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Sample GSM2048197 Query DataSets for GSM2048197
Status Public on Jan 28, 2016
Title Dhp1-1_rep2
Sample type RNA
 
Channel 1
Source name rRNA depleted RNA of Dhp1-1
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: dhp1-1
strain: p1088
Treatment protocol RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
Growth protocol 30ºC liquid cultures grown to log phase in full media (YEA)
Extracted molecule total RNA
Extraction protocol Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. The rRNA-depleted samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20 and random hexamers.
Label Cy5
Label protocol The cDNAs from WT and mutant strains were labeled with Cy3(WT) and Cy5(mutant) (GE Healthcare)
 
Channel 2
Source name rRNA depleted RNA of wildtype
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: wildtype
strain: p1087
Treatment protocol RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions
Growth protocol 30ºC liquid cultures grown to log phase in full media (YEA)
Extracted molecule total RNA
Extraction protocol Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. The rRNA-depleted samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20 and random hexamers.
Label Cy3
Label protocol The cDNAs from WT and mutant strains were labeled with Cy3(WT) and Cy5(mutant) (GE Healthcare)
 
 
Hybridization protocol Hybridization, blocking, and washing was performed following the Agilent instructions
Scan protocol Scanning of arrays was performed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.)
Data processing Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Substraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False p-value filtering (p<=0.05) and background filtering (BG=median of negative control probes for green channel and red channel, probes with gProcessedSignal < 2x gBG AND rProcessedSignal < 2x rBG are filtered out) Filtered probes value set to 1
 
Submission date Jan 27, 2016
Last update date Jan 28, 2016
Contact name Tamas Fischer
E-mail(s) tamas.fischer@bzh.uni-heidelberg.de
Phone +49 6221 544728
Organization name Biochemie Zentrum Heidelebrg
Department BZH
Lab AG Fischer
Street address Im Neuenheimer Feld 328
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL19654
Series (2)
GSE77289 A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE [gene expression]
GSE77291 A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE

Data table header descriptions
ID_REF
VALUE filtered log2(rProcessedSignal/gProcessedSignal)

Data table
ID_REF VALUE
sp40c_1 0
sp40c_3 0
sp40c_5 0
sp40c_7 0.4352975
sp40c_9 0.5895845
sp40c_11 1.0568584
sp40c_13 1.6382879
sp40c_15 1.4713125
sp40c_17 1.5137711
sp40c_19 1.0675696
sp40c_21 1.490727
sp40c_23 0
sp40c_25 2.2177758
sp40c_27 0
sp40c_29 0
sp40c_31 0
sp40c_33 2.0870084
sp40c_35 0
sp40c_37 0
sp40c_39 0

Total number of rows: 174063

Table truncated, full table size 2831 Kbytes.




Supplementary file Size Download File type/resource
GSM2048197_0023expression_dhp1-1.fw.bedgraph.gz 564.7 Kb (ftp)(http) BEDGRAPH
GSM2048197_0023expression_dhp1-1.rev.bedgraph.gz 565.5 Kb (ftp)(http) BEDGRAPH
GSM2048197_253622710023_201307021831_S01-2_GE2_107_Sep09_2_Tamas_1_1.txt.gz 17.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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