NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE1944 Query DataSets for GSE1944
Status Public on Nov 10, 2004
Title Genome-wide binding of Fhl1 and Ifh1 +/- Rapamycin
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary Array design

-Platform: amino-silane coated glass slides (GAPS II, Corning)
-S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. A complete description of the primers can be obtained on the web site (ftp://ftp.resgen.com/pub/genepairs/yeast_intergenic).
-The PCR products were purified and spotted using an automated arrayer (MicroGrid II, BioRobotics)


Experiment design
-Type of experiment: genome wide binding analysis
-Experimental factor: genotype (Wild-Type, Fhl1-myc, Ifh1-myc); drug (rapamycin)
-Number of hybridization performed in the experiment: 15 (four conditions with three to five biological replicates each)
-Reference used for each condition: ChIP from the wild-type strain
-Quality control: one dye-swap per condition

Samples used, extract preparation and labeling
-The origin of the biological sample:
o Species: S. cerevisiae
o Cell type: (1) W303; (2) W303+IFH1-13myc-TRP1MX6;(3) W303+FHL1-13myc-HIS3MX6.
-Growth conditions: log phase (2x107/mL) at 30ºC in YPD medium; when indicated rapamycin was added at the final concentration of 200 ng/mL for 90 min.
-Cross-linking for 30 min at 30ºC
-Chromatin immunoprecipitation: Dynabeads M280 coupled to sheep anti-mouse IgG or sheep anti-rabbit IgG and mouse monoclonal antibodies against the myc epitope (culture supernatant of 9E10) were used for immunoprecipitation according to standard techniques.
-Labeling protocol(s): each IP was blunt-ended, ligated to linker DNA, then subjected to Ligation Mediated (LM)-PCR in the presence of amino-allyl dUTP. Labeling was performed for 1 hour at room temperature in the presence of NHS-ester Cy3 or Cy5 in 0.1 M Sodium Carbonate. The labeling reaction was stopped with 2 M Hydroxylamine and the labeled DNA purified.

Hybridization procedures and parameters
-Standard protocols were used

Measurement data and specifications
-Software for scanning: GenePix Pro 4.0 (Axon Instruments, Inc.)
-Scanner: GenePix 4000A (Axon Instruments, Inc.)
Keywords: dose response
 
 
Contributor(s) Schawalder SB, Kabani M, Choudhurry U, Howald I, Werner M, Shore D
Citation(s) 15616569
Submission date Nov 08, 2004
Last update date Mar 15, 2012
Contact name Stephan B. Schawalder
E-mail(s) [email protected]
Phone +41 22 379 61 77
Organization name University of Geneva
Department Departement of Molecular biology
Lab Group Shore
Street address Quai Ansermet 30
City Geneva
ZIP/Postal code 1211
Country Switzerland
 
Platforms (1)
GPL1695 yeast intergenic array
Samples (15)
GSM34772 Fhl1-(1)
GSM34773 Fhl1-(2)
GSM34774 Fhl1-(3)
Relations
BioProject PRJNA90441

FHL1_untreated_enriched header descriptions
Intergenic
Ratio
P-value
ORFc
ORFw
GO (except for RPGs)

Data table
Intergenic Ratio P-value ORFc ORFw GO (except for RPGs)
iYLR023C 2.33 5.76E-09 - YLR023C hypothetical ORF
iYIL019W 3.66 1.61E-07 RPL2B - -
iYHR141C 6.35 1.91E-07 CHS7 RPL42B ER to Golgi transport
iYGR117C 4.75 2.57E-07 RPS23A YGR117C unknown
iYIL133C 5.00 3.92E-07 - RPL16A -
iYER044C-A 2.03 4.06E-07 - mei4 meiosis-specific gene required for meiotic recombination
iYLR029C 2.00 4.54E-07 YLR030W RPL15A hypothetical ORF
iYJL192C 3.31 7.44E-07 RPS14B SOP4 ER to Golgi transport
iYBR189W 4.30 7.71E-07 YBR190W,RPL21A - -
iYMR142C 5.02 7.95E-07 RPS16A RPL13B -
iYER116C 4.62 1.88E-06 RPL23B SLX8 DNA recombination
iYKL065C 2.06 2.54E-06 MNR2 YET1 unknown (putative magnesium transporter) / yeast endoplasmic reticulum 24 kDa transmembrane protein (homolog of BAP31)
iYNL307C 2.24 2.55E-06 MRPS18 MCK1 Mitochondrial ribosomal protein of the small subunit / 43.1 kDa serine/threonine/tyrosine protein kinase (glycogen synthase kinase 3 activity); chromosome segregation; entry in meiosis; NHEJ
iYGL189C 4.55 4.14E-06 - RPS26A -
iYLR047C 5.58 4.16E-06 RPS0B YLR047C hypothetical ORF
iYJL136C 5.73 4.71E-06 YJL135W,LCB3 RPS21B hypothetical ORF/ sphingolipids biosynthesis
iYDR416W 3.18 6.14E-06 RPL12B - -
iYOL120C 2.02 7.36E-06 - RPL18A -
iYPL249C-A 2.57 7.50E-06 - RPL36B -
iYJR122W 6.15 7.57E-06 RPS5 - -

Total number of rows: 100

Table truncated, full table size 5 Kbytes.




FHL1_Rapa_enriched header descriptions
Intergenic
Ratio
P-value
ORFc
ORFw
GO (except RPGs)

Data table
Intergenic Ratio P-value ORFc ORFw GO (except RPGs)
iYLR184W 1.99 2.20E-10 RPL37A - -
iYJL136C 3.03 8.33E-10 YJL135W,LCB3 RPS21B hypothetical ORF/ sphingolipids biosynthesis
iYIL133C 4.62 6.60E-09 - RPL16A -
iYHL033C 2.10 1.09E-08 - RPL8A -
iYML073C 5.21 2.47E-08 - RPL6A -
iYGL136C 2.67 2.52E-08 RPL1B MRM2 mitochondrial 21S rRNA methyltransferase
iYER116C 3.58 3.51E-08 RPL23B SLX8 DNA recombination
iYLR047C 4.98 5.13E-08 RPS0B YLR047C hypothetical ORF
iYGR117C 4.43 5.43E-08 RPS23A YGR117C unknown
iYPL249C-A 2.16 6.13E-08 - RPL36B -
iYFR031C-A 4.59 7.34E-08 - RPL2A -
iYGL104C 3.34 7.63E-08 RPL28 VPS73 vacuolar targeting
iYIL069C 3.08 8.90E-08 - RPS24B -
iYDR449C 2.29 9.21E-08 RPS18A UTP6 part of small ribosomal subunit processosome
iYOR292C 3.90 1.25E-07 RPS10A YOR292C hypothetical ORF
iYML026C 4.66 1.27E-07 - RPS18B -
iYML025C 3.63 1.43E-07 RPS17A YML6 mitochondrial ribosomal protein of the large subunit
iYDL076C 4.28 1.43E-07 RPL31A YDL076C putative histone deactylase
iYEL054C 3.07 2.47E-07 - RPL12A -
iYHR141C 4.66 2.59E-07 CHS7 RPL42B ER to Golgi transport

Total number of rows: 99

Table truncated, full table size 5 Kbytes.




IFH1_untreated_enriched header descriptions
Intergenic
Ratio
P-value
ORFc
ORFw
GO (except RPGs)

Data table
Intergenic Ratio P-value ORFc ORFw GO (except RPGs)
iYIL133C 3.00 7.25E-09 - RPL16A -
iYHR141C 4.39 9.26E-08 CHS7 RPL42B ER to Golgi transport
iYMR142C 2.75 2.10E-07 RPS16A RPL13B -
iYIL069C 3.72 2.47E-07 - RPS24B -
iYOR234C 3.05 3.15E-07 snr17a RPL33B snoRNA
iYIL052C 3.72 3.41E-07 - RPL34B -
iYPL144W 1.92 4.63E-07 RPL33A - -
iYJR122W 3.79 4.93E-07 RPS5 - -
iYDR416W 2.41 8.80E-07 RPL12B - -
iYJL137C 2.09 1.03E-06 - GLG2 self-glucosylating initiator of glycogen synthesis
iYDL184C 2.26 1.23E-06 - RPL41A -
iYBL093C 2.65 1.32E-06 RPL32 ROX3 RNA polymerase II holoenzyme component
iYOR292C 2.05 1.90E-06 RPS10A YOR292C hypothetical ORF
iYOR312C 3.30 1.91E-06 - RPL20B -
iYOL128C 1.81 2.19E-06 RPL25 YGK3 glycogen synthase kinase 3 activity
iYHR203C 2.32 3.32E-06 MNL1 RPS4B ER alpha-mannosidase-like involved in ERAD
iYNL096C 1.90 3.40E-06 - RPS7B -
iYKL006C-A 2.34 4.70E-06 RPL14A SFT1 v-SNARE (Golgi)
iYML025C 2.70 4.93E-06 RPS17A YML6 mitochondrial ribosomal protein of the large subunit
iYNL302C 3.52 6.65E-06 - RPS19B -

Total number of rows: 92

Table truncated, full table size 4 Kbytes.




IFH1_Rapa_enriched header descriptions
Intergenic
Ratio
P-value
ORFc
ORFw
GO (except RPGs)

Data table
Intergenic Ratio P-value ORFc ORFw GO (except RPGs)
iYHR136C 2.84 1.01E-06 ARO9 SPL2 aromatic amino acid aminotransferase II / identical to PHO81 (inhibitor of of a cyclin (Pho80p)-dependent protein kinase (Pho85p) complex (Cdk))
iYDR112W 3.01 2.32E-06 - YDR111C putative alanine transaminase (glutamyc pyruvic transaminase)
iYJL180C 2.22 5.82E-06 PFD1 ATP12 bovine prefoldin subunit 1 homolog / essential for assembly of a functional F1-ATPase; binds the alpha subunit of F1-ATPase
iYPL214C 2.18 1.87E-05 YPL213W THI6 pre-mRNA splicing factor activity; looks exceptionally like U2A / thiamin biosynthetic bifunctional enzyme (TMP pyrophosphorylase hydroxyethylthiazole kinase)
iYPL273W 1.81 3.08E-05 - - -
iYDL157C 2.58 4.07E-05 YDL156W YDL157C,YDL158C hypothetical ORFs
iYCR021C 1.83 4.77E-05 - HSP30 heat-shock protein
iYBR217W 2.31 5.10E-05 - - -
iYHR039C 1.95 6.14E-05 - YHR039C Meiotic Sister-Chromatid recombination
iYDR033W 1.92 6.24E-05 - - -
iYDR168W 2.21 6.97E-05 - - -
iYER155C 1.86 1.33E-04 - BEM2 Rho GTPase activating protein (GAP); involved in bud emergence
iYGR075C 2.18 1.51E-04 - PRP38,YGR073C PRP38; RNA splicing factor / hypothetical ORF
iYGR120C 1.92 1.52E-04 - SEC35 Conserved Oligomeric Golgi complex; required for ER to Golgi vesicle docking
INTYCR097W-A2 4.59 1.58E-04 - - -
iCEN12 1.89 1.85E-04 - - -
iYLL024C 1.94 1.89E-04 - SSA2 member of the 70 kDa heat-shock protein family
iYGR081C 1.86 2.69E-04 TOM20 SLX9 20 kDa mitochondrial outer membrane protein import receptor / unknown
iYDR060W 1.96 2.73E-04 YDR061W - hypothetical ORF
iYDR125C 2.20 3.41E-04 SWF1 ECM18 spore wall formation / unknown

Total number of rows: 68

Table truncated, full table size 5 Kbytes.




FHL1_untreated_normalized header descriptions
Systematic
Normalized
StdDev Norm
t-test P-value
ORFc
ORFw

Data table
Systematic Normalized StdDev Norm t-test P-value ORFc ORFw
iYLR023C 2.3313599 0.10155304 5.76399E-09 0 YLR023C
iYAL039C-0 1.7093858 0.075459294 9.56625E-08 0 CYC3
iYIL019W 3.658913 0.4264997 1.61104E-07 RPL2B 0
iYHR141C 6.347859 0.31338555 1.90723E-07 YHR142W RPL42B
iYJL038C 1.5544562 0.06364098 1.95275E-07 YJL037W YJL038C
iYGR117C 4.748974 0.71913433 2.57102E-07 RPS23A YGR117C
iYLR285W 1.5762938 0.07263187 3.27835E-07 0 0
iYIL133C 5.00259 0.8403895 3.92043E-07 0 RPL16A
iYER044C-A 2.034157 0.15158765 4.05684E-07 0 mei4
iYLR029C 1.9950892 0.14737986 4.53986E-07 YLR030W RPL15A
iYNL038W 1.6099362 0.08344234 5.03712E-07 0 0
iYKR015C 1.4139215 0.05345283 5.12154E-07 YKR016W YKR015C
iYJL192C 3.3110757 0.4607944 7.44075E-07 RPS14B YJL192C
iYKL110C-0 1.3834 0.052487973 7.69841E-07 0 KTI12
iYBR189W 4.3042536 0.73464113 7.70937E-07 "YBR190W,RPL21A" 0
iYMR142C 5.023509 0.30959097 7.94966E-07 RPS16A RPL13B
iYBR056W 1.4117993 0.0592596 9.77467E-07 0 0
iYBR108W 0.37468272 0.04555447 1.08365E-06 0 0
iYPL274W 1.5855511 0.094314806 1.38227E-06 YPL273W 0
iYBL101C 0.66217524 0.03654699 1.71813E-06 YBL101W-A ECM21

Total number of rows: 14062

Table truncated, full table size 445 Kbytes.




FHL1_Rapa_normalized header descriptions
Systematic
Normalized
StdDev Norm
t-test P-value
ORFc
ORFw

Data table
Systematic Normalized StdDev Norm t-test P-value ORFc ORFw
iYLR184W 1.9867891 0.09978632 2.20111E-10 RPL37A 0
iYJL136C 3.0262747 0.48106325 8.33011E-10 "YJL135W,LCB3" RPS21B
YGLWdelta10 1.6202087 0.08606276 5.64424E-09 0 0
iYIL133C 4.6246963 1.2565523 6.59864E-09 0 RPL16A
iYHL033C 2.1014473 0.29157746 1.09003E-08 0 RPL8A
iYLR155C-0 0.6936697 0.047823805 1.18727E-08 YLR156W ASP3A
iYML073C 5.212459 1.7496691 2.46596E-08 0 RPL6A
iYGL136C 2.666682 0.5329906 2.52127E-08 RPL1B YGL136C
iYER116C 3.578297 0.9620409 3.50689E-08 RPL23B YER116C
iYLR047C 4.981734 1.1649904 5.12969E-08 RPS0B YLR047C
iYGR117C 4.4250526 0.96552646 5.43473E-08 RPS23A YGR117C
iYPL249C-A 2.1590977 0.12698317 6.12575E-08 0 RPL36B
iYOR096W 1.4234371 0.11264152 6.28712E-08 0 0
iYFR031C-A 4.5866637 1.5913743 7.34E-08 0 RPL2A
iYGL104C 3.3388143 0.92062986 7.62817E-08 RPL28 YGL104C
iYIL069C 3.0815358 0.80613065 8.90283E-08 0 RPS24B
iYDR449C 2.294968 0.44473428 9.21068E-08 RPS18A YDR449C
iYOR292C 3.8973227 1.0732378 1.25338E-07 RPS10A YOR292C
iYML026C 4.6648703 1.1748185 1.27156E-07 0 RPS18B
iYML025C 3.6258779 0.77504367 1.42591E-07 RPS17A YML025C

Total number of rows: 14063

Table truncated, full table size 445 Kbytes.




IFH1_untreated_normalized header descriptions
Systematic
Normalized
StdDev Norm
t-test P-value
ORFc
ORFw

Data table
Systematic Normalized StdDev Norm t-test P-value ORFc ORFw
iYIL133C 3.0024028 0.37505284 7.25274E-09 0 RPL16A
iYHR141C 4.3915596 0.7713855 9.25566E-08 YHR142W RPL42B
iYMR142C 2.7524192 0.48602203 2.10106E-07 RPS16A RPL13B
iYIL069C 3.7170646 0.86912584 2.47255E-07 0 RPS24B
iYOR234C 3.0505478 0.6249867 3.14559E-07 snr17a RPL33B
iYIL052C 3.7174847 0.90587807 3.40583E-07 0 RPL34B
iYPL144W 1.9209564 0.24213132 4.62933E-07 RPL33A 0
iYJR122W 3.7942193 0.98482054 4.92819E-07 RPS5 0
iYLR083C 1.5828363 0.14883773 7.28922E-07 0 EMP70
iYDR416W 2.406198 0.44330186 8.79578E-07 RPL12B 0
iYJL137C 2.093127 0.3311486 1.03032E-06 0 GLG2
iYLLCDELTA1 1.5021961 0.13284487 1.15209E-06 0 0
iYDL184C 2.2578392 0.4029682 1.2285E-06 0 RPL41A
iYBL093C 2.6514807 0.57199574 1.32098E-06 RPL32 ROX3
iYOR292C 2.054312 0.34321865 1.90403E-06 RPS10A YOR292C
iYOR312C 3.3038054 0.53802586 1.90648E-06 0 RPL20B
iYOL128C 1.8071432 0.25281206 2.19353E-06 RPL25 YOL128C
iTN(GUU)O1 1.7298704 0.13934015 2.97818E-06 YOL054W 0
iYKL110C-0 1.4240056 0.12426218 3.04844E-06 0 KTI12
iYHR203C 2.3175898 0.48638338 3.32185E-06 YHR204W RPS4B

Total number of rows: 14063

Table truncated, full table size 445 Kbytes.




IFH1_Rapa_normalized header descriptions
Systematic
Normalized
StdDev Norm
t-test P-value
ORFc
ORFw

Data table
Systematic Normalized StdDev Norm t-test P-value ORFc ORFw
RDN58-1 0.5026124 0.035301797 3.44445E-07 0 0
iYLR057W 1.6199466 0.051906683 4.34899E-07 0 0
iYHR136C 2.8359973 0.36179376 1.00981E-06 ARO9 SPL2
iYIL170W-1 0.65553373 0.03494154 1.21213E-06 0 0
iYBR013C 0.5919412 0.040345356 1.4425E-06 0 "YBR013C,YBR012C"
iYDR170C 1.7217785 0.12538442 1.72835E-06 0 SEC7
iTS(AGA)D1 1.5594249 0.09446672 1.91239E-06 RPT2 0
Q0125 0.5961771 0.04290698 2.15704E-06 0 0
iYDR112W 3.0070531 0.1652715 2.31937E-06 0 YDR111C
YOLCdelta9 0.57877576 0.045766328 2.70585E-06 0 0
iYLL026W 1.6586001 0.12632154 3.42725E-06 0 0
iSNR69 0.4942665 0.052450456 3.43601E-06 RGT1 0
Q0275 0.74240047 0.033703826 3.6879E-06 0 0
iYLR296W 0.52344865 0.051852692 3.77691E-06 YLR297W 0
iYLRWDELTA6-B 0.5798667 0.033696357 4.56896E-06 0 YLR154C
iYLR091W 1.4600588 0.060935635 5.39433E-06 SUL2 0
CEN14 0.7374038 0.036739312 5.5815E-06 0 0
iYJL180C 2.2156487 0.29038015 5.82263E-06 PFD1 ATP12
iYGR173W 0.6050313 0.050640192 6.21236E-06 0 0
iYBR152W 0.71297824 0.04087123 6.86705E-06 RIB7 0

Total number of rows: 14062

Table truncated, full table size 445 Kbytes.




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
GSE1944_RAW.tar 362.4 Mb (http)(custom) TAR (of TIFF)

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap