title: HSC#10, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S161
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_121
Short description:			RNA extracted from second stem cell fraction of primary human hematopoietic cells.
Estimated purity:				> 99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

source_name: Second stem cell fraction of primary human hematopoietic cells, Cord blood

tag: Defining markers:				CD34+, CD38-, CD36-


title: Primary Myoblast Rb(-) D, chip MOE430B

status: Public on Feb 13 2008

type: RNA

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S324
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_371
Short description:			Satellite cell derived primary myoblasts. Myoblasts lacking retinoblastoma gene product. Differentiation defective. Biological triplicates, !Sample_description = Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			2-3 x 10^6
Sample volume:				5 ul

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: pRb Null Primary Myoblasts, Skeletal muscle

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol:
Growth medium:				Hams F-10 20% FBS
Media supplements:			bFGF
Culture conditions:			37 0C, 5% Co2

extract_protocol:
RNA prep method:				Qiagen Mini
Cell purification method:			Cultured homogenous populations
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Desmin, MyoD staining

treatment_protocol: Assays to confirm viability:		Staining and trypan blue exclusion

tag: Strain:					Balb/C

tag: Gender:					Female

tag: Karyotype:				Diploid

tag: Defining markers:				MyoD, Pax7


title: Primary Myoblast WT C, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S323
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_370
Short description:			Satellite cell derived primary myoblasts. Wild types controls.Biological triplicates
Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			2-3 x 10^6
Sample volume:				5 ul

source_name: Wild Type Primary Myoblasts, Skeletal muscle


title: Primary Myoblast WT A, chip MOE430B


title: HSC#1, chip HG-U133A

type: other

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E120
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=120
SCGP Sample ID:				S160
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=120#SAMPLE_120
Short description:			RNA extracted from first stem cell fraction of primary human hematopoietic cells.
Estimated purity:				> 99%
Num cells for RNA prep:			20,000-100,000
Sample volume:				5.0 ul

molecule: other

organism: Homo sapiens

source_name: First stem cell fraction of primary human hematopoietic cells, Cord blood

extract_protocol:
RNA prep method:				TRIzol and RNeasy
Amplification method:			T7-based
Cell purification method:			FACS-sorting
Method for estimating purity:		FACS

tag: Strain:

tag: Defining markers:				CD34+, CD38-, Lin-


title: Primary Myoblast WT B, chip MOE430B


title: HSC#4, chip HG-U133A


title: HSC#5, chip HG-U133A


title: HeLa (2.5) template ds-cDNA, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E5
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=5
SCGP Sample ID:				S64
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=5#SAMPLE_48
Short description:			HeLa (2.5) template ds-cDNA: T7 based RNA amplification from 40 ng of total RNA, and then template ds-cDNA was generated from amplified RNA.
RNA concentration:			2.0 ug/ul
Sample volume:				5.0 ul

source_name: HeLa ds-cDNA, Cervical epithelium

extract_protocol: RNA prep method:				TRIzol extraction, RNeasy purification


title: HSC#9, chip HG-U133A


title: HSC#2, chip HG-U133A


title: Primary Myotube MCK-cre Rb flox J, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S326
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_373
Short description:			Primary MCK-cre Rb flox myotube RNA. Day 6 in low serum differenciation conditions. Samples are ffrom 3 independent cell lines.
Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			3-6x 10^6
Sample volume:				5 ul

source_name: MCK-cre Rb flox Primary Myotube, Skeletal muscle

growth_protocol:
Growth medium:				5% horse serum DMEM
Media supplements:			2% pen/strep
Culture conditions:			37 0C, 5% Co2

extract_protocol:
RNA prep method:				Qiagen Mini
Cell purification method:			Tissue dissociation, selective plating, marker staining
Contaminating cell type:			Fibroblasts
Method for estimating purity:		Desmin, MyoD staining

treatment_protocol: Assays to confirm viability:		Staining and TUNEL

tag: Defining markers:				MHC, muscle creatine kinase, myosine light chain


title: HeLa (1.5) template ds-cDNA, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E5
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=5
SCGP Sample ID:				S63
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=5#SAMPLE_47
Short description:			T7-based RNA amplification from 1.0 ug of total RNA followed by the generation of template ds-cDNA from amplified RNA.
RNA concentration:			5.0 ug/ul
Sample volume:				5.0 ul


title: Primary Myotube MCK-cre Rb flox K, chip MOE430A


title: Primary Myotube MCK-cre Rb flox L, chip MOE430A


title: E2F4KO, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID:			E236
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=236
SCGP Sample ID:				S328
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=236#SAMPLE_366
Short description:			E2F4 knockout neurospheres from E12.5 forebrain. E2F4 transcription factor regulates the expression of the genes which are required for neural stem cell expansion in the developing mouse brain. The results of microarray analysis will help to identify the signaling pathways affected by E2F4 deletion and refine the neural stem cell regulatory mechanism.
RNA concentration:			2.0 ug/ul
Sample volume:				10 ul

source_name: Knockout embryonic neurospheres, Forebrain E12.5 (ventral telencephalon)

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			none

tag: Strain:					CS7B6


title: HeLa total RNA, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. John Dick (jdick@uhnres.utoronto.ca; Room 6-608; 620 University Avenue) for analysis.
Stembase Experiment ID:			E5
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=5
SCGP Sample ID:				S6
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=5#SAMPLE_5
Short description:			HeLa total RNA
RNA concentration:			7.0 ug/ul
Sample volume:				10 ul

source_name: HeLa total RNA, Cervix epithelium


title: E2F4WT, chip MOE430B

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Ruth Slack (rslack@uottawa.ca; ) for analysis.
Stembase Experiment ID:			E236
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=236
SCGP Sample ID:				S327
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=236#SAMPLE_365
Short description:			E2F4 wild type neurospheres from E12.5 forebrain. E2F4 transcription factor regulates the expression of the genes which are required for neural stem cell expansion in the developing mouse brain. The results of microarray analysis will help to identify the signaling pathways affected by E2F4 deletion and refine the neural stem cell regulatory mechanism.
RNA concentration:			2.0 ug/ul
Sample volume:				10 ul

source_name: Wild type embryonic neurospheres, Forebrain E12.5 (ventral telencephalon)


title: Primary Myotube WT I, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E238
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=238
SCGP Sample ID:				S325
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=238#SAMPLE_372
Short description:			Primary wild type myotube RNA. Day 6 in low serum differenciation conditions. Samples are ffrom 3 independent cell lines.
Estimated purity:				~99-100%
RNA concentration:			2 ug/ul
Num cells for RNA prep:			3-6x 10^6
Sample volume:				5 ul

source_name: Wild Type Primary Myotube, Skeletal muscle


title: 3JM 3, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E204
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=204
SCGP Sample ID:				S273
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=204#SAMPLE_245
Short description:			Human myoblast differentiated 4 days.
RNA concentration:			200ng/uL
Sample volume:				15uL

source_name: differentiated myoblast/myotube, muscle

growth_protocol: Growth medium:				Differentation Media, DMEM + 2.5% horse serum

extract_protocol: RNA prep method:				Protocol not specified

tag: Gender:					Male


title: Primary Myotube WT G, chip MOE430A


title: 3JM 2, chip HG-U133A


title: Primary Myotube WT H, chip MOE430A


title: Primary Myoblast Rb(-) F, chip MOE430A


title: 2JM#3, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E204
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=204
SCGP Sample ID:				S268
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=204#SAMPLE_244
Short description:			Undifferentiated FM95-14 human embryonic myoblasts contain myogenic stem/progenitor cells. Gene expression analysis and comparison to FM95-14 cells that have been allowed to differentiate will allow the ascertainment of genes that are implicated in myogenic lineage commitment.
Cell line clone ID:			FM95-14
RNA concentration:			200 ng/uL
Num cells for RNA prep:			2.5 x 10^6 cells
Sample volume:				10uL

source_name: Undifferentiated FM95-14 myoblast, muscle

growth_protocol:
Growth medium:				SKBM-2 (cambrex)
Media supplements:			dexamethasone, glutamine, FBS 10%, hEGF

extract_protocol: RNA prep method:				RNeasy


title: Primary Myoblast Rb(-) E, chip MOE430A


title: 3JM 1, chip HG-U133A


title: 2JM#2, chip HG-U133A


title: Primary Myoblast WT B, chip MOE430A


title: Primary Myoblast WT C, chip MOE430A


title: E2F4KO, chip MOE430A


title: 2JM#1, chip HG-U133A


title: 1JM#1, chip HG-U133A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E204
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=204
SCGP Sample ID:				S267
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=204#SAMPLE_243
Short description:			293FT-human embryonal kidney, To be used as human control cell line for human myoblast study.
RNA concentration:			200 ng/uL
Num cells for RNA prep:			2 x 10^6 cells
Sample volume:				5 uL

source_name: 293FT, kidney

growth_protocol:
Growth medium:				DMEM (high glucose)
Media supplements:			10% pen/strep , 10%FBS , G418 500 ug/uL


title: Primary Myoblast Rb(-) D, chip MOE430A


title: Primary Myoblast WT A, chip MOE430A


title: 1JM#2, chip HG-U133A


title: HCT116 expression analysis

status: Public on Feb 12 2008

city: New York

first: Neri

last: Minsky

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

description: expression data

hyb_protocol: Array hybridization was carried out using the Affymetrix HG-U133_Plus_2 array according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G per manufacturer's protocol.

data_processing: Algorithm: 5.0 ExpressionStat

label: biotin

molecule: polyA RNA

source_name: colorectal cancer cell line

label_protocol: Carried out according to the manufacturer’s instructions.

growth_protocol: HCT116 cells were grown in McCoy's 5A medium supplemented with 10% FCS and antibiotics

extract_protocol: RNA was extracted using the QIAGEN RNeasy kit according to the manufacturer's protocol.

treatment_protocol: Treatment: no treatment

tag: Age

value: cell line

tag: Human colorectal cancer


title: 1JM#3, chip HG-U133A


title: E2F4WT, chip MOE430A


title: Colon adenocarcinoma (15556T)

city: Bethesda

first: Curtis

middle: C

last: Harris

state: MD

address: Building 37, Room 3068A

department: Center for Cancer Research

institute: National Cancer Institute

description: No additional information.

hyb_protocol: OSU - Sample Hybridization Protocol Qty. of labeled target: 5 ug of total RNA Other: Labeled targets from 5ug of total RNA were used for hybridization on each miRNA microarray chip containing human and mouse miRNA genes. All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6x SSPE (0.9 M NaCl / 60 mM NaH2PO4 H20 / 8 mM EDTA, pH 7.4) / 30% formamide at 25C for 18 hr, washed in 0.75x TNT (Tris HCL/NaCl/Tween 20) at 37C for 40 min.

scan_protocol: OSU - Scanning Protocol Other: Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at Power 80 and PMT 70 setting, and a scan resolution of 10 um.

data_processing:
Data Processing Protocol
Calculation Method: The microarrays used for this analysis were pin-spotted microRNA microarrays (from the Ohio State University Comprehensive Cancer Center, version 2.0). Intensities of each spot were the median intensities of foreground. Each of 170 microarrays used for this study contained 11520 spots. All spots where foreground intensity was less than background were reassigned as NA (NA marks missing data spots). All spots flagged as deficient by the scanner were also reassigned as NA. All blank (no oligo) spots with high foreground intensity were reassigned as NA. Each microRNA oligo is represented by quadruplicate spots on these arrays as two distant pairs of two adjacent spots. If there were 0 or 1 NA for an oligo quadruple, and the means of the distant oligo pairs differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned as NA. If there were 2 NAs for an oligo quadruple and the two non-NA spot intensities differed by > 1 on the log2 scale, all of the quadruplicate spots were reassigned NA. If there were 3 NA spots for a quadruple, the final spot was reassigned as NA. In total, 1,082,689 of 1,958,400 spots were reassigned as NA using these methods. LOESS (Locally Weighted Scatterplot Smoothing) normalization was performed using the R software package. All data was then imported into BRB array tools version 3.5.0 for analysis and all replicate spots were averaged. There were originally 85 pairs (tumor and paired nontumorous tissue) of arrays used. One case that was originally identified as an incident colon carcinoma patient was later found to have been diagnosed as carcinoma in situ and was removed from the analysis leaving the study population of 84 subjects.

label: alexa 647

label_protocol:
OSU - Labeling Protocol
Other: Processed by using a method of direct detection of the biotin-containing transcripts by streptavidin-Alexa647 conjugate.

extract_protocol:
OSU - Tri-Reagent Protocol
Other: RNA isolation was performed using TRIZOL Reagent (Invitrogen, Carlsbad) according to manufacturer's instructions. Briefly, colon tissue was homogenized in TRIZOL reagent and chloroform was added and liquid phases were separated with centrifugation. The supernatant was collected and RNA was precipitated with isopropanol washed with 75% ethanol. RNA was resuspended in DEPC treated water and 5 micrograms were used for each microarray experiment.

tag: Tissue

value: Colon

tag: Disease state

value: colon adenocarcinoma

tag: Individual

tag: Clinical info

value: Follow up status:Alive or censored


title: Paired nontumorous tissue (15556n)

description: No additional information.

value: paired nontumorous tissue


title: Paired nontumorous tissue (15430n)

description: No additional information.


title: Paired nontumorous tissue (15527n)

description: No additional information.


title: Colon adenocarcinoma (15527T)

description: No additional information.


title: Paired nontumorous tissue (15422n)

description: No additional information.

value: Follow up status:Died from Cancer


title: Colon adenocarcinoma (15422T)

description: No additional information.


title: Colon adenocarcinoma (15313T)

description: No additional information.


title: Paired nontumorous tissue (15313n)

description: No additional information.


title: Primary Myotube WT H, chip MOE430B


title: Colon adenocarcinoma (15363T)

description: No additional information.


title: Colon adenocarcinoma (15021T)

description: No additional information.


title: Paired nontumorous tissue (14915n)

description: No additional information.


title: Colon adenocarcinoma (15430T)

description: No additional information.


title: Colon adenocarcinoma (15214T)

description: No additional information.


title: Colon adenocarcinoma (14933T)

description: No additional information.


title: Paired nontumorous tissue (15214n)

description: No additional information.


title: Colon adenocarcinoma (15059T)

description: No additional information.


title: Paired nontumorous tissue (15149n)

description: No additional information.


title: Colon adenocarcinoma (14554T)

description: No additional information.


title: Colon adenocarcinoma (14559T)

description: No additional information.


title: Paired nontumorous tissue (15021n)

description: No additional information.


title: Paired nontumorous tissue (14559n)

description: No additional information.


title: Carcinoma in situ (14779T)

description: No additional information.

value: carcinoma in situ


title: Paired nontumorous tissue (15363n)

description: No additional information.


title: Paired nontumorous tissue (14933n)

description: No additional information.


title: Paired nontumorous tissue (15059n)

description: No additional information.


title: Colon adenocarcinoma (15149T)

description: No additional information.


title: Colon adenocarcinoma (14467T)

description: No additional information.


title: Paired nontumorous tissue (14779n)

description: No additional information.


title: Paired nontumorous tissue (14554n)

description: No additional information.


title: Colon adenocarcinoma (14445T)

description: No additional information.


title: Paired nontumorous tissue (14445n)

description: No additional information.


title: Paired nontumorous tissue (14278n)

description: No additional information.


title: Paired nontumorous tissue (14467n)

description: No additional information.


title: Colon adenocarcinoma (14278T)

description: No additional information.


title: Colon adenocarcinoma (14062T)

description: No additional information.


title: Paired nontumorous tissue (14273n)

description: No additional information.


title: Colon adenocarcinoma (14915T)

description: No additional information.


title: Colon adenocarcinoma (14022T)

description: No additional information.


title: Paired nontumorous tissue (14070n)

description: No additional information.


title: Colon adenocarcinoma (14070T)

description: No additional information.


title: Colon adenocarcinoma (14273T)

description: No additional information.


title: Paired nontumorous tissue (14022n)

description: No additional information.


title: Colon adenocarcinoma (13822T)

description: No additional information.


title: Paired nontumorous tissue (13799n)

description: No additional information.


title: Colon adenocarcinoma (13701T)

description: No additional information.


title: Colon adenocarcinoma (13799T)

description: No additional information.


title: Colon adenocarcinoma (13736T)

description: No additional information.


title: Paired nontumorous tissue (13822n)

description: No additional information.


title: Paired nontumorous tissue (13736n)

description: No additional information.


title: Colon adenocarcinoma (13687T)

description: No additional information.


title: Paired nontumorous tissue (13687n)

description: No additional information.


title: Paired nontumorous tissue (13701n)

description: No additional information.


title: Paired nontumorous tissue (13547n)

description: No additional information.


title: Colon adenocarcinoma (13273T)

description: No additional information.


title: Paired nontumorous tissue (14062n)

description: No additional information.


title: Colon adenocarcinoma (12892T)

description: No additional information.


title: Paired nontumorous tissue (13201n)

description: No additional information.


title: Colon adenocarcinoma (13201T)

description: No additional information.


title: Paired nontumorous tissue (13273n)

description: No additional information.


title: Paired nontumorous tissue (12892n)

description: No additional information.


title: Paired nontumorous tissue (12879n)

description: No additional information.


title: Paired nontumorous tissue (12874n)

description: No additional information.


title: Colon adenocarcinoma (13547T)

description: No additional information.


title: Colon adenocarcinoma (12874T)

description: No additional information.


title: Paired nontumorous tissue (12814n)

description: No additional information.


title: Colon adenocarcinoma (12829T)

description: No additional information.


title: Colon adenocarcinoma (12861T)

description: No additional information.


title: Paired nontumorous tissue (12829n)

description: No additional information.


title: Paired nontumorous tissue (12861n)

description: No additional information.


title: Colon adenocarcinoma (12879T)

description: No additional information.


title: Paired nontumorous tissue (12792n)

description: No additional information.


title: Paired nontumorous tissue (12755n)

description: No additional information.


title: Colon adenocarcinoma (12792T)

description: No additional information.


title: Colon adenocarcinoma (12755T)

description: No additional information.


title: Colon adenocarcinoma (12814T)

description: No additional information.


title: Colon adenocarcinoma (12742T)

description: No additional information.


title: Paired nontumorous tissue (12742n)

description: No additional information.


title: Colon adenocarcinoma (12740T)

description: No additional information.


title: Paired nontumorous tissue (12740n)

description: No additional information.


title: Colon adenocarcinoma (12663T)

description: No additional information.


title: Colon adenocarcinoma (12724T)

description: No additional information.


title: Paired nontumorous tissue (12663n)

description: No additional information.


title: Paired nontumorous tissue (12724n)

description: No additional information.


title: Colon adenocarcinoma (12633T)

description: No additional information.


title: Paired nontumorous tissue (12633n)

description: No additional information.


title: Colon adenocarcinoma (12464T)

description: No additional information.


title: Colon adenocarcinoma (12531T)

description: No additional information.


title: Colon adenocarcinoma (12462T)

description: No additional information.


title: Paired nontumorous tissue (12462n)

description: No additional information.


title: Paired nontumorous tissue (12447n)

description: No additional information.


title: Paired nontumorous tissue (12450n)

description: No additional information.


title: Colon adenocarcinoma (12417T)

description: No additional information.


title: Paired nontumorous tissue (12531n)

description: No additional information.


title: Colon adenocarcinoma (12447T)

description: No additional information.


title: Paired nontumorous tissue (12417n)

description: No additional information.


title: Paired nontumorous tissue (12464n)

description: No additional information.


title: Colon adenocarcinoma (12385T)

description: No additional information.


title: Colon adenocarcinoma (12450T)

description: No additional information.


title: Paired nontumorous tissue (12294n)

description: No additional information.


title: Paired nontumorous tissue (12385n)

description: No additional information.


title: Colon adenocarcinoma (12298T)

description: No additional information.


title: Colon adenocarcinoma (12231T)

description: No additional information.


title: Colon adenocarcinoma (12375T)

description: No additional information.


title: Paired nontumorous tissue (12231n)

description: No additional information.


title: Colon adenocarcinoma (12294T)

description: No additional information.


title: Paired nontumorous tissue (12298n)

description: No additional information.


title: Colon adenocarcinoma (12163T)

description: No additional information.


title: Paired nontumorous tissue (12375n)

description: No additional information.


title: Colon adenocarcinoma (12169T)

description: No additional information.


title: Paired nontumorous tissue (12169n)

description: No additional information.


title: Paired nontumorous tissue (12163n)

description: No additional information.


title: Paired nontumorous tissue (12158n)

description: No additional information.


title: Colon adenocarcinoma (12158T)

description: No additional information.


title: Colon adenocarcinoma (12146T)

description: No additional information.


title: Paired nontumorous tissue (12146n)

description: No additional information.


title: Colon adenocarcinoma (12139T)

description: No additional information.


title: Paired nontumorous tissue (12139n)

description: No additional information.


title: Colon adenocarcinoma (12124T)

description: No additional information.


title: Colon adenocarcinoma (12122T)

description: No additional information.


title: Paired nontumorous tissue (12124n)

description: No additional information.


title: Paired nontumorous tissue (12122n)

description: No additional information.


title: Colon adenocarcinoma (12051T)

description: No additional information.


title: Paired nontumorous tissue (12004n)

description: No additional information.


title: Colon adenocarcinoma (11918T)

description: No additional information.


title: Colon adenocarcinoma (12031T)

description: No additional information.


title: Paired nontumorous tissue (11918n)

description: No additional information.


title: Paired nontumorous tissue (12076n)

description: No additional information.


title: Paired nontumorous tissue (12051n)

description: No additional information.


title: Paired nontumorous tissue (11916n)

description: No additional information.


title: E coli Treated with Paromomycin and Rifampicin

city: La Jolla

first: Michael

last: Sykes

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description:
E. coli treated with Paromomycin and Rifampicin
virtual dual channel sample, derived from technically single channel submission

hyb_protocol: As per Sigma Genosys manufacturer's instructions

scan_protocol: Blots exposed to a PhosphorImager screen for 48 hours, and then scanned by a Storm PhosphorImager scanner

data_processing:
Background corrected signal intensity were then normalized using total intensity normalization.  The average volume difference between the two experiment and two control spots on a single array was calculated, and then averaged between two replicate arrays.  This volume difference was divided by the error estimate, to give a relative volume difference.
Attached raw data represents the background corrected signal intensity.

organism: Escherichia coli

label_protocol: As per Sigma Genosys' cDNA labeling instructions

extract_protocol: Phenol extraction

source_name: control of Paromomycin and Rifampicin

tag: control of Paromomycin and Rifampicin


title: E coli Treated with Paromomycin and Streptomycin

description:
E. coli treated with Paromomycin and Streptomycin
virtual dual channel sample, derived from technically single channel submission

source_name: control of Paromomycin and Streptomycin

tag: control of Paromomycin and Streptomycin


title: Colon adenocarcinoma (11873T)

description: No additional information.


title: Paired nontumorous tissue (12031n)

description: No additional information.


title: Colon adenocarcinoma (12076T)

description: No additional information.


title: Paired nontumorous tissue (11873n)

description: No additional information.


title: E coli Treated with Erythromycin and Promethazine

description:
E. coli treated with Erythromycin and Promethazine
virtual dual channel sample, derived from technically single channel submission

source_name: control of Erythromycin and Promethazine


title: Paired nontumorous tissue (11854n)

description: No additional information.


title: Colon adenocarcinoma (12004T)

description: No additional information.


title: Colon adenocarcinoma (11854T)

description: No additional information.


title: Colon adenocarcinoma (11916T)

description: No additional information.


title: E coli Treated with Tetracycline

description:
E. coli treated with Tetracycline
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Tetracycline

tag: E. coli treated with Tetracycline

source_name: control of Tetracycline

tag: control of Tetracycline


title: Colon adenocarcinoma (11731T)

description: No additional information.


title: Colon adenocarcinoma (11847T)

description: No additional information.


title: Paired nontumorous tissue (11847n)

description: No additional information.


title: E coli Treated with Streptomycin

description:
E. coli treated with Streptomycin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Streptomycin

tag: E. coli treated with Streptomycin

source_name: control of Streptomycin

tag: control of Streptomycin


title: Paired nontumorous tissue (11731n)

description: No additional information.


title: 14GRp_Blood_PNA_HRT

city: Tromsoe

first: Vanessa

last: Dumeaux

address: University of Tromsoe

country: Norway

institute: "The Norwegian Women and Cancer project"

description: Briefly, 10 μg of labeled cRNA targets from each sample were first fragmented, mixed with internal control target (24-mer oligo labeled with LIZ® fluorescent dye) and hybridized to a pre-hybridized microarray at 55°C for 16 hr. After washing to remove unhybridized DIG-labeled molecules, an alkaline phosphatase-antibody conjugate was added to bind to the DIG-labeled target. The addition of substrate and a chemiluminescence enhancer initiates the chemiluminescent reaction. Eight images were collected for each microarray using the 1700 analyzer including 2 “short” chemiluminescent images (5 seconds exposure length each) and 2 “long” chemiluminescent images (25 seconds exposure length each) for gene expression analysis, 2 fluorescent images for feature finding and spot normalization and 2 QC images for spectrum cross-talk correction. Applied Biosystems Expression System software was used to extract signal intensities, signal to noise ratios (S/N) and flagging values from the microarray images.

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit

data_processing: Using Applera package in R, we set the filtering criteria so that each gene had flagging value < 2 and a signal to noise ratio (S/N) ≥ 3 in at least 50% of the samples. After filtration, we proceed with quantile normalization of the log-intensities.

label: digoxigenin

source_name: blood samples in PAXgene, globin reduction using PNA, HRT user

label_protocol: NanoAmp™ RT-IVT Labeling Kit from Applied Biosystems

extract_protocol: PAXgene Blood RNA Kit (PreAnalytiX, Hombrechtikon, Switzerland)

tag: postmenopausal women


title: 15_Blood_noGR_noHRT

scan_protocol: Applied Biosystems Chemiluminescence Detection Kit

source_name: blood samples in PAXgene, no globin reduction, no HRT user


title: 14_Blood_noGR_HRT

source_name: blood samples in PAXgene, no globin reduction, HRT user


title: 41_Blood_noGR_HRT


title: Colon adenocarcinoma (11716T)

description: No additional information.


title: 41GRp_Blood_PNA_HRT


title: E coli Treated with Rifampicin

description:
E. coli treated with Rifampicin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Rifampicin

tag: E. coli treated with Rifampicin

source_name: control of Rifampicin

tag: control of Rifampicin


title: E coli Treated with Sulfisoxazole

description:
E. coli treated with Sulfisoxazole
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Sulfisoxazole

tag: E. coli treated with Sulfisoxazole

source_name: control of Sulfisoxazole

tag: control of Sulfisoxazole


title: E coli Treated with Spectinomycin

description:
E. coli treated with Spectinomycin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Spectinomycin

tag: E. coli treated with Spectinomycin

source_name: control of Spectinomycin

tag: control of Spectinomycin


title: 17GRp_Blood_PNA_noHRT

source_name: blood samples in PAXgene, globin reduction using PNA, no HRT user


title: E coli Treated with Promethazine

description:
E. coli treated with Promethazine
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Promethazine

tag: E. coli treated with Promethazine

source_name: control of Promethazine

tag: control of Promethazine


title: Paired nontumorous tissue (11716n)

description: No additional information.

tag: Tissue

tag: Disease state

tag: Individual


title: Colon adenocarcinoma (11692T)

description: No additional information.

tag: Clinical info


title: E coli Treated with Puromycin

description:
E. coli treated with Puromycin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Puromycin

tag: E. coli treated with Puromycin

source_name: control of Puromycin

tag: control of Puromycin


title: Colon adenocarcinoma (11642T)

description: No additional information.


title: Paired nontumorous tissue (11692n)

description: No additional information.


title: 14GRa_Blood_GlobinClear_HRT

source_name: blood samples in PAXgene, globin reduction using GlobinClear kit from ambion, HRT user


title: 15GRp_Blood_PNA_noHRT


title: 15GRa_Blood_GlobinClear_noHRT

source_name: blood samples in PAXgene, globin reduction using GlobinClear kit from ambion, non HRT user


title: 7GRp_r2_Blood_PNA_noHRT


title: 17GRa_Blood_GlobinClear_noHRT


title: 17_Blood_noGR_noHRT


title: 41GRa_Blood_GlobinClear_HRT


title: 31GRp_r2_Blood_PNA_HRT


title: 7_r2_Blood_noGR_noHRT


title: E coli Treated with Paromomycin

description:
E. coli treated with Paromomycin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Paromomycin

tag: E. coli treated with Paromomycin

source_name: control of Paromomycin

tag: control of Paromomycin


title: 31_r2_Blood_noGR_HRT

tag: postmenopausal women


title: Colon adenocarcinoma (11437T)

description: No additional information.


title: 33GRp_r2_Blood_PNA_noHRT


title: Paired nontumorous tissue (11642n)

description: No additional information.


title: Paired nontumorous tissue (11437n)

description: No additional information.


title: E coli Treated with Nalidixic Acid

description:
E. coli treated with Nalidixic Acid
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Nalidixic Acid

tag: E. coli treated with Nalidixic Acid

source_name: control of Nalidixic Acid

tag: control of Nalidixic Acid


title: E coli Treated with Kanamycin

description:
E. coli treated with Kanamycin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Kanamycin

tag: E. coli treated with Kanamycin

source_name: control of Kanamycin

tag: control of Kanamycin


title: E coli Treated with Hygromycin B

description:
E. coli treated with Hygromycin B
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Hygromycin B

tag: E. coli treated with Hygromycin B

source_name: control of Hygromycin B

tag: control of Hygromycin B


title: E coli Treated with Erythromycin

description:
E. coli treated with Erythromycin
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Erythromycin

tag: E. coli treated with Erythromycin

source_name: control of Erythromycin

tag: control of Erythromycin


title: 33_r2_Blood_noGR_noHRT

source_name: blood samples in PAXgene, no globin reduction, no HRT user


title: 34GRp_r2_Blood_PNA_HRT

source_name: blood samples in PAXgene, globin reduction using PNA, HRT user


title: 46_r2_Blood_noGR_noHRT


title: 36_r2_Blood_noGR_noHRT

source_name: blood samples in PAXgene, globin reduction using PNA, no HRT user


title: 45_r2_Blood_noGR_HRT

source_name: blood samples in PAXgene, no globin reduction, HRT user


title: Colon adenocarcinoma (11303T)

description: No additional information.

tag: Tissue


title: 34GRp_r3_Blood_PNA_HRT


title: 34GRp_Blood_PNA_HRT


title: 34GRa_Blood_GlobinClear_HRT


title: 12_r2_Blood_noGR_HRT


title: Paired nontumorous tissue (11303n)

description: No additional information.

tag: Disease state


title: Colon adenocarcinoma (11275T)

description: No additional information.

tag: Individual


title: Paired nontumorous tissue (11275n)

description: No additional information.

tag: Clinical info


title: 33GRa_Blood_GlobinClear_noHRT


title: E coli Treated with Chloramphenicol

description:
E. coli treated with Chloramphenicol
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with Chloramphenicol

tag: E. coli treated with Chloramphenicol

source_name: control of Chloramphenicol

tag: control of Chloramphenicol


title: Colon adenocarcinoma (11230T)

description: No additional information.


title: E coli Treated with IPTG

description:
E. coli treated with IPTG
virtual dual channel sample, derived from technically single channel submission

source_name: E. coli treated with IPTG

tag: E. coli treated with IPTG

source_name: control of IPTG

tag: control of IPTG


title: Paired nontumorous tissue (11230n)

description: No additional information.


title: 33_Blood_noGR_noHRT

source_name: blood samples in PAXgene, globin reduction using GlobinClear kit from ambion, non HRT user

tag: postmenopausal women


title: Colon adenocarcinoma (11181t)

description: No additional information.


title: 31GRa_Blood_GlobinClear_HRT

source_name: blood samples in PAXgene, globin reduction using GlobinClear kit from ambion, HRT user


title: 33GRp_Blood_PNA_noHRT


title: Paired nontumorous tissue (11181n)

description: No additional information.


title: CAPE Replicate 2

city: San Antonio

first: Xinyu

last: Wang

state: TX

address: 3400 Rawley E. Chambers Ave., Bldg. 3611

institute: US Army Institute of Surgical Research

description: 5 µg/ml CAPE treatment-2 (2005-09).

hyb_protocol: Cy5 and Cy3-labelled cDNA were hybridized using 3DNA Array 900 kit (Genisphere Inc., Hatfield, PA) according to the manufacturer's instructions.

scan_protocol: Dried array slides were scanned using a GenePix scanner 4000B (Axon Instruments, Inc., Union City, CA) and tabulated with GenePix pro 6.0 software. The Genepix reports (.gpr files) were imported into BRB array tools (Biometric Research Branch, National Cancer Institute) for further analysis.

data_processing: LOWESS smooth normalized, background subtracted, and spotflag filtered VALUE data obtained from the log of the processed Red signal/processed Green signal were used.

source_name: Total RNA from CAPE (5 µg/ml) treated human embilical vein endothelial cells for 6 hours

label_protocol: Total RNA was labelled using 3DNA Array 900 kit (Genisphere Inc., Hatfield, PA) according to the manufacturer's instructions.

growth_protocol: HUVEC were cultivated at 37 °C in a humidified atmosphere of 95% air and 5% CO2 with medium changed every 2 days until confluent.

extract_protocol: Total RNA was extracted with TRI reagent according to the manufacturer's instructions (Molecular Research Center, Cincinnati, OH).

treatment_protocol: Confluent HUVEC were indubated with 5 µg/ml CAPE for 6 hours.

tag: Total RNA were from human umbilical vein endothelial cells, HUVEC (pooled).

source_name: Human universal reference RNA

label_protocol: Human universal reference RNA was labelled using 3DNA Array 900 kit (Genisphere Inc., Hatfield, PA) according to the manufacturer's instructions.

extract_protocol: Human universal reference RNA was extracted by Stratagene (Catalog#740000).

tag: Universal reference RNA was obtained from Stratagene.


title: CAPE Replicate 3

description: 5 µg/ml CAPE treatment-3 (2005-09).


title: 34_Blood_noGR_HRT


title: 7GRp_Blood_PNA_noHRT


title: 46GRp_Blood_PNA_noHRT

tag: Postmenopausal women


title: 46GRa_Blood_GlobinClear_noHRT


title: Colon adenocarcinoma (11148T)

description: No additional information.


title: Colon adenocarcinoma (11157T)

description: No additional information.


title: CAPE Replicate 1

description: 5 µg/ml CAPE treatment-1 (2005-09).


title: DMSO Control Replicate 3

description: DMSO vehicle control-3 (2005-09).

source_name: Total RNA from DMSO (0.1%) vehicle control treated human embilical vein endothelial cells for 6 hours

treatment_protocol: Confluent HUVEC were indubated with 0.1% DMSO for 6 hours.

tag: Total RNA was from human umbilical vein endothelial cells, HUVEC (pooled).


title: 46_Blood_noGR_noHRT


title: 7GRa_Blood_GlobinClear_noHRT


title: Paired nontumorous tissue (11157n)

description: No additional information.


title: 7_Blood_noGR_noHRT


title: iah.ma0208

type: mixed

city: Roslin

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

country: United Kingdom

institute: The Roslin Institute

description: Comparison of RNA to genomic DNA reference

hyb_protocol: Hybridised according to previously published protocol: Fardini et al (2007) The YfgL lipoprotein is essential for type III secretion system expression and virulence of Salmonella enterica Serovar Enteritidis.  Infect Immun. 2007 (1):358-70

scan_protocol: Slides were scanned using a GenePix scanner

data_processing:
Fluorescence was quantified using GenePix Pro 6.0.
Data analysed using limma and R.
Background was not subtracted from foreground.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Amplified RNA from day-old chick caecums infected with S. typhimurium F98

label_protocol: Superscript II (Invitrogen) and random hexamers (Amersham) indirect labeling using amino acyll dUTP with Cy5.

extract_protocol: Total RNA was extracted from infected caecums (TriReagent, Sigma)

molecule: genomic DNA

source_name: DNA Reference from S. typhimurium F98

label_protocol: DNA was labeled using Invitrogen BioPrime DNA labeling kit

extract_protocol: DNA was extracted using Qiagen genomic DNA kit

tag: S. typhimurium F98


title: iah.ma0209

tag: Amplified RNA from day-old chick caecums infected with S. typhimurium F98


title: iah.ma0207


title: DMSO Control Replicate 2

description: DMSO vehicle control-2 (2005-09).


title: 45GRa_Blood_GlobinClear_HRT


title: DMSO Control Replicate 1

description: DMSO vehicle control-1 (2005-09).


title: 45_Blood_noGR_HRT


title: Paired nontumorous tissue (11148n)

description: No additional information.


title: Paired nontumorous tissue (10515n)

description: No additional information.


title: Colon adenocarcinoma (10515T)

description: No additional information.


title: 45GRp_Blood_PNA_HRT


title: iah.ma0206


title: CAPE Treatment Replicate 3

description: 5 µg/ml CAPE treatment-3 (2004-04).

label_protocol: Human universal reference RNA were labelled using 3DNA Array 900 kit (Genisphere Inc., Hatfield, PA) according to the manufacturer's instructions.


title: iah.ma0205


title: Colon adenocarcinoma (10212T)

description: No additional information.


title: 36GRa_Blood_GlobinClear_noHRT


title: Colon adenocarcinoma (10186T)

description: No additional information.


title: CAPE Treatment Replicate 2

description: 5 µg/ml CAPE treatment-2 (2004-04).


title: 36_Blood_noGR_noHRT


title: DMSO Vehicle Control Replicate 3

description: DMSO vehicle control-3 (2004-04).


title: iah.ma0029

source_name: Amplified RNA from batch cultured S. typhimurium F98

extract_protocol: Total RNA was extracted (TriReagent, Sigma)


title: CAPE Treatment Replicate 1

description: 5 µg/ml CAPE treatment-1 (2004-04).


title: Paired nontumorous tissue (10212n)

description: No additional information.


title: 36GRp_Blood_PNA_noHRT


title: iah.ma0030

tag: Amplified RNA from batch cultured S. typhimurium F98


title: Paired nontumorous tissue (10186n)

description: No additional information.


title: DMSO Vehicle Control Replicate 2

description: DMSO vehicle control-2 (2004-04).


title: iah.ma0028


title: Colon adenocarcinoma (10167T)

description: No additional information.


title: 12GRa_Blood_GlobinClear_HRT


title: Paired nontumorous tissue (10167n)

description: No additional information.


title: 12_Blood_noGR_HRT


title: DMSO Vehicle Control Replicate 1

description: DMSO vehicle control-1 (2004-04).

extract_protocol: Total RNA was extracted with TRI reagent according to the manufacturer's instructions (Molecular Research Center, Cincinnati, OH)

treatment_protocol: Confluent HUVEC were indubated with 0.1% DMSO for 6 hours

tag: Total RNA were from human umbilical vein endothelial cells, HUVEC (pooled)


title: 12GRp_Blood_PNA_HRT


title: 1736925319_F

status: Public on Feb 11 2008

city: Urbana

first: jun

last: cai

state: IL

address: Springfield Ave, DCL

institute: UIUC

description: LUC RNAi Day 2 (Day 2 Control) repeat 2

hyb_protocol: According to protocol provided by Sentrix Mouse-6 Expression BeadChip (Illumina)

scan_protocol: Image scanning hardware and software, and processing procedures and parameters: Illumina BeadStation 500; Illumina BeadStudio; Rank Invariant Normalization

data_processing: Rank Invariant Normalisation→ Convert all signal less than 0 to 0.1

source_name: E14TG2a mouse embryonic stem cells (ATCC, CRL-1821)

label_protocol: According to protocol provided by Illumina

growth_protocol: Mouse embryonic stem cells were transfected with constructs expressing Klf2, Klf4 and Klf5 shRNA or luciferase shRNA vectors (2 ug), using Lipofectamine 2000 (Invitrogen) protocol. The cells were selected with 1ug/ml of Puromycin (Sigma) 24-hours after transfection for 2, 4 or 6 days.

extract_protocol: Total RNA isolated using TRIzol followed by QIAGEN RNA Clean-up. Total RNA

tag: Luc 2days – mES cells 2 days post-transfection with shRNA vector against luciferase


title: 1736925319_B

description: LUC RNAi Day 6 (Day 6 Control) repeat 2

tag: Luc 6days – mES cells 6 days post-transfection with shRNA vector against luciferase


title: 1736925320_F

description: LUC RNAi Day 2 (Day 2 Control) repeat 3


title: 1736925319_A

description: Triple KLF RNAi Day 6 repeat 2

tag: Klf 6days –  mES cells 6 days post-transfection with shRNA vector against Klf2, Klf4, and Klf5


title: 1736925247_E

description: Triple KLF RNAi Day 2 repeat 1

tag: Klf 2days –  mES cells 2 days post-transfection with shRNA vector against Klf2, Klf4, and Klf5


title: 1736925320_B

description: LUC RNAi Day 6 (Day 6 Control) repeat 3


title: 1736925247_C

description: Triple KLF RNAi Day 4 repeat 1

tag: Klf 4days –  mES cells 4 days post-transfection with shRNA vector against Klf2, Klf4, and Klf5


title: 1736925319_D

description: LUC RNAi Day 4 (Day 4 Control) repeat 2

tag: Luc 4days – mES cells 4 days post-transfection with shRNA vector against luciferase


title: 1736925319_C

description: Triple KLF RNAi Day 4 repeat 2


title: 1736925319_E

description: Triple KLF RNAi Day 2 repeat 2


title: 1736925247_B

description: LUC RNAi Day 6 (Day 6 Control) repeat 1


title: 31_Blood_noGR_HRT


title: 1736925320_C

description: Triple KLF RNAi Day 4 repeat 3


title: MLIV_rep4

city: brescia

first: andrea

last: bozzato

address: viale europa 11

country: Italy

institute: university of brescia

description:
Fibroblast cell line from individuals affected by Mucolipidosis type IV (Cy5 labelled) versus fibroblast cell line from normal control individuals (Cy3 labelled). RNA samples extracted from different subjects were pooled into a single RNA mix. Each pair of TIFF image files was processed using GenePix Pro 4.1 (Axon Instruments). These files were firstly examined for quality control: spots showing no signal or obvious defects were accordingly flagged by GenePix Pro and excluded from analysis; besides, all �negative� control spots were manually flagged and excluded from further analysis. All statistical and graphical analysis were carried out in the R computing environment using the Linear models for Microarray data package (Smyth, 2004) from Bioconductor project (www.bioconductor.org) (Gentleman et al., 2004). For each microarray it was performed local background subtraction followed by global lowess normalization within each slide followed by scale normalization between slides.
The two replicate spots per gene in each array were used to maximize the robustness of statistical analysis on each gene via the �lmFit� function within Limma (Smyth, 2004).  Differential expression of genes was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and p-value.

data_processing: Global lowess normalization within and scale normalization between arrays by Limma package

source_name: AB pool

tag: Normal control fibroblast pool

source_name: MLIV pool

tag: Mucolipidosis type IV patient's poolMLIV pool


title: 1736925320_A

description: Triple KLF RNAi Day 6 repeat 3


title: 1736925247_F

description: LUC RNAi Day 2 (Day 2 Control) repeat 1


title: 1736925320_E

description: Triple KLF RNAi Day 2 repeat 3


title: MLIV_rep3

tag: Mucolipidosis type IV patient's pool


title: 1736925247_D

description: LUC RNAi Day 4 (Day 4 Control) repeat 1


title: MLIV_rep2

description:
Fibroblast cell line from individuals affected by Mucolipidosis type IV (Cy5 labelled) versus fibroblast cell line from normal control individuals (Cy3 labelled). RNA samples extracted from different subjects were pooled into a single RNA mix. Each pair of TIFF image files was processed using GenePix Pro 4.1 (Axon Instruments). These files were firstly examined for quality control: spots showing no signal or obvious defects were accordingly flagged by GenePix Pro and excluded from analysis; besides, all “negative” control spots were manually flagged and excluded from further analysis. All statistical and graphical analysis were carried out in the R computing environment using the Linear models for Microarray data package (Smyth, 2004) from Bioconductor project (www.bioconductor.org) (Gentleman et al., 2004). For each microarray it was performed local background subtraction followed by global lowess normalization within each slide followed by scale normalization between slides.
The two replicate spots per gene in each array were used to maximize the robustness of statistical analysis on each gene via the “lmFit” function within Limma (Smyth, 2004).  Differential expression of genes was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and p-value.


title: 1736925247_A

description: Triple KLF RNAi Day 6 repeat 1


title: MLIV_rep1

description:
Fibroblast cell line from individuals affected by Mucolipidosis type IV (Cy5 labelled) versus fibroblast cell line from normal control individuals (Cy3 labelled). RNA samples extracted from different subjects were pooled into a single RNA mix. Each pair of TIFF image files was processed using GenePix Pro 4.1 (Axon Instruments). These files were firstly examined for quality control: spots showing no signal or obvious defects were accordingly flagged by GenePix Pro and excluded from analysis; besides, all control spots were manually flagged and excluded from further analysis. All statistical and graphical analysis were carried out in the R computing environment using the Linear models for Microarray data package (Smyth, 2004) from Bioconductor project (www.bioconductor.org) (Gentleman et al., 2004). For each microarray it was performed local background subtraction followed by global lowess normalization within each slide followed by scale normalization between slides.
The two replicate spots per gene in each array were used to maximize the robustness of statistical analysis on each gene within Limma (Smyth, 2004).  Differential expression of genes was determined using an empirical Bayes (EB) approach within Limma (Smyth, 2004). After EB analysis, genes were ranked as being differentially expressed in decreasing order of the B-statistic and p-value.


title: PostMet replicate 1

status: Public on Feb 10 2008

city: Halifax

first: Jason

last: Williams

state: Nova Scotia

address: 1411 Oxford Street

department: Institute for Marine Biosciences

institute: National Research Council

description: Combined Reference sample, equal representation from all replicates of growth stages.

hyb_protocol: Hybridization buffer (Roche) containing the labeled targets (60 uL) was carefully applied to one corner of the Lifter Slip on the slide and immediately placed in the hybridization chamber (Die Tech, San Jose, CA, USA) for ON hyb. After hybridization slides were washed.

scan_protocol: Scanned on Perkin Elmer ScanArray 5000XL, ScanArray Express software v3.0.1 Images were quantified using SpotReader software (version).

data_processing: Limma LOWESS normalized, background subtracted data obtained from log2 of processed Experimental signal/processed Reference signal. Arraypipe software was used.

organism: Hippoglossus hippoglossus

label_protocol: RNA (7.5 ug) from universal RNA reference and experimental samples was reverse transcribed and labeled using the SuperscriptTM Plus Direct cDNA labeling system (Invitrogen, Carlsbad, CA, USA) with Alexa 555 (experimental) and Alexa 647 (reference) fluorophores according to manufacturers instructions.

extract_protocol: Total RNA extracted using Rneasy Plus Mini kit (Qiagen) according to the manufacturers protocol

tag: whole larval tissue

tag: Age

value: 104 days post-hatch

source_name: Total RNA from all 5 stages


title: PostMet replicate 3


title: PostMet replicate 2


title: PreMet replicate 3

value: 91 days post-hatch


title: MidMet replicate 3

value: 64 days post-hatch


title: MidMet replicate 2


title: PreMet replicate 1


title: MidMet replicate 1


title: colon_il22_rep2

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

hyb_protocol: as described in In situ Hybridization kit-plus

scan_protocol: Agilent scanner, manufacturer's protocol

data_processing: Agilent Feature Extraction software 8.5

source_name: Stratagene Universal Mouse Reference

label_protocol: standard

extract_protocol: commercial

tag: Stratagene #740100

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit

extract_protocol: Qiagen RNeasy


title: colon_control_rep1

source_name: Control

tag: Control 1


title: PostHatch replicate 3

value: 1 day post-hatch


title: colon_control_rep3

tag: Control 3


title: PostHatch replicate 2


title: PostHatch replicate 1

scan_protocol: Scanned on Perkin Elmer ScanArray 5000XL, ScanArray Express software v3.0.1.

data_processing: Image data aquired using ScanArray Express software v3.0.1. Limma LOWESS normalized, background subtracted data obtained from log2 of processed Experimental signal/processed Reference signal. Arraypipe software was used.


title: MouthOpening replicate 3

value: 21 days post-hatch


title: MouthOpening replicate 1


title: colon_il22_rep1


title: colon_control_rep2

tag: Control 2


title: MouthOpening replicate 2


title: Sample #6 SCOMP-amplified

type: genomic

city: Toronto

first: Susan

last: Done

address: 610 University Ave

institute: Ontario Cancer Institute

description: Purchased from Sigma, www.sigmaaldrich.com

hyb_protocol: Labeled products were combined, 80μg of Human Cot-1 DNA and 200mg of yeast tRNA (Invitrogen) were added.  The mixture was concentrated in a speed-vac at 37°C down to 10μl and resuspended in 80μl of DIG Easy Hybe buffer (Roche, Switzerland), denatured at 100°C for 1.5 min., cooled on ice and incubated for 30 min at 37°C, then hybridized to 19K human cDNA arrays (University Health Network Microarray Centre, Toronto, Canada, www.microarrays.ca) for 16 hours at 42°C.

scan_protocol: GenePix 4000B slide scanner and GenePix Pro 6.0 software package (Molecular Devices, California, USA)

data_processing: Log2 ratios filtered to exclude cDNA clones without mapping info and those spots flagged as anomalous, cenetered by the median and scale normalized.

source_name: DNA from breast carcinoma #6

label_protocol: 1.0μg of amplified test and reference DNA was mixed with 21.5μl ddH2O and 20μl of 2.5X Random Primer/Reaction Mix Buffer (Invitrogen, www.invitrogen.com), boiled for 5 min. and 5μl of ‘low C’ dNTP mix with either 2.5μl Cy5-dCTP (Amersham Biosciences, USA) for test or Cy3 for the reference DNA with 1μl of Klenow solution, then incubated at 37°C for 2 hrs.  The reaction was stopped by adding EDTA, then 450μl of TE pH 7.4 added and the mix loaded onto a micron-30 filter (Fisher/Millipore), spun for 8-10 min. at 10,000 rpm, inverted and spun for 1 min to recover the purified probe.

extract_protocol:
DNA extracted  using a QIAGEN DNA Mini Kit (QUIAGEN Inc., Canada) after a 72 hr period in lysis buffer at 56°C.
DOP amplification: Degenerate oligonucleotide primed (DOP)-PCR: 10-100 ng of genomic DNA was amplified by Thermo Sequenase (Amersham Biosciences) in a low stringency pre-amplification step (5 cycles) followed by regular PCR amplification in less stringent conditions, several replicate reactions were pooled together and a negative control (template = water) was used to ensure absence of contamination.  The resulting amplified DNA was purified using the Qiaquick PCR Purification Kit (Qiagen, Canada) and quantified using a DynaQuant Fluorimeter (Amersham Biosciences).
SCOMP amplification: Genomic DNA was digested with 2 U MseI (New England Biolabs) for 3 hours in One-Phor-All Buffer (Amersham) in a final volume of 5 mL.  Base pairing of the adaptor nucleotides was done in a final volume of 3 mL using 0.5 mL    One-Phor-All Buffer, 0.5m 100 mM Lib1 oligonucleotide (5’-AGTGGGATTCCTGCTGTCAGT-3’) and 0.5 mL 100 mM ddMse11 oligonucleotide (5’-TAACTGACAGCdd-3’) in a MJ Research PT100 thermocycler programmed for a gradient of 65°C to 15°C ramped down at 1°C per minute.   1 mL T4 DNA Ligase (40U/mL) (Roche), 1 mL of 10 mM ATP and the MseI digested genomic DNA was added and allowed to incubate at 15°C overnight. For PCR amplification the following was added to the ligation mix: 3 mL Expand Long Template buffer 1 (Roche), 2 mL 10 mM dNTPs, 35 mL H2O and 1 mL Expand-Long-Template PolMix (3.5U/mL).  Thermocycler conditions were as follows:  1 cycle, 68°C for 3 mins; 15 cycles 40 sec @ 94°C, 30 sec @ 57°C, 1 min 30 sec + 1 sec/cycle @ 68°C; 8 cycles 40 sec @ 94°C, 30 sec @ 57°C + 1°C/cycle, 1 min 45 sec + 1 sec/cycle @ 68°C; 22 cycles 40 sec @ 94°C, 30 sec @ 65°C, 1 min 53 sec + 1 sec/cycle @ 68°C; 1 cycle 3 min 40 sec @ 68°C.   Several reactions were pooled together.  A negative control (template=water) was used for all steps to ensure there was no contamination.  Following PCR amplification, the resulting products were cleaned with the Qiaquick PCR Purification Kit (Qiagen, Canada) and quantitated using a DynaQuant Fluorimeter (Amersham Biosciences).

tag: Microdissected sections of fresh fixed paraffin embedded tissue

source_name: Human placenta

tag: Fresh tissue


title: Sample #4 SCOMP-amplified

source_name: DNA from breast carcinoma #4


title: Sample #5 SCOMP-amplified

source_name: DNA from breast carcinoma #5


title: Sample #3 SCOMP-amplified

source_name: DNA from breast carcinoma #3


title: Sample #3 DOP-amplified


title: Sample #1 SCOMP-amplified

source_name: DNA from breast carcinoma #1


title: Sample #1DOP-amplified


title: Sample #2 DOP-amplified

source_name: DNA from breast carcinoma #2


title: Sample #6 non-amplified control


title: Sample #5 non-amplified control


title: Sample #4 non-amplified control


title: Sample #3 non-amplified control


title: Sample #1 non-amplified control


title: Sample #2 non-amplified control


title: Sample #2 SCOMP-amplified


title: 13500959 - Root e2 exp2 vs Root eH exp2

status: Public on Feb 09 2008

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Characterisation of the transcriptional changes (host genes up- and down-regulated) during the P. brassicae / A. thaliana interaction.

hyb_protocol: Root eH exp2 Cy5 / Root e2 exp2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

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

organism: Arabidopsis thaliana

source_name: Root eH exp2

label_protocol: labelling  , amplification=,   .

growth_protocol: root - Media=[2/3 compost, 1/3 vermiculite] mix sterilized by autoclave	 Temperature=22°C day,19°C night	 Light=16 hours

extract_protocol: Root eH exp2:10ug.

treatment_protocol: Name:Inoculated eH - biotic stress - pathogen infection,isolate eh:. Inoculation was performed by applying 1mL of resting spore suspension (107 spores.ml-1) to the crown of each 7-days-old seedling. Experiments were done in a climatic chamber with 16 hours light at 22degre Celsius and 8 hours dark at 19degre Celsius.

tag: Arabidopsis thaliana (burren)  - dev.stage (Boyes et al. Plant Cell 2001):1.08,boyes

source_name: Root e2 exp2

extract_protocol: Root e2 exp2:10ug.

treatment_protocol: Name:Inoculated e2 - biotic stress - pathogen infection,isolate e2:. Inoculation was performed by applying 1mL of resting spore suspension (107 spores.ml-1) to the crown of each 7-days-old seedling. Experiments were done in a climatic chamber with 16 hours light at 22degre Celsius and 8 hours dark at 19degre Celsius.


title: PreMet replicate 2


title: 13501857 - Plant e2 exp2 vs Plant eH exp2

hyb_protocol: Plant eH exp2 Cy5 / Plant e2 exp2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Plant eH exp2

growth_protocol: whole plant - Media=[2/3 compost, 1/3 vermiculite] mix sterilized by autoclave	 Temperature=22°C day,19°C night	 Light=16 hours

extract_protocol: Plant eH exp2:10ug.

tag: Arabidopsis thaliana (burren)  - dev.stage (Boyes et al. Plant Cell 2001):boyes,1.08

source_name: Plant e2 exp2

extract_protocol: Plant e2 exp2:10ug.


title: 13501837 - Plant eH exp2 vs Plant e2 exp2

hyb_protocol: Plant e2 exp2 Cy5 / Plant eH exp2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501833 - Plant eH exp1 vs Plant e2 exp1

hyb_protocol: Plant e2 exp1 Cy5 / Plant eH exp1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Plant e2 exp1

growth_protocol: whole plant - Media=[2/3 compost, 1/3 vermiculite] mix sterilized by autoclave	 Temperature=22°C day, 19°C night	 Light=16 hours

extract_protocol: Plant e2 exp1:10ug.

source_name: Plant eH exp1

extract_protocol: Plant eH exp1:10ug.


title: 13500958 - Root eH exp2 vs Root e2 exp2

hyb_protocol: Root e2 exp2 Cy5 / Root eH exp2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501835 - Plant e2 exp1 vs Plant eH exp1

hyb_protocol: Plant eH exp1 Cy5 / Plant e2 exp1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501858 - Root eH exp1 vs Root e2 exp1

hyb_protocol: Root e2 exp1 Cy5 / Root eH exp1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Root e2 exp1

extract_protocol: Root e2 exp1:10ug.

source_name: Root eH exp1

growth_protocol: root - Media=[2/3 compost, 1/3 vermiculite] mix sterilized by autoclave	 Temperature=22°C day, 19°C night	 Light=16 hours

extract_protocol: Root eH exp1:10ug.


title: 13500957 - Root e2 exp1 vs Root eH exp1

hyb_protocol: Root eH exp1 Cy5 / Root e2 exp1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Breed = Occidental, Day 25 Fetus C

city: Raleigh

first: Nicholas

middle: Eldon

last: Hardison

state: NC

address: 4700 Hillsborough St., Room 318A

institute: North Carolina State University

hyb_protocol: The fragmented cRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20, Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 and Eukaryotic Hybridization Controls (Affymetrix). The hybridization cocktail was denatured at 99°C for 5 min, incubated at 45°C for 5 min and then injected into a GeneChip cartridge. The GeneChip array was incubated at 42°C for at least 16 hr in a rotating oven at 60 rpm. GeneChips were washed with a series of nonstringent (25°C) and stringent (50°C) solutions containing variable amounts of MES, Tween20 and SSPE. The microarrays were then stained with Streptavidin Phycoerythrin and the fluorescent signal was amplified using a biotinylated antibody solution.

scan_protocol: Fluorescent images were detected in a GeneChip® Scanner 3000.

data_processing: Expression data were extracted using the MicroArray Suite 5.0 software (Affymetrix). All GeneChips were scaled to a median intensity setting of 500.

label: biotin-cRNA, streptavidin-phycoerythrin

organism: Sus scrofa

source_name: Placenta

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: The RNA was extracted using RNAqueous Kit (Ambion) as per the instructions of the manufacturer. Briefly, media was removed from the plates and cells were lysed in 1 ml lysis buffer. To this was added 1 ml of 64% alcohol. The contents were mixed and passed through the column. The RNA bound to the column was washed once with wash solution 1 and twice with wash solution 2/3. Finally RNA was eluted in 40 ul of hot elution buffer. RNA was quantified by spectrophotometry and quality verified by running 5 ug of RNA on 1% agarose gel. The resulting RNA was used for microarray analyses.

tag: Breed = Occidental, Day 25 Fetus


title: Breed = Occidental, Day 25 Fetus B


title: Breed = Meishan, Day 25 Fetus C

tag: Breed = Meishan, Day 25 Fetus


title: Breed = Meishan, Day 25 Fetus C (SFP)


title: Breed = Meishan, Day 25 Fetus B


title: Breed = Occidental, Day 30 Fetus FC2-1 (SFP)

source_name: Fibroblast

tag: Breed = Occidental, Day 30 Fetus


title: colon_il22_rep3

source_name: Stratagene Universal Mouse Reference


title: Breed = Occidental, Day 30 Fetus FC3 (SFP)


title: Breed = Occidental, Day 25 Fetus A


title: Breed = Occidental, Day 30 Fetus FC1 (SFP)


title: Breed = Meishan, Day 25 Fetus A


title: Breed = Meishan, Day 25 Fetus B (SFP)


title: Breed = Meishan, Day 25 Fetus A (SFP)


title: HCT116_miRcont

status: Public on Apr 30 2008

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: Human colorectal cancer cell line with pre-miR negative control

hyb_protocol: Agilent protocol

scan_protocol: Agilent scanner and Agilent scan control software

data_processing: Feature Extraction ver 9.5

source_name: Human colorectal cancer cell line HCT116

label_protocol: Agilent protocol

extract_protocol: Trizol and RNeasy Mini Elute Cleanup kit

treatment_protocol: HCT116 cells were transfected with 100 pmol of Pre-miR miRNA Molecules Negative Control #1 (Ambion) using a Cell Line Nucleofector kit V (Amaxa) with a Nucleofector I electroporation device (Amaxa) according to the manufacturer’s instructions.  Total RNA was extracted 48 h after transfection.

tag: HCT116 transfected with pre-miR negative control


title: HGDP-1398

status: Public on Feb 08 2008

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

description: Genomic DNA extracted from lymphoblastoid cell lines from a ethnically diverse series was genotyped using Infinium HumanHap550 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC3/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 3.1.4 (Illumina).

label: C-Bio and A-DNP

source_name: lymphoblastoid cell lines

label_protocol: Genotyping was performed using Illumina Infinium HumanHap550 Genotyping BeadChips according to the manufacturerÕs protocol (Illumina Inc., San Diego, CA, www.illumina.com). 1000ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted at the Foundation Jean Dausset (CEPH) in Paris using standard protocols.

tag: Population

value: Adygei

tag: Country

value: Russia-Caucasus

tag: Region

value: EUROPE

tag: Gender

value: Female


title: HGDP-1396

value: Male


title: 1736925320_D

description: LUC RNAi Day 4 (Day 4 Control) repeat 3

source_name: E14TG2a mouse embryonic stem cells (ATCC, CRL-1821)

tag: Luc 4days – mES cells 4 days post-transfection with shRNA vector against luciferase


title: HGDP-1404


title: HGDP-1388


title: HGDP-1385


title: HGDP-323

value: Kalash

value: Pakistan


title: HGDP-1386


title: HGDP-1399


title: HGDP-1370

value: Basque

value: France


title: HGDP-1387


title: HGDP-1371


title: HGDP-1382


title: HGDP-1383


title: HGDP-1367


title: HGDP-1381


title: HGDP-1397


title: HGDP-1365


title: HGDP-1403


title: HGDP-1364


title: HGDP-1366


title: HGDP-1363


title: HGDP-1384


title: 1year_90/0 (060706_02)

status: Public on Mar 01 2008

city: Cincinnati

first: Bhuvaneswari

last: Sakthivel

state: OH

address: 3333 Burnet Ave

department: Biomedical Informatics

institute: CCHMC

description: Sham Control and 30, 60 and 90 minutes of ischemia.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 µg/µL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer.  Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 µL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 µL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0001. Arrays were stained with R-Phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using and anti-streptavidin antibody (goat) biotinylated  [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a GeneChip Scanner 3000 [Affymetrix]

data_processing:
Affymetrix murine MOE 430 2.0  gene chips were used.GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.3.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine whether the hybridization of target RNA to the array occurred properly.
The data were analyzed with GeneSpring version 7.3 (Agilent Technologies, Palo Alto, CA) using RMA normalization with a custom CDF file(Mm430_Mm_REFSEQ_8]), then normalized to the mean of the sham samples of the same age

source_name: liver of 4-5 weeks (young) and 12-14 month (adult) old mice

label_protocol: 10 µg of total murine liver RNA from the 8 groups (n=3 of young Sham controls, old Sham control, young 30 min. of ischemia, old 30 min. of ischemia, 60 min. of ischemia, old 60 min. of ischemia, young 90 min. of ischemia, old 90 min. of ischemia) was amplified with the Genechip Expression 3’ Amplification One-Cycle Target Labeling and Control Reagents Kit (Affymetrix) to prepare biotin-labeled fragmented cRNA. Specifically, the One-Cycle cDNA Synthesis Kit (Affymetrix) was used to make double-stranded cDNA from total RNA. cRNA was labeled with biotin-UTP and biotin-CTP by an in vitro transcription reaction using the IVT Labeling Kit (Affymetrix).

extract_protocol:
The median and left lobe of the liver were dissected from young (4-5 weeks) and old (12-14month) mice that underwent either ischemia or Sham control operations and immediately submerged in RNAlater [Ambion, Inc., Austin, TX].
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Sham treatment; 30, 60 or 90 minutes of partial hepatic ischemia


title: HGDP-1323

value: Lahu

value: China


title: HGDP-1360


title: HGDP-1359


title: HGDP-1326


title: HGDP-1362


title: HGDP-1358


title: HGDP-1318


title: HGDP-1322


title: HGDP-1321


title: HGDP-1319


title: HGDP-1303

value: Uygur


title: HGDP-1317


title: HGDP-1320


title: HGDP-1361


title: HGDP-1357


title: HGDP-1306


title: HGDP-1304


title: HGDP-1305


title: HGDP-1298


title: HGDP-1299


title: HGDP-1300


title: HGDP-1302


title: HGDP-1301


title: HGDP-1297


title: HGDP-1230

value: Mongola


title: HGDP-1231


title: HGDP-1229


title: HGDP-1225


title: HGDP-1228


title: HGDP-1224


title: HGDP-1222

value: Daur


title: HGDP-1223


title: HGDP-1227


title: HGDP-1226


title: HGDP-1219


title: HGDP-1215


title: HGDP-1216


title: HGDP-1220


title: HGDP-1221


title: HGDP-1188

value: Yizu


title: HGDP-1214


title: HGDP-1213


title: HGDP-1217


title: HGDP-1218


title: HGDP-1186


title: HGDP-1183


title: HGDP-1182


title: HGDP-1179


title: HGDP-1184


title: HGDP-1187


title: HGDP-1059

value: Pima

value: Mexico

value: AMERICA


title: HGDP-1185


title: HGDP-1060


title: HGDP-1181


title: HGDP-1180


title: HGDP-1058


title: HGDP-1061


title: HGDP-1051


title: HGDP-1038


title: HGDP-1037


title: HGDP-1050


title: HGDP-1049


title: HGDP-1039


title: HGDP-963

value: Yakut

value: Siberia


title: HGDP-956

value: Female


title: HGDP-960

value: Male


title: HGDP-962


title: HGDP-1046


title: HGDP-954


title: HGDP-959


title: HGDP-953


title: HGDP-970

value: Colombian

value: Colombia


title: HGDP-948


title: HGDP-951


title: HGDP-952


title: HGDP-947


title: HGDP-949


title: HGDP-946


title: HGDP-903

value: Russian

value: Russia

value: EUROPE


title: HGDP-902


title: HGDP-945


title: HGDP-895


title: HGDP-894


title: HGDP-950


title: HGDP-892


title: HGDP-893


title: PMNCs_total RNA Pool_Wash Out_Aliquot N1

status: Public on Feb 21 2008

city: Barcelona

first: MONTSERRAT

last: FITO COLOMER

address: DR.AIGUADER 88

country: Spain

institute: IMIM

description: reference sample

hyb_protocol: Microarrays were prehybridized during 1h at 55ºC. During prehybridization, 10 micrograms of DIG-labeled cRNA were fragmented and used for hybridization (55 ºC, 16 h, 100 rpm agitation), according to Applied Biosystems Chemiluminescence Detection Kit. Same manufacturer´s protocol was used for hybridization washes and for performing Antibody Binding (anti-digoxigenin-AP) and antibody washes. The next steps, chemiluminescent reaction and detection, were performed with only one microarray at a time and following manufactures´ procedures.

scan_protocol: Microarrays were scanned with the Applied Biosystems 1700 Chemiluminescent Analyzer and quantified using the AB1700 software

data_processing: The algorithm's quality metrics “flags” and the ratio of signal/noise were used, on each microarray, to quantify probe quality and detectability (1700 Chemiluminescent Microarray Analyzer Users Guide). Probes with a signal/noise ratio <3 and/or flags >5,000 were excluded. From the initial 32,878 probeset, 15,308 high-quality probes were kept, and their signal were normalized among arrays by using the quantile technique

label: DIG-UTP

source_name: Periferal Blood Mononuclear cells

label_protocol: One microgram of total RNA was reverse-transcribed using T7-oligo (dT) primer. After first and second strand cDNA synthesis, the cDNA was purified and used for in vitro transcription (IVT) labeling with DIG-UTP, rendering labeled cRNA, according to the Applied Biosystems instructions for Chemiluminescent RT-IVT labeling kit V.2.0.

growth_protocol: Prior to the intervention, volunteers followed a one week washout period in which sunflower oil was provided as a source of fat for all purposes. During the first four days of the washout period, participants were asked to follow an antioxidant-controlled diet. Participants were allowed to eat per day less than: 2 pieces of fruit, 2 servings of vegetables or legumes, 2 cups of tea or coffee, and to avoid wine, beer, and olive oil consumption. During the last 3 days before, and on the intervention day, volunteers followed a strict low-phenolic compound diet., according to which  several foods, rich in phenolic compounds, were excluded from their diet (vegetables, legumes, fruit, juice, wine, coffee, tea, caffeine-containing soft drinks, beer, cacao, marmalade, olive oil and olives).

extract_protocol: Blood was collected at 8 a.m., at fasting state, prior to first (0 hours, pre-dose), 6 h after acute (50 ml (44 g) virgine olive oil) and at 8 a.m., at fasting state, after 3-weeks (25 ml (22 g) virgine olive oil per day) interventions. Periferal Blood Mononuclear Cells (PBMCs) were isolated within two hours after blood drawing using Vacuntainer CPT tubes (Beckton Dickinson, Franklin Lakes, NJ, USA) and following manufacturer´ instructions. Harvested PMNCs were preserved in 1 ml of Ultraspec solution (Biotecx Laboratories, Houston, TX, USA) and were stored at -80ºC prior to RNA extraction. Total RNA was extracted from Ultraspec preserved PMNCs following manufacturer´instructions. RNA concentration (A260) and RNA purity (A260/A280 and A260/A280 ratios) were estimated spectrometrically (NanoDrop® ND-1000, NanoDrop Technologies, USA). RNA integrity was assessed by micro capillary gel electrophoresis (Bioanalyzer, NanoChip, Agilent Technologies, Wilmington, DE, USA) and was estimated by both the rRNA ratio (28S/18S rRNA ratio) and the RIN value (RNA integrity number) using Agilent 2100 Expert Software . The purity of isolated individual RNA samples was greater than 1.8 by A260/A280 and 1.75 by A260/A280, with integrity values not lower than 1.7 and 8.5 by 28S/18S rRNA ratio and by RIN, respectively.The weight equivalents of individual total RNA samples corresponding to baseline, acute and to 3-week intervention were combined into three RNA pooles, respectively. The pooled RNA samples were concentrated using the Rneasy Mini Elute Cleanup system (Qiagen, Barcelona, Spain), till the required by microarray service concentration (0.1 μg/μl). The prepared RNA pools had purity not lower than 1.9 by both A260/A280 and A260/A280 ratios and the integrity was at score of 9.0 according to RIN.The aliquoted pooled and individual RNAs samples were stored at -80º C prior to use.

treatment_protocol: At first intervention day, at fasting state, 50 mL (44 g) of virgin olive oil were administered in a single dose (experiment 1), following this, volunteers continued with consumption of 25 ml (22 g) of virgin olive oil per day during 3 consequent weeks (experiment 2).

tag: total RNA pool

tag: 6 males

tag: wash out

tag: AGE

tag: 3 smokers + 3 non-smokers

tag: BMI


title: HGDP-891


title: HGDP-883


title: LZ23 Normal Control 42 weeks

status: Public on Feb 20 2008

city: Denver

first: Robert

middle: S

last: Stearman

state: CO

address: 4200 E Ninth Ave

department: Medicine/Pulmonary

institute: UCHSC

description: Gene expression data from normal mouse lung tissue

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MGU74Av2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method arbitrarily set to 500

source_name: A/J mouse (Jackson Labs) lung tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 to 5 microg total RNA

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

tag: Age matched Control, no treatment


title: HGDP-882


title: HGDP-879


title: HGDP-890


title: HGDP-880


title: HGDP-877

value: Maya


title: HGDP-881


title: HGDP-876


title: HGDP-878


title: HGDP-875


title: PMNCs_total RNA Pool_PostPrandial_Aliquot N2

description: experiment 1

tag: post prandial (6 hours)


title: HGDP-867


title: cDNA Analysis of Fe Deficiency on NILs E04

city: Ames

first: Randy

last: Shoemaker

state: IA

address: 100 Osbourne Dr. G401

department: Agronomy

institute: Iowa State University

description: Slides were hybridized at Iowa State University.  Scanning and data analysis was done at the University of Illinois.

hyb_protocol: Arrays were hybridized at 42 degrees for 18 hours.  After overnight hybridization, arrays were washed (wash 1: 1XSSC, 0.2%SDS; wash 2: 0.2XSSc, 0.2%SDS; wash 3: 0.1%SDS) to remove unbounds cDNAs.  Slides were then centrifuged for 5 min. to dry.

scan_protocol: Slides were scanned using ScanArray Express.  Resulting images were overlaid and spots identified by the ImaGene Program.

data_processing: Differential expression between the samples was identified by a federated ratio of above 2.0 or below 0.5 corresponding to a positive or negative two fold difference respectively between the two samples.

organism: Glycine max

source_name: Fe Inefficient Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1XBuffer, 10mM DTT, 500uM low T dNTPs, 100um Cy dye and 13u/uL SuperScript II were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees C.

extract_protocol: Total RNA extracted using the modified Phenol:Chloroform total RNA extraction described by Vodkin et al. BMC Genomics 2005.

tag: Roots of Fe Inefficient soybeans grown under 50uM Fe(NO3)3 hydroponic conditions for 14 days.

source_name: Fe Efficient Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1X Buffer, 10mM DDTT, 500uM low T dNTPs, 100uM of Cy Dye, and 13 u/uL SuperScript II were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees.

extract_protocol: Total RNA was extracted using a Modified Phenol:Chloroform extraction protocol described by Vodkin et. al BMC Genomics 2005.

tag: Roots of Fe Efficient soybeans grown under 50uM Fe(NO3)3 hydroponic conditions for 14 days


title: HGDP-855

city: Bethesda


title: HGDP-863


title: HGDP-874


title: HGDP-865


title: HGDP-864


title: HGDP-866


title: HGDP-862


title: HGDP-720

value: Cambodian

value: Cambodia


title: HGDP-721


title: HGDP-787

value: Melanesian

value: Bougainville

value: OCEANIA


title: HGDP-714


title: HGDP-854

value: Mexico


title: HGDP-715


title: HGDP-712


title: HGDP-713


title: HGDP-717


title: HGDP-719


title: HGDP-716


title: HGDP-710

value: AMERICA


title: HGDP-701

value: Bedouin

value: Israel-Negev


title: HGDP-704

value: Female


title: HGDP-711

value: Male


title: HGDP-703

value: Colombian