title: post-transplantation for sample 9

status: Public on Feb 13 2008

type: protein

city: Stanford

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

hyb_protocol: 1. Add 5 ml serum diluted (1:500) in PBST Probing Buffer at the indented numeral end of the 4-chamber incubation tray without touching the array surface. Allow the serum to flow across the array surface. Avoid pipetting serum directly onto the array surface. 2. Incubate the tray for 90 minutes at 4ºC on a shaker set at 50 rpm (circular shaking). 3. Aspirate the serum using vacuum or pipette as described on the previous page (Step 5). 4. Wash each array with 5 ml PBST Probing Buffer with gentle shaking on a shaker set at 50 rpm for 5 minutes at room temperature. Aspirate the PBST Probing Buffer as described on the previous page (Step 5). 5. Repeat Step 4 four more times using fresh PBST Probing Buffer each time to obtain a total of 5 wash steps. 6. During the wash steps, mix 2.5 μl Alexa Fluor® 647 goat anti-human IgG antibody (secondary antibody) with 5 ml PBST Probing Buffer per array to obtain a final antibody concentration of 1 μg/ml. Store on ice until use. 7. Add 5 ml Alexa Fluor® 647 antibody solution from Step 6 to the incubation tray at the indented numeral end of the tray without touching the array surface. Allow the solution to flow across the array surface. Avoid pipetting solution directly onto the array surface. 8. Incubate the tray for 90 minutes at 4ºC on a shaker set at 50 rpm (circular shaking). 9. Aspirate the antibody solution. 10. Wash each array with 5 ml PBST Probing Buffer with gentle shaking on a shaker set at 50 rpm for 5 minutes at room temperature. Aspirate the PBST Probing Buffer. 11. Repeat Step 10 four more times using fresh PBST Probing Buffer each time to obtain a total of 5 wash steps. 12. Proceed immediately to Drying the Microarray.

scan_protocol: The scanning time for each array is ~7-8 minutes. 1. Start the appropriate array acquisition and analysis software on the computer connected to the fluorescence microarray scanner. 2. Open the microarray enclosure on the scanner. 3. Place the ProtoArray® Microarray in the holder such that the nitrocellulosecoated side of the array faces the laser source and barcode on the array is closest to the outside of the instrument. 4. Close the microarray enclosure on the scanner. 5. Set the following settings to image the microarray: • Wavelength: 635 nm • PMT Gain: 600 • Laser Power: 100% • Pixel Size: 10 μm • Lines to Average: 1.0 • Focus Position: 0 μm 6. Preview the microarray. Adjust settings, if needed. Scan the microarray in detail and include the barcode for record 7. Save the image to a suitable location as ‘multi-image TIFF’ file. Remove the microarray from the scanner. 8. Proceed to downloading lot-specific information available on the ProtoArray® Central Portal, next page. GenePix® Pro microarray data acquisition software. Adjust the subarray grid to ensure the grid is in proper location for each subarray. After the grid is properly adjusted and all features are aligned, utilize the automatic spot finding functionalities of the image acquisition software program, if desired. Then, acquire the pixel intensity data for each feature by clicking the Analyze button in GenePix® Pro, and save/export the results as a .GPR (GenePix® Results) file.

data_processing: VALUE = Signal - Background

label: Alexa Fluor 647

molecule: protein

source_name: serum sample after kidney allograft transplantation

label_protocol: Add 5 ml Alexa Fluor® 647 (secondary) antibody solution to the incubation tray at the indented numeral end of the tray without touching the array surface. Allow the solution to flow across the array surface. Avoid pipetting solution directly onto the array surface

extract_protocol:
1. Draw 4.5 mL of blood into red top tubes
2. Let stand for 30 minutes until clot is formed
3. Centrifuge the tube for 5 minutes at 2000g using a swing-out rotor or other non-desk top centrifuge
4. Transfer (pipette) the clear supernatant (serum) carefully without disturbing the clot, to a 5 mL labeled cryotube

tag: sex

value: female


title: pre-transplantation for sample 29

first: Li

last: Li

state: CA

country: USA

organism: Homo sapiens

source_name: serum sample before kidney allograft transplantation

value: male


title: pre-transplantation for sample 7


title: post-transplantation for sample 8


title: pre-transplantation for sample 9


title: Cerebellar granular layer, biological rep 1

status: Public on Feb 24 2008

type: RNA

city: Lawrence

first: Xinkun

last: Wang

state: KS

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

description:
total RNA extracted from neurons collected from brain cryosections
Fisher 344/BN F1, 6-month-old

hyb_protocol: standard

scan_protocol: standard

data_processing: Affymetrix MAS 5.0 default processing, all chips scaled to the same target value of 500.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Cerebellar granular layer

label_protocol: two-cycle target labeling

extract_protocol: standard

tag: tissue

value: Cerebellar granular layer

tag: biological rep

tag: strain

value: Fisher 344/BN

tag: hybrid

tag: age


title: post-transplantation for sample 6


title: pre-transplantation for sample 23


title: pre-transplantation for sample 24


title: post-transplantation for sample 5


title: post-transplantation for sample 28


title: post-transplantation for sample 24


title: pre-transplantation for sample 8


title: post-transplantation for sample 7


title: post-transplantation for sample 23


title: post-transplantation for sample 20


title: Day14 BM45 #2

status: Public on Jul 01 2008

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Standard Affymetrix Procedure

scan_protocol: Standard Affymetrix Procedure

data_processing: Standard Affymetrix Procedure, MAS5.0

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Day14 BM45

label_protocol: Standard Affymetrix Procedure

extract_protocol: Hot Phenol Method

tag: replicate

tag: time

value: Day 14 of fermentation


title: post-transplantation for sample 16


title: pre-transplantation for sample 20


title: pre-transplantation for sample 17


title: post-transplantation for sample 12


title: pre-transplantation for sample 12


title: pre-transplantation for sample 14


title: post-transplantation for sample 15


title: pre-transplantation for sample 15


title: pre-transplantation for sample 28


title: post-transplantation for sample 11


title: pre-transplantation for sample 11


title: post-transplantation for sample 17


title: pre-transplantation for sample 16


title: post-transplantation for sample 14


title: post-transplantation for sample 3


title: pre-transplantation for sample 1

description: none.


title: post-transplantation for sample 29


title: pre-transplantation for sample 5


title: pre-transplantation for sample 6

description: none.


title: post-transplantation for sample 1

description: none.


title: pre-transplantation for sample 3