GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE2218

Query DataSets for GSE2218

Status

Public on May 31, 2005

Title

Changes in transcript abundance and association with large polysomes in response to hypoxia stress

Organism

Arabidopsis thaliana

Experiment type

Expression profiling by array

Summary

7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes.

TABLE 1 - Comparison between transcript abundance in non-stress and hypoxia-stress conditions.

TABLE 2 - Comparison between transcript abundance in large polysome complexes (5 or more ribosomes per mRNA) in non-stress and 12 hypoxia-stress conditions.

TABLE 3 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under non-stress conditions. Raw data (not normalized)

TABLE 4 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under 12h of hypoxia-stress. Raw data (not normalized)

Keywords: time-course

Contributor(s)

Branco-Price C, Kawaguchi R, Ferreira RB, bailey-Serres J

Citation(s)

16081496

Submission date

Jan 31, 2005

Last update date

Aug 28, 2018

Contact name

Cristina Branco-Price

E-mail(s)

[email protected]

Phone

951 827 6276

Fax

951 827 4437

Organization name

University of California, Riverside

Department

Botany and Plant Sciences

Lab

Julia Bailey-Serres

Street address

2215 batchelor Hall

City

Riverside

State/province

ZIP/Postal code

92521

Country

USA

Platforms (1)

GPL198

[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array

Samples (4)

More...

GSM40552	Total RNA, non-stressed
GSM40553	Total RNA - hypoxia stress
GSM40554	Polysomal mRNA, non-stress

Relations

BioProject

PRJNA91467

TABLE 1: Change in Total mRNA abundance in response to hypoxia header descriptions
ID_REF	Probeset on Affymetrix GeneChip Arabidopsis ATH1 Genome Array
VALUE	Log2 of signal ratio (signal_HS: signal_NS): SLR
Change	Increase (I), decrease (D) or no-change (NC)
Change p-value	statistical value that validates change call
Descriptions	gene annotation

Data table
ID_REF	VALUE	Change	Change p-value	Descriptions
AFFX-BioB-5_at	-0.2	NC	0.975915	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_at	-0.3	NC	0.967223	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_at	-0.3	NC	0.91689	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioC-5_at	-0.1	NC	0.626498	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_at	-0.4	NC	0.937277	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_at	-0.3	D	0.999243	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_at	-0.3	D	0.999724	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-5_at	-0.2	D	0.995951	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-3_at	0	NC	0.5	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-DapX-5_at	0.2	NC	0.373502	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-M_at	0.4	NC	0.5	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-3_at	-0.8	NC	0.836757	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-5_at	0.8	NC	0.229871	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-M_at	0.4	NC	0.163243	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-3_at	0	NC	0.5	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-5_at	0.4	NC	0.5	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-M_at	0.3	NC	0.5	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-3_at	0.2	NC	0.28164	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-5_at	0.2	NC	0.425368	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-M_at	0.5	NC	0.042672	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

Total number of rows: 22810

Table truncated, full table size 2360 Kbytes.

TABLE 2: Change in Large Polysome RNA abundance in response to hypoxia header descriptions
ID_REF	Probeset on Affymetrix GeneChip Arabidopsis ATH1 Genome Array
VALUE	Log2 of signal ratio (polysomal RNA HS : polysomal RNA NS): SLR
Change	Increase (I), decrease (D) or no-change (NC)
Change p-value	statistical value that validates change call
Descriptions	gene annotation

Data table
ID_REF	VALUE	Change	Change p-value	Descriptions
AFFX-BioB-5_at	0.3	NC	0.5	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_at	0.5	I	0.000009	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_at	0.4	NC	0.008999	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioC-5_at	0.3	NC	0.012832	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_at	0.4	I	0.000005	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_at	0.4	I	0.000001	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_at	0.2	NC	0.0873	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-5_at	0.3	I	0.000003	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-3_at	0.3	I	0.000001	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-DapX-5_at	0	NC	0.333554	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-M_at	0.1	NC	0.5	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-3_at	0.2	NC	0.542816	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-5_at	0	NC	0.548143	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-M_at	0.5	NC	0.075186	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-3_at	1.2	NC	0.5	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-5_at	0.4	NC	0.010768	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-M_at	0.4	NC	0.066107	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-3_at	-0.1	NC	0.221792	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-5_at	0.3	NC	0.103208	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-M_at	1.1	NC	0.441229	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

Total number of rows: 22810

Table truncated, full table size 2360 Kbytes.

TABLE 3: Polysome Loading under non-stress conditions header descriptions
ID_REF	Probeset on Affymetrix GeneChip Arabidopsis ATH1 Genome Array
VALUE	Log2 signal ratio (Polysomal RNA non-stress: Total RNA non-stress): SLR
Change	Increase (I), decrease (D) and no-change (NC)
Change p-value	statistical value that validates change call
Descriptions	gene annotation

Data table
ID_REF	VALUE	Change	Change p-value	Descriptions
AFFX-BioB-5_at	-0.5	D	0.999999	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_at	-0.8	D	1	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_at	-0.6	D	0.999998	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioC-5_at	-0.4	D	1	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_at	-0.7	D	1	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_at	-0.6	D	1	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_at	-0.6	D	1	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-5_at	-0.5	D	1	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-3_at	-0.5	D	1	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-DapX-5_at	0.2	NC	0.5	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-M_at	-0.7	NC	0.980134	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-3_at	-1.2	NC	0.849661	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-5_at	-0.1	NC	0.141119	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-M_at	-0.1	NC	0.290785	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-3_at	-4.5	NC	0.937277	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-5_at	-0.4	NC	0.935602	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-M_at	-0.2	NC	0.957328	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-3_at	0.3	NC	0.5	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-5_at	-0.3	NC	0.793869	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-M_at	0	NC	0.409628	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

Total number of rows: 22810

Table truncated, full table size 2359 Kbytes.

TABLE 4: Polysome loading in response to 12h hypoxia stress header descriptions
ID_REF	Probeset on Affymetrix GeneChip Arabidopsis ATH1 Genome Array
VALUE	Log2 signal ratio (Polysomal mRNA_hypoxia stress: Total mRNA_hypoxia stress): SLR
Change	Increase (I), decrease (D) or no-change (NC)
Change p-value	statistical value that validates change call
Descriptions	gene annotation

Data table
ID_REF	VALUE	Change	Change p-value	Descriptions
AFFX-BioB-5_at	-0.1	NC	0.5	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-M_at	0.1	NC	0.5	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioB-3_at	-0.1	NC	0.5	J04423 E coli bioB gene biotin synthetase (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-BioC-5_at	-0.1	NC	0.5	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioC-3_at	-0.1	NC	0.5	J04423 E coli bioC protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-5_at	0	NC	0.5	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-BioDn-3_at	-0.2	NC	0.656614	J04423 E coli bioD gene dethiobiotin synthetase (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-5_at	0	NC	0.5	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-CreX-3_at	-0.1	NC	0.5	X03453 Bacteriophage P1 cre recombinase protein (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)
AFFX-DapX-5_at	-0.9	NC	0.786122	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-M_at	-1.6	D	0.996551	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-3_at	-0.2	NC	0.5	L38424 B subtilis dapB, jojF, jojG genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-5_at	-0.1	NC	0.574632	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-M_at	0	NC	0.268189	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-3_at	-0.8	NC	0.727363	X17013 B subtilis lys gene for diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of X17013 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-5_at	-0.4	NC	0.680982	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-M_at	-0.5	NC	0.5	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-3_at	0	NC	0.110635	M24537B subtilis pheB, pheA genes corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-5_at	-0.2	NC	0.5	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-M_at	0.4	NC	0.542816	X04603 B subtilis thrC, thrB genes corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime respectively)

Total number of rows: 22810

Table truncated, full table size 2359 Kbytes.

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE2218_RAW.tar	13.6 Mb	(http)(custom)	TAR (of CEL, EXP)