title: F-Genome: slide8

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57980.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 12/29/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 12/29/2006; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

source_name: Fiber at 5 DPA derived from A-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 12/23/2006; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A25A_A5A_A5c5; Parameter Date performed = 12/28/2006; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = A25A_A5A_A5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 5 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 5 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 12/23/2006; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 12/22/2006; Parameter Tube label = A25A_A5A_A25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = A25A_A5A_A25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 25 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: T0004 (parental) vs 43264 (congenic)

status: Public on Mar 04 2008

type: RNA

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

country: USA

institute: The George Washington University Medical Center

description: T0004 (parental) vs 43264 (congenic)

hyb_protocol: Printed arrays were pre-hybridized in a prehybridization buffer (5x SSC; 0.1% SDS; 1% BSA) for 45 minutes at 42C. Labeled cDNA samples (one labeled with Cy3 and a second with Cy5) were combined and lyophilized. The lyophilized pellet was resuspended in a hybridization buffer (50% formamide; 5x SSC; 0.1% SDS) and heated to 95C for 5 minutes and immediately snap-cooled. The labeled cDNA was then applied to the pre-hybridzed array under glass coverslip. The array was sealed in a hyb chamber and incubated overnight at 42C. The array was subsequently washed three times in buffers of increasing stringency (Low: 1.0x SSC, 0.2% SDS; Medium: 0.1x SSC, 0.2% SDS; High: 0.1x SSC). The arrays were quickly dried and immediately scanned.

scan_protocol: The hybridized microarray chips were scanned on an Axon GenePix 4000B scanner under the two-color mode for Cy3 and Cy5 fluorophores.

data_processing: The Cy3 and Cy5 images were analyzed through GenePix Pro 4.0 to calculate spot intensities and exported obtaining a .gpr file. The .gpr file was run through TIGR Express Converter to generate a .mev file. The .mev file was through the TIGR MIDAS using a lowess normalization.

molecule: total RNA

organism: Rattus norvegicus

source_name: T0004 (Inbred Dahl salt-sensitive (SS/Jr) rat )

label_protocol: Single-stranded cDNA was generated through reverse transcription of total RNA by Superscript III (Invitrogen) and random primers. Amino-allyl dUTP (in a ratio of 2:3 with dTTP) was incorporated during the reverse transcription. The RNA was then degraded by hydrolysis under alkaline conditions and the amino-allyl cDNA was subsequently purified with PCR Purification columns (Qiagen) substituting a phosphate wash buffer and phosphate elution buffer for the Tris-containing buffers in the kit. The purified sample was lyophilized and resuspended in sodium carbonate buffer and allowed to couple to the Cy3 fluorophore for an hour at room temperature. The reaction was stopped by sodium acetate and then the labeled cDNA was purified to remove uncoupled dye with PCR Purification columns (Qiagen) as per manufacturer's protocol.

extract_protocol: Tissue was processed using Trizol reagent (Invitrogen), and total RNA was extracted using RNeasy columns (Qiagen) according to manufacturer's protocols.

tag: Inbred Dahl salt-sensitive (SS/Jr) adult male rat; tissue

value: kidney

label_protocol: Single-stranded cDNA was generated through reverse transcription of total RNA by Superscript III (Invitrogen) and random primers. Amino-allyl dUTP (in a ratio of 2:3 with dTTP) was incorporated during the reverse transcription. The RNA was then degraded by hydrolysis under alkaline conditions and the amino-allyl cDNA was subsequently purified with PCR Purification columns (Qiagen) substituting a phosphate wash buffer and phosphate elution buffer for the Tris-containing buffers in the kit. The purified sample was lyophilized and resuspended in sodium carbonate buffer and allowed to couple to the Cy5 fluorophore for an hour at room temperature. The reaction was stopped by sodium acetate and then the labeled cDNA was purified to remove uncoupled dye with PCR Purification columns (Qiagen) as per manufacturer's protocol.

tag: Congenic strain S.LEW (5)x6x9 adult male rat; tissue


title: F-Genome: slide31

status: Public on Mar 05 2008

city: Athens

first: Alan

middle: R

last: Gingle

state: GA

address: 111 Riverbend Rd.

department: Center for Applied Genetics Technologies

institute: University of Georgia

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58003.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/30/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/30/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Gossypium longicalyx

source_name: Fiber at 20 DPA derived from F-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F20B_A20B_F20c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F20B_A20B_F20c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 20 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 20 DPA; Parameter Transgenes = none

organism: Gossypium herbaceum

source_name: Fiber at 20 DPA derived from A-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F20B_A20B_A20c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F20B_A20B_A20c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

treatment_protocol: Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse

tag: Fiber at 20 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 20 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide24

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57996.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = Gal file; Software: type: feature extraction Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Applied Precision; Parameter Scan Temperature = RT; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/29/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Temperature = RT; Parameter Scanner Make = Applied Precision; Parameter Exposure (secs) = 0.5; Parameter Scan Date = 1/29/2007; Parameter Pixel Size = 10 um; Parameter Scanner Model = arrayWoRx Biochip Reader; Parameter Resolution (um) = 0.1; Parameter Scanning software version = 2.1.4; Parameter Scanning software = arrayWoRx Software Suite

source_name: Fiber at 25 DPA derived from A-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/22/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = A25B_A5B_A25c5; Parameter Date performed = 1/28/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = A25B_A5B_A25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 25 DPA derived from A-genome

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 25 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/22/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/28/2007; Parameter Tube label = A25B_A5B_A5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = A25B_A5B_A5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

tag: Parameter Species = Gossypium herbaceum; Parameter Genome = A1; Parameter Tissue type = Fiber 5 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: T0002 (parental) vs 43259 (congenic) oligo

source_name: T0002 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: F-Genome: slide25

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/57997.gif

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = A1; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F5B_A5B_A5c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F5B_A5B_A5c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

source_name: Fiber at 5 DPA derived from F-genome

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F5B_A5B_F5c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F5B_A5B_F5c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA

treatment_protocol: Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse

tag: Fiber at 5 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Tissue type = Fiber 5 DPA; Parameter Polyploid level = 2x; Parameter Transgenes = none


title: F-Genome: slide32

description:
Simple annotation: CEGC_cat_1, F-Genome
Image: http://cagt12.agtec.uga.edu/Microarray/gifs/2007-10/58004.gif

source_name: Fiber at 25 DPA derived from F-genome

label_protocol:
Treatment - Channel 1; Experimentally pertinent treatments performed on the original biological sample used to generate the extract that was labelled and scanned in Channel 1 (green).; Protocol Type = Treatment; Parameter Genome = F; Parameter Growth Condition = Pohl Conservatory and Horticulture Greenhouse
Amplification - Channel 1; Methods for amplifying extracted samples prior to labeling and using for the channel 1 (green) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Type of in-vitro transcription = Epicentre; Parameter Date performed = 1/28/2007; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Tube label = F25B_A25B_F25c5; Parameter Date performed = 1/29/2007; Parameter Labeling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy5; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 1 reference name = F25B_A25B_F25c5; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Extracted molecule = RNA; Parameter Name = Ran

tag: Fiber at 25 DPA derived from F-genome

tag: Parameter Species = Gossypium longicalyx; Parameter Genome = F; Parameter Polyploid level = 2x; Parameter Tissue type = Fiber 25 DPA; Parameter Transgenes = none

label_protocol:
Amplification - Channel 2; Methods for amplifying extracted samples prior to labeling and using for the channel 2 (red) scan.; Protocol Type = Amplification; Parameter Approx RNA yield = 50 ug; Parameter Date performed = 1/28/2007; Parameter Type of in-vitro transcription = Epicentre; Parameter Primers round 1 = T7-Oligo(dT); Parameter number of rounds = 1; Parameter Approx start quantity = 0.5 ug
Parameter Date performed = 1/29/2007; Parameter Tube label = F25B_A25B_A25c3; Parameter Labelling method = indirect; Parameter Amount of extract labeled = 8 ug; Parameter Type of label = Cy3; Parameter Name = Ran

extract_protocol: Parameter Date performed = Nov-06; Parameter Extraction method reference = "Wilkins and Smart; Parameter Channel 2 reference name = F25B_A25B_A25c3; Parameter Extraction method = Hot-borate / Li precipitation method; Parameter Extraction description = Vortex ovules with 600um glass beads under liquid nitrogen.; Parameter Name = Ran; Parameter Extracted molecule = RNA


title: T0008 (parental) vs 43265 (congenic)

description: T0008 (parental) vs 43265 (congenic)

source_name: T0008 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43267 (congenic) vs T0010 (parental) oligo

source_name: T0010 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43265 (congenic) vs T0008 (parental) oligo


title: T0003 (parental) vs 43260 (congenic)

description: T0003 (parental) vs 43260 (congenic)

source_name: T0003 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43266 (congenic) vs T0009 (parental) oligo

source_name: T0009 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43264 (congenic) vs T0007 (parental) oligo

description: 43264 (congenic) vs T0007 (parental)

source_name: T0007 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43270 (congenic) vs T0016 (parental)

description: 43270 (congenic) vs T0016 (parental)

source_name: T0016 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43267 (congenic) vs T0010 (parental)

description: 43267 (congenic) vs T0010 (parental)


title: 43265 (congenic) vs T0008 (parental)

description: 43265 (congenic) vs T0008 (parental)


title: T0002 (parental) vs 43259 (congenic)

description: T0002 (parental) vs 43259 (congenic)


title: 43259 (congenic) vs T0002 (parental)

description: 43259 (congenic) vs T0002 (parental)


title: 43264 (congenic) vs T0004 (parental)

description: 43264 (congenic) vs T0004 (parental)


title: 43266 (congenic) vs T0009 (parental)

description: 43266 (congenic) vs T0009 (parental)


title: 66672 (congenic) vs T2952 (parental)

description: 66672 (congenic) vs T2952 (parental)

tag: Congenic strain S.LEW (5)x6x11 adult male rat; tissue

source_name: T2952 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: T2936 (parental) vs 66670 (congenic)

description: T2936 (parental) vs 66670 (congenic)

source_name: T2936 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: T2945 (parental) vs 66668 (congenic)

description: T2945(parental) vs 66668 (congenic)

source_name: T2945 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 43260 (congenic) vs T0003 (parental)

description: 43260 (congenic) vs T0003 (parental)


title: 66674 (congenic) vs T2954 (parental)

description: 66674 (congenic) vs T2954 (parental)

source_name: T2954 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: 66666 (congenic) vs T2934 (parental)

description: 66666 (congenic) vs T2934 (parental)

source_name: T2934 (Inbred Dahl salt-sensitive (SS/Jr) rat )


title: T2934 (parental) vs 66666 (congenic)

description: T2934 (parental) vs 66666 (congenic)


title: Exp4: CH1/Cy3 = B49.5   74t3  (tethered), CH2/cy5 = B49.5 (untethered)

city: Edinburgh

first: Lee

middle: Edward

last: Finlan

state: Lothian

address: Crewe Road South

department: Chromosomes & Gene Expression Laboratory

country: United Kingdom

institute: MRC Human Genetics Unit

description: Biological replicate 4 of 4.

hyb_protocol: Differentially labelled RNAs from cell lines with and without the lacI-lap2b tether (tethered/untethered) were cohybridised to an oligonucleotide microarray representing ~30,000 human genes

scan_protocol: Microarray slides were scanned under optimal scanning powers that produced a 1:1 ratio of Cy3:Cy5 across ~20%  of the Microarray slide using the GenePix 4000B (Axon Instruments) connected to Genepix pro 4.1 scanning programme . Scanned images were Block Lowess normalised using Bluefuse v3.2 and the distributions of log2 (tethered/untethered) ratios were assessed from boxplots.

data_processing:
LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Bluefuse software was used.
The data is arranged into a series of columns that are annotated in a corresponding fashion, such as gene position, chromosome #,  log 2 ratio,  cy signal values etc that are interconnected.

molecule: polyA RNA

organism: Homo sapiens

source_name: B49.5 74t3 cells

label_protocol: DNase treated, purified RNA was  requantified and 20ug of total treated RNA was used to create cDNA using the Superscript Direct cDNA module (Invitrogen) labelled with either Cy3 or Cy5 respectively.

growth_protocol: cells were grown DMEM supplemented with 10% FCS plus antibiotic selection were required.  Cell harvested at ~70-80% confluency

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Stable cell transfection of the LacO integrations were selected for using 5ug/ml blasticidinS , lacI-lap2b Tethered stable cell lines were selected with 220 ug/ml zeocin.

tag: Fibrosarcoma cells

source_name: B49.5 cells


title: 66668 (congenic) vs T2945 (parental)

description: 66668 (congenic) vs T2945 (parental)


title: T2954 (parental) vs 66674 (congenic)

description: T2954 (parental) vs 66674 (congenic)


title: Exp4: CH1/Cy3 = J21.c3, CH2/cy5 = J21.c3    (Self-Self Hybridization)

description: Biological replicate 4 of 4.

source_name: J21.c3 cells

tag: Stable cell transfection of the LacO integrations were selected for using 5ug/ml blasticidinS


title: Exp3: CH1/Cy3 =B49.5 (untethered), CH2/cy5 = B49.5   74t3  (tethered)

description: Biological replicate 3 of 4.


title: Exp3: CH1/Cy3 =B49.5 , CH2/cy5 = B49.5     (Self-Self Hybridization)

description: Biological replicate 3 of 4.


title: 66670 (congenic) vs T2936 (parental)

description: 66670 (congenic) vs T2936 (parental)

tag: Inbred Dahl salt-sensitive (SS/Jr) adult male rat; tissue


title: Exp1: CH1/Cy3 =J21.c3 (untethered), CH2/cy5 = J21.c3   lap2  (tethered)

description: Biological replicate 1 of 5.

source_name: J21.c3 lacI-ap2b


title: Exp5: CH1/Cy3 = J21.c3   lap2  (tethered), CH2/cy5 = J21.c3 (untethered)

description: Biological replicate 5 of 5.


title: Exp1: CH1/Cy3 =B49.5 (untethered), CH2/cy5 = B49.5   74t3  (tethered)

description: Biological replicate 1 of 4.


title: Exp3: CH1/Cy3 =J21.c3 (untethered), CH2/cy5 = J21.c3   lap2  (tethered)

description: Biological replicate 3 of 5.


title: Exp2: CH1/Cy3 = B49.5   74t3  (tethered), CH2/cy5 = B49.5 (untethered)

description: Biological replicate 2 of 4.


title: Exp2: CH1/Cy3 = J21.c3, CH2/cy5 = J21.c3   (Self-Self Hybridization)

description: Biological replicate 2 of 4.


title: Exp1: CH1/Cy3 =B49.5 , CH2/cy5 = B49.5  (Self-Self Hybridization)

description: Biological replicate 1 of 4.


title: Patient 6 skin treated

city: Hershey

first: Diane

middle: M

last: Thiboutot

state: PA

address: 500 University Drive

department: Department of Dermatology; Jake Gittlen Res. Fnd.

institute: The Pennsylvannia State University College of Medicine

description: Subjects included males and females ages 14 to 40 years who were scheduled by their dermatologist to receive treatment with 13-cis RA (isotretinoin, brand not noted) for severe acne.  All aspects of the patients’ treatment with 13-cis RA apart from the skin biopsies were standard of care and were not part of this research.  Exclusion criteria included patients with underlying medical conditions requiring treatment with systemic medications that might interfere with the gene array analysis.

hyb_protocol: Biotinylated cRNA, produced through in vitro transcription, was fragmented and hybridized to an Affymetrix human U133A 2.0 microarray

scan_protocol: The arrays were processed on a Gene Chip Fluidics Station 450 and scanned on a Affymetrix GeneChip Scanner (Santa Clara, CA).

data_processing: The expression values were normalized by using the R-Affy package from Bioconductor version 1.1 to remove background noise and non-biologival variations among arrays. The background noise was removed from the PM probe intensities using the "RMA" method. Normalization was performed using the quantile normalization method (Bolstad et. al., 2003).  To remove the effects of outlier probes and sumerize probe intensities within one probe set to a single expression value, the "medianpolish" method was applied to the background adjusted, normalized PM intensities and not the PM-MM, because it is believed that MM intensities reflect background noise as well as probe-specific signals. Significant gene expression alterations were identified using the computer software: Significance Analysis of Microarrays (Tusher et. al.,2001).

label: biotin

source_name: skin, 1 week isotretinoin treatment

extract_protocol: Biopsies were sectioned using a cryostat to facilitate tissue homogenization. Total RNA was isolated and DNase I treated using the Rneasy Fibrous Tissue Kit (Qiagen, Valencia, CA). RNA was ethanol precipitated and quantified using a spectrophotometer. Approximately 2 micrograms of total RNA from each sample was used to generate double-stranded cDNA using a T7-oligo (dT) primer.

treatment_protocol: Human skin biopsies were obtained from patients before isotretinoin and after 1-week isotretinoin treatment. Biospies were flash frozen and stored at -80C until RNA isolation


title: Patient 4 skin baseline

source_name: skin, no treatment

label_protocol: Biotinylated cRNA, produced through in vitro transcription


title: Patient 4 skin treated


title: Patient 6 skin baseline


title: Patient 2 skin treated


title: Patient 7 skin treated


title: Patient 7 skin baseline


title: Patient 1 skin baseline


title: DBM/control, 4h, rep4

city: Vancouver

first: Juergen

last: Ehlting

state: BC

address: 321 - 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 4 of 4 comparing DBM treatment for 4h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

hyb_protocol: We pre-hybridized microarray slides for 45 min at 48°C in 5 x SSC, 0.1 % SDS, 0.2 % BSA. Slides were washed twice with water for 1 min, dipped 5 times in isopropanol, and spun dry in Falcon tubes at 100 g for 3 min. The hybridization solution was applied to the microarray slides and covered with untreated glass cover slips (Fisher Scientific, Nepean, ON, Canada). Arrays were incubated over night in CMT hybridization chambers (Corning, Corning, NY, USA) submerged in a water bath at 42°C with moderate vertical shaking. Hybridization chambers were disassembled and slides were washed for 15 min at 42°C in 2 x SSC, 0.5 % SDS, and for 2 times 15 min in 0.5 x SSC, 0.5 % SDS. Subsequently, arrays were dipped five times in 0.1 x SSC and spun dry as described above.

scan_protocol: Microarrays were scanned with a ScanArray Express (Perkin Elmer, Woodbridge, ON, Canada) scanner with laser power set to 95% and photo-multiplier-tube set to 54 to 64. We identified and quantified spots using the ImaGene software (BioDiscovery, Marina Del Rey, CA, USA). Grids were manually placed and spot finding was performed using the ‘Auto adjust’ spot function repeated for three times. Spot finding was subsequently verified by visual inspection and manually adjusted when necessary. Poor spots were manually flagged (flag 1) and were not used in further data analyses. For all analyses, the median pixel intensities for each spot were used.

data_processing: For all analyses, the median pixel intensities for each spot were used. Analyses were performed using customized scripts for R and Bioconducter. For background correction, we defined the mean of the lowest 10% of spot intensities from a particular subgrid as the background for that subgrid. This mean was subtracted from each spot in the subgrid. Signal intensities that did not exceed the background plus 3 standard deviations thereof were defined as not detectable and were excluded from further analyses. We normalized using loess curves thus generating log2 transformed expression ratios comparing DBM treatment with control.

organism: Arabidopsis thaliana

source_name: whole rosette, untreated control, 4h, rep 4

label_protocol: Total RNA was used for a direct labelling procedure. 80 μg total RNA was incubated with 0.27 μM T17VN primer, 0.15 mM dATP, dCTP, and dGTP, 0.05 mM dTTP (Invitrogen), 0.025 mM Cyanidin3- or Cyanidin5-conjugated dUTP (Amersham, Piscataway, NJ, USA), 40 U RNAseInh (Promega, San Luis Obispo CA, USA), and 400 U SuperscriptII (Invitrogen) in 10 mM DTT and 1 x first strand buffer in a total volume of 40 μl. In addition, 0.3 fmole human cRNAs complementary to the human negative control oligonucleotides were used in labelling reactions (HsD17B1, KRT1, and MB). Prior to addition of enzymes the solution was heated to 65°C for 5 min and for primer annealing cooled to 42°C. Following an incubation at 42°C for 2.5 h, the RNA was degraded with 8 μl 1 M sodium hydroxide for 15 min at 65°C, neutralized with 8 μl 1 M hydrochloric acid and buffered with 4 μl 1M Tris-pH 7.5. Subsequently, the labelled cDNA was purified using a PCR purification kit according to the manufacturer’s protocol (Qiagen, Mississauga, ON, Canada). DNA was eluted in 100 μl 10 mM Tris, pH 8.5, the two labeling reactions were combined, and 1μl Cyanidin5-labelled GFP was added. Following an ethanol/sodium acetate precipitation (Sambrook and Russel, 2001) the air-dried cDNA pellet was resuspended in 3 μl water, denatured at 95°C for 3 min, added to 50 μl pre-warmed array hybridization buffer #1 (Ambion, Austin, TX, USA), and kept at 65°C until use.

extract_protocol: Total RNA was isolated using a modified TRIZOL extraction method as follows.  Approximately 1g of plant material was ground in liquid nitrogen using a mortar and pestle, resuspended in 15 ml TRIZOL reagent (Invitrogen, Carlsbad CA, USA), vortexed and incubated at 65°C for 5 min with regular mixing. Cell debris was pelleted by centrifugation for 30 min at 12,000 g and 4°C and the supernatant was extracted with 3 ml chloroform twice. After centrifugation for 20 min at 12,000 g, the aqueous phase was recovered and RNA was precipitated at room temperature for 5 min with 0.5 volumes of 0.8 M sodium citrate and 0.5 volumes isopropanol. After centrifugation for 30 min at 12,000 g, the pellet was washed with 70% ethanol and re-centrifuged. The RNA pellet was air dried for 5 min and resuspended in 200 μl RNAse free water. Following a spectrophotometric determination of RNA concentration, the RNA was precipitated with 2.5 volumes of ethanol and a 1/10 volume of 3 M sodium acetate at –20°C overnight, and subsequently pelleted at 20,000 g for 30 min at 4°C. The precipitate was washed with 70% ethanol, re-centrifuged, air dried and resuspended in RNAse free water to an approximate concentration of 5 μg/μl. Actual concentration was determined spectrophotometrically, and RNA quality was determined using a 2100 Bioanalyzer (Agilent Technologies, Mississauga ON, Canada).

treatment_protocol: Two days before the onset of the experiment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod). As control, Arabidopsis plants were maintained under the same condition without exposure to DBM larvae.  All rosette leaves were harvested at 4h after onset of the experiment and flash frozen in liquid nitrogen.

tag: Ecotype

value: Landsberg erecta (Ler)

tag: Growth stage

tag: Organ

value: whole rosette leaves

tag: Treatment

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 4h, rep 4

growth_protocol: Arabidopsis thaliana plants (ecotype Landsberg erecta) were grown in plastic pots (10cm wide x 8cm tall) containing Terra-lite Redi-earth (W.R. Grace and Co., Ajax, Ontario, Canada).  Each pot contained four or five plants, which were grown in a growth chamber (Controlled Environment Ltd., Winnipeg, MB, Canada) at 20˚C constant temperature, 8 hr/16 hr Light/Dark photoperiod at 50-60% ambient humidity, for 8 to 9 weeks.  Short day conditions prevented the onset of flowering and the plants were thus maintained in growth stage 1 (leaf production) with 13 to 15 rosette leaves larger than 1mm (stage 1.13 to 1.14). Diamondback moth (DBM, Plutella xylostella) larvae were maintained on cabbage (Brassica oleracea) plants in a climate-controlled room at 25ºC, 12 hr photoperiod with 50%-60% relative humidity

treatment_protocol: Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod).  For insect treatment, seven Diamondback moth (DBM, Plutella xylostella)  larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately.  All rosette leaves were harvested at 4h after onset of continuous herbivory and flash frozen in liquid nitrogen.

value: Plutella xylostella, 4h


title: DBM/control, 8h, rep4

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 8h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 4 of 4 comparing DBM treatment for 8h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 8h, rep 4

growth_protocol: Arabidopsis thaliana plants (ecotype Landsberg erecta) were grown in plastic pots (10cm wide x 8cm tall) containing Terra-lite Redi-earth (W.R. Grace and Co., Ajax, Ontario, Canada).  Each pot contained four or five plants, which were grown in a growth chamber (Controlled Environment Ltd., Winnipeg, MB, Canada) at 20˚C constant temperature, 8 hr/16 hr Light/Dark photoperiod at 50-60% ambient humidity, for 8 to 9 weeks.  Short day conditions prevented the onset of flowering and the plants were thus maintained in growth stage 1 (leaf production) with 13 to 15 rosette leaves larger than 1mm (stage 1.13 to 1.14).

treatment_protocol: Two days before the onset of the experiment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod). As control, Arabidopsis plants were maintained under the same condition without exposure to DBM larvae.  All rosette leaves were harvested at 8h after onset of the experiment and flash frozen in liquid nitrogen.

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 8h, rep 4

treatment_protocol: Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod).  For insect treatment, seven Diamondback moth (DBM, Plutella xylostella)  larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately.  All rosette leaves were harvested at 8h after onset of continuous herbivory and flash frozen in liquid nitrogen.

value: Plutella xylostella, 8h


title: DBM/control, 24h, rep1

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 24h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 1 of 4 comparing DBM treatment for 24h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 24h, rep 1

treatment_protocol: Two days before the onset of the experiment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod). As control, Arabidopsis plants were maintained under the same condition without exposure to DBM larvae.  All rosette leaves were harvested at 24h after onset of the experiment and flash frozen in liquid nitrogen.

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 24h, rep 1

treatment_protocol: Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod).  For insect treatment, seven Diamondback moth (DBM, Plutella xylostella)  larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately.  All rosette leaves were harvested at 24h after onset of continuous herbivory and flash frozen in liquid nitrogen.

value: Plutella xylostella, 24h


title: Patient 5 skin baseline


title: Patient 1 skin treated


title: DBM/control, 24h, rep2

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 24h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 2 of 4 comparing DBM treatment for 24h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 24h, rep 2

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 24h, rep


title: Patient 2 skin baseline


title: DBM/control, 24h, rep4

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 24h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 4 of 4 comparing DBM treatment for 24h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 24h, rep 4

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 24h, rep 4


title: DBM/control, 24h, rep3

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 24h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 3 of 4 comparing DBM treatment for 24h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 24h, rep 3

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 24h, rep 3


title: DBM/control, 4h, rep3

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 3 of 4 comparing DBM treatment for 4h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 4h, rep 3

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 4h, rep 3


title: DBM/control, 8h, rep2

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 8h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 2 of 4 comparing DBM treatment for 8h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 8h, rep 2

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 8h, rep 2


title: DBM/control, 8h, rep1

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 8h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 1 of 4 comparing DBM treatment for 8h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 8h, rep 1

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 8h, rep 1


title: DBM/control, 1h, rep4

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 4 of 4 comparing DBM treatment for 1h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 1h, rep 4

treatment_protocol: Two days before the onset of the experiment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod). As control, Arabidopsis plants were maintained under the same condition without exposure to DBM larvae.  All rosette leaves were harvested at 1h after onset of the experiment and flash frozen in liquid nitrogen.

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 1h, rep 4

treatment_protocol: Two days before exposing A. thaliana plants to herbivore treatment, plants were transferred to a climate-controlled room (22ºC, 50-60% humidity, 12 hr photoperiod).  For insect treatment, seven Diamondback moth (DBM, Plutella xylostella)  larvae (third to fifth instars) were placed on a group of four or five plants until time of harvest, for each time point separately.  All rosette leaves were harvested at 1h after onset of continuous herbivory and flash frozen in liquid nitrogen.

value: Plutella xylostella, 1h


title: DBM/control, 8h, rep3

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 8h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 3 of 4 comparing DBM treatment for 8h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 8h, rep 3

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 8h, rep 3


title: DBM/control, 4h, rep1

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 1 of 4 comparing DBM treatment for 4h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 4h, rep 1

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 4h, rep 1


title: DBM/control, 4h, rep2

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 2 of 4 comparing DBM treatment for 4h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 4h, rep 2

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 4h, rep 2


title: DBM/control, 1h, rep3

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 3 of 4 comparing DBM treatment for 1h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3)

source_name: whole rosette, untreated control, 1h, rep 3

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 1h, rep 3


title: Belgrade b/b Duodenum replicate 2

status: Public on Mar 03 2008

city: Buffalo

first: James

middle: F.

last: Collins

state: NY

address: 3435 Main Street

department: Exercise and Nutrition Sciences

institute: University at Buffalo

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

label: Biotin

source_name: duodenal scrape

label_protocol: Standard Affymetrix Protocol

extract_protocol: Trizol followed by purification with RNEasy Mini Kit (Invitrogen)

tag: Belgrade, hohozygote, adult


title: T cell_activated_48h_rep2

type: other

city: Stanford

first: Michael

middle: George

last: Kattah

state: CA

address: 269 Campus Dr., CCSR 2250

department: Medicine

institute: Stanford University

description: Biological replicate 2 of 3. Donor 2 activated T cells versus Donor 2 resting T cells

hyb_protocol: Tags were amplified, labeled, and purified (see 'Label protocol'). These tags were hybridized in hybridization buffer [20μg salmon sperm DNA (Invitrogen), 25μg yeast tRNA (Invitrogen), 4X SSC, 0.1% SDS] on spotted Codelink slides in in a microarray hybridization chamber (Corning) in a 47.5 C circulating water bath (GE Healthcare) for 16-20 h.  After hybridization, slides were washed three times for 5 min in 1x TNT wash buffer [(100 mM Tris-HCl pH 8.0, 150 mM sodium chloride, 0.05% Tween-20 (Sigma Aldrich), 2 mM EDTA], washed once for 5 min in 0.5x TNT wash buffer, rinsed for <1 s in ddH2O and centrifuged to dryness at 600 x g for  5 min.

scan_protocol: Scanned on an GenePix 4000B scanner. Images were quantified using GenePix Pro 5.0.1.24

data_processing: We averaged the median of 635nm/532nm ratios from replicate features.  The fold-change for each tag was calculated by taking the log2 of the ratios.  We applied a low-intensity cut-off filter during analysis as follows:  spots with over 50% of the pixels exhibiting fluorescent intensities less than two standard deviations above background in both 635nm and 532nm channels were set to a fold-change of zero.  The arrays were median-centered by subtracting the median log value, and analyzed by one class significance analysis of microarrays to identify markers with statistically-significant differences.  Because the HIT reaction is 48-plex, each 48-plex data set was analyzed separately.  Tags that had a fold-change of zero in all of the samples were deleted prior to SAM analysis.  For the dye-swap column (D1A / D3A), the parity of each fold-change was reversed.

molecule: other

source_name: Activated T cells Donor 2

label_protocol:
Staining of CD4+ helper T cells with DNA-antibody conjugates:
DNA oligos were conjugated to secondary monovalent Goat anti-mouse Fab fragments by hydrazone bond formation (Solulink)
To prepare the HIT cocktail, we placed 2.5 ug of each antibody  and 3.4 ug of each Fab-oligo conjugate (4:1 Fab-oligo:Antibody molar ratio) in a 96-well V-bottom polypropylene plate (Corning) and incubated at 4 C for 2 h.
We then added 5 ul of HIT cocktail dilution buffer [1.5% bovine serum albumin (BSA) (Sigma Aldrich), 15 mM EDTA, 2.2 mg/ml mouse gamma globulin (Jackson ImmunoResearch Laboratories, Inc.), 150 ug/ml salmon sperm DNA(ssDNA) (Invitrogen), PBS] to each well and incubated for 10 min.
We then added 50 ul of the HIT cocktail to 25ul of the samples and incubated for 30 min at 4 C.  We washed the samples 3 times with wash buffer [1.5% BSA, 15 mM EDTA, PBS], fixed them for 15 min at 21–23 C in fixation buffer [1.6% paraformaldehyde (Polysciences, Inc.) in wash buffer], and then washed twice in PBS.  After washing, we aspirated the remaining PBS and brought the reaction to a final volume of 50 μl in T7 amplification mix.
Tag amplification and labeling:
RNA tags were amplified in amplification mix [250 U T7 RNA Polymerase-Plus (Ambion), 1x transcription buffer (Ambion),  0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.33 mM UTP, and 0.17 mM Cy3-UTP  or 0.17 mM Cy5-UTP (PerkinElmer)] for 4-6 hours at 37 C.
Tag purification:
The amplified labeled RNA tags were purified using mirVana (Ambion)

growth_protocol: Cells were cultured in complete X-VIVO 15 media (Lonza) [X-VIVO 15 supplemented with 10% heat-inactivated FCS (Omega Scientific), 100 units/ml penicillin/streptomycin (Invitrogen), 14.3 μM β-mercaptoethanol (Sigma-Aldrich), and L-glutamine (Invitrogen)].  For T cell activation, anti-CD3/anti-CD28 coated beads (Miltenyi Biotec) were added at a bead-to-cell ratio of 1:1 and a final cell density of 1 x 10^6 cells/ml.

extract_protocol: not applicable

treatment_protocol: activated 48 h in vitro with anti-CD3/anti-CD28 coated beads

tag: Normal human donor purified primary naïve CD4+ helper T cells

source_name: Resting T cells Donor 2

label_protocol: same as Channel 1 'Label protocol'

treatment_protocol: rested 48 h in vitro without anti-CD3/anti-CD28 coated beads


title: T cell_activated_48h_rep1

description: Biological replicate 1 of 3. Donor 1 activated T cells versus Donor 1 resting T cells

source_name: Activated T cells Donor 1

source_name: Resting T cells Donor 1


title: Belgrade b/b Jejunum replicate 2

description: Standard Affymetrix protocol.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Standard Affymetrix protocol.

source_name: jejunal scrape

label_protocol: Standard Affymetrix protocol.

extract_protocol: Trizol followed by cleanup with RNEasy mini kit (Invitrogen)

tag: Belgrade, homozygote, adult


title: Exp2: CH1/Cy3 = J21.c3   lap2  (tethered), CH2/cy5 = J21.c3 (untethered)

description: Biological replicate 2 of 5.

source_name: J21.c3 lacI-ap2b


title: Belgrade b/b Duodenum replicate 1


title: DBM/control, 1h, rep2

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 2 of 4 comparing DBM treatment for 1h (Channel 2, Cy3) with control rosettes (Channel 1, Cy5)

source_name: whole rosette, untreated control, 1h, rep 2

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 1h, rep 2


title: T cell_activated_48h_rep3 (dyeswap)

description: Biological replicate 3 of 3. Donor 3 resting T cells versus Donor 3 activated T cells (dye-swap)

source_name: Resting T cells Donor 3

source_name: Activated T cells Donor 3


title: Belgrade b/b Jejunum replicate 1


title: T2952 (parental) vs 66672 (congenic)

description: T2952 (parental) vs 66672 (congenic)

source_name: T2952 (Inbred Dahl salt-sensitive (SS/Jr) rat )

label_protocol: Single-stranded cDNA was generated through reverse transcription of total RNA by Superscript III (Invitrogen) and random primers. Amino-allyl dUTP (in a ratio of 2:3 with dTTP) was incorporated during the reverse transcription. The RNA was then degraded by hydrolysis under alkaline conditions and the amino-allyl cDNA was subsequently purified with PCR Purification columns (Qiagen) substituting a phosphate wash buffer and phosphate elution buffer for the Tris-containing buffers in the kit. The purified sample was lyophilized and resuspended in sodium carbonate buffer and allowed to couple to the Cy3 fluorophore for an hour at room temperature. The reaction was stopped by sodium acetate and then the labeled cDNA was purified to remove uncoupled dye with PCR Purification columns (Qiagen) as per manufacturer's protocol.


title: Belgrade b/b Jejunum replicate 3

description: Standard Affymetrix protocol.


title: Belgrade b/b Duodenum replicate 3

source_name: doudenal scrape

tag: Balgrade, homozygote, adult


title: Belgrade +b Duodenum replicate 1

source_name: Duodenual scrape

tag: Belgrade rat, heterozygote, adult


title: spxB deletion Spn_D39vsD39ΔspxB_BHI_rep3

status: Public on Feb 22 2008

city: Bloomington

first: Ho-Ching

middle: Tiffany

last: Tsui

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

data_processing: Data were normalized with GeneTraffic 3.2 software (Iobion Informatics) using the Lowess (subgrid) method without background subtraction.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae bacterial strain D39 rpsL41

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight. Overnight cultures which displayed no lysis were diluted to an OD620 of ~0.005 into BHI and grown at 37C and an atmosphere of 5% CO2. Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520

tag: S. pneumoniae bacterial strain D39 (NCTC) rpsL1, virulent, type 2 capsule, designated as IU1781 in Malcolm Winkler's lab

source_name: S. pneumoniae bacterial strain D39 (NCTC) rpsL41ΔspxB

label_protocol: see above

growth_protocol: see above

extract_protocol: see above

tag: S. pneumoniae bacterial strain D39 (NCTC) with rpsL1 (IU1781) and deletion of spxB gene.  It was constructed by tranformation of ΔspxB amplicon into strain IU1781. However, sebsequent studies showed that there is a secondary mutation that causes a capsule defect in this strain (IU1819). Hence this strain is not isogenic with strain IU1781.


title: DBM/control, 1h, rep1

description:
Arabidopsis thaliana Ler plants (growth stage 1) were exposed to Diamondback moth (DBM, Plutella xylostella) larvae for 1h (continuous feeding experiment).  Control plants were harvested at the same time point. Whole rosettes were used for RNA isolation, labelling and array
This file describes results for replicate 1 of 4 comparing DBM treatment for 1h (Channel 2, Cy5) with control rosettes (Channel 1, Cy3).

source_name: whole rosette, untreated control, 1h, rep 1

source_name: whole rosette, treated with diamond back moth (Plutella xylostella), 1h


title: Belgrade +/b Jejunum replicate 1

tag: Belgrade, heterozygous, adult


title: Exp4: CH1/Cy3 =J21.c3 (untethered), CH2/cy5 = J21.c3   lap2  (tethered)

description: Biological replicate 4 of 5.


title: Belgrade +b Duodenum replicate 3

source_name: duodenal scrape


title: Cancer tissue from patient 771522-1

status: Public on Feb 18 2008

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42C under LifterSlipTM (Erie, Portsmouth, NH) in a hybridization chamber which was placed in a 3D-tilting agitator BioMixerTM  II (CapitalBio) to provide continuous mixing of the hybridization buffer that results in more uniform hybridization across the entire slide surface, preventing edge effects and giving improved signal intensity, the efficiency of which has been demonstrated with our genome-wide mRNA expression profiling (Patterson et al., Nat Biotechnol. 2006, 24:1140-1150).The array was then washed with two consecutive washing solutions of 0.2% SDS, 2X SSC at 42C for 5 min, and 0.2% SSC for 5 min at room temperature.

scan_protocol: Arrays were scanned with a LuxScanTM 10K-A laser confocal scanner and the images obtained were then analyzed using LuxScan 3.0TM software (both from CapitalBio, Beijing, China).

data_processing: After average values of the replicate spots of each miRNA were background subtracted, faint spots were filtered out when expression signal were lower than 800 in all samples.  Signal was normalized using the median center tool for genes in the Cluster 3.0 software before performing the unsupervised clustering with complete linkage and uncentered Pearson correlation to underlying the structure of the miRNA expression (Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns (Proc Natl Acad Sci U S A 1998;95:14863-8).

source_name: Cancer tissue from patient 771522-1

label_protocol: 4 ug of low-molecular-weight RNA was labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon, Lafayette, CO) with 2 units T4 RNA ligase (New England Biolabs, Ipswich, MA).  The labeling reaction was performed at 4C for 2 h.  Labeled RNA was precipitated with 0.3 M sodium acetate and 2.5 volumes ethanol and after washing with ethanol and drying was resuspended in 15 ul of hybridization buffer containing 3X SSC, 0.2% SDS and 15% formamide.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Carlsbad, CA) and the low-molecular-weight RNA was isolated by using the Ambion miRNA Isolation Kit

tag: Cancer tissue from patient 771522-1


title: Adjacent normal tissue from patient 771522-1

description: the microRNA expression in the tissue


title: spxB deletion Spn_D39vsD39ΔspxB_BHI_rep1

scan_protocol: Performed as per microarray manufacturer’s recommendations (OciChip Application Guide from Ocimum Biosolutions). Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer. Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

source_name: S. pneumoniae bacterial strain D39 rpsL1

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.2) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520.

source_name: S. pneumoniae bacterial strain D39 (NCTC) rpsL1ΔspxB

tag: S. pneumoniae bacterial strain D39 (NCTC) with rpsL1 (IU1781) and deletion of spxB gene.  It was constructed by tranformation of ΔspxB amplicon into strain IU1781. However, sebsequent studies showed that there is a secondary mutation that causes a capsule defect in this strain (IU1819). Hence this strain is not isogenic with strain IU1718.


title: Adjacent normal tissue from patient 771522-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 770681-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 770681-1

tag: Cancer tissue from patient 770681-1


title: cDNA Analysis of Fe Deficiency on NILs E01

status: Public on Feb 20 2008

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 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 Fe(NO3)3 hydroponic conditions for 14 days.

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.


title: Cancer tissue from patient 770681-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 770681-2

tag: Cancer tissue from patient 770681-2


title: Patient 5 skin treated

description: Subjects included males and females ages 14 to 40 years who were scheduled by their dermatologist to receive treatment with 13-cis RA (isotretinoin, brand not noted) for severe acne.  All aspects of the patients’ treatment with 13-cis RA apart from the skin biopsies were standard of care and were not part of this research.  Exclusion criteria included patients with underlying medical conditions requiring treatment with systemic medications that might interfere with the gene array analysis.

source_name: skin, 1 week isotretinoin treatment


title: cDNA Analysis of Fe Sufficient Hydroponic Conditions on NILs 198

description: Slides weree hybridized in the Shoemaker Lab and scanned at the Microarray Core Facility at Iowa State University.

hyb_protocol: Arrays were hybridized at 42 degrees C. for 18 hours.  After overnight hybridization, arrays were washed (wash 1: 1X SSC, 0.2%SDS; wash2: 0.2X SSC, 0.2%SDS; wash 3: 0.1% SDS) to remove unbound cDNAs.  Slides were then centrifuged for 5 minutes to dry.

scan_protocol: Slides were scanned using a Pro Scan Array HT at the Center for Plant Genomics Microarray Facility at Iowa State University.  Resulting images were overlaid and spots identified by the ImaGene program.

data_processing: Differential Expression between iron efficient and iron inefficient samples was identified by a log ratio of positive or negative 2 using the GeneTraffic analysis program.

source_name: Iron Sufficient Iron Efficient Clark Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1X Buffer, 110mM DTT, 500uM low T dNTPs, 100uM Cy5, and 13u/uL SuperScriptII were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees C.

extract_protocol: Total RNA was extracted using a modified phenol:chloroform extraction protocol described by Vodkin et al. BMC Genomics 2005.  Qiagen RNeasy kit provided further purification of the extracted total RNA

tag: Roots of iron efficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditons for 14 days.

source_name: Iron Sufficient Iron Inefficient IsoClark Roots

label_protocol: 90ug of RNA was combined with oligo dT for 10 min.  20uL 1X Buffer, 110mM DTT, 500uM low T dNTPs, 100uM Cy3, and 13u/uL SuperScriptII were incubated with RNA/Oligo dT mix for 2 hours at 42 degrees C.

tag: Roots of Iron Inefficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditons for 14 days.


title: Adjacent normal tissue from patient 770681-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 770681-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 768865-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 768865-1

tag: Cancer tissue from patient 768865-1


title: Cancer tissue from patient 768865-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 768865-2

tag: Cancer tissue from patient 768865-2


title: cDNA Analysis of Fe Sufficient Hydroponic Conditions on NILs 197

tag: Roots of iron inefficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditions for 14 days.


title: cDNA Analysis of Fe Sufficient Hydroponic Conditions on NILs 196

tag: Roots of Iron efficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditions for 14 days.

tag: Roots of Iron inefficient soybeans grown under iron sufficient (100uM Fe(NO3)3) hydroponic conditions for 14 days.


title: cDNA Analysis of Fe Deficiency on NILs B07

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


title: Affymetrix 250k StyI, JW S2

status: Public on Feb 29 2008

type: genomic

city: Houston

first: Omar

last: Alvi

state: TX

address: 1 Baylor Plaza

department: Human Genome Sequencing Center

institute: Baylor College of Medicine

description: Genotyping data for JW (Affymetrix 500k SNPs)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Gene Chip Scanner 3000 with autoloader and 7G upgrade and GCOS 1.4

data_processing: Affymetrix files (CEL) were processed using GCOS 1.4 software, Genotype calls were made using the BRLMM software from Affymetrix in Gene Chip Genotype Analysis software v 4.0

molecule: genomic DNA

source_name: JW DNA extracted from blood

label_protocol: Standard Affymetrix protocol

extract_protocol: DNA extracted from blood using FlexiGene DNA kit from Qiagen

tag: Blood from JW


title: Adjacent normal tissue from patient 774270-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 774270-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 774270-1

tag: Cancer tissue from patient 774270-1


title: Adjacent normal tissue from patient 768865-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 769799-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 769799-1

tag: Cancer tissue from patient 769799-1


title: Affymetrix 250k StyI, JW S1


title: Adjacent normal tissue from patient 774270-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 769799-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 769799-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 769799-2

tag: Cancer tissue from patient 769799-2


title: Cancer tissue from patient 212086-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 212086-1

tag: Cancer tissue from patient 212086-1


title: Adjacent normal tissue from patient 769799-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 768865-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215826-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 215826-1

tag: Cancer tissue from patient 215826-1


title: Cancer tissue from patient 209134-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 209134-1

tag: Cancer tissue from patient 209134-1


title: Cancer tissue from patient 209134-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 209134-2

tag: Cancer tissue from patient 209134-2


title: Cancer tissue from patient 215826-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 215826-2

tag: Cancer tissue from patient 215826-2


title: spxB deletion Spn_D39vsD39ΔspxB_BHI_rep2

source_name: S. pneumoniae bacterial strain D39 rpsL41

tag: S. pneumoniae bacterial strain D39 (NCTC) rpsL1, virulent, type 2 capsule, designated as IU1781 in Malcolm Winkler's lab

source_name: S. pneumoniae bacterial strain D39 (NCTC) rpsL41ΔspxB

tag: S. pneumoniae bacterial strain D39 (NCTC) with rpsL1 (IU1781) and deletion of spxB gene.  It was constructed by tranformation of ΔspxB amplicon into strain IU1781. However, sebsequent studies showed that there is a secondary mutation that causes a capsule defect in this strain (IU1819). Hence this strain is not isogenic with strain IU1718.


title: Affymetrix 250k NspI, JW S2


title: Cancer tissue from patient 192884-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 192884-2

tag: Cancer tissue from patient 192884-2


title: Adjacent normal tissue from patient 209134-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 192884-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 192884-1

tag: Cancer tissue from patient 192884-1


title: Cancer tissue from patient 774270-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 774270-2

tag: Cancer tissue from patient 774270-2


title: Cancer tissue from patient 205484-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205484-1

tag: Cancer tissue from patient 205484-1


title: Cancer tissue from patient 205484-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205484-2

tag: Cancer tissue from patient 205484-2


title: T cell_activated_48h_self

description: Self-Self comparison. Donor 1 activated T cells versus Donor 3 activated T cells

source_name: Activated T cells Donor 1

tag: Normal human donor purified primary naïve CD4+ helper T cells

source_name: Activated T cells Donor 3


title: Adjacent normal tissue from patient 212086-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 212623-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 212086-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 197838-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 197838-1

tag: Cancer tissue from patient 197838-1


title: Cancer tissue from patient 197838-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 197838-2

tag: Cancer tissue from patient 197838-2


title: Cancer tissue from patient 212623-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 212623-2

tag: Cancer tissue from patient 212623-2


title: Cancer tissue from patient 212623-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 212623-1

tag: Cancer tissue from patient 212623-1


title: Cancer tissue from patient 205650-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205650-1

tag: Cancer tissue from patient 205650-1


title: Cancer tissue from patient 205650-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205650-2

tag: Cancer tissue from patient 205650-2


title: Adjacent normal tissue from patient 215826-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 203081-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203081-2

tag: Cancer tissue from patient 203081-2


title: Cancer tissue from patient 203081-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203081-1

tag: Cancer tissue from patient 203081-1


title: Cancer tissue from patient 192982-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 192982-2

tag: Cancer tissue from patient 192982-2


title: Cancer tissue from patient 198125-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 198125-2

tag: Cancer tissue from patient 198125-2


title: Cancer tissue from patient 192982-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 192982-1

tag: Cancer tissue from patient 192982-1


title: Cancer tissue from patient 203894-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203894-1

tag: Cancer tissue from patient 203894-1


title: Cancer tissue from patient 203173-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203173-2

tag: Cancer tissue from patient 203173-2


title: Cancer tissue from patient 203173-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203173-1

tag: Cancer tissue from patient 203173-1


title: Cancer tissue from patient 203894-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203894-2

tag: Cancer tissue from patient 203894-2


title: Adjacent normal tissue from patient 203173-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 192884-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205484-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205484-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205650-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 198125-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 198125-1

tag: Cancer tissue from patient 198125-1


title: Cancer tissue from patient 213728-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 213728-2

tag: Cancer tissue from patient 213728-2


title: Adjacent normal tissue from patient 203081-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 206458-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 206458-1

tag: Cancer tissue from patient 206458-1


title: Cancer tissue from patient 206458-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 206458-2

tag: Cancer tissue from patient 206458-2


title: Belgrade +b Duodenum replicate 2

source_name: duodenal scrape

tag: Belgrade, heterozygous, adult


title: Cancer tissue from patient 205873-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205873-1

tag: Cancer tissue from patient 205873-1


title: Cancer tissue from patient 205873-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 205873-2

tag: Cancer tissue from patient 205873-2


title: Cancer tissue from patient 204477-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204477-1

tag: Cancer tissue from patient 204477-1


title: Cancer tissue from patient 204477-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204477-2

tag: Cancer tissue from patient 204477-2


title: Adjacent normal tissue from patient 203894-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203894-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205650-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 204939-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204939-1

tag: Cancer tissue from patient 204939-1


title: Cancer tissue from patient 204939-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204939-2

tag: Cancer tissue from patient 204939-2


title: Adjacent normal tissue from patient 203081-2

description: the microRNA expression in the tissue


title: Affymetrix 250k NspI, JW S1

source_name: JW DNA extracted from blood

tag: Blood from JW


title: Adjacent normal tissue from patient 203173-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 213728-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 213728-1

tag: Cancer tissue from patient 213728-1


title: Adjacent normal tissue from patient 198125-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 192982-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 192982-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 198125-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 206458-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 213728-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205873-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204939-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 206458-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 205873-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204939-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204477-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 213728-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204477-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 211526-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 211526-2

tag: Cancer tissue from patient 211526-2


title: Cancer tissue from patient 208450-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 208450-1

tag: Cancer tissue from patient 208450-1


title: Cancer tissue from patient 208450-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 208450-2

tag: Cancer tissue from patient 208450-2


title: Cancer tissue from patient 204434-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204434-2

tag: Cancer tissue from patient 204434-2


title: Adjacent normal tissue from patient 211526-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 203326-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203326-2

tag: Cancer tissue from patient 203326-2


title: Cancer tissue from patient 193512-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 193512-2

tag: Cancer tissue from patient 193512-2


title: Cancer tissue from patient 203326-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 203326-1

tag: Cancer tissue from patient 203326-1


title: Adjacent normal tissue from patient 208450-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 206219-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 206219-2

tag: Cancer tissue from patient 206219-2


title: Cancer tissue from patient 211526-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 211526-1

tag: Cancer tissue from patient 211526-1


title: Adjacent normal tissue from patient 211526-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 193512-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 193512-1

tag: Cancer tissue from patient 193512-1


title: Belgrade +/b Jejunum replicate 3

source_name: jejunal scrape

tag: Belgrade, heterozygous, adult


title: Adjacent normal tissue from patient 208450-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 204434-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 204434-1

tag: Cancer tissue from patient 204434-1


title: Cancer tissue from patient 206219-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 206219-1

tag: Cancer tissue from patient 206219-1


title: Adjacent normal tissue from patient 204434-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 206219-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 206219-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203326-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 204434-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 193512-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 193512-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 197838-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 203326-1

description: the microRNA expression in the tissue


title: cDNA Analysis of Fe Sufficient Hydroponic Conditions on NILs 195

source_name: Iron Sufficient Iron Inefficient IsoClark Roots

tag: Roots of iron  inefficient IsoClark soybean grown in iron sufficient (100uM Fe (NO3)3) hydroponics solutions for 14 days.

source_name: Iron Sufficient Iron Efficient Clark Roots

tag: Roots of iron efficient Clark soybean grown in iron sufficient (100uM Fe (NO3)3) hydroponics solutions for 14 days.


title: Adjacent normal tissue from patient 197838-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 208087-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 208087-2

tag: Cancer tissue from patient 208087-2


title: Cancer tissue from patient 200303-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 200303-2

tag: Cancer tissue from patient 200303-2


title: Belgrade +/b Jejunum replicate 2


title: Cancer tissue from patient 200303-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 200303-1

tag: Cancer tissue from patient 200303-1


title: Adjacent normal tissue from patient 208087-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 194969-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 194969-2

tag: Cancer tissue from patient 194969-2


title: Cancer tissue from patient 208087-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 208087-1

tag: Cancer tissue from patient 208087-1


title: Adjacent normal tissue from patient 208087-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 209186-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 209186-2

tag: Cancer tissue from patient 209186-2


title: Adjacent normal tissue from patient 200303-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 194969-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 194969-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 194969-1

tag: Cancer tissue from patient 194969-1


title: Cancer tissue from patient 209186-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 209186-1

tag: Cancer tissue from patient 209186-1


title: Adjacent normal tissue from patient 194969-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 209186-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 207367-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 207367-2

tag: Cancer tissue from patient 207367-2


title: Cancer tissue from patient 210973-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 210973-2

tag: Cancer tissue from patient 210973-2


title: Adjacent normal tissue from patient 210973-2

description: the microRNA expression in the tissue


title: Cancer tissue from patient 207367-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 207367-1

tag: Cancer tissue from patient 207367-1


title: Cancer tissue from patient 215270-2

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 215270-2

tag: Cancer tissue from patient 215270-2


title: Cancer tissue from patient 210973-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 210973-1

tag: Cancer tissue from patient 210973-1


title: Adjacent normal tissue from patient 207367-1

description: the microRNA expression in the tissue


title: Cancer tissue from patient 215270-1

description: the microRNA expression in the tissue

source_name: Cancer tissue from patient 215270-1

tag: Cancer tissue from patient 215270-1


title: Adjacent normal tissue from patient 215270-1

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 215270-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 207367-2

description: the microRNA expression in the tissue


title: Adjacent normal tissue from patient 209186-1

description: the microRNA expression in the tissue


title: TS#9 in differentiation medium day 4 Grp D

status: Public on Nov 07 2007

city: La Jolla

first: Roy

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: Ets2 type: TS differ f/f; medium DM; Grp D replicate

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by Illumina using the Illumina scanner.

data_processing: None: raw data from Beadstudio

label: Streptavidin Cy3

organism: Mus musculus

source_name: Mouse TS#9 in differentiation medium day 4

label_protocol: As described in the illumina Mouse-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

growth_protocol: TS cells were isolated from blastocysts and grown as previously described (Tanaka et al., 1998). Briefly, Growth medium (GM) was RPMI 1640 supplemented with 20% FBS, 1 mM sodium pyruvate, 100 μM b-mercaptoethanol, 100 U/ml penicillin, 100μg/ml streptomycin, 2 mM L-glutamine, 25 ng/ml human recombinant FGF4 (Sigma), 1 μg/ml heparin, and 70% EFCM. TS cell differentiation was induced by withdrawal of FGF4 and EFCM after trypsinization and replating at appropriate density. For TS colony formation assay, optimally growing TS cells were trypsinized and replated at 500-2000 cells per 6-cm dish onto feeder cells, and fed with fresh GM every 2-3 days for 1-2 weeks.

extract_protocol: Illumina TotalPrep RNA amplification kit (Ambion Catalog#IL1791)

tag: Ets2 type

value: TS differ f/f; TS#9 in differentiation medium day 4; medium DM


title: HV3-20-66CGH

status: Public on Oct 23 2007

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: PC3 125-1L

hyb_protocol: DNA samples were hybridized onto the array for 16-18 hours at 42°C utilizing the MAUI 4-bay hybridization system and MAUI Mixer A0 (BioMicro System, Salt Lake City, UT, USA). After hybridization arrays and MAUI Mixer were disassembled in 42°C 1xSSC and 0.05% SDS (wash solution 1) and subsequently washed two times in wash solution 1 for 5 minutes followed by two washes in 0.1xSSC (wash solution 2) for 5 minutes.

scan_protocol: Dried array slides were scanned using a ScanLite Express microarray scanner (Perkin Elmer, Wellesley, MA, USA). Raw image files of the arrays were processed using DeArray software (Chen et al, 1997) and resulting image data were imported into R environment using bioconductor packages (Gentleman RC et al., 2004) for further analysis.

data_processing: Loess normalization

label_protocol: 10 µg of amplified and purified DNA were labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen) according to the manufacturer¢â¬â„¢s instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy5-dUTP or Cy3-dUTP. Labeled DNA was purified using QIAquick PCR purification columns (Qiagen). Tumor and reference DNA were pooled, mixed with 50 µg Cot-1 DNA (Invitrogen) and concentrated to a volume of 20 µl in a vacuum centrifuge. DNA was then mixed with an equal amount of 2x formamide buffer, denaturated at 95°C for 5 min and preincubated at 37°C for 30 min in a waterbath.

extract_protocol: DNA was isolated using the QiAmp DNA isolation kit (Qiagen, Hilden, Germany) and subsequently quantified by a fluorometric assay (Quant-iT Pico Green dsDNA Kit, Invitrogen, Karlsruhe, Germany). Fluorescence was measured using a TECAN (Salzburg, Austria) SpectrafluorPLUS microplate fluorescence reader with an excitation wavelength at 485 nm and an emission wavelength at 535 nm. DNA concentrations were calculated from a standard curve of double-stranded control DNA provided with the kit that was measured in triplicate at the concentrations 30, 3, 0.3, and 0.03 ng/µl (measured by fluorometry).A volume of 2.5 µl out of 4 ng/µl dilutions from cell lines and control DNA was used as starting material for the amplification. The phi29-amplification was carried out according to the Repli-G kit manufacturer's instructions (Qiagen) using an incubation time of 16 h. Repli-G reactions were checked by a real time based intra Alu-PCR assay. Additionally DNA concentration was fluorimetrically measured with Quant-iT Pico Green dsDNA Kit (Invitrogen) and ranged between 10-30 Ž¼g.

source_name: male DNA


title: HV3-20-67CGH

description: male DNA

tag: male DNA

source_name: LNCaP-CN4 2


title: TS#9/AdGFP day1 in GM Grp A

description: TS#9/AdGFP day1 in GM

source_name: Mouse TS#9/AdGFP day1 in GM

tag: Ets2 type f/f; medium GM; AdenoGFP; TS#9/AdGFP day1 in GM


title: HV3-7-18CGH

description: male DNA


title: Tri TS#15(ets2flox/flox) AdCreGFP 3dpi Grp B

description: Tri TS#15(ets2flox/flox) AdCreGFP, 3dpi; GrpB replicate

source_name: Mouse Tri TS#15(ets2flox/flox) AdCreGFP, 3dpi

tag: Ets2 type f/f; medium GM; Adeno CRE; Tri TS#15(ets2flox/flox) AdCreGFP, 3dpi


title: TS#7 GMd4 (6-well) Grp C

description: Ets2 type: TS cellsf/f; medium GM; GrpC replicate

source_name: Mouse TS#7 GMd4 (6-well)

value: TS cellsf/f; medium GM;


title: TS#9/AdCreGFP day3 in GM Grp B

description: TS#9/AdCreGFP day3 in GM; GrpB replicate

source_name: Mouse TS#9/AdCreGFP day3 in GM

tag: Ets2 type f/f; medium GM; Adeno CRE ; TS#9/AdCreGFP day3 in GM; GrpB


title: TS#9 in growth medium Grp C

description: Ets2 type: TS cellsf/f; medium GM;TS#9 in growth medium; GrpC replicate

source_name: Mouse TS#9 in growth medium

value: TS cellsf/f; medium GM; TS#9 in growth medium


title: HV3-20-60CGH

description: male DNA

source_name: PC3 NIH


title: TS#7 DMd4 (6-well) Grp D

source_name: Mouse TS#7 DMd4 (6-well)

value: TS differ f/f; medium DM;


title: HV3-20-61CGH

description: male DNA

source_name: CWR22 Rv1


title: Adjacent normal tissue from patient 210973-1

description: the microRNA expression in the tissue


title: HV3-20-64CGH

description: male DNA


title: HV3-20-70CGH

description: male DNA


title: HV3-20-63CGH

description: PC3 HOM

source_name: PC3 HOM

tag: PC3 HOM