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| Status |
Public on Feb 19, 2018 |
| Title |
BloodGT136 |
| Sample type |
genomic |
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| Source name |
wild
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| Organism |
Parus major |
| Characteristics |
tissue: blood
Sex: female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole blood samples were stored in either 1 ml Cell Lysis Solution (Gentra Puregene Kit, Qiagen, USA) or Queens buffer. DNA was extracted by using the FavorPrep 96-Well Genomic DNA Extraction Kit (Favorgen Biotech corp.). DNA quality and DNA concentration were measured on a Nanodrop 2000 (Thermo Scientific).
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| Label |
Biotin
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| Label protocol |
As per manufacturer (Affymetrix)
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| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
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| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
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| Description |
DishQualityControl 0.998
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| Data processing |
A total of 3.116 great tits were genotyped using a custom made Affymetrix® great tit 650K SNP chip at Edinburgh Genomics (Edinburgh, United Kingdom). SNP calling was done following the Affymetrix® best practices workflow by using the Axiom® Analysis Suite 1.1.
The processed data file "SamValuesAll.txt" includes the Genotype Call (SNP call): AA (0), AB (1), BB (2), and NoCall (3); Columns with header 'A' or 'B' represent the raw signal intensity from the probes targeting each allele (i.e. A and B).
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| Submission date |
Oct 18, 2017 |
| Last update date |
Feb 19, 2018 |
| Contact name |
Veronika Laine |
| E-mail(s) |
v.laine@nioo.knaw.nl
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| Organization name |
NIOO-KNAW
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| Department |
Animal Ecology
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| Street address |
Droevendaalsesteeg 10
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| City |
Wageningen |
| ZIP/Postal code |
6708 PB |
| Country |
Netherlands |
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| Platform ID |
GPL24144 |
| Series (1) |
| GSE105131 |
Affymetrix SNP array data for wild Dutch great tits (Parus major) |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM2819954_GT1885.CEL.gz |
12.4 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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