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Sample GSM4971513 Query DataSets for GSM4971513
Status Public on Feb 03, 2021
Title 6HA-Sgs1
Sample type genomic
 
Source name G2/M arrest with Nocodazole
Organism Saccharomyces cerevisiae
Characteristics strain: HY3707
strain genotype: W303 MATa RAD5+, sgs1::pADH1-tc3-6xHA-Sgs1 (KanMX4)
antibody: anti-HA (F-7) Santa Cruz Biotechnology
Treatment protocol G2/M synchronization was performed by 10-20 μg/ml Nocodazole for 120-180 minutes at 25°C and validated by microscopy. Cells were treated with 0.2 mg/ml of Auxin (stock 50 mg/ml) during the arrest, if mentioned. Cells were collected and fixed with 1% formaldehyde for 30 min at room temperature for further ChIP.
Growth protocol Cells were grown in YP+Glucose 2% (YPD) media at 25°C in 500 ml flask for a density of 1.2×10^7 cells/ml.
Extracted molecule genomic DNA
Extraction protocol Binding profiles by ChIP-on-chip were determined as described in (Bermejo et al., 2009).
Label Dynabeads Protein A invitrogen
Label protocol Sample preparation and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.
 
Hybridization protocol Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays.
Scan protocol Arrays were scanned on an Affymetrix Scanner.
Description Binding pattern of Sgs1 by ChIP-on-chip after arrest of cells in G2/M with Nocodazole
Data processing BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]
 
Submission date Dec 11, 2020
Last update date Feb 03, 2021
Contact name Dana Branzei
E-mail(s) dana.branzei@ifom.eu
Organization name IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation
Lab DNA Repair lab
Street address Via Adamello 16
City Milan
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL7250
Series (1)
GSE147452 Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites

Supplementary file Size Download File type/resource
GSM4971513_6HA_Sgs1_pvalue.bar.gz 15.5 Mb (ftp)(http) BAR
GSM4971513_6HA_Sgs1_pvalue.bar.txt.gz 16.2 Mb (ftp)(http) TXT
GSM4971513_6HA_Sgs1_signal.bar.gz 15.3 Mb (ftp)(http) BAR
GSM4971513_6HA_Sgs1_signal.bar.txt.gz 16.2 Mb (ftp)(http) TXT
GSM4971513_R1422_Sgs1_IP.CEL.gz 29.1 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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