BMC Genomics
Volume 9

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Kumar V
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Bailey MJ
Thomas TL
Cassone VM

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Thomas TL
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Research article

Circadian genomics of the chick pineal gland in vitro

Stephen P Karaganis¹ , Vinod Kumar² , Phillip D Beremand¹ , Michael J Bailey³ , Terry L Thomas¹ and Vincent M Cassone¹

¹Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA

²Department of Zoology, University of Lucknow, Lucknow 226007, India

³Department of Poultry Science, Texas A&M University, College Station, TX 77843-3258, USA

author email corresponding author email

BMC Genomics 2008, 9:206doi:10.1186/1471-2164-9-206


Published:	3 May 2008

Additional files

Additional file 1:

Rhythmic transcripts (t-test analysis). This file lists gene transcripts determined to be rhythmic using t-test analysis. Separate tabs contain lists of gene transcripts which exhibit rhythm amplitudes of at least 1.5-fold or 2-fold in either LD or DD. Lists are presented as two columns of data displaying each clone ID and associated reference number as listed in the Texas A&M Biology Department's Laboratory for Functional Genomics chicken pineal database [32]. Data are listed in alphabetical order by clone ID.

Format: XLS Size: 83KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Rhythmic transcripts (ANOVA). This file lists gene transcripts determined to be rhythmic using ANOVA. Separate tabs contain lists of gene transcripts which exhibit rhythm amplitudes of at least 1.5-fold or 2-fold in either LD or DD. Lists are presented as two columns of data displaying each clone ID and associated reference number. Data are listed in alphabetical order by clone ID.

Format: XLS Size: 44KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Functional clustering of rhythmic transcripts. This file lists functional categorizations of non-redundant gene transcripts determined to be rhythmic using t-test analysis. Separate tabs contain lists of gene transcripts which rhythmic in either LD or DD. Lists are presented as two columns of data displaying each clone ID and functional cluster. Data are listed in alphabetical order by clone ID.

Format: XLS Size: 46KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

Light regulated transcripts. This file lists gene transcripts regulated by 6-hour exposure to light. Separate tabs contain lists of gene transcripts that were upregulated or downregulated at least 1.5-fold or 2-fold at either CT6 or CT18. Lists are presented as two columns of data displaying each clone ID and associated reference number. Data are listed in alphabetical order by clone ID.

Format: XLS Size: 39KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

NE regulated transcripts. This file lists gene transcripts regulated by 6-hour exposure to norepinephrine. Separate tabs contain lists of gene transcripts that were upregulated or downregulated at least 1.5-fold or 2-fold at either CT6 or CT18. Lists are presented as two columns of data displaying each clone ID and associated reference number. Data are listed in alphabetical order by clone ID.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 6:

Comparative analysis. This file contains non-overlapping unigene lists, clustered as follows: LD: rhythmic genes with at least 1.5-fold amplitude mRNA expression in LD; DD: rhythmic genes with at least 1.5-fold amplitude mRNA expression in DD; Light: gene mRNA regulated at least 1.5-fold by light; NE: gene mRNA regulated at least 1.5-fold by norepinephrine. Data are listed in alphabetical order by clone ID. Genes for which returned no blast hit was returned are listed by reference number.

Format: XLS Size: 49KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 7:

Candidate genes. This file contains a brief discussion of several candidate genes from the genomics screen.

Format: DOC Size: 34KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional file 8:

Primer sequences. This table lists primer sequences for all qPCR targets.

Format: DOC Size: 34KB Download file

This file can be viewed with: Microsoft Word Viewer