymerase, cleaned up with the Qiagen Reaction Cleanup Kit, amplified with 22 PCR cycles, and subsequently cleaned up according to the Agilent Mammalian ChIP-on-chip Kit protocol. 2ug of DNA was fragmented, and labeled with Cyanine 3-dUTP, and Cyanine 5-dUTP according to the Agilent Mammalian ChIP-on-chip Kit protocol.

growth_protocol: upb1-1 / ProUPB1:UPB1:GFP and wildtype lines were germinated and grown on MS media for 6 days  as described in Tsukagoshi et. al. 2010

extract_protocol: Chromatin Immunoprecipitation as described in Tsukagoshi et. al. 2010

treatment_protocol: Whole root tissue was fixed as described in Tsukagoshi et. al. 2010

tag: growth protocol

value: whole roots from 6d on MS-media grown seedlings

value: whole roots

tag: genotype

tag: antibody

value: anti-GFP

tag: antibody manufacturer

value: ABCAM

tag: antibody catalog #

tag: lot #

source_name: wt

value: wt


title: Control #2: mock transfection of HCT116 dicer- cell line, 24 h timepoint

value: HCT-116 dicer- cells


title: Trophoblast Stem Cell 129R3 repeat 1

tag: strain


title: Worm_wildtype_rep2

description: Slide 125

tag: tissue


title: Worm_wildtype_swap_rep2

description: Slide 126


title: Worm_wildtype_rep1

description: Slide 123


title: Rice root treated with 100 µM of Pb, biological rep2

status: Public on Nov 11 2010

city: Lucknow

first: Debasis

last: Chakrabarty

address: Rana Pratap Marg

institute: NBRI

description: Gene expression data from rice root treated with 100 µM of Pb.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Gene Chip Rice Genome Arrays (Gene Expression Omnibus platform accession no. GPL2025). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Scanner 3300 (Affymetrix, USA).

data_processing: The hybridization data were analyzed using dCHIP software. Satisfactory image files were analyzed to generate probe intensity (.cel) files using the default settings of GCOS. The normalization of all arrays was performed following default setting of dCHIP [54].  To identify statistically significant differentially expressed genes, a combined criterion of 2-fold or more change and t test p value, <0.005 was adopted. To obtain annotations for the probe sets, target sequences were from the sequence information file for the rice genome array. The target sequences were then searched using BLASTN against the TIGR rice pseudomolecules, release 6.1 (http://rice.plantbiology.msu.edu/).

organism: Oryza sativa Indica Group

source_name: Rice root treated with 100 µM of Pb

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: The rice variety IR-64 was germinated and allowed to grow for 5 d at 37 oC and then transferred to Hewitt solution to grow for 10 days.

extract_protocol: Total RNA was extracted from the treated rice roots using the QIAGEN RNeasy Plant Maxi Kit (QIAGEN, MD).

treatment_protocol: After 10 d of growth, seedlings of uniform size and growth were treated with 100 µM of Cr (VI), As (V), Cd, and Pb under standard physiological conditions of 16 h light (115 μmol m−2 s−1) and 8 h dark photoperiod at 25 ± 2°C for 24 h.

tag: cultivar

value: IR 64

value: root

tag: treatment

value: 100 µM of Pb

tag: age

value: 10 days


title: Worm_wildtype_swap_rep4

description: Slide 130


title: root_UPB1_1_2

description: ProUPB1:UPB1:GFP transcription factor ChIP sample v wildtype control (no GFP) ChIP sample, gProcessedSignal and rProcessedSignal were used to calculate the probewise ratio and subsequent analysis


title: root_UPB1_1_1


title: Trophoblast Stem Cell 129R3 repeat 2

value: 129 x Rosa26-rtTA


title: Rice root treated with 100 µM of AsV, biological rep2

description: Gene expression data from rice root treated with 100 µM of AsV.

source_name: Rice root treated with 100 µM of AsV

value: 100 µM of AsV


title: Rice root treated with 100 µM of Cd, biological rep1

description: Gene expression data from rice root treated with 100 µM of Cd.

source_name: Rice root treated with 100 µM of Cd

value: 100 µM of Cd


title: Rice root treated with 100 µM of AsV, biological rep3


title: Rice root treated with 100 µM of Cr (VI), biological rep1

description: Gene expression data from rice root treated with 100 µM of Cr (VI).

value: 100 µM of Cr (VI)


title: Rice root treated with 100 µM of Cr (VI), biological rep2


title: Rice root treated with 100 µM of Cr (VI), biological rep3


title: Rice root treated with 100 µM of Cd, biological rep2


title: Rice root treated with 100 µM of Cd, biological rep3


title: Rice root treated with 100 µM of Pb, biological rep1


title: Control rice root, biological rep2

description: Gene expression data from rice roots treated with water.

source_name: Control rice root


title: Rice root treated with 100 µM of AsV, biological rep1


title: Control rice root, biological rep3


title: Control rice root, biological rep1


title: Rice root treated with 100 µM of Pb, biological rep3


title: Root, biological rep2

city: Mishima

first: Nori

last: Kurata

state: Shizuoka

address: 1111 Yata

institute: National Institute of Genetics

description: Gene expression data from mature root.

hyb_protocol: 3.3 ug of labeled and fragmented cRNA was hybridized to GeneChip Rice Genome Array using  GeneChip Hybridization Oven 640 (Affymetrix). Wash and stain was performed by GeneChip Fluidics Station 450 (Affymetrix). All operations were performed with Hybridization, Stain and Wash Kit (Affymetrix) according to manufacturer's protocol (hws_kit_manual).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix).

data_processing: CEL files produced by GCOS 1.3 were analyzed using the statistical software R with bioconductor package “affy”. Signal intensities were extracted by expresso algorithm with parameters : bgcorrect.method = “mas”, normalize = “F”, pmcorrect.method = “pmonly”, summary.method = “mas”. Extracted signal intensities were introduced into GeneSpring 7.3.1 (Agilent) and scaled to 75th percentile per chip. Mas5calls algorithm in package “affy” was used for detection call.

organism: Oryza sativa

source_name: Whole root, 4th leaf growing stage

label_protocol: Biotinylated cRNA were prepared from 500 ng total RNA using One-Cycle cDNA Synthesis Kit (Affymetrix) according to manufacturers protocol (hws_kit_manual).

growth_protocol: Young leaves and roots were collected from plants grown in a green house. Calli were generated from seeds for three weeks on MS medium at 30C, transferred to regeration medium, cultured for indicated days and collected. Shoots were collected from plants grown at 30C in a growth chamber for four weeks.

extract_protocol: Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.

treatment_protocol: Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.

tag: cv. Nipponbare


title: Regenerating callus 4 days, biological rep1

description: Gene expression data from regenerating callus.

source_name: 4 days regenerated callus


title: Young leaf, biological rep3

description: Gene expression data from young leaf.

source_name: 4th leaf blade


title: Young leaf, biological rep2

description: Gene expression data from young leaf.


title: Regenerating callus 2 days, biological rep2

description: Gene expression data from regenerating callus. Excess amount of poly (A) controls were used accidentally.

source_name: 2 days regenerated callus


title: Growing callus, biological rep1

description: Gene expression data from growing callus.

source_name: Growing callus


title: Regenerating callus 8 days, biological rep2

source_name: 8 days regenerated callus


title: Shoot, biological rep3

description: Gene expression data from shoot.

source_name: 4 weeks old shoot


title: Regenerating callus 6 days, biological rep3

source_name: 6 days regenerated callus


title: Root, biological rep3

description: Gene expression data from mature root.


title: Root, biological rep1

description: Gene expression data from mature root.


title: Regenerating callus 2 days, biological rep1


title: Young leaf, biological rep1

description: Gene expression data from young leaf.


title: Regenerating callus 4 days, biological rep3


title: Growing callus, biological rep3


title: Shoot, biological rep2

description: Gene expression data from shoot.


title: Regenerating callus 8 days, biological rep1


title: Regenerating callus 4 days, biological rep2


title: Growing callus, biological rep2

description: Gene expression data from growing callus. Excess amount of poly (A) controls were used accidentally.


title: Shoot, biological rep1

description: Gene expression data from shoot.


title: Regenerating callus 6 days, biological rep2


title: 4 DAP embryosac_top, biological rep2

description: Gene expression data from top 3/4 part of pollinated embryo sac.

source_name: Embyo and ovary, top 3/4 part, 4 DAP

growth_protocol: Plants were grown in paddy fields under normal condition at Mishima, Japan.

treatment_protocol: Tissue samples were collected on August - September. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.


title: Regenerating callus 8 days, biological rep3


title: Young leaf, biological rep4

description: Gene expression data from young leaf.


title: 4 DAP embryosac_top, biological rep3


title: Regenerating callus 6 days, biological rep1


title: 4 DAP embryosac_top, biological rep1


title: 2 DAP embryosac_top, biological rep1

source_name: Embyo and ovary, top 3/4 part, 2 DAP


title: 2 DAP embryosac_top, biological rep2


title: 3 DAP embryosac_top, biological rep2

source_name: Embyo and ovary, top 3/4 part, 3 DAP


title: 1 DAP embryosac_top, biological rep2

source_name: Embyo and ovary, top 3/4 part, 1 DAP


title: Embryosac control_top, biological rep1

description: Gene expression data from top 3/4 part of unpollinated embryo sac.

source_name: Unpollinated embyo and ovary, top 3/4 part


title: 3 DAP embryosac_bottom, biological rep2

description: Gene expression data from bottom 1/4 part of pollinated embryo sac.

source_name: Embyo and ovary, bottom 1/4 part, 3 DAP


title: 3 DAP embryosac_top, biological rep1


title: Embryosac control_top, biological rep3


title: 1 DAP embryosac_top, biological rep1


title: 2 DAP embryosac_bottom, biological rep3

source_name: Embyo and ovary, bottom 1/4 part, 2 DAP


title: 4 DAP embryosac_bottom, biological rep2

source_name: Embyo and ovary, bottom 1/4 part, 4 DAP


title: 4 DAP embryosac_bottom, biological rep3


title: 3 DAP embryosac_bottom, biological rep1


title: 2 DAP embryosac_bottom, biological rep2


title: 1 DAP embryosac_bottom, biological rep3

source_name: Embyo and ovary, bottom 1/4 part, 1 DAP


title: 3 DAP embryosac_bottom, biological rep3


title: 2 DAP embryosac_bottom, biological rep1


title: 4 DAP embryosac_bottom, biological rep1


title: Embryosac control_top, biological rep2


title: 1 DAP embryosac_bottom, biological rep2


title: Regenerating callus 2 days, biological rep3


title: root_UPB1_2_1

source_name: wt


title: Fertilization, biological rep3

description: Gene expression data from pollinated stigma and ovary. Pollinated pollen grains were included in collected samples.

source_name: Stigma and Ovary 40-50 min after pollination

treatment_protocol: Tissue samples were collected on August - October. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.


title: 1 DAP embryosac_bottom, biological rep1


title: Embryosac control_bottom, biological rep1

description: Gene expression data from bottom 1/4 part of unpollinated embryo sac.

source_name: Unpollinated embyo and ovary, bottom 1/4 part


title: Fertilization, biological rep1


title: Zygote formation, biological rep1

source_name: Stigma and Ovary 5-7 hrs after pollination


title: Embryosac control_bottom, biological rep3


title: Ovary control, biological rep2

description: Gene expression data from unpollinated ovary.

source_name: Unpollinated ovary


title: Pollen tube growth, biological rep2

source_name: Stigma and Ovary 15-25 min after pollination


title: Pollinating ovary, biological rep2

description: Gene expression data from ovary just after pollination. Pollinated pollen grains were included in collected samples.

source_name: Ovary 5 min after pollination


title: Fertilization, biological rep2


title: Zygote formation, biological rep2


title: Embryosac control_bottom, biological rep2


title: Ovary control, biological rep3


title: Pollinating stigma, biological rep1

description: Gene expression data from stigma just after pollination. Pollinated pollen grains were included in collected samples.

source_name: Stigma 5 min after pollination


title: Pollen tube growth, biological rep1


title: Zygote formation, biological rep3


title: Stigma control, biological rep3

description: Gene expression data from unpollinated stigma.

source_name: Unpollinated stigma


title: Pollinating stigma, biological rep2


title: Pollen tube growth, biological rep3


title: Ovary control, biological rep1


title: Pollinating ovary, biological rep3


title: Stigma control, biological rep2


title: Stigma control, biological rep1


title: Pollinating ovary, biological rep1


title: Anther at P3, biological rep3

description: Gene expression data from developing anther.

source_name: Anther, tri-cellular mature pollen stage

extract_protocol:
Tissue samples were collected on July - October. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.
Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.


title: Anther at P3, biological rep1


title: Anther at P3, biological rep2


title: Sample exposed to melittin, replicate 3

city: PATERNA

first: MONICA

last: GANDIA

state: VALENCIA

address: AVDA. AGUSTIN ESCARDINO 7

department: CIENCIA DE LOS ALIMENTOS

country: Spain

institute: IATA

hyb_protocol: The nylon filters from the macroarray containing 6,020 yeast ORFs (Laboratory of DNA chips, Universitat de València, http://scsie.uv.es/chipsdna/) were hybridized with 33P-labelled cDNA probes and stripped. A total of three different filters were used, and each biological replicate from each of the three treatments (control, 5 μM PAF26, and 5 μM melittin) was hybridized to a distinct filter. Therefore, each individual filter was subjected to three cycles of hybridization and stripping.

scan_protocol: Filters were exposed for 5–7 days to an imaging plate (BAS-MP 2040, FujiFilm), which was scanned in a phosphorimaging scanner (FLA-3000, FujiFilm).

data_processing:
Raw image quantitation background subtracted: Macroarray hybridization images were quantified with the software package ArrayVision v8.0 (Imaging Research Inc.). The local background was defined as the mean signal intensity of an area around each block of 16 hybridized spots, and subtracted from each signal.

Values were submitted to statistical analysis (ArrayStat v1.0 software) as described in López-García et al. (2010), BMC Microbiology.

organism: Saccharomyces cerevisiae

source_name: Yeast cells exponentially grown in YPD medium and exposed to melittin

label_protocol: Radiolabelled cDNA was obtained by reverse transcription (RT) of 20 μg of total RNA, after annealing to 3.75 µg of the anchor oligonucleotide oligo(dT)VN (Invitrogen), in the presence of 5 mM DTT, 800 μM each of dATP, dTTP and dGTP, 5 μM dCTP, 5 μl of 3000 Ci/mmol α33P-dCTP, 10 units RNase inhibitor (Invitrogen), and 400 units SuperScript III reverse transcriptase (Invitrogen), at 50ºC for 2h. Template RNA was removed by alkaline hydrolysis, followed by neutralization. Unincorporated nucleotides were separated from the 33P-labelled cDNA probe by passage through MicroSpin S-300HR columns (Amersham).

growth_protocol: 25 ml cultures of 10E+05 colony-forming units (CFU)/ml of S. cerevisiae FY1679 were grown with shaking at 30ºC in 20% YPD medium (100% YPD is 1% yeast extract, 2% peptone and 2% dextrose) for three hours.

extract_protocol: Yeast cells were collected by centrifugation and kept at  80ºC until processed for RNA isolation. Total RNA was extracted from cell pellets and ethanol precipitated.

treatment_protocol: 250 μl of a 100X stock solution of each peptide were added to each yeast culture (final concentration 5 μM). The same volume of MOPS buffer was added to the control sample. Cultures were grown at 30ºC with shaking for 3 additional hours. Three independent biological replicates were conducted for each treatment.

value: melittin


title: Sample exposed to melittin, replicate 2


title: Anther at P2, biological rep1

source_name: Anther, bi-cellular gametopyte stage


title: Anther at P1, biological rep2

source_name: Anther, uni-nucleated gametopyte stage


title: Anther at P2, biological rep3


title: Anther at P1, biological rep3


title: Sample exposed to melittin, replicate 1


title: Anther at M3, biological rep1

source_name: Anther, pollen mother cells at meiotic diplotene-tetrad stage


title: Anther at M3, biological rep2


title: Anther at M3, biological rep3


title: Sample exposed to PAF26, replicate 3

source_name: Yeast cells exponentially grown in YPD medium and exposed to PAF26


title: Anther at P2, biological rep2


title: Anther at P1, biological rep1


title: Anther at M2, biological rep2

source_name: Anther, pollen mother cells at meiotic zygotene-pachytene stage


title: Sample exposed to PAF26, replicate 2


title: Sample exposed to PAF26, replicate 1


title: Anther at M2, biological rep3


title: Anther at M1, biological rep3

source_name: Anther, pollen mother cells at meiotic leptotene stage


title: Anther at M1, biological rep1


title: Control sample, replicate 3

source_name: Yeast cells exponentially grown in YPD medium and exposed to MOPS buffer

value: no antimicrobial peptide


title: Anther at M2, biological rep1


title: Anther at Mei1, biological rep2

source_name: Anther, pollen mother cells at pre-meiotic S/G2 stage


title: Anther at Mei1, biological rep3


title: Anther at Mei1, biological rep1


title: Anther at An1, biological rep2

source_name: Anther, hypodermal archesporial cells forming stage


title: Anther at M1, biological rep2


title: Anther at M1, biological rep4


title: Anther at An1, biological rep1


title: Anther at An1, biological rep3


title: Control sample, replicate 1


title: Control sample, replicate 2


title: Escherichia coli_Rep1

city: Singapore

first: Hua

last: Ling

address: 62 Nanyang Drive

department: Department of Chemical and Biomolecular Engineering, SCBE

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 1 of 2

hyb_protocol: Standard Agilent procedures

scan_protocol: Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1

data_processing: Agilent Feature Extraction Software v. 9.5.3.1  was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: LW12, 30min after OD600 reaches 1.0

label_protocol: Approximately 10 µg of total RNA was processed to produce Cy5 or Cy3-labelled cDNA targets

growth_protocol: In LB plus 0.8% glucose cells grew overnight, and then diluted to OD600=0.02, followed by culture until OD600 reaches 1.0. The culture was preformed at 37 Celsius degree and 250rpm.

extract_protocol: Total RNA was isolated using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol

treatment_protocol: One condition: 37 Celsius degree, 250rpm, 30min after OD600 reaches 1.0

tag: genome/variation

value: luxS mutant LW12

source_name: W3110, 30min after OD600 reaches 1.0

value: wild type W3110


title: Escherichia coli_Rep2

description: Biological replicate 1 of 2


title: Anther at M3, biological rep4


title: NT1

city: Hong Kong

first: William

last: Niu

address: #21, Rd. Sassoon

department: Dept. Biochemistry

country: Hong Kong

institute: The University of Hong Kong

description: gene expression data from early passage mouse embryonice fibroblsts

hyb_protocol: According to The GeneChip® Mouse Genome 430 2.0 protocol.  Array

data_processing: GCOS

source_name: Zmpste24-/- mouse embryonic fibroblasts (P3)

growth_protocol: Three pairs of wild-type and Zmpste24-/- MEFs were generated from E13.5 embryos at passage 0, subcultured into passage 3 and collected for total RNA extraction.

extract_protocol: RNA was isolated by TRIzol (Invitrogen) following the manufacturer protocol.

treatment_protocol: A total of 5 x 105 MEFs were plated on multiple 100-mm dishes for each line in 10% fetal calf serum and Dulbecco's Modified Eagle's Medium (DMEM).

tag: cell type

value: mouse embryonic fibroblasts


title: NT2

scan_protocol: According to The GeneChip® Mouse Genome 430 2.0 protocol.  Array


title: HRPE-rep2

city: Bethesda

first: R

middle: Krishnan

last: Kutty

address: 6 Center Dr., Room 112

department: National Eye Institute

institute: National Institutes of Health

description: Biological replicate 2 of 2

hyb_protocol: hybridization performed using dual-channel microarray μParafloTM microfluidic chip containing miRNA transcripts (LC Sciences)

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: LOWESS normalized, background subtracted

source_name: Control HRPE cells

label_protocol: Control labeled with Cy3. Treated labeled wit Cy5

growth_protocol: Human retinal pigment epithelial (HRPE) cell cultures established from adult donor eyes were grown in a medium containing 10% featal bovine serum and was used between passages 7 and 10

extract_protocol: RNA extracted with Ambion mirVana miRNA Isolation Kit

treatment_protocol: Cells were treated with an inflammatory cytokine mix containing IFN-γ (100 u/ml), TNF-α (10 ng/ml) and IL-1β (10 ng/ml) for 16 hours in a serum-free medium

value: Human retinal pigment epithelial (HRPE) cells

tag: treatment group

value: control

source_name: Treated HRPE cells


title: WT3

source_name: Zmpste24+/+ mouse embryonic fibroblasts (P3)

label_protocol: According to The GeneChip® Mouse Genome 430 2.0 protocol.  Array


title: WT2


title: Kidney Cortical Collecting Duct

type: SAGE

city: Paris

first: Lydie

last: Cheval

address: 15 rue de l'école de Médecine

institute: Institut des Cordeliers

description: Library was obtained from 1000 microdissected Cortical Collecting Duct from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

data_processing: Automatic tag detection and counting was performed with SADELAB (CEA Saclay, France), a web-based integrated platform dedicated to the management of SAGE project.

molecule: polyA RNA

source_name: microdissected cortical collecting duct from kidney

extract_protocol: Dynabeads mRNA direct kit (Dynal) was used to extract mRNA.

tag: gender

value: male

value: 10 weeks

value: kidney cortical collecting duct


title: Kidney Proximal Tubule, S3

description: Library was obtained from microdissected Proximal tubule S3 from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected proximal tubule, S3 from kidney

value: kidney proximal tubule, S3


title: Kidney Glomerulus

description: Library was obtained from microdissected glomeruli from male CD1 mice under control condition. The lirary was generated using Sau3AI as anchoring enzyme and BsmFI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data are provided after curation as described in the publication.

source_name: microdissected glomeruli from kidney

value: kidney glomeruli


title: WT1

tag: genotype/variation


title: Kidney Proximal Tubule, S1

description: .Library was obtained from microdissected Proximal tubule S1 from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected proximal tubule, S1 from kidney

value: kidney proximal tubule, S1


title: Kidney Distal Convoluted Tubule

description: Library was obtained from 1000 microdissected Distal Convoluted Tubule from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected distal convoluted tubule from kidney

value: kidney distal convoluted tubule


title: Kidney Proximal Tubule, S2

description: Library was obtained from microdissected Proximal tubule S2 from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected proximal tubule, S2 from kidney

value: kidney proximal tubule, S2


title: Kidney Outer Medullary Collecting Duct

description: Library was obtained from 1000 microdissected Outer Medullary Collecting Duct from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected outer medullary Collecting Duct from kidney

value: kidney outer medullary collecting duct


title: Kidney Medullary Thick Ascending Limb of Henle's Loop (MTAL)

description: Library was obtained from microdissected medullary thick ascending limb of Henle's loop from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected medullary thick ascending limb of Henle's loop from kidney

value: kidney medullary thick ascending limb of Henle's loop (MTAL)


title: Kidney Connecting Tubule (CNT)

description: Library was obtained from 1000 microdissected Connecting Tubule from male CD1 mice under control condition. The library was generated using Sau3AI as anchoring enzyme and MmeI as tagging enzyme.The SAGE Adaptation method for Downsized Extracts was used to generate the library. Data were provided after curation as described in the publication.

source_name: microdissected connecting tubule from kidney

value: kidney connecting tubule