NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE11300 Query DataSets for GSE11300
Status Public on Oct 01, 2008
Title Genome-Wide Microarray Analysis Reveals Massive Changes in Gene Expression During Conjugation in Tetrahymena thermophila
Organism Tetrahymena thermophila
Experiment type Expression profiling by array
Summary A genome wide microarray platform containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila is described, validated and used to study gene expression in growing, starved and conjugating cells. Of the ~27,400 predicted open reading frames in Tetrahymena, transcripts homologous to 5876 are not detectable in one or more of these life cycle stages, indicating that this organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels 5X background and 95 genes are expressed at 250X background in all stages. Transcripts homologous to 94 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, and 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1073 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the previously described developmental stages of meiosis, nuclear differentiation and DNA elimination. Genes encoding proteins known to be complexed show similar expression patterns, indicating that co-ordinate expression with putative genes of known function should identify new genes with related functions.
Keywords: growth (three cell densities); Starvation (seven time points); Conjugation (ten time points)
 
Overall design For growth, CU428 cells at low, medium and high cell densities (~100Kcells/ml, ~350Kcells/ml and ~1000Kcells/ml; referred to as L-l, L-m and L-h) were collected.
For starvation, CU428 cells were starved at 2x105 cells/ml in 10 mM Tris (pH 7.5) for 3, 6, 9, 12, 15 and 24 hours (referred to as S-0, S-3, S-6, S-9, S-12, S-15 and S-24.
For conjugation, B2086 and CU428 cells that had been starved for 18 hours were resuspended in 10 mM Tris (pH 7.5) at 2x105 cells/ml, mixed, and samples were collected at 2, 4, 6, 8, 10, 12, 14, 16, 18 hours after the mixture (referred to as C-0, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18).
For each growing and starved Tetrahymena sample, hybridizations were performed on three independent microarrays (e.g. L1, L2 and L3; S1, S2 and S3). For analysis of conjugation, hybridizations were performed on two independent microarrays (e.g. C1 and C2).
Each individual microarray represents a separate experiment; total RNA was isolated from independent cell cultures then independently labeled and hybridized.
 
Contributor(s) Miao W, Xiong J, Bowen J, Gorovsky M
Citation(s) 21637855, 20977778, 19204800
Submission date Apr 29, 2008
Last update date Aug 28, 2019
Contact name Martin Gorovsky
E-mail(s) goro@mail.rochester.edu
Phone 585 275-6988
Fax 585 275-2070
Organization name University of Rochester
Department Department of Biology
Street address Hutchison Hall 432
City Rochester
State/province NY
ZIP/Postal code 14627
Country USA
 
Platforms (1)
GPL6759 Tetrahymena thermophila genome-wide oligonucleotide microarray
Samples (50)
GSM283687 Tetrahymena_L1-l
GSM283690 Tetrahymena_L1-m
GSM283691 Tetrahymena_L1-h
Relations
BioProject PRJNA106605

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11300_RAW.tar 22.1 Mb (http)(custom) TAR
GSE11300_Raw_C1_Samples.txt.gz 12.2 Mb (ftp)(http) TXT
GSE11300_Raw_C2_Samples.txt.gz 12.2 Mb (ftp)(http) TXT
GSE11300_Raw_L1_Samples.txt.gz 5.1 Mb (ftp)(http) TXT
GSE11300_Raw_L2_Samples.txt.gz 5.2 Mb (ftp)(http) TXT
GSE11300_Raw_L3_Samples.txt.gz 5.1 Mb (ftp)(http) TXT
GSE11300_Raw_S1_Samples.txt.gz 9.2 Mb (ftp)(http) TXT
GSE11300_Raw_S2_Samples.txt.gz 9.2 Mb (ftp)(http) TXT
GSE11300_Raw_S3_Samples.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.