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| Status |
Public on Oct 31, 2016 |
| Title |
kin28-AA_plusrap_Srb2 |
| Sample type |
SRA |
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| Source name |
Saccharomyces cerevisiae_YJ146
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YJ146
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Description |
Chip-seq of Myc-tagged Mediator subunit
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| 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
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| Submission date |
May 31, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Natalia Petrenko |
| Organization name |
Harvard Medical School
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| Department |
BCMP
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| Lab |
Struhl lab
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| Street address |
240 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL17143 |
| Series (1) |
| GSE82082 |
A study of Mediator subunit enhancer-promoter binding |
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| Relations |
| BioSample |
SAMN05192341 |
| SRA |
SRX1810794 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2183230_kin28-AA_plusrap_Srb2.bigwig |
30.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM2183230_kin28-AA_plusrap_Srb2.sgr.gz |
7.1 Mb |
(ftp)(http) |
SGR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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