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Sample GSM758890 Query DataSets for GSM758890
Status Public on Jul 13, 2011
Title Sef1myc_L_ChIP1
Sample type genomic
 
Channel 1
Source name Myc ChIP DNA from myc-tagged Sef1 strain in low iron
Organism Candida albicans
Characteristics strain: SN423
genotype/variation: myc-tagged Sef1 strain
chip antibody: Anti-c-Myc 9E10
antibody vendor, cat. number: COVANCE (MMS-150R)
Treatment protocol Cells were fixed, lysed, immunoprecipitated with anti-Myc antibody and genomic DNAs were sheared by sonication
Growth protocol Saturated cultures of Sef1-Myc (SN423) was inoculated into iron depleted (YEPD+BPS) liquid medium to OD600=0.05. Cultures were incubated with shaking at 30°C until OD600 0.4.
Extracted molecule genomic DNA
Extraction protocol Saturated cultures of untagged wild type C. albicans (SN250), Sef1-Myc (SN423), Hap43-Myc (SN840), and Sfu1-Myc (SN646) were inoculated into low iron (untagged, Sef1-Myc, Hap43-Myc) or iron replete (untagged, Sfu1-Myc) liquid medium to OD600=0.05. Cultures were incubated with shaking at 30°C until OD600 0.4, when formaldehyde was added to 1% final (with shaking, room temperature, 15 minutes), followed by glycine to 125mM final (with shaking, room temperature, 5 minutes). Cells were collected by centrifugation at 4°C and washed twice with 20 mM Tris-HCl pH 7.5/150 mM NaCl, followed by freezing in liquid N2 and storage at -80°C. Cell lysis, DNA shearing, and ChIP-Chip were performed as described (Nobile et al., 2009).
Label Cy5
Label protocol IP genomic DNA samples were labeled with Cy5 and input genomic DNA samples were labeled with Cy3. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58)
 
Channel 2
Source name Input DNA from myc-tagged Sef1 in low iron
Organism Candida albicans
Characteristics strain: SN423
Treatment protocol Cells were fixed, lysed, immunoprecipitated with anti-Myc antibody and genomic DNAs were sheared by sonication
Growth protocol Saturated cultures of Sef1-Myc (SN423) was inoculated into iron depleted (YEPD+BPS) liquid medium to OD600=0.05. Cultures were incubated with shaking at 30°C until OD600 0.4.
Extracted molecule genomic DNA
Extraction protocol Saturated cultures of untagged wild type C. albicans (SN250), Sef1-Myc (SN423), Hap43-Myc (SN840), and Sfu1-Myc (SN646) were inoculated into low iron (untagged, Sef1-Myc, Hap43-Myc) or iron replete (untagged, Sfu1-Myc) liquid medium to OD600=0.05. Cultures were incubated with shaking at 30°C until OD600 0.4, when formaldehyde was added to 1% final (with shaking, room temperature, 15 minutes), followed by glycine to 125mM final (with shaking, room temperature, 5 minutes). Cells were collected by centrifugation at 4°C and washed twice with 20 mM Tris-HCl pH 7.5/150 mM NaCl, followed by freezing in liquid N2 and storage at -80°C. Cell lysis, DNA shearing, and ChIP-Chip were performed as described (Nobile et al., 2009).
Label Cy3
Label protocol IP genomic DNA samples were labeled with Cy5 and input genomic DNA samples were labeled with Cy3. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58)
 
 
Hybridization protocol 10 independent hybridization experiments were performed on 4 biological replicates of the untagged control and 2 biological replicates each of Sef1-Myc, Sfu1-Myc, and Hap43-Myc. Protocol is available in Hernday et al. (Methods Enzymol. 2010;470:737-58)
Scan protocol Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol
Description Genomic wide Sef1 enrichment
Data processing Agilent Chip Analytics software v1.2 (Agilent Technologies) was used for initial data normalization and analysis (Tuch et al., 2008), followed by visualization and additional analysis using MochiView v.1.39 (http://johnsonlab.ucsf.edu/). High confidence regulatory events were associated with Agilent segment p-values of ≥ 4 (-log10 p-value based on the enrichment statistic for each probe in the region) and minimum 2-fold (Sef1-Myc and Hap43-Myc) or 1.5-fold (Sfu1-Myc) enrichment in both biological replicates of the epitope-tagged strains (Table S2). Genes with enrichment peaks in untagged controls were excluded.
 
Submission date Jul 12, 2011
Last update date Jul 13, 2011
Contact name Changbin Chen
E-mail(s) Changbin.Chen@ucsf.edu
Phone 4154768992
Fax 4154768201
Organization name University of California, San Francisco
Department Department of Microbiology & Immunology
Lab Dr. Suzanne Noble LAB
Street address HSE450, 513 Parnassus Avenue
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platform ID GPL13696
Series (2)
GSE30591 A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis [ChIP_chip]
GSE30593 A unique iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis

Data table header descriptions
ID_REF
VALUE normalized log2 ratios (Cy5/Cy3)

Data table
ID_REF VALUE
1 -0.078965314
2 -0.078965314
3 -0.084799975
4 -0.084799975
5 -0.19542532
6 -0.19542532
7 -0.19609356
8 -0.19609356
9 -0.2059729
10 -0.28276414
11 -0.28276414
12 -0.10437739
13 -0.10437739
14 -0.2877863
15 -0.2877863
16 -0.32614103
17 0.06680101
18 -0.23952399
19 -0.2052968
20 -0.13346446

Total number of rows: 243504

Table truncated, full table size 4298 Kbytes.




Supplementary file Size Download File type/resource
GSM758890_Sef1myc_L_rep1.gpr.gz 25.3 Mb (ftp)(http) GPR
Processed data included within Sample table

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