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Series GSE61737 Query DataSets for GSE61737
Status Public on Sep 25, 2014
Title Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation
Organism Agrobacterium fabrum str. C58
Experiment type Expression profiling by genome tiling array
Summary This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery.
A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once.
The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky.
Validations are performed by subjecting Agrobacterium tumefaciens C58 under various growth conditions and then using the tling microarrays to verify expected gene expression patterns.
Overall design Agrobacterium tumefaciens C58 was grown under 10 different conditions: a standard condition and 9 stressful conditions. 2 replications were measured for each condition.
Contributor(s) Cho H, Chou H
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Submission date Sep 24, 2014
Last update date Sep 26, 2014
Contact name Hui-Hsien Chou
Phone 515-294-9242
Organization name Iowa State University
Department Genetics, Development and Cell Biology
Lab Complex Computation Lab
Street address 503 Science II
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
Platforms (1)
GPL19222 NimbleGen Agrobacterium tumefaciens C58 72K x 4 array v1.0
Samples (20)
GSM1512005 Agrobacterium tumefaciens C58_standard_condition_rep1
GSM1512006 Agrobacterium tumefaciens C58_standard_condition_rep2
GSM1512007 Agrobacterium tumefaciens C58_under_ColdShock_rep1
This SubSeries is part of SuperSeries:
GSE61738 Prokaryote whole-genome tiling microarray design and validation
BioProject PRJNA261977

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
GSE61737_Normalized_data_with_annotation.txt.gz 5.8 Mb (ftp)(http) TXT
GSE61737_RAW.tar 27.1 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table
Processed data are available on Series record

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