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Series GSE119211 Query DataSets for GSE119211
Status Public on Aug 29, 2020
Title SFP1 (ChIP-seq)
Organisms Saccharomyces cerevisiae; Naumovozyma castellii; Saccharomyces paradoxus; Kluyveromyces lactis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We set out to determine how Sfp1 binding targets evolved over time. We sampled our species of interest to include one pre-whole genome duplicaton (WGD) species containing SFP1A (K. lactis), one post-WGD species containing both SFP1 and SFP1PL (N. castellii), two post-WGD species containing only SFP1 (S. cerevisiae and S. paradoxus) and performed ChIP for each Sfp1 homolog in each species using an antibody that recognizes a conserved subdomain of Sfp1 common to both Sfp1, Sfp1a, and Sfp1pl. Because Sfp1pl was also present in N. castellii, a second antibody was used that is more specific to Sfp1pl (denoted as IP3). We also performed ChIP in SFP1 deletion mutants in each species tested, as a control."
 
Overall design Polyclonal antibodies were created (Bethyl, Inc) to bind a peptide from the conserved c-terminal portion of Sfp1 designated, αSfp1-1, while αSfp1-3 was raised to recognize was raised to bind specifically to the N. castellii Sfp1pl The ChIP protocol was performed as described by Lefrancois et al. in The Guide to Yeast Genetics (Weissman, Jonathan F., Guthrie, 2010); modifications noted below) with 2-3 replicates per sample. Strains were grown to optical densities (OD600) between 0.6 and 0.8 in 500 mL of BMW (Thompson et al., 2013). Fixation took place with 37% formaldehyde for 15 minutes at room temperature, with occasional shaking every 5 minutes. Samples were sheared on the Covaris E210 with the following settings: 20% / 8 intensity/ 200 cycles per burst in 1-minute cycles for 16 minutes. Sequencing libraries were prepared from the input and immunoprecipitated DNA and were sequenced on an Illumina HiSeq 2500 with 25 base pair, paired end reads. Reads were mapped to the reference genomes of each species (S288C R64 for S. cerevisiae, YGOB v7 Aug 2012 for K. lactis and N. castellii, and Scannell et al. for S. paradoxus (Scannell et al., 2011), using bowtie2.
 
Contributor(s) Delorey T, de Boer C, Knaack S, Roy S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Aug 29, 2018
Last update date Aug 31, 2020
Contact name Carl G de Boer
Organization name The Broad Institute
Lab Aviv Regev
Street address 415 Main St
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platforms (4)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
GPL19759 Illumina HiSeq 2500 (Kluyveromyces lactis)
GPL20787 Illumina HiSeq 2500 (Saccharomyces paradoxus)
Samples (70)
GSM3360763 Klac_Sfp1d_IP1_1
GSM3360764 Klac_Sfp1d_IP1_2
GSM3360765 Klac_Sfp1d_IP1_3
This SubSeries is part of SuperSeries:
GSE119238 The roles of duplication and divergence in the evolution of a transcription factor
Relations
BioProject PRJNA488473
SRA SRP159103

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
GSE119211_Klac_WT-vs-Sfp1d_IP1-vs-input.R1.bw 44.5 Mb (ftp)(http) BW
GSE119211_Klac_WT-vs-Sfp1d_IP1-vs-input.R2.bw 44.5 Mb (ftp)(http) BW
GSE119211_Klac_WT-vs-Sfp1d_IP1-vs-input.R3.bw 44.5 Mb (ftp)(http) BW
GSE119211_Klac_WT-vs-Sfp1d_IP1-vs-input_3-3.logRatio.bw 46.4 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP1-vs-input.R1.bw 46.9 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP1-vs-input.R2.bw 47.3 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP1-vs-input.R3.bw 46.6 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP1-vs-input.logRatio.bw 48.8 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP3-vs-input.R1-1.bw 47.2 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP3-vs-input.R2-1.bw 47.2 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP3-vs-input.R3-1.bw 47.1 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-551_IP3-vs-input.logRatio.bw 48.9 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-719_IP1-vs-input.R1.bw 47.0 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-719_IP1-vs-input.R2.bw 47.2 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-719_IP1-vs-input.R3.bw 47.2 Mb (ftp)(http) BW
GSE119211_Ncas_WT-vs-719_IP1-vs-input.logRatio.bw 48.9 Mb (ftp)(http) BW
GSE119211_RAW.tar 2.4 Gb (http)(custom) TAR (of BW)
GSE119211_Scer_WT-vs-Sfp1d_IP1-vs-input.R1.bw 51.6 Mb (ftp)(http) BW
GSE119211_Scer_WT-vs-Sfp1d_IP1-vs-input.R2.bw 51.9 Mb (ftp)(http) BW
GSE119211_Scer_WT-vs-Sfp1d_IP1-vs-input.logRatio.bw 52.3 Mb (ftp)(http) BW
GSE119211_Spar_WT-vs-Sfp1d_IP1-vs-input.R1.bw 47.3 Mb (ftp)(http) BW
GSE119211_Spar_WT-vs-Sfp1d_IP1-vs-input.R2.bw 47.3 Mb (ftp)(http) BW
GSE119211_Spar_WT-vs-Sfp1d_IP1-vs-input.R3.bw 47.4 Mb (ftp)(http) BW
GSE119211_Spar_WT-vs-Sfp1d_IP1-vs-input.logRatio.bw 50.3 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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