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Platform GPL2677 Query DataSets for GPL2677
Status Public on Jul 28, 2005
Title Human Array 1.0
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Homo sapiens
Manufacturer C.R.I.B.I. Biotechnology Center (University of Padova)
Manufacture protocol 2688 different cDNA inserts were PCR amplified directly from bacterial cultures. Bacterial clones were inoculated in 96-well, 2 ml Assay Block (Corning), containing 600 µl LB/Ampicillin (50 µl /ml) and incubated at 37 °C for 16 hrs. Approximately 1µl of culture suspension was transferred in 96 well plate (Corning), loaded in each single well with 100 µl of the following solution: 1X PCR buffer, 1.5 mM MgCl2, 0.15 mM for each of the four dNTPs, 0.2 µM for each of primer A and B, 0.02U/µl of Taq Polimerase (New England Biolabs). PCR buffer and unincorporated nucleotides were removed by filtering through 96-well multiscreen filter plates (Millipore, Bedford, MA, USA). The purification protocol was automated using the 96 channel robotic workstation Multimek (Beckman) to avoid errors due to the manual handling of large number of samples. Quality control and quantification of the amplified products was done by separation of 3 µl samples on agarose gels containing EtBr and gel image analysis with Chemi Doc UV transilluminator equipped with the Quantity One software (Bio-Rad, Hercules, CA, USA). PCR products were then lyophilized and plates were sealed using thermowell sealers (Corning) and stored at –20°C. For microarray printing, PCR products were dissolved in 15 µl of Micro Spotting Solution (ArrayIt, Telechem, Sunnyvale, CA, USA) by vigorous shaking of plates for 4-5 hrs at 4°C, and transferred in 384 well plates. Spotting was performed using the robotic system Genpak Array 21 (Genetix, Hampshire, UK) equipped with 32 Stealth Micro Spotting Pins SMP 3B (ArrayIt) settled to obtain spots with an average diameter of 120 µm. Samples were spotted in duplicate on derivatized glass slides (MICROMAX Glass Slides: SuperChip™ I, PerkinElmer, Wellesley, MA, USA) to obtain more consistent fluorescence measures. Spotting was performed at 50% relative humidity to obtain the best spot morphology and to reduce the plate evaporation. Microarrays were then processed in a UV cross linker (Stratagene, La Jolla, CA, USA) (total power of 300 mJoules) for the binding the DNA to the slides. Microarrays were finally processed to remove any unbound PCR product, dried and stored under vacuum at room temperature in sealed boxes.
Support glass
Coating aminosilane
 
Description Human Array 1.0 was constructed arraying on glass slides PCR-amplified cDNAs obtained from our archive of recombinant bacterial clones. This archive consists of 2688 different cDNA clones collected after systematic sequencing of human skeletal muscle cDNA libraries that contain only the 300-500 bp long 3’-portions of muscle transcripts.
 
Web link http://microcribi.cribi.unipd.it/
Contributor(s) Campanaro S, Pacchioni B, Trevisan S, Laveder P, De Pittà C, Lanfranchi G
Citation(s) 12471055
Submission date Jul 27, 2005
Last update date Oct 28, 2005
Contact name Gerolamo Lanfranchi
E-mail(s) stefano.cagnin@unipd.it
Phone +39-0498276219
Organization name University of Padova
Department CRIBI - Biotechnology Center and Biology Department
Lab Functional Genomics Lab
Street address Via U. Bassi, 58/B
City Padova
ZIP/Postal code 35131
Country Italy
 
Samples (16) GSM66023, GSM66024, GSM66025, GSM66026, GSM66027, GSM66028 
Series (2)
GSE3014 The Ankrd2, Cdkn1c and Calcyclin Genes are Under the Control of MyoD During Myogenic Differentiation
GSE3022 Gene expression profiling in dysferlinopathies using a dedicated muscle microarray

Data table header descriptions
ID
Array Row array row position in Human Array 1.0
Array Column array column position in Human Array 1.0
Row row probe position in sub-array
Column column probe position in sub-array
Name cDNA identifier at CRIBI
GB_ACC GenBank accession number
SPOT_ID
Description cDNA probe description

Data table
ID Array Row Array Column Row Column Name GB_ACC SPOT_ID Description
1 1 4 1 20 1-001A01 NM_001020 Homo sapiens ribosomal protein S16 (RPS16), mRNA
2 1 4 11 20 1-001A01 NM_001020 Homo sapiens ribosomal protein S16 (RPS16), mRNA
3 3 4 1 20 1-001A02 NM_001824 Homo sapiens creatine kinase, muscle (CKM), mRNA
4 3 4 11 20 1-001A02 NM_001824 Homo sapiens creatine kinase, muscle (CKM), mRNA
5 1 4 2 20 1-001A03 NM_002046 Homo sapiens glyceraldehyde-3-phosphate dehydrogenase (GAPD), mRNA
6 1 4 12 20 1-001A03 NM_002046 Homo sapiens glyceraldehyde-3-phosphate dehydrogenase (GAPD), mRNA
7 3 4 2 20 1-001A04 NM_000432 Homo sapiens myosin, light polypeptide 2, regulatory, cardiac, slow (MYL2), mRNA
8 3 4 12 20 1-001A04 NM_000432 Homo sapiens myosin, light polypeptide 2, regulatory, cardiac, slow (MYL2), mRNA
9 1 4 3 20 1-001A05 NM_003673 Homo sapiens titin-cap (telethonin) (TCAP), mRNA
10 1 4 13 20 1-001A05 NM_003673 Homo sapiens titin-cap (telethonin) (TCAP), mRNA
11 3 4 3 20 1-001A06 NM_001927 Homo sapiens desmin (DES), mRNA
12 3 4 13 20 1-001A06 NM_001927 Homo sapiens desmin (DES), mRNA
13 1 4 4 20 1-001A07 NM_000517 Homo sapiens alpha one globin (HBA1) mRNA, complete cds
14 1 4 14 20 1-001A07 NM_000517 Homo sapiens alpha one globin (HBA1) mRNA, complete cds
15 3 4 4 20 1-001A08 NM_144617 Homo sapiens mRNA for HEAT-SHOCK 20 KD LIKE-PROTEIN P20, patent sequence AX013767 (bladder), probable alpha crystallin chain b (AC002398) , Telethon(ItalyB41)HSPD00019_FL151
16 3 4 14 20 1-001A08 NM_144617 Homo sapiens mRNA for HEAT-SHOCK 20 KD LIKE-PROTEIN P20, patent sequence AX013767 (bladder), probable alpha crystallin chain b (AC002398) , Telethon(ItalyB41)HSPD00019_FL151
17 1 4 5 20 1-001A09 NM_005205 Homo sapiens cytochrome c oxidase subunit VIa polypeptide 2 (COX6A2), mRNA
18 1 4 15 20 1-001A09 NM_005205 Homo sapiens cytochrome c oxidase subunit VIa polypeptide 2 (COX6A2), mRNA
19 3 4 5 20 1-001A10 NM_001100 Homo sapiens actin, alpha 1, skeletal muscle (ACTA1), mRNA
20 3 4 15 20 1-001A10 NM_001100 Homo sapiens actin, alpha 1, skeletal muscle (ACTA1), mRNA

Total number of rows: 5376

Table truncated, full table size 594 Kbytes.






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