title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - SC1b

status: Public on Mar 21 2009

type: RNA

city: Manhattan

first: Daniel

last: Marcus

state: KS

address: 228 Coles Hall

department: Anatomy & Physiology

country: USA

institute: Kansas State University

description: Absolute and comparison analysis are conducted using the following settings: Scaling - All Probe Sets: Target Signal = 500 Normalization – User Defined: Scale Factor = 1

hyb_protocol: GENECHIP HYBRIDIZATION PROTOCOL: Hybridization cocktail composition: (for standard array format) Note: 10% DMSO is added for targets Prepared using the GeneChip Expression 3’-Amplificaton IVT Labeling Protocol. 30ul fragmented cRNA 15ug (0.05ug/ul final conc.) 5ul control Biotin labeled oligo B2 (3nM) (Affymetrix) (50pM final conc.) 15ul 20x Eukaryotic Hybridization spike controls (bioB, bioC, BioD, cre) (Affymetrix) (1.5, 5, 25 and 100pM final conc. respectively) 3ul Herring Sperm DNA (10mg/ml)(blocking reagent) (0.1mg/ml final conc.) 3ul Acetylated BSA (50mg/ml)(blocking reagent) (0.5mg/ml final conc.) 150ul 2x Hybridization Buffer (Final 1x conc. is 100mM MES {12X stock: 70.4g MES free-acid monohydrate, 193.3g MES sodium Salt/L pH 6.6}, 1M [Na+], 20mM EDTA, 0.01% Tween 20) - DEPC H2O to 300ul. - Denatured at 99C 5min prior to applying to GeneChip Hybridization Conditions: - GeneChip is prehybridized with 200ul 1x Hybridization buffer (see above) at 45C 10min at 60rpm - 200ul denatured Hybridization cocktail is applied to GeneChip - GeneChip is hybridized 16 hr at 45C and 60rpm in GeneChip Hybridization Oven 640. Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard Array Format. Enzo BioArray High Yield RNA Transcript Labeling Washing and Staining Protocol Post Hyb wash #1 - 10 cycles of 2 mixes/ cycle with wash buffer A at 25C - non-stringent (6xSSPE, 0.01% Tween 20) Post Hyb wash #2 - 4 cycles of 15 mixes/ cycle with wash buffer B at 50C - stringent (100mM MES, 0.1M [Na+], 0.01% Tween 20) 1st Stain - 10 min. at 25C (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES, 92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O}, 24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin conjugate, 270ul DEPC H2O, 600ul total vol.) Post Stain Wash - 10 cycles of 4 mixes/cycle with wash buffer A at 25C 2nd Stain - 10 min. at 25C (Antibody Stain: 300ul 2x MES stain buffer {see above}, 24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG, 3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O, 600ul total vol.) 3rd Stain - 10 min at 25C (SAPE stain: see above, 600ul total vol.) Final Wash - 15 cycles of 4 mixes/cycle with wash buffer A at 30C. The GeneChip remains filled with wash buffer A for the scanning procedure. GeneChip Expression 3’-Amplification IVT Labeling Washing and Staining Protocol Post Hyb wash #1 - 10 cycles of 2 mixes/ cycle with wash buffer A at 30ºC - non-stringent (6xSSPE, 0.01% Tween 20) Post Hyb wash #2 - 6 cycles of 15 mixes/ cycle with wash buffer B at 50ºC - stringent (100mM MES, 0.1M [Na+], 0.01% Tween 20) 1st Stain - 5 min. at 30ºC (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES, 92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O}, 24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin conjugate, 270ul DEPC H2O, 600ul total vol.) Post Stain Wash - 10 cycles of 4 mixes/cycle with wash buffer A at 30ºC 2nd Stain - 5 min. at 35ºC (Antibody Stain: 300ul 2x MES stain buffer {see above}, 24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG, 3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O, 600ul total vol.) 3rd Stain - 5 min at 35ºC (SAPE stain: see above, 600ul total vol.) Final Wash - 15 cycles of 4 mixes/cycle with wash buffer A at 35ºC. The GeneChip remains filled with wash buffer A for the scanning procedure.

scan_protocol: Scanning: Automated process conducted using the Agilent GeneArray Scanner. - 2x scans are conducted for the Enzo protocol and 1x scans are conducted for the GeneChip Expression protocol as follows: Pixel value = 3um Wavelength = 570nm

data_processing: Data was generated and calculated using GCOS1.4

molecule: total RNA

organism: Rattus norvegicus

source_name: IEC6 cells - ACTT Commercially available

label_protocol: Affymetrix Small Sample Labeling Protocol vII (2xIVT) First Cycle of Amplification Step 1. First cycle, first strand cDNA synthesis Note: Use C thermal cycler with a heated lid for incubations in this step. Use the 4 Chold 42 minutes C 104 C 60for the addition of reagents. 70 C hold6 minutes with 1ul of4 a. Mix 1ul of total RNA (50ng/ul) C in thermal70 C holdminutes 5uM T7(dT)24 in 0.2ul PCR tube and incubate at 70 cycler with heated lid for 6 min. (5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’) b. Cool to 4 c. Spin briefly. d. Add 3ul of RT-Premix-1 master mixC for 2 min. using the following components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes. 1 rxn DEPC treated water 0.375ul 5x first strand buffer 1ul DTT, 0.1M 0.5ul dNTP mix, 10mM 0.375ul Rnase inhibitor, 40 U/ul e.0.25ul SuperScript II, 200 U/ul 0.5ul Total Volume 3ul C 60 minutes. atIncubated at 42 f. Heat sample C for 10 minutes to inactivate SuperScript II. sample to 4 Step 2. First cycle, second strand70 g. Spin briefly and cool C. thermal cycler without heated lid forcDNA synthesis Note: Use C hold for 16 Cincubations in this step. Use 4 the addition of reagents. C 120 minutes 4 a Prepare the SS-Premix-1 as follows using the16 minutes C hold4 C 10hold components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes. 1 rxn DEPC treated water 22.75ul 5x second strand buffer 7.5ul dNTP mix, 10mM 0.75ul DNA ligase, E. coli, 10U/ul 0.25ul DNA polymerase I, E. coli 10U/ul 1ul Rnase H, 2U/ul 0.25ul Total Volume 32.5ul b. Add 32.5ul of the SS-Premix-1 to each first strand reaction making a final volume of 37.5ul. c. Incubate the samples at 16Mix by pipetting and spin briefly. d. C for 2 hours. e. Add 1ul of T4 DNA polymerase (5U/ul) to the reaction and mix by pipetting. f. Continue incubation at 16 for 10 minutes. Step 3. First cycle,C double-stranded cDNA cleanup by ethanol precipitation. a. Transfer the reaction to a 1.5 ml centrifuge tube. b. Add 80ul of DEPC treated water to dilute reaction. c. Add 2ul of glycogen (5 mg/ml), 0.6 volumes (72ul) of 5M NH4OAc, and 2.5 volumes (480ul) of cold absolute ethanol. Mix by pipetting. d. Precipitate e. Centrifuge at 14,000rpm forat -20 C.the double-stranded cDNA C for 2 hours. 20 minutes at 4 f. Wash pellet with 800ul of 70% cold ethanol. g. Centrifuge at minutes at 4 h. Remove ethanol and dry pellet in speed vacuum14,000rpm for 5 C. for 10 minutes. Step 4. First cycle, IVT for cRNA amplification using MEGAscript T7 kit (Ambion). a. At room temperature, add the following reagents to the dried double-stranded cDNA pellet, in the order indicated. 1rxn DEPC treated water 4ul Premixed NTPs, 18.75mM each 4ul 10x reaction buffer 1ul 10x enzyme mix 1ul Total Volume 10ul b. Mix well by pipetting. Spin briefly. C for 5 hours mixing every c. Incubate at 37 Step 5. First cycle, cRNA cleanup with Qiagen30 minutes. RNeasy columns. a. Add 90ul of Rnase-free water to sample. b. Follow the RNeasy Mini Protocol for RNA Cleanup as directed in the RNeasy Mini Kit handbook. c. In the last step of the purification, elute the cRNA sample with 30ul of Rnase-free water first, and follow with an additional 20ul of water for the second elution. d. Determine the cRNA yield by conducting a 1/10 dilution in water and measuring the absorbance at 260nm. e. Transfer 400ng of cRNA to a new 1.5ml tube and use speed vacuum to concentrate sample to 4ul. Avoid drying the sample completely. Note: If the yield is less that 400ng, use the entire sample for the second cycle of cDNA synthesis. Second Cycle of Amplification and Labeling Step 6. Second cycle, first strand cDNA synthesis. Note: Use heating blocks for incubation in this step. a. Add random primers to the cRNA sample and mix well. cRNA, 400ng 4ul Random primers, 0.2 ug/ul 1ul Total Volume 5ul C for 10 minutes b. Incubate at 70 c. Cool sample on ice for 2 minutes. d.to denature cRNA. Prepare the RT-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least two reactions to avoid pipetting small volumes. 1rxn 5x first strand buffer 2ul DTT, 0.1M 1ul dNTP mix, 10mM 0.5ul RNase Inhibitor, 40 U/ul 0.5ul SuperScript II, 200 U/ul 1ul Total Volume 5ul e. Add 5ul of the RT-Premix-2 to the denatured RNA and primer mixture, making a final volume 10ul. Mix well by f. Incubate the sample atpipetting. Spin briefly. C for 1 hour. Spin briefly. 42 g. To remove the RNA template, add 1ul of RNase H (2 U/ul) and incubate the h. Heat the sample37 C for 5 minutes to inactivatesample at C for 20 minutes. at 95 RNase H. i. Cool sample on ice 2 minutes. Spin briefly. Step 7. Second cycle, second strand cDNA synthesis Note: Transfer sample to a 0.2 ml PCR tube and perform the incubations in a thermal cycler without a heated lid. Use C hold 4 C 1016 minutes C hold4 C 12070 C holdthe 4 C 6 minutesto add reagents. 4 a. Add 2.0ul of the 5uM T7(dT)24 promoter primer to the16 C holdminutes chilled sample from the previous step. b. Mix well. Spin briefly. C for 6 sample to 4 e.c. Incubate sample at 70 d. Cool the C and spin briefly.minutes. Prepare the SS-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). 1rxn DEPC treated water 43.5ul 5x second strand buffer 15ul dNTP mix, 10mM 1.5ul DNA polymerase I, E. coli, 10 U/ul 2ul Total Volume 62ul f. Add 62ul of the SS-Premix-2 to the sample making a total volume g. Incubate at 16of 75ul. Mix well by pipetting. Spin briefly. C for 2 hours. i.h. Add 2ul of T4 DNA polymerase (5 U/ul) to the reaction. Mix well. C for 10 Incubate at 16 minutes. Step 8. Second cycle, double-strand cDNA cleanup by ethanol precipitation. a. Add 2ul of 5 mg/ml glycogen, 0.6 volume 5M NH4OAc, and 2.5 volumes of cold absolute ethanol. b. Mix well by pipetting. c. C for 30 the samplePrecipitate the double-stranded cDNA at -20 d. Centrifuge C.minutes. at 14,000 rpm for 20 minutes at 4 e. Carefully remove supernatant and wash the Centrifuge the tube atcDNA pellet by adding 800ul of 70% cold ethanol. f. C. 14,000 rpm for 5 minutes at 4 g. Carefully remove the ethanol. Dry pellet in a atspeed vacuum for 10 minutes. h. Store dry pellet C or proceed to next step. –20 Step 9. Second cycle, IVT for cRNA amplification and labeling with ENZO BioArray High Yield RNA Transcription Labeling Kit (Affymetrix) or GeneChip Expression 3’-Amplification IVT Labeling kit (Affymetrix). a. At room temperature, add the following reagents to the dried double-stranded cDNA pellet. Enzo BioArray High Yield RNA Transcription Labeling kit 1rxn DEPC treated water 22ul 10X HY reaction buffer 4ul 10X Biotin labeled ribonucleotides 4ul 10X DTT 4ul 10X RNase inhibitor mix 4ul 20X T7 RNA polymerase 2ul Total Volume 40ul 1. Mix the components well after adding each reagent; especially 2.after adding water, ensuring the cDNA pellet is completely dissolved. C for Incubate at 37 5 hours mixing every 30 minutes. GeneChip Expression 3’-Amplification IVT Labeling Kit 1rxn DEPC treated water 20ul 10x IVT Labeling Buffer 4ul IVT Labeling NTP Mix 12ul IVT Labeling Enzyme Mix 4ul Total Volume 40ul 1. Mix components well after adding each reagent, especially after adding water, ensuring the cDNA pellet is completely dissolved. 2. Incubate at 37ºC for 16 hours in a hybridization oven or thermal cycler with a heated lid to prevent condensation.

growth_protocol: Incubated for 72 hours at 37C in 5% CO2.

extract_protocol: Total RNA was extracted from IEC6 cells using a RNeasy Micro kit following the manufacturer's protocol (no.74004, Qiagen; Valencia, CA).

treatment_protocol: Vehicle Control with 1µM SC-560 for 72 hours

tag: Tissue

value: Intestinal Crypt Cells

tag: Animal

value: Rat


title: KSUAP-DM mReissners Membrane F0hrC

description:
Absolute and comparison analysis are conducted using the following settings:
      Scaling - All Probe Sets: Target Signal = 500
      Normalization – User Defined: Scale Factor = 1

hyb_protocol: GENECHIP HYBRIDIZATION PROTOCOL: Hybridization cocktail composition: (for standard array format) Note: 10% DMSO is added for targets 								 Prepared using the GeneChip 								 Expression 3’-Amplificaton  IVT 								 Labeling Protocol.      30ul     fragmented cRNA 15ug                                                      (0.05ug/ul final conc.)        5ul     control Biotin labeled oligo B2 (3nM) (Affymetrix)          (50pM final conc.)      15ul     20x Eukaryotic Hybridization spike controls        (bioB, bioC, BioD, cre) (Affymetrix)                             (1.5, 5, 25 and 100pM final conc.                                                                                respectively)        3ul     Herring Sperm DNA (10mg/ml)(blocking reagent)            (0.1mg/ml final conc.)        3ul     Acetylated BSA (50mg/ml)(blocking reagent)                    (0.5mg/ml final conc.)    150ul     2x Hybridization Buffer        (Final 1x conc. is 100mM MES {12X stock: 70.4g MES free-acid monohydrate, 193.3g MES         sodium Salt/L pH 6.6}, 1M [Na+], 20mM EDTA, 0.01% Tween 20)   - DEPC H2O to 300ul.                  - Denatured at 99C 5min prior to applying to GeneChip Hybridization Conditions:        - GeneChip is prehybridized with 200ul 1x Hybridization buffer (see above) at 45C 10min at 60rpm        - 200ul denatured Hybridization cocktail is applied to GeneChip        - GeneChip is hybridized 16 hr at 45C and 60rpm in GeneChip Hybridization Oven 640. Washing and Staining: Automated process using the GeneChip Fluidics Station 400 with the Standard             Array Format. Enzo BioArray High Yield RNA Transcript Labeling Washing and Staining Protocol          Post Hyb wash #1 - 10 cycles of 2 mixes/ cycle with wash buffer A at 25C - non-stringent (6xSSPE, 0.01% Tween 20)          Post Hyb wash #2 - 4 cycles of 15 mixes/ cycle with wash buffer B at 50C - stringent   (100mM MES, 0.1M [Na+], 0.01% Tween 20)          1st Stain                 - 10 min. at 25C  (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES,  92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O},                                             24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin  conjugate, 270ul DEPC H2O, 600ul total vol.)          Post Stain Wash     - 10 cycles of 4 mixes/cycle with wash buffer A at 25C          2nd Stain                 - 10 min. at 25C   (Antibody Stain: 300ul 2x MES stain buffer {see above},              	  24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG,                                              3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O,   600ul total vol.)          3rd Stain                  - 10 min at 25C   (SAPE stain: see above, 600ul total vol.)          Final Wash              - 15 cycles of 4 mixes/cycle with wash buffer A at 30C. The GeneChip remains   filled with wash buffer A for the scanning procedure. GeneChip Expression 3’-Amplification IVT Labeling Washing and Staining Protocol Post Hyb wash #1 - 10 cycles of  2 mixes/ cycle with wash buffer A at 30ºC - non-stringent (6xSSPE, 0.01% Tween 20)          Post Hyb wash #2 - 6 cycles of 15 mixes/ cycle with wash buffer B at 50ºC - stringent   (100mM MES, 0.1M [Na+], 0.01% Tween 20)          1st Stain                 - 5 min. at 30ºC  (SAPE Stain: 300ul 2x MES stain buffer {41.7ml 12x MES,  92.5ml 5M NaCl, 2.5ml 10% Tween 20/ 250ml total vol. in DEPC H2O},                                             24ul 50mg/ml acetylated BSA, 6ul 1mg/ml Streptavidin-R-Phycoerythrin  conjugate, 270ul DEPC H2O, 600ul total vol.)          Post Stain Wash     - 10 cycles of 4 mixes/cycle with wash buffer A at 30ºC          2nd Stain                 - 5 min. at 35ºC   (Antibody Stain: 300ul 2x MES stain buffer {see above},              	  24ul 50 mg/ml acetylated BSA, 6ul 10mg/ml normal goat IgG,                                              3.6ul 0.5mg/ml biotinylated anti-streptavidine antibody, 266.4ul DEPC H2O,   600ul total vol.)          3rd Stain                  - 5 min at 35ºC   (SAPE stain: see above, 600ul total vol.)          Final Wash              - 15 cycles of 4 mixes/cycle with wash buffer A at 35ºC. The GeneChip remains   filled with wash buffer A for the scanning procedure.

scan_protocol: Scanning: Automated process conducted using the Agilent GeneArray Scanner.         - 2x scans are conducted for the Enzo protocol and 1x scans are conducted for the GeneChip Expression protocol as follows:                       Pixel value = 3um                       Wavelength = 570nm

data_processing: Data was generated and calculated in GCOS1.2

label: Affymetrix Small Sample Labeling Protocol vII (2xIVT)

organism: Mus musculus

source_name: Fresh Reissner's Membrane (unincubated)

label_protocol:
First Cycle of Amplification
Step 1. First cycle, first strand cDNA synthesis
Note:  Use thermal cycler with a heated lid for incubations in this step. Use the 4C hold for the addition of reagents.  70C	6 minutes
	  4C	hold
	  42C	60 minutes
	  70C	10 minutes
	  4C	hold
a.	Mix 1ul of total RNA (50ng/ul) with 1ul of 5uM T7(dT)24 in 0.2ul PCR tube and incubate at 70C in thermal cycler with heated lid for 6 min.
(5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’)
b.	Cool to 4C for 2 min.
c.	Spin briefly.
d.	Add 3ul of RT-Premix-1 master mix using the following components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
	DEPC treated water			0.375ul
	5x first strand buffer			1ul
	DTT, 0.1M				0.5ul
	dNTP mix, 10mM			0.375ul
	Rnase inhibitor, 40 U/ul		0.25ul
	SuperScript II, 200 U/ul		0.5ul
	Total Volume			3ul
e.	Incubated at 42C 60 minutes.
f.	Heat sample at 70C for 10 minutes to inactivate SuperScript II.
g.	Spin briefly and cool sample to 4C.
Step 2. First cycle, second strand cDNA synthesis
Note:  Use thermal cycler without heated lid for incubations in this step. Use 4C hold for the addition of reagents.
16C	120 minutes
4C	hold
16C	10 minutes
4C	hold
a	Prepare the SS-Premix-1 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
					1 rxn
	DEPC treated water		22.75ul
	5x second strand buffer		7.5ul
	dNTP mix, 10mM		0.75ul
	DNA ligase, E. coli, 10U/ul	0.25ul
	DNA polymerase I, E. coli 10U/ul	1ul
	Rnase H, 2U/ul			0.25ul
	Total Volume			32.5ul
b.	Add 32.5ul of the SS-Premix-1 to each first strand reaction making a final volume of 37.5ul.
c.	Mix by pipetting and spin briefly.
d.	Incubate the samples at 16C for 2 hours.
e.	Add 1ul of T4 DNA polymerase (5U/ul) to the reaction and mix by pipetting.
f.	Continue incubation at 16C for 10 minutes.
Step 3. First cycle, double-stranded cDNA cleanup by ethanol precipitation.
a.	Transfer the reaction to a 1.5 ml centrifuge tube.
b.	Add 80ul of DEPC treated water to dilute reaction.
c.	Add 2ul of glycogen (5 mg/ml), 0.6 volumes (72ul) of 5M NH4OAc, and 2.5 volumes (480ul) of cold absolute ethanol. Mix by pipetting.
d.	Precipitate the double-stranded cDNA at -20C for 2 hours.
e.	Centrifuge at 14,000rpm for 20 minutes at 4C.
f.	Wash pellet with 800ul of 70% cold ethanol.
g.	Centrifuge at 14,000rpm for 5 minutes at 4C.
h.	Remove ethanol and dry pellet in speed vacuum for 10 minutes.
Step 4.  First cycle, IVT for cRNA amplification using MEGAscript T7 kit (Ambion).
a.	At room temperature, add the following reagents to the dried double-stranded cDNA pellet, in the order indicated.

						1rxn
DEPC treated water		4ul
Premixed NTPs, 18.75mM each	4ul
10x reaction buffer		1ul
10x enzyme mix			1ul
Total Volume			10ul
b.	Mix well by pipetting. Spin briefly.
c.	Incubate at 37C for 5 hours mixing every 30 minutes.
Step 5.  First cycle, cRNA cleanup with Qiagen RNeasy columns.
a.	Add 90ul of Rnase-free water to sample.
b.	Follow the RNeasy Mini Protocol for RNA Cleanup as directed in the RNeasy Mini Kit handbook.
c.	In the last step of the purification, elute the cRNA sample with 30ul of Rnase-free water first, and follow with an additional 20ul of water for the second elution.
d.	Determine the cRNA yield by conducting a 1/10 dilution in water and measuring the absorbance at 260nm.
e.	Transfer 400ng of cRNA to a new 1.5ml tube and use speed vacuum to concentrate sample to 4ul. Avoid drying the sample completely.  Note: If the yield is less that 400ng, use the entire sample for the second cycle of cDNA synthesis.
Second Cycle of Amplification and Labeling
Step 6.  Second cycle, first strand cDNA synthesis.
Note: Use heating blocks for incubation in this step.
a.	Add random primers to the cRNA sample and mix well.
cRNA, 400ng			4ul
Random primers, 0.2 ug/ul		1ul
Total Volume			5ul
b.	Incubate at 70C for 10 minutes to denature cRNA.
c.	Cool sample on ice for 2 minutes.
d.	Prepare the RT-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least two reactions to avoid pipetting small volumes.

					1rxn
5x first strand buffer			2ul
DTT, 0.1M				1ul
dNTP mix, 10mM			0.5ul
RNase Inhibitor, 40 U/ul			0.5ul
SuperScript II, 200 U/ul			1ul
Total Volume				5ul
e.	Add 5ul of the RT-Premix-2 to the denatured RNA and primer mixture, making a final volume 10ul. Mix well by pipetting. Spin briefly.
f.	Incubate the sample at 42C for 1 hour. Spin briefly.
g.	To remove the RNA template, add 1ul of RNase H (2 U/ul) and incubate the sample at 37C for 20 minutes.
h.	Heat the sample at 95C for 5 minutes to inactivate RNase H.
i.	Cool sample on ice 2 minutes. Spin briefly.
Step 7.  Second cycle, second strand cDNA synthesis
Note:  Transfer sample to a 0.2 ml PCR tube and perform the incubations in a thermal cycler without a heated lid. Use the 4C hold to add reagents.
70C		6 minutes
4C		hold
16C		120 minutes
4C		hold
16C		10 minutes
4C		hold
a.	Add 2.0ul of the 5uM T7(dT)24 promoter primer to the chilled sample from the previous step.
b.	Mix well. Spin briefly.
c.	Incubate sample at 70C for 6 minutes.
d.	Cool the sample to 4C and spin briefly.
e.	Prepare the SS-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen).
					1rxn
DEPC treated water			43.5ul
5x second strand buffer			15ul
dNTP mix, 10mM			1.5ul
DNA polymerase I, E. coli, 10 U/ul		2ul
Total Volume				62ul
f.	Add 62ul of the SS-Premix-2 to the sample making a total volume of 75ul. Mix well by pipetting. Spin briefly.
g.	Incubate at 16C for 2 hours.
h.	Add 2ul of T4 DNA polymerase (5 U/ul) to the reaction. Mix well.
i.	Incubate at 16C for 10 minutes.
Step 8.  Second cycle, double-strand cDNA cleanup by ethanol precipitation.
a.	Add 2ul of 5 mg/ml glycogen, 0.6 volume 5M NH4OAc, and 2.5 volumes of cold absolute ethanol.
b.	Mix well by pipetting.
c.	Precipitate the double-stranded cDNA at -20C for 30 minutes.
d.	Centrifuge the sample at 14,000 rpm for 20 minutes at 4C.
e.	Carefully remove supernatant and wash the cDNA pellet by adding 800ul of 70% cold ethanol.
f.	Centrifuge the tube at 14,000 rpm for 5 minutes at 4C.
g.	Carefully remove the ethanol. Dry pellet in a speed vacuum for 10 minutes.
h.	Store dry pellet at –20C or proceed to next step.
Step 9.  Second cycle, IVT for cRNA amplification and labeling with ENZO BioArray High Yield RNA Transcription
              Labeling Kit  (Affymetrix)  or GeneChip Expression 3’-Amplification IVT Labeling kit (Affymetrix).
a.	At room temperature, add the following reagents to the dried double-stranded cDNA pellet.
Enzo BioArray High Yield RNA Transcription Labeling kit
					1rxn
DEPC treated water		22ul
10X HY reaction buffer		4ul
10X Biotin labeled ribonucleotides	4ul
10X DTT			4ul
10X RNase inhibitor mix		4ul
20X T7 RNA polymerase		2ul
Total Volume			40ul
1. Mix the components well after adding each reagent; especially after adding water, ensuring the cDNA
    pellet is completely dissolved.
	2. Incubate at 37C for 5 hours mixing every 30 minutes.
GeneChip Expression 3’-Amplification IVT Labeling Kit
					1rxn
	DEPC treated water		20ul
	10x IVT Labeling Buffer		  4ul
	IVT Labeling NTP Mix		12ul
	IVT Labeling Enzyme Mix	  4ul
	Total Volume			40ul
	1. Mix components well after adding each reagent, especially after adding water, ensuring the cDNA pellet
	    is completely dissolved.
	2. Incubate at 37ºC for 16 hours in a hybridization oven or thermal cycler with a heated lid to prevent
	    condensation.
Step 10. Second cycle, labeled cRNA target cleanup with Qia

growth_protocol: Native tissue; no proliferation in organ culture

extract_protocol: RNA was extracted using a RNeasy Microkit following the manufacturer's protocol (no. 74004, Qiagen; Valencia, CA)

treatment_protocol: Reissner's Membrane explants unincubated

value: Reissner's Membrane

value: Mouse

tag: Age

value: adult


title: KSU Dr.Lillich - IEC6 cells treated with NSAIDS - I1b

treatment_protocol: Vehicle Control with 100µM Indomethacin for 72 hours


title: KSU-Dr.Lillich - IEC6 cells treated with NSAIDS - C2

growth_protocol: Incubated for 72 hours at 37C in 5% CO2

treatment_protocol: Vehicle Control with DMSO for 72 hours


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - NS2b

treatment_protocol: Vehicle Control with 100µM NS-398 for 72 hours


title: KSU Dr.Lillich - IEC6 cells treated with NSAIDS - C1

description:
Absolute and comparison analysis are conducted using the following settings:
Scaling - All Probe Sets: Target Signal = 500
Normalization – User Defined: Scale Factor = 1

label_protocol:
Affymetrix Small Sample Labeling Protocol vII (2xIVT)
First Cycle of Amplification
Step 1. First cycle, first strand cDNA synthesis
Note: Use C holdthermal cycler with a heated lid for incubations in this step. Use the 4 C 6 minutesfor the addition of reagents. 70
C hold4
C 6042 minutes
C 10 minutes70
C hold4
a. Mix 1ul of total RNA (50ng/ul) C in thermalwith 1ul of 5uM T7(dT)24 in 0.2ul PCR tube and incubate at 70 cycler with heated lid for 6 min.
(5’-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3’)
b. C for 2 min.Cool to 4
c. Spin briefly.
d. Add 3ul of RT-Premix-1 master mix using the following components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
DEPC treated water 0.375ul
5x first strand buffer 1ul
DTT, 0.1M 0.5ul
dNTP mix, 10mM 0.375ul
Rnase inhibitor, 40 U/ul 0.25ul
SuperScript II, 200 U/ul 0.5ul
Total Volume 3ul
C 60 minutes.e. Incubated at 42
f. Heat sample C for 10 minutes to inactivate SuperScript II.at 70
g. Spin briefly and cool C.sample to 4
Step 2. First cycle, second strand cDNA synthesis
Note: Use C hold forthermal cycler without heated lid for incubations in this step. Use 4 the addition of reagents.
C 120 minutes16
C hold4
C 1016 minutes
C hold4
a Prepare the SS-Premix-1 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least four reactions to avoid pipetting small volumes.
1 rxn
DEPC treated water 22.75ul
5x second strand buffer 7.5ul
dNTP mix, 10mM 0.75ul
DNA ligase, E. coli, 10U/ul 0.25ul
DNA polymerase I, E. coli 10U/ul 1ul
Rnase H, 2U/ul 0.25ul
Total Volume 32.5ul
b. Add 32.5ul of the SS-Premix-1 to each first strand reaction making a final volume of 37.5ul.
c. Mix by pipetting and spin briefly.
d. C for 2 hours.Incubate the samples at 16
e. Add 1ul of T4 DNA polymerase (5U/ul) to the reaction and mix by pipetting.
Cf. Continue incubation at 16 for 10 minutes.
Step 3. First cycle, double-stranded cDNA cleanup by ethanol precipitation.
a. Transfer the reaction to a 1.5 ml centrifuge tube.
b. Add 80ul of DEPC treated water to dilute reaction.
c. Add 2ul of glycogen (5 mg/ml), 0.6 volumes (72ul) of 5M NH4OAc, and 2.5 volumes (480ul) of cold absolute ethanol. Mix by pipetting.
d. Precipitate the double-stranded cDNA C for 2 hours.at -20
C.e. Centrifuge at 14,000rpm for 20 minutes at 4
f. Wash pellet with 800ul of 70% cold ethanol.
g. Centrifuge at 14,000rpm for 5 C.minutes at 4
h. Remove ethanol and dry pellet in speed vacuum for 10 minutes.
Step 4. First cycle, IVT for cRNA amplification using MEGAscript T7 kit (Ambion).
a. At room temperature, add the following reagents to the dried double-stranded cDNA pellet, in the order indicated.
1rxn
DEPC treated water 4ul
Premixed NTPs, 18.75mM each 4ul
10x reaction buffer 1ul
10x enzyme mix 1ul
Total Volume 10ul
b. Mix well by pipetting. Spin briefly.
C for 5 hours mixing every 30 minutes.c. Incubate at 37
Step 5. First cycle, cRNA cleanup with Qiagen RNeasy columns.
a. Add 90ul of Rnase-free water to sample.
b. Follow the RNeasy Mini Protocol for RNA Cleanup as directed in the RNeasy Mini Kit handbook.
c. In the last step of the purification, elute the cRNA sample with 30ul of Rnase-free water first, and follow with an additional 20ul of water for the second elution.
d. Determine the cRNA yield by conducting a 1/10 dilution in water and measuring the absorbance at 260nm.
e. Transfer 400ng of cRNA to a new 1.5ml tube and use speed vacuum to concentrate sample to 4ul. Avoid drying the sample completely. Note: If the yield is less that 400ng, use the entire sample for the second cycle of cDNA synthesis.
Second Cycle of Amplification and Labeling
Step 6. Second cycle, first strand cDNA synthesis.
Note: Use heating blocks for incubation in this step.
a. Add random primers to the cRNA sample and mix well.
cRNA, 400ng 4ul
Random primers, 0.2 ug/ul 1ul
Total Volume 5ul
C for 10 minutes to denature cRNA.b. Incubate at 70
c. Cool sample on ice for 2 minutes.
d. Prepare the RT-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen). It is recommended to assemble the master mix for at least two reactions to avoid pipetting small volumes.
1rxn
5x first strand buffer 2ul
DTT, 0.1M 1ul
dNTP mix, 10mM 0.5ul
RNase Inhibitor, 40 U/ul 0.5ul
SuperScript II, 200 U/ul 1ul
Total Volume 5ul
e. Add 5ul of the RT-Premix-2 to the denatured RNA and primer mixture, making a final volume 10ul. Mix well by pipetting. Spin briefly.
C for 1 hour. Spin briefly.f. Incubate the sample at 42
g. To remove the RNA template, add 1ul of RNase H (2 U/ul) and incubate the sample at C for 20 minutes.37
C for 5 minutes to inactivateh. Heat the sample at 95 RNase H.
i. Cool sample on ice 2 minutes. Spin briefly.
Step 7. Second cycle, second strand cDNA synthesis
Note: Transfer sample to a 0.2 ml PCR tube and perform the incubations in a thermal cycler without a heated lid. Use C hold to add reagents.the 4
C 6 minutes70
C hold4
C 12016 minutes
C hold4
C 10 minutes16
C hold4
a. Add 2.0ul of the 5uM T7(dT)24 promoter primer to the chilled sample from the previous step.
b. Mix well. Spin briefly.
C for 6 minutes.c. Incubate sample at 70
d. Cool the C and spin briefly.sample to 4
e. Prepare the SS-Premix-2 as follows using the components from the SuperScript Choice System (Invitrogen).
1rxn
DEPC treated water 43.5ul
5x second strand buffer 15ul
dNTP mix, 10mM 1.5ul
DNA polymerase I, E. coli, 10 U/ul 2ul
Total Volume 62ul
f. Add 62ul of the SS-Premix-2 to the sample making a total volume of 75ul. Mix well by pipetting. Spin briefly.
C for 2 hours.g. Incubate at 16
h. Add 2ul of T4 DNA polymerase (5 U/ul) to the reaction. Mix well.
C for 10i. Incubate at 16 minutes.
Step 8. Second cycle, double-strand cDNA cleanup by ethanol precipitation.
a. Add 2ul of 5 mg/ml glycogen, 0.6 volume 5M NH4OAc, and 2.5 volumes of cold absolute ethanol.
b. Mix well by pipetting.
c. C for 30 minutes.Precipitate the double-stranded cDNA at -20
d. Centrifuge C.the sample at 14,000 rpm for 20 minutes at 4
e. Carefully remove supernatant and wash the cDNA pellet by adding 800ul of 70% cold ethanol.
f. C.Centrifuge the tube at 14,000 rpm for 5 minutes at 4
g. Carefully remove the ethanol. Dry pellet in a speed vacuum for 10 minutes.
h. Store dry pellet C or proceed to next step.at –20
Step 9. Second cycle, IVT for cRNA amplification and labeling with ENZO BioArray High Yield RNA Transcription
Labeling Kit (Affymetrix) or GeneChip Expression 3’-Amplification IVT Labeling kit (Affymetrix).
a. At room temperature, add the following reagents to the dried double-stranded cDNA pellet.
Enzo BioArray High Yield RNA Transcription Labeling kit
1rxn
DEPC treated water 22ul
10X HY reaction buffer 4ul
10X Biotin labeled ribonucleotides 4ul
10X DTT 4ul
10X RNase inhibitor mix 4ul
20X T7 RNA polymerase 2ul
Total Volume 40ul
1. Mix the components well after adding each reagent; especially after adding water, ensuring the cDNA
pellet is completely dissolved.
C for2. Incubate at 37 5 hours mixing every 30 minutes.
GeneChip Expression 3’-Amplification IVT Labeling Kit
1rxn
DEPC treated water 20ul
10x IVT Labeling Buffer 4ul
IVT Labeling NTP Mix 12ul
IVT Labeling Enzyme Mix 4ul
Total Volume 40ul
1. Mix components well after adding each reagent, especially after adding water, ensuring the cDNA pellet
is completely dissolved.
2. Incubate at 37ºC for 16 hours in a hybridization oven or thermal cycler with a heated lid to prevent
condensation.
Step


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - SC2b


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - SC2


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - I2b


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - NS1b


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - C2b


title: KSU Dr.Lillich - IEC6 cells treated with NSAIDS - C1b

value: Intestinal Crypt Cells Animal:Rat


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - SC1


title: Fibroblasts from normal histology lung tissue, NL-6

status: Public on Mar 19 2009

city: Pittsburgh

first: Louis

middle: Justine

last: Vuga

state: PA

address: 3459 Fifth Ave, 628NW

department: Pulmonary Allergy, and Critical Care Medicine

institute: University of Pittsburgh

description: 8396 genes that had an Entrez gene ID demonstrate minimal changes in gene expression between fibroblasts from UIP histology lung tissue and normal histology lung tissue. Among them, 236 genes were substantially changed (TNoM=0 and t-test p-value <0.05).

hyb_protocol: Fragmented cRNA was hybridized to Codelink Uniset I slides. After hybridization, arrays were washed and stained with streptavidin-AlexaFluor 647.

scan_protocol: The arrays were scanned using a Genepix 4000B microarray scanner. Images were analyzed using Codelink expression II analysis suite, and visually inspected for defects and quality control parameters as recommended by the manufacturer.

data_processing: Median-Normalization

label: Biotin

organism: Homo sapiens

label_protocol: The extracted total RNA was used as a template to generate double-stranded cDNA and biotin-labeled cRNA, as recommended by the manufacturer of the arrays.

growth_protocol: Early passages of cells were cultured in a humidified atmosphere containing 5% of CO2 in Dulbecco's modified Eagle's medium (DMEM) (Cellgro, Herndon, VA), supplemented with 10% Fetal Bovine Serum (ATCC, Manassas, VA), 1% penicillin (Cellgro), and kept in a humidified incubator (Kendro Lab, New Town, CT) at 37°C.

extract_protocol: Total RNA was extracted from fibroblasts of UIP histology lung tissue or normal histology lung tissue using TRIzol reagent (GIBCO-BRL, Gaithersburg, MD) according to the manufacturer protocol for RNA extraction and purification. RNA was stored at - 80°C until use.

tag: Normal donor Lung


title: Fibroblasts from normal histology lung tissue, NL-7


title: Fibroblasts from UIP histology lung tissue, IPF-22

tag: UIP lung explant


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - NS1


title: Fibroblasts from UIP histology lung tissue, IPF-21


title: KSU Dr.Lillich - IEC6 - cells treated with NSAIDS - NS2


title: Fibroblasts from normal histology lung tissue, NL-5


title: Fibroblasts from UIP histology lung tissue, IPF-19


title: Fibroblasts from UIP histology lung tissue, IPF-20


title: Rectal cancer 21

status: Public on Mar 01 2009

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Rectal cancer_21

hyb_protocol: The two labeled cDNAs were hybridized to the microarray slide at 50°C overnight using a 3DNA Array 50 kit (Genisphere Inc, Hatfield, PA)

scan_protocol: After hybridization, each microarray was washed twice with 2X SSC, 0.2% SDS at room temperature for 5 min, and finally with 95% ethanol at room temperature for 1 min. The hybridized slide was scanned using a ScanArray 5000 Scanner

data_processing: Scanned images were analyzed using the GenePix Pro 4.0 program. The raw data were normalized using the print-tip Lowess method available in the OLIN package (http://www.bioconductor.org/).

source_name: Rectal cancer

label_protocol: Aliquots of tumor and adjacent normal RNAs (20 microgram respectively) were used as templates for the synthesis of cDNA, labeled with Cy5 or Cy3, respectively, using SuperScript II reverse transcriptase (Invitrogen, Carlsbard, CA) for 2 hr at 42°C.

growth_protocol: Tissue specimen prepared after surgical tumor resection

extract_protocol: RNA was extracted using Qiagen RNA extraction kit according to the manufacturer's instructions

tag: tumor location

value: rectum

tag: APC (1=WT; 2=Mutation; NA=Not available) mutation status

tag: BER (1=WT; 2=Mutation) mutation status

tag: MMR (1=WT; 2=Mutation) mutation status

tag: P53 (1=WT; 2=Mutation) mutation status

tag: RAF (1=WT; 2=Mutation) mutation status

tag: WNT (1=WT; 2=Mutation) mutation status

source_name: Normal rectum


title: Rectal cancer 20

description: Rectal cancer_20


title: Rectal cancer 19

description: Rectal cancer_19


title: T00251332 vastus lateralis COPD exacerbation

status: Public on Mar 14 2009

city: Leuven

first: Tim

last: Crul

address: Herestraat 49 - 706

department: Pathophysiology

country: Belgium

institute: University of Leuven

description:
COPD patients (forced expiratory volume in the first second/forced vital capacity (FEV1/FVC) <70%) hospitalized for an acute exacerbation were compared to clinically stable COPD patients visiting the outpatient clinic (FEV1/FVC <70%, no hospitalizations for acute exacerbations within 1 year before testing, no participation in training programs). On day 4 of hospitalization, percutaneous Bergström needle biopsies were taken from the vastus lateralis muscle. All participants gave oral and written informed consent to participate in the present study.
Total RNA from the vastus lateralis muscle was isolated using the Trizol method (Gibco BRL, Life Technologies, Merelbeke, Belgium). Microarray analysis was performed on CodeLink UniSet Human 20 K Bioarray (Amersham Biosciences, Diegem, Belgium) according to the manufacturer’s protocol at the VIB MicroArray Facility (MAF, Flanders Interuniversity Institute for Biotechnology, Leuven, Belgium). In brief, the quality of the total RNA was assessed with the Agilent Bio-analyser and Nanodrop followed by two rounds of cDNA synthesis. Biotin-labelled cRNA was synthesized by in vitro transcription and quality checked with the Nanodrop. 10 µg of biotin-labelled cRNA was fragmented and hybridized on the microarray slides and subsequently scanned with an Agilent Scanner. Gene expression was measured with the Codelink Expression Analysis software.

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection Protocol overview Hybridisation is performed overnight in a temperature-controlled shaking incubator. 1. Fragment cRNA. In 25 μl total volume, add 10 μg of cRNA to 5 μl of 5× fragmentation buffer and incubate at 94 ºC for 20 minutes. 2. Prepare hybridization reaction mixture. Bring 10 μg of fragmented cRNA, 78 μl of hybridization buffer component A, and 130 μl of hybridization buffer component B to a final volume of 260 μl with water. Incubate at 90 ºC for 5 minutes and immediately chill on ice for 5–30 minutes. 3. Loading reaction mixtures into array chambers. Slowly inject 250 μl of hybridization reaction mixture into array input port and seal ports with sealing strips. 4. Hybridization. Set the shaker speed to 300 rpm and incubate slides for 18–24 h at 37 ºC, maintaining a consistent hybridization time for comparative experiments. 5. Post-hybridization wash. Remove the Flex Chamber using the hybridization removal tool to hold the bioarray in place while peeling the Flex Chamber off at a 60º angle. Then, place the bioarrays into the bioarray rack while it sits inside the medium reagent reservoir containing 0.75× TNT. Transfer the bioarray rack to the large reagent reservoir containing preheated 0.75× TNT, and incubate at 46 °C for exactly 1 h. Do not exceed 1 h incubation. 6. Detection with streptavidin-dye conjugate. Fill each slot of the small reagent reservoir with 3.4 ml of Cy5-Streptavidin working solution. Transfer the bioarray rack from the large reagent reservoir into the small reagent reservoir and incubate bioarrays at ambient temperature for 30 minutes. Wash the bioarrays four times with 1× TNT (5 minutes each wash) in large reagent reservoirs. Rinse the bioarrays in 0.1× SSC/0.05% Tween™ for 30 seconds. Immediately follow the rinse with centrifugation to dry bioarrays, and store dried bioarrays in the dark.

scan_protocol: Bioarray scanning and analysis. Scan bioarrays and analyze with CodeLink Expression Analysis software. Scanning with GenePix™ 4000B is described in this booklet. For use of CodeLink Bioarrays with other scanners, visit the CodeLink website (www.amershambiosciences.com). In brief: For scanning with a GenePix Array Scanner, use the following steps. For information on use of alternative scanners with CodeLink bioarrays, visit the CodeLink website (www.amershambiosciences.com). 7.1 Turn the scanner on 15 minutes prior to use. 7.2 Open the cover to expose the slide holder. 7.3 Lift the latch of the slide holder and lift the upper clip. 7.4 Wearing latex gloves, load the bioarray into the tray with the label side down and closest to the front of the scanner. 7.5 Pull the clip on the left of the slide out and let the bioarray fall into place. Release the clip to put pressure against the bioarray. 7.6 Grab bioarray by the edges and move the bioarray toward you. 7.7 Lower upper clip and press down on the latch until it clicks. 7.8 Slide the cover to the right to cover the slide holder. 7.9 Open the GenePix software and select the following settings: expand setting file name: Expression_5um.gps: whole genome products Expression_10um.gps: 10K and 20K products wavelength: 635 nm PMT voltage: 600 V laser power: 100% pixel size: 5μm for Whole Genome products 10μm for 10K and 20K products focus position: 0 μm 7.10 In the Report tab, open the scanning script by clicking Scan CodeLink Slide. 7.11 Enter the bioarray serial number and click Next. The Experiment and Scan Information interface is displayed. 7.12 Type in the project name, experiment name, and sample name. The username is automatically captured. When opening this interface for the first time, a message box may ask whether to allow an ActiveX interaction to proceed. Click Yes. 7.13 Select a setting (.gps) file. The standard setting file is CodeLinkExpr.gps. If a settings file was previously selected, the name and path are displayed under Current Settings File. To select a new file, click Browse under Select New Settings File. The values for project name, experiment name, user name, and settings file that were entered for a previous bioarray are retained but may be changed. 7.14 In the Load and Scan Slide screen, the standard TIF file name for the current bioarray is displayed. If desired, the name may be modified, however, the slide number as the first part of the name cannot be altered. 7.15 Click Browse to select the image path or the location where the image files will be stored. If a Security Alert message box is displayed, click Yes. 7.16 Click Scan Slide. The Image tab will display, and the instrument will perform the scan. 7.17 When complete, the view will return to the Report tab. 7.18 Click Save Image to save the scanned image at the appropriate file location. 7.19 Slide the cover to the left and remove the bioarray. 7.20 To scan the next bioarray, click New Slide and enter the serial number for the next bioarray. The setting information previously entered will be retained. 7.21 Analyze the image from each bioarray using CodeLink Expression Analysis software.

data_processing: All the data processing was done by CodeLink™ Bioarrays software using default parameters set by the manufacturer.

source_name: Human vastus lateralis muscle biopsy

label_protocol:
Biotin-labelled cRNA target is prepared by a linear amplification method. The poly(A)+
RNA subpopulation (within the total RNA population) is primed for reverse transcription
by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5′ to a d(T)24
sequence. After second-strand cDNA synthesis, the cDNA serves as the template
for an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT is
performed in the presence of biotinylated nucleotides to label the target cRNA. This
method produces approximately 1000-fold to 5000-fold linear amplification of the
input poly(A)+ RNA.

extract_protocol: Total RNA from the vastus lateralis muscle was isolated using the Trizol method (Gibco BRL, Life Technologies, Merelbeke, Belgium). In brief, approximately 0.1 g of muscle tissue was homogenized using an Ultra-Turrax homogenizer (Janke & Kunkel, Germany) in 1 ml Trizol Reagent. The homogenized samples were incubated at room temperature for five minutes and 0.2 ml chloroform was added. After shaking for 15 seconds the samples were incubated at room temperature for 2 minutes. Samples were centrifuged at 12,000 x g for 15 minutes at 4 ºC and the upper aqueous phase was transferred to a fresh tube. 0.5 ml isopropyl alcohol was added to precipitate the RNA. Samples were incubated at room temperature for 10 minutes and centrifuged at 12,000 x g for 10 minutes at 4 ºC. RNA pellet was washed with 75% ethanol and centrifuged at 12,000 x g for 5 minutes at 4 ºC. RNA pellets were briefly dried and dissolved in H2O.

tag: Human vastus lateralis muscle biopsy taken at day 4 of hospitalization for an acute COPD exacerbation


title: Rectal cancer 28

description: Rectal cancer_28


title: T00252622 Vastus lateralis stable COPD

tag: Human vastus lateralis muscle biopsy form stable COPD patient


title: Rectal cancer 18

description: Rectal cancer_18


title: T00252619 vastus lateralis COPD exacerbation


title: T00251333 vastus lateralis stable COPD

source_name: Human vastus lateralis muscle biospy

tag: Human vastus lateralis muscle biopsy from stable COPD patient


title: T00252618 Vastus lateralis stable COPD


title: T00252620 vastus lateralis stable COPD


title: T00251335 vastus lateralis stable COPD


title: Rectal cancer 27

description: Rectal cancer_27


title: Rectal cancer 22

description: Rectal cancer_22


title: Rectal cancer 26

description: Rectal cancer_26


title: Rectal cancer 24

description: Rectal cancer_24


title: T00252617 vastus lateralis COPD exacerbation

source_name: human vastus lateralis muscle biopsy


title: Rectal cancer 23

description: Rectal cancer_23


title: Rectal cancer 17

description: Rectal cancer_17


title: Rectal cancer 16

description: Rectal cancer_16


title: T00252621 vastus lateralis COPD exacerbation


title: Rectal cancer 13

description: Rectal cancer_13


title: Rectal cancer 10

description: Rectal cancer_10


title: Rectal cancer 14

description: Rectal cancer_14


title: Rectal cancer 7

description: Rectal cancer_7


title: Rectal cancer 6

description: Rectal cancer_6


title: Rectal cancer 15

description: Rectal cancer_15


title: Rectal cancer 8

description: Rectal cancer_8


title: Rectal cancer 9

description: Rectal cancer_9


title: Colon cancer descending 23

source_name: Colon cancer descending

value: descending

source_name: Normal colon descending


title: Rectal cancer 11

description: Rectal cancer_11


title: Rectal cancer 5

description: Rectal cancer_5


title: Rectal cancer 4

description: Rectal cancer_4


title: Colon cancer descending 29


title: Rectal cancer 12

description: Rectal cancer_12


title: Rectal cancer 1

description: Rectal cancer_1


title: Colon cancer descending 25


title: Colon cancer descending 24


title: Rectal cancer 2

description: Rectal cancer_2


title: Rectal cancer 3

description: Rectal cancer_3


title: Colon cancer descending 28


title: Colon cancer descending 15


title: Colon cancer descending 27


title: Colon cancer descending 17


title: Colon cancer descending 26


title: Colon cancer descending 20


title: Colon cancer descending 14


title: Colon cancer descending 11


title: Colon cancer descending 6


title: Colon cancer descending 7


title: Colon cancer descending 19


title: Colon cancer descending 22


title: Colon cancer descending 21


title: Colon cancer descending 18


title: Colon cancer descending 5


title: Colon cancer descending 16


title: Colon cancer descending 2


title: Colon cancer descending 13


title: Colon cancer ascending 27

description: Colon cancer_ascending_27

source_name: Colon cancer ascending

value: ascending

source_name: Normal colon ascending


title: Rectal cancer 25

description: Rectal cancer_25


title: Colon cancer descending 10


title: Colon cancer ascending 24

description: Colon cancer_ascending_24


title: Colon cancer ascending 25

description: Colon cancer_ascending_25


title: Colon cancer descending 12


title: Colon cancer ascending 23

description: Colon cancer_ascending_23


title: Colon cancer ascending 21

description: Colon cancer_ascending_21


title: Colon cancer descending 9


title: Colon cancer descending 8


title: Colon cancer ascending 20

description: Colon cancer_ascending_20


title: Colon cancer descending 4


title: Colon cancer descending 3


title: Colon cancer ascending 19

description: Colon cancer_ascending_19


title: Colon cancer ascending 14

description: Colon cancer_ascending_14


title: Colon cancer ascending 22

description: Colon cancer_ascending_22


title: Colon cancer descending 1


title: Colon cancer ascending 11

description: Colon cancer_ascending_11


title: Colon cancer ascending 17

description: Colon cancer_ascending_17


title: Colon cancer ascending 10

description: Colon cancer_ascending_10


title: Colon cancer ascending 26

description: Colon cancer_ascending_26


title: Colon cancer ascending 9

description: Colon cancer_ascending_9


title: Colon cancer ascending 5

description: Colon cancer_ascending_5


title: Colon cancer ascending 18

description: Colon cancer_ascending_18


title: Colon cancer ascending 7

description: Colon cancer_ascending_7


title: Colon cancer ascending 16

description: Colon cancer_ascending_16


title: Colon cancer ascending 8

description: Colon cancer_ascending_8


title: Colon cancer ascending 2

description: Colon cancer_ascending_2


title: Colon cancer ascending 13

description: Colon cancer_ascending_13


title: Colon cancer ascending 15

description: Colon cancer_ascending_15


title: Colon cancer ascending 12

description: Colon cancer_ascending_12


title: Colon cancer ascending 6

description: Colon cancer_ascending_6


title: Sample#11 Tumor DNA

type: genomic

city: Fukuoka

first: DAISUKE

last: KUGA

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

description: SNP array data from microdissected GBM tissue

hyb_protocol: Standard Affymetrix procedures using Fluidics Station 400

scan_protocol: Standard Affymetrix procedures using GeneChip Scanner 3000

data_processing: Raw intensity values were calculated using the dChip software package.

label: biotin

molecule: genomic DNA

source_name: Primary glioblastoma 11

label_protocol: Standard Affymetrix protocol starting from 250 ng of DNA

extract_protocol: Extraction of genomic DNA was performed according to the Qiagen DNeasy kit instructions.

tag: gender

value: F, age :55


title: Sample#12 Tumor DNA

source_name: Primary glioblastoma 12

value: M, age :55


title: Colon cancer ascending 3

description: Colon cancer_ascending_3


title: Colon cancer ascending 4

description: Colon cancer_ascending_4


title: Sample#12 Blood DNA

description: SNP array data from matched blood sample

source_name: Matched blood 12


title: Sample#9 Tumor DNA

source_name: Primary glioblastoma 9

value: M, age :69


title: Colon cancer ascending 1

description: Colon cancer_ascending_1


title: Sample#9 Blood DNA

source_name: Matched blood 9


title: Sample#14 Blood DNA

source_name: Matched blood 14

value: F, age :10


title: Sample#7 Blood DNA

source_name: Matched blood 7

value: F, age :56


title: Sample#4 Blood DNA

source_name: Matched blood 4


title: Sample#11 Blood DNA

source_name: Matched blood 11


title: Sample#6 Blood DNA

source_name: Matched blood 6

value: F, age :73


title: Sample#13 Tumor DNA

source_name: Primary glioblastoma 13

value: M, age :41


title: Sample#3 Blood DNA

source_name: Matched blood 3

value: M, age :65


title: Sample#5 Blood DNA

source_name: Matched blood 5

value: F, age :61


title: Sample#5 Tumor DNA

source_name: Primary glioblastoma 5


title: Sample#7 Tumor DNA

source_name: Primary glioblastoma 7


title: Sample#3 Tumor DNA

source_name: Primary glioblastoma 3


title: Sample#1 Blood DNA

source_name: Matched blood 1


title: Sample#13 Blood DNA

source_name: Matched blood 13


title: Sample#1 Tumor DNA

source_name: Primary glioblastoma 1


title: Sample#10 Tumor DNA

source_name: Primary glioblastoma 10

value: F, age :44


title: Sample#2 Blood DNA

source_name: Matched blood 2

value: M, age :71


title: Sample#2 Tumor DNA

source_name: Primary glioblastoma 2


title: Sample#8 Tumor DNA

source_name: Primary glioblastoma 8

value: F, age :64


title: Sample#14 Tumor DNA

source_name: Primary glioblastoma 14


title: Sample#10 Blood DNA

source_name: Matched blood 10


title: Sample#6 Tumor DNA

source_name: Primary glioblastoma 6


title: Sample#8 Blood DNA

source_name: Matched blood 8


title: Sample#4 Tumor DNA

source_name: Primary glioblastoma 4


title: UIP, biological rep22

status: Public on Feb 20 2009

first: Kazuhisa

last: Konishi

address: 1212 Kaufmann Building  3471 Fifth Ave

department: Pulmonry, Allergy, and Critical Care Medicine

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a lung with usual interstitial pneumonia.

hyb_protocol: Following fragmentation, 1.5 ug of cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Scanner protocol

data_processing: Agilent Feature Extraction

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep22

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

extract_protocol: Trizol extraction of total RNA followed by RNeasy cleanup was performed according to the manufacturers' instructions.

tag: Tissue from a patient with pathological diagnosis of usual interstitial pneumonia.


title: Day 14 liver array #4

city: Raleigh

first: Melissa

last: Ashwell

state: NC

address: Campus Box 7621

institute: North Carolina State University

description: Analysis of RNA from liver tissue extracted from polygenic obese male mice at day 14 of trial.  Each sample (treatment and control) represents pools of either five or four samples.

hyb_protocol: Hybridizations were for 16 hours in a rotating hybridization oven, using the Agilent 60-mer-oligo microarray processing protocol. Slides were subsequently washed with a 6x SSC-0.005% Triton X-102 wash solution for 10 min at room temperature, followed by a second wash with a solution of 0.1x SSC-0.005% Triton X-102 for 5 min. Slides were dried under a nitrogen stream.

scan_protocol: Slides were scanned with an Agilent G2565BA microarray scanner

data_processing: Gene expression data were obtained with the use of Agilent G2567AA Feature Extraction software, using defaults for all parameters except ratio terms, which were changed according to Agilent protocol to fit the direct labeling procedure.

source_name: Treated (Conjugated Linoleic Acid Fed)

label_protocol: Used the Agilent Fluorescent Direct Label kit protocol using 10 micrograms of starting material

extract_protocol: Total RNA was extracted using TriReagent and the Qiagen RNeasy Mini kit

tag: M16 polyobese line of male mice fed CLA for 14 days

source_name: Control (Linoleic Acid Fed)

tag: M16 polyobese line of male mice fed LA for 14 days


title: Day 14 liver array #2

description: Analysis of RNA from liver tissue extracted from polygenic obese male mice at day 14 of trial.  Each sample (treatment and control) represent pools of either five or four samples.


title: UIP, biological rep18

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep18


title: UIP, biological rep19

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep19


title: UIP, biological rep23

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep23


title: UIP, biological rep17

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep17


title: Day 14 liver array #3


title: UIP, biological rep13

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep13


title: UIP, biological rep16

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep16


title: UIP, biological rep10

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep10


title: UIP, biological rep14

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep14


title: UIP, biological rep8

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep8


title: UIP, biological rep11

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep11


title: UIP, biological rep20

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep20


title: UIP, biological rep15

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep15


title: UIP, biological rep5

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep5


title: UIP, biological rep9

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep9


title: UIP, biological rep4

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep4


title: UIP, biological rep21

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep21


title: UIP, biological rep3

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep3


title: UIP, biological rep2

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep2


title: control, biological rep15

description: Lung tissue samples obtained from the University of Pittsburgh Health Sciences Tissue Bank. Gene expression data from a control lung.

source_name: normal lung tissues, control, biological rep15

tag: Normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection.


title: UIP, biological rep7

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep7


title: UIP, biological rep12

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep12


title: Day 14 liver array #1

description: Analysis of RNA from liver tissue extracted from polygenic obese male mice at day 14 of trial.  Each sample (treatment an control) represent pools of either five or four samples.

source_name: Control (Linoleic Acid Fed)

label_protocol: Used the Agilent Flourescent Direct Label kit protocol using 10 micrograms of starting material

tag: M16 polygenic obese male mice fed linoleic acid for 14 days

source_name: Treated (Conjugated Linoleic Acid Fed)

label_protocol: Used the Agilent Flourescent Direct Label kit using 10 micrograms of starting material

tag: M16 polygenic obese male mice fed conjugated linoleic acid for 14 days


title: control, biological rep14

source_name: normal lung tissues, control, biological rep14


title: UIP, biological rep6

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep6


title: UIP, biological rep1

source_name: Lung tissue with usual interstitial pneumonia (UIP), biological rep1


title: control, biological rep13

source_name: normal lung tissues, control, biological rep13


title: control, biological rep9

source_name: normal lung tissues, control, biological rep9


title: control, biological rep5

source_name: normal lung tissues, control, biological rep5


title: control, biological rep10

source_name: normal lung tissues, control, biological rep10


title: control, biological rep6

source_name: normal lung tissues, control, biological rep6


title: control, biological rep4

source_name: normal lung tissues, control, biological rep4


title: control, biological rep2

source_name: normal lung tissues, control, biological rep2


title: control, biological rep8

source_name: normal lung tissues, control, biological rep8


title: control, biological rep7

source_name: normal lung tissues, control, biological rep7


title: 13705738 - gB2 vs MS2

status: Public on Feb 18 2009

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

description: Effect of carnitine on the transcriptome of A. thaliana ?

hyb_protocol: MS2 Cy5 / gB2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: plantlet - media : MS hygrometry : 43% temperature : 24°C light : 150 µmol.m-2.s-1

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - harvest date:24-11-08

treatment_protocol: Name:RS07-01_g-butyrobétaïne - compound based treatment - compound addition,g-butyrobétaïne:quantity 1mM . The butyrobetaine 1 mM is added in the growth media MS. Wild type ecotype columbia 0 are seeded in this media. 3 days of stratification at 4°C to synchronize germination. 7 days of culture. Prelevement at 7 days.


title: control, biological rep12

source_name: normal lung tissues, control, biological rep12


title: 13705735 - MS1 vs gB1

hyb_protocol: gB1 Cy5 / MS1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  - harvest date:17-11-08


title: 13705721 - gB1 vs MS1

hyb_protocol: MS1 Cy5 / gB1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13705743 - MS2 vs gB2

hyb_protocol: gB2 Cy5 / MS2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: control, biological rep3

source_name: normal lung tissues, control, biological rep3


title: HF_LD200_label1_rep2

status: Public on Jan 15 2009

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

hyb_protocol: Microarray hybridisation was performed at the Transcriptome Core Facility of OuestGenopole according to recommended protocols for glass-spotted oligonucleotide microarray.

scan_protocol: Hybridized arrays were scanned at 10 µm/pixel resolution on a ScanArray Express 4000 XL (Packard Bioscience). Image analyses were performed with Genepix Pro 5.0 (Axon Instruments, Union City, CA, USA).

data_processing: Intensities of selected spots were transformed into log (Cy3/Cy5) and data were normalized by both spot and chip by weighted linear regression (LOWESS) method with Genespring GX software (Silicon Genetics, Redwood, CA).

organism: Sus scrofa

source_name: high intramuscular fat, LD200, label1, rep2

label_protocol: Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion)

extract_protocol: Chomczynski and Sacchi, 1987

tag: D116, LD200, 110 kg LW pig, HF group

source_name: reference pool

tag: reference pool composed of an equal amount of RNA isolated from 8 LF samples


title: LF_LD869_rep1

source_name: low intramuscular fat, LD869, rep1

tag: D116, LD869, 110 kg LW pig, LF group


title: HF_LD643_label2_rep2

source_name: high intramuscular fat, LD643, label2, rep2

tag: D116, LD643, 110 kg LW pig, HF group


title: HF_LD874_label2_rep1

source_name: high intramuscular fat, LD874, label2, rep1

tag: D116, LD874, 110 kg LW pig, HF group


title: HF_LD200_label2_rep1

source_name: high intramuscular fat, LD200, label2, rep1


title: LF_LD343_rep2

source_name: low intramuscular fat, LD343, rep2

tag: D116, LD343, 110 kg LW pig, LF group


title: HF_LD253_label2_rep2

source_name: high intramuscular fat, LD253, label2, rep2

tag: D116, LD253, 110 kg LW pig, HF group


title: HF_LD231_label1_rep2

source_name: high intramuscular fat, LD231, label1, rep2

tag: D116, LD231, 110 kg LW pig, HF group


title: control, biological rep1

source_name: normal lung tissues, control, biological rep1


title: LF_LD261_rep1

source_name: low intramuscular fat, LD261, rep1

tag: D116, LD261, 110 kg LW pig, LF group


title: LF_LD869_rep2

source_name: low intramuscular fat, LD869, rep2


title: HF_LD253_label1_rep1

source_name: high intramuscular fat, LD253, label1, rep1


title: LF_LD343_rep1

source_name: low intramuscular fat, LD343, rep1


title: LF_LDN16_rep1

source_name: low intramuscular fat, LDN16, rep1

tag: D116, LDN16, 110 kg LW pig, LF group


title: HF_LD226_label1_rep2

source_name: high intramuscular fat, LD226, label1, rep2

tag: D116, LD226, 110 kg LW pig, HF group


title: LF_LD719_rep1

source_name: low intramuscular fat, LD719, rep1

tag: D116, LD719, 110 kg LW pig, LF group


title: HF_LD226_label1_rep1

source_name: high intramuscular fat, LD226, label1, rep1


title: HF_LD231_label1_rep1

source_name: high intramuscular fat, LD231, label1, rep1

source_name: reference pool


title: HF_LD643_label1_rep1

source_name: high intramuscular fat, LD643, label1, rep1

tag: D116, LD643, 110 kg LW pig, LF group


title: LF_LD224_rep1

source_name: low intramuscular fat, LD224, rep1

tag: D116, LD224, 110 kg LW pig, LF group


title: HF_LD874_label1_rep1

source_name: high intramuscular fat, LD874, label1, rep1


title: LF_LDN16_rep2

source_name: low intramuscular fat, LDN16, rep2


title: LF_LD348_rep1

source_name: low intramuscular fat, LD348, rep1

tag: D116, LD348, 110 kg LW pig, LF group


title: HF_LD200_label1_rep1

source_name: high intramuscular fat, LD200, label1, rep1


title: HF_LD643_label2_rep1

source_name: high intramuscular fat, LD643, label2, rep1


title: HF_LD514_label2_rep1

source_name: high intramuscular fat, LD514, label2, rep1

tag: D116, LD514, 110 kg LW pig, HF group


title: HF_LD514_label1_rep2

source_name: high intramuscular fat, LD514, label1, rep2


title: LF_LD348_rep2

source_name: low intramuscular fat, LD348, rep2


title: LF_LD194_rep1

source_name: low intramuscular fat, LD194, rep1

tag: D116, LD194, 110 kg LW pig, LF group


title: HF_LD226_label2_rep1

source_name: high intramuscular fat, LD226, label2, rep1


title: HF_LD667_label2_rep1

source_name: high intramuscular fat, LD667, label2, rep1

tag: D116, LD667, 110 kg LW pig, HF groups


title: HF_LD231_label2_rep1

source_name: high intramuscular fat, LD231, label2, rep1

tag: reference pool composed of an equal amount of RNA isolated from 8 LF samples


title: HF_LD667_label2_rep2

source_name: high intramuscular fat, LD667, label2, rep2

tag: D116, LD667, 110 kg LW pig, HF group


title: control, biological rep11

source_name: normal lung tissues, control, biological rep11

tag: Normal lung tissues obtained from the disease free margins with normal histology of lung cancer resection.


title: HF_LD874_label2_rep2

source_name: high intramuscular fat, LD874, label2, rep2

tag: D116, LD874, 110 kg LW pig, HF group

source_name: reference pool


title: LF_LD719_rep2

source_name: low intramuscular fat, LD719, rep2


title: HF_LD643_label1_rep2

source_name: high intramuscular fat, LD643, label1, rep2

tag: D116, LD643, 110 kg LW pig, HF group


title: LF_LD261_rep2

source_name: low intramuscular fat, LD261, rep2


title: HF_LD514_label1_rep1

source_name: high intramuscular fat, LD514, label1, rep1


title: LF_LD194_rep2

source_name: low intramuscular fat, LD194, rep2


title: HF_LD667_label1_rep1

source_name: high intramuscular fat, LD667, label1, rep1


title: HF_LD253_label2_rep1

source_name: high intramuscular fat, LD253, label2, rep1

tag: D116, LD253, 110 kg LW pig, HF group


title: HF_LD667_label1_rep2

source_name: high intramuscular fat, LD667, label1, rep2


title: HF_LD200_label2_rep2

source_name: high intramuscular fat, LD200, label2, rep2

tag: D116, LD200, 110 kg LW pig, HF group


title: HF_LD231_label2_rep2

source_name: high intramuscular fat, LD231, label2, rep2

tag: D116, LD231, 110 kg LW pig, HF group


title: HF_LD253_label1_rep2

source_name: high intramuscular fat, LD253, label1, rep2


title: HF_LD874_label1_rep2

source_name: high intramuscular fat, LD874, label1, rep2


title: LF_LD224_rep2

source_name: low intramuscular fat, LD224, rep2


title: HF_LD514_label2_rep2

source_name: high intramuscular fat, LD514, label2, rep2


title: normal liver tissue 4 NL4

status: Public on Dec 31 2008

city: Shanghai

first: JIANREN

last: GU

address: No.25/Ln.2200, Xietu Road,

department: State Key Laboratory of Oncogenes and Related Genes

country: China

institute: Shanghai Cancer Institute, Shanghai Jiao Tong University

description: MicroRNAs expression profile in human hepatocellular carcinoma

hyb_protocol: Labeled RNA was precipitated with 0.3 M sodium acetate and 2.5 volumes ethanol, then resuspended in 15 μl of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. All hybridizations were performed in duplicate.The hybridization was performed at 42°C overnight and then washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Images were scanned with a confocal LuxScanTM scanner and quantified with LuxScan TM software (CapitalBio Corp, Beijing, China).

data_processing: Raw data preprocessing included: local background subtraction, quantile normalization across multiple slides,14 the natural log transformation of expression levels, average of within-slide replicates and technical across-slide replicates. This was performed in R package (version 2.5.0).

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270481/suppl/GSM270481_060217 NL4 Cy3 135-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270481/suppl/GSM270481_060217 NL4 Cy3 135-2.gpr.gz

source_name: normal liver tissue

label_protocol: Four μg of low molecular weight RNA was labeled with 500 ng 5'-phosphate-cytidyl- uridyl-cy3-3' (Dharmacon, Chicago, IL) with 2 units T4 RNA ligase (NEB, Ipswich, MD), and 4 μg of the negative control was added to each miRNA sample. The labeling reaction was performed at 4 for 2 h.

extract_protocol: Small RNA with a miRNA-rich fraction was prepared from tissue samples using miRNA Isolation Kit (Ambion, Austin, TX) according to the manufacturer’s instructions.

tag: normal liver tissue


title: normal liver tissue NL9

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270486/suppl/GSM270486_060311 NL9cy3 197-1 80800.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270486/suppl/GSM270486_060311 NL9cy3 197-2 85 800.gpr.gz


title: normal liver tissue 7 NL7


title: normal liver tissue 5 NL5


title: normal liver tissue 8 NL8

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270485/suppl/GSM270485_060217 NL8 Cy3 138-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270485/suppl/GSM270485_060217 NL8 Cy3 138-2.gpr.gz


title: normal liver tissue 3 NL3


title: normal liver tissue 6 NL6

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270483/suppl/GSM270483_060217 NL6 Cy3 137-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270483/suppl/GSM270483_060217 NL6 Cy3 137-2.gpr.gz


title: 165N, patient 77, corresponding noncancerous liver tissue tissues

source_name: corresponding noncancerous liver tissue

tag: Survival Period

value: more than 45

tag: Pathological stage

value: HCC-III

tag: Cirrhosis

value: no

tag: Metastasis

tag: HBV infection

value: yes

tag: Alcohol abuse


title: 162N, patient 76, corresponding noncancerous liver tissue tissues

value: more than 46


title: 166N, patient 78, corresponding noncancerous liver tissue tissues

tag: AGE

value: HCC-II


title: 160N, patient 75, corresponding noncancerous liver tissue tissues


title: normal liver tissue 2 NL2

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270479/suppl/GSM270479_060217 NL2 Cy3 134-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270479/suppl/GSM270479_060217 NL2 Cy3 134-2.gpr.gz


title: normal liver tissue 1NL1

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270478/suppl/GSM270478_060310 NL1 cy3 193-1.gpr.gz


title: normal liver tissue NL10

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270487/suppl/GSM270487_060311 NL10 Cy3 208-2.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270487/suppl/GSM270487_060311 NL10cy3 208-1 95 900.gpr.gz


title: 1360, Npatient 71, corresponding noncancerous liver tissue tissues

value: more than 53


title: 144N, patient 73, corresponding noncancerous liver tissue tissues


title: HF_LD226_label2_rep2

source_name: high intramuscular fat, LD226, label2, rep2

tag: D116, LD226, 110 kg LW pig, HF group

source_name: reference pool


title: 158N, patient 74, corresponding noncancerous liver tissue tissues


title: 123N, patient 69, corresponding noncancerous liver tissue tissues

value: more than 42


title: 1320, Npatient 70, corresponding noncancerous liver tissue tissues

tag: Survival Period:15


title: 121N, patient 68 , corresponding noncancerous liver tissue tissues


title: 139N, patient 72, corresponding noncancerous liver tissue tissues


title: 114N, patient 65, corresponding noncancerous liver tissue tissues


title: 115N, patient 66, corresponding noncancerous liver tissue tissues


title: 112N, patient 64, corresponding noncancerous liver tissue tissues


title: 111N, patient 63, corresponding noncancerous liver tissue tissues


title: 107N, patient 59, corresponding noncancerous liver tissue tissues

value: more than 68


title: 108N, patient 60, corresponding noncancerous liver tissue tissues

tag: Survival Period:2


title: 106N, patient 58, corresponding noncancerous liver tissue tissues


title: 9N, patient 57, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270456/suppl/GSM270456_060406 9N cy3 009-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270456/suppl/GSM270456_060407 9N cy3 071-1.gpr.gz


title: 43N, patient 48, corresponding noncancerous liver tissue tissues

tag: Survival Period:9


title: 120N, patient 67, corresponding noncancerous liver tissue tissues


title: 51N, patient 49, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270448/suppl/GSM270448_060718 HK51N cy3 107-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270448/suppl/GSM270448_060718 HK51N cy3 107-2.gpr.gz

tag: Survival Period:13.5

value: HCC


title: 109N, patient 61, corresponding noncancerous liver tissue tissues


title: 70N, patient 53, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270452/suppl/GSM270452_060719 HK70N cy3 089-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270452/suppl/GSM270452_060719 HK70N cy3 089-2.gpr.gz


title: 8N, patient 56, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270455/suppl/GSM270455_060407 8N Cy3 057-1 88,850.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270455/suppl/GSM270455_060407 8N Cy3 057-2 85,850.gpr.gz


title: 54N, patient 50, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270449/suppl/GSM270449_060718 HK54N cy3 109-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270449/suppl/GSM270449_060718 HK54N cy3 109-2.gpr.gz

value: HCC II-III


title: 71N, patient 54, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270453/suppl/GSM270453_060719 HK71N cy3 087-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270453/suppl/GSM270453_060719 HK71N cy3 087-2.gpr.gz


title: 42N, patient 47, corresponding noncancerous liver tissue tissues

value: more than 49


title: 110N, patient 62, corresponding noncancerous liver tissue tissues


title: 80N,  patient 55, corresponding noncancerous liver tissue tissues


title: 345N, patient 40, corresponding noncancerous liver tissue tissues


title: 60N, patient 52, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270451/suppl/GSM270451_060718 HK60N cy3 100-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270451/suppl/GSM270451_060718 HK60N cy3 100-2.gpr.gz


title: 344N, patient 39, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270438/suppl/GSM270438_060310 344N Cy3 015-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270438/suppl/GSM270438_060310 344N Cy3 015-2.gpr.gz


title: 347N, patient 42, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270441/suppl/GSM270441_060310 347N Cy3 206-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270441/suppl/GSM270441_060310 347N Cy3 206-2.gpr.gz

value: more than 20


title: 346N, patient 41, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270440/suppl/GSM270440_060704 346N Cy3 015-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270440/suppl/GSM270440_060704 346N Cy3 015-2.gpr.gz


title: 41N, patient 46, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270445/suppl/GSM270445_060630 41N cy3 050-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270445/suppl/GSM270445_060630 41N cy3 050-2.gpr.gz

value: more than 48


title: 343N, patient 38, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270437/suppl/GSM270437_060704 343N Cy3 049-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270437/suppl/GSM270437_060704 343N Cy3 049-2.gpr.gz


title: 341N, patient 37, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270436/suppl/GSM270436_060228 341N Cy3 163-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270436/suppl/GSM270436_060228 341N Cy3 163-2.gpr.gz


title: 340N, patient 36, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270435/suppl/GSM270435_060308 340N Cy3 198-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270435/suppl/GSM270435_060308 340N Cy3 198-2.gpr.gz


title: 56N, patient 51, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270450/suppl/GSM270450_060718 HK56N cy3 097-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270450/suppl/GSM270450_060718 HK56N cy3 097-2.gpr.gz


title: 39N, patient 45, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270444/suppl/GSM270444_060629 39N cy3 063-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270444/suppl/GSM270444_060629 39N cy3 063-2.gpr.gz


title: 338N, patient 34, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270433/suppl/GSM270433_060307 338N Cy3 177-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270433/suppl/GSM270433_060307 338N Cy3 177-2.gpr.gz


title: 35N, patient 43, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270442/suppl/GSM270442_061115 35N CY3 1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270442/suppl/GSM270442_061115 35N CY3 2.gpr.gz


title: 337N, patient 33, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270432/suppl/GSM270432_060630 337N cy3 054-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270432/suppl/GSM270432_060630 337N cy3 054-2.gpr.gz


title: 317N, patient 26, corresponding noncancerous liver tissue tissues


title: 26N, patient 21, corresponding noncancerous liver tissue tissues


title: 321N, patient 29, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270428/suppl/GSM270428_060704 321N Cy3 017-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270428/suppl/GSM270428_060704 321N Cy3 017-2.gpr.gz

value: more than 27


title: 32N, patient 31, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270430/suppl/GSM270430_060629 32N cy3 056-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270430/suppl/GSM270430_060629 32N cy3 056-2.gpr.gz


title: 31N, patient 28, corresponding noncancerous liver tissue tissues


title: 314N, patient 23, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270422/suppl/GSM270422_060120 314N cy3 7013-1 95 950-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270422/suppl/GSM270422_060123 314N 7006-1 cy3 75 700.gpr.gz

value: more than 30


title: 339N, patient 35, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270434/suppl/GSM270434_060307 339N Cy3 186-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270434/suppl/GSM270434_060307 339N Cy3 186-2.gpr.gz

value: more than 23


title: 156N, patient 17, corresponding noncancerous liver tissue tissues


title: 17N, patient 19, corresponding noncancerous liver tissue tissues

tag: Survival Period:17.5


title: 18N, patient 20, corresponding noncancerous liver tissue tissues


title: 316N, patient 25, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270424/suppl/GSM270424_060120 316N cy3 7196-1 99 950.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270424/suppl/GSM270424_060123 316N 7044-1 cy3 75 700.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270424/suppl/GSM270424_060215 316N cy3 126-2.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270424/suppl/GSM270424_060215 316N cy3 128-2.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270424/suppl/GSM270424_060216 316N cy3 129-2.gpr.gz


title: 313N, patient 22, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270421/suppl/GSM270421_060120 313N cy3 7015-1 99 950.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270421/suppl/GSM270421_060120 313Ncy3 7015-1 99 950.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270421/suppl/GSM270421_060123 313N 7001-1 cy3 75 700.gpr.gz


title: 154N, patient 15, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270414/suppl/GSM270414_060921 154N CY3 OP-3041-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270414/suppl/GSM270414_060921 154N CY3 OP-3041-2.gpr.gz

tag: Survival Period:2.5


title: 152N , patient 13, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270412/suppl/GSM270412_060920 152N CY3 OP-4032-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270412/suppl/GSM270412_060920 152N CY3 OP-4032-2.gpr.gz


title: 336N, patient 32, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270431/suppl/GSM270431_060301 336N Cy3 171-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270431/suppl/GSM270431_060301 336N Cy3 171-2.gpr.gz


title: 137N, patient 10, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270409/suppl/GSM270409_060901 137N CY3 063-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270409/suppl/GSM270409_060901 137N CY3 064-1.gpr.gz


title: 134N, patient 7, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270406/suppl/GSM270406_060922 134N CY3 OP-9108-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270406/suppl/GSM270406_060922 134N CY3 OP-9108-2.gpr.gz

tag: SEX

value: male


title: 157N, patient 18, corresponding noncancerous liver tissue tissues


title: 155N, patient 16, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270415/suppl/GSM270415_061101 155N CY3 1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270415/suppl/GSM270415_061101 155N CY3 2.gpr.gz

value: HCC-III


title: 133N,patient 6 , corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270405/suppl/GSM270405_060907 133N CY3 7082-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270405/suppl/GSM270405_060907 133N CY3 7082-2.gpr.gz

value: more than 56


title: 136N, patient 9, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270408/suppl/GSM270408_061108 136N CY3 1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270408/suppl/GSM270408_061108 136N CY3 2.gpr.gz

value: more than54

value: no

value: yes


title: 315N, patient 24, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270423/suppl/GSM270423_060123 315N 7043-1 cy3 75 700.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270423/suppl/GSM270423_060215 315N cy3 126-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270423/suppl/GSM270423_060215 315N cy3 128-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270423/suppl/GSM270423_060216 315N cy3 129-1.gpr.gz


title: 135N, patient 8, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270407/suppl/GSM270407_060922 135N CY3 OP-9110-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270407/suppl/GSM270407_060922 135N CY3 OP-9110-2.gpr.gz

value: HCC-II


title: 318N, patient 27, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270426/suppl/GSM270426_060630 318N cy3 052-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270426/suppl/GSM270426_060630 318N cy3 052-2.gpr.gz


title: 323N, patient 30, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270429/suppl/GSM270429_060301 323N Cy3 165-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270429/suppl/GSM270429_060308 323N Cy3 200-2.gpr.gz

value: more than 26


title: 132N,patient 5, corresponding noncancerous liver tissue tissues

value: more than 58


title: 153N, patient 14, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270413/suppl/GSM270413_060921 153N CY3 OP-3030-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270413/suppl/GSM270413_060921 153N CY3 OP-3030-2.gpr.gz


title: 138N, patient 11, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270410/suppl/GSM270410_061031 138N CY3 1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270410/suppl/GSM270410_061031 138N CY3 2.gpr.gz


title: 14N, patient 12, corresponding noncancerous liver tissue tissues


title: 38N, patient 44, corresponding noncancerous liver tissue tissues


title: 162K, patient 76, HCC tissues

source_name: primary liver cancer

value: more than 46


title: 128N, patient2 , corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270401/suppl/GSM270401_060919 128N CY3 OP-4033-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270401/suppl/GSM270401_060919 128N CY3 OP-4033-2.gpr.gz


title: 131N,  patient4 , corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270403/suppl/GSM270403_061101 131N CY3 1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270403/suppl/GSM270403_061101 131N CY3 2.gpr.gz

value: more than 57


title: 165K, patient 77, HCC tissues

value: more than 45


title: 130N, patient 3, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270402/suppl/GSM270402_060915 130N CY3 op-3035-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270402/suppl/GSM270402_060915 130N CY3 op-3035-2.gpr.gz


title: 160K, patient 75, HCC tissues


title: 166K, patient 78, HCC tissues


title: 1320, Kpatient 70, HCC tissues


title: 158K, patient 74, HCC tissues


title: 144K, patient 73, HCC tissues


title: 139K, patient 72, HCC tissues


title: 114K, patient 65, HCC tissues


title: 115K, patient 66, HCC tissues


title: 120K, patient 67, HCC tissues


title: 111K, patient 63, HCC tissues


title: 123K, patient 69, HCC tissues

value: more than 42


title: 112K, patient 64, HCC tissues


title: 121K, patient 68 , HCC tissues


title: 106K, patient 58, HCC tissues


title: 127N, patient 1, corresponding noncancerous liver tissue tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270400/suppl/GSM270400_060914 127N CY3  OP-3047-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270400/suppl/GSM270400_060914 127N CY3  OP-3047-2.gpr.gz


title: 110K, patient 62, HCC tissues

value: HCC II-III


title: 107K, patient 59, HCC tissues

value: more than 68


title: 8K, patient 56, HCC tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270377/suppl/GSM270377_060407 8K Cy3 058-1 88,850.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270377/suppl/GSM270377_060407 8K Cy3 058-2 85,850.gpr.gz


title: 108K, patient 60, HCC tissues


title: 109K, patient 61, HCC tissues


title: 70K, patient 53, HCC tissues

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270374/suppl/GSM270374_060719 HK70K cy3 090-1.gpr.gz

supplemental_files: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM270nnn/GSM270374/suppl/GSM270374_060719 HK70K cy3 090-2.gpr.gz

value: HCC