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Sample GSM2183239 Query DataSets for GSM2183239
Status Public on Oct 31, 2016
Title kin28-AA_minusrap_Srb10
Sample type SRA
 
Source name Saccharomyces cerevisiae_KHW333
Organism Saccharomyces cerevisiae
Characteristics strain: KHW333
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extraction protocol as described in Fan, X., Lamarre-Vincent, N., Wang, Q., and Struhl, K. (2008). Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucl. Acids Res. 36, e125. Antibodies used in this study include 9E10 anti-Myc antibodies from Santa Cruz and 8WG16 antibodies from Covance.
Library construction as described in Wong, K.-H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7, Unit 7.11.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Description Chip-seq of Myc-tagged Mediator subunit
Data processing map using Bowtie in Galaxy (Penn State). Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 .
Sam-to-Bam using Galaxy
Bam-to-Bed using Galaxy (Concatenate the two kin28-AA_minusrap_Gal11 files).
MACS using Galaxy to create a shifted raw tag count at every bp in a wiggle file and save as bigwig. All libraries have an average fragment size of 200-300, except the Srb4 libraries, which are 80-200
for plotting, normalize to # of sequenced reads
Genome_build: sacCer3
Supplementary_files_format_and_content: every processed file contains a shifted raw tag count at every bp in a bigwig file
 
Submission date May 31, 2016
Last update date May 15, 2019
Contact name Natalia Petrenko
Organization name Harvard Medical School
Department BCMP
Lab Struhl lab
Street address 240 Longwood Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL17143
Series (1)
GSE82082 A study of Mediator subunit enhancer-promoter binding
Relations
BioSample SAMN05192350
SRA SRX1810803

Supplementary file Size Download File type/resource
GSM2183239_kin28-AA_minusrap_Srb10.bigwig 33.4 Mb (ftp)(http) BIGWIG
GSM2183239_kin28-AA_minusrap_Srb10.sgr.gz 12.4 Mb (ftp)(http) SGR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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