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Sample GSM1199774 Query DataSets for GSM1199774
Status Public on Oct 21, 2013
Title Mot1_IP_10min_MNase_no_rapamycin_(20130705_2_3)
Sample type SRA
 
Source name Mot1 IP
Organisms Saccharomyces cerevisiae; Drosophila melanogaster
Characteristics cell: nuclei
mutant: WT
strain: W303
genotype: tor1-1 fpr1::natMX RPL13A-2xFKBP12::TRP1 TBP-FRB-kanMX6 MOT1-3FLAG-hphMX4
antibody: anti-FLAG beads (Sigma #8823)
Extracted molecule genomic DNA
Extraction protocol Nuclear isolation, chromatin preparation, and immunoprecipitation were performed as described (PMID 23468649). Sequencing libraries were prepared as described (PMID 22025700), except that TruSeq adapters were used for multiplexing and the ratio of sample to Ampure beads was changed from 5:9 to 1:1 in the two cleanup steps to compensate for the longer length of the TruSeq adapters.
 
Library strategy ChIP-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2500
 
Description Mot1 IP, 10' MNase, no rapamycin treatment
Data processing 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. We also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads that were only mapped to one organism (Supplementary files .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary files .wig)
 
Submission date Aug 01, 2013
Last update date May 15, 2019
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platform ID GPL17524
Series (1)
GSE44200 Mot1 redistributes TBP from TATA-containing to TATA-less promoters
Relations
BioSample SAMN02298805
SRA SRX330679

Supplementary file Size Download File type/resource
GSM1199774_Mot1_IP_10min_MNase_no_rapamycin.fly_only.bed.gz 30.3 Mb (ftp)(http) BED
GSM1199774_Mot1_IP_10min_MNase_no_rapamycin.fly_only.wig.gz 85.0 Mb (ftp)(http) WIG
GSM1199774_Mot1_IP_10min_MNase_no_rapamycin.yeast_only.bed.gz 19.8 Mb (ftp)(http) BED
GSM1199774_Mot1_IP_10min_MNase_no_rapamycin.yeast_only.wig.gz 61.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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