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| Status |
Public on May 23, 2013 |
| Title |
Lsm1-TAP |
| Sample type |
SRA |
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| Source name |
yeast cells grown in YPD
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
background strain: yMC458
genotype/variation: LSM1-TAP
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| Growth protocol |
cells grown in YPD
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1% formahldehyde-fixed cells were lysed in buffer 50 mM HEPES 150 mM NaCl, 2 mM EDTA (pH 8.0), 1% Triton X‐100 0.1% NaDeoxycholate. Lysis done with zirconium silicate beads for 6min in mini-beadbeater
Shear the chromatin to a median size of 250‐300 bp by sonication: using Diagenode Bioruptor Standard (power setting: high, 30 seconds on / 30 seconds off, 30 cycles)
ChIP was performed with Rabbit IgG sepharose beads (Bethyl P120-101). After several rounds of wash, beads were treated with enzymes in the following order: T4 DNA polymerase, then T4 Polynucleotide Kinase, then Klenow Fragment (3’→5’ exo‐) (these steps are for polishing the DNA ends), then ligation to PCR adaptors and elongation using phi29 DNA polymerase
DNA on beads was then digested with Lambda exonulease, followed by RecJf Exonuclease. DNA was eluted from beads at 65C.
For complete protocol see: Rhee & Pugh (2012) curr. Protoc. Mol. Biol. Chapter 21:Unit 21.24. doi: 10.1002/0471142727.mb2124s100
To complete library construction for high‐throughput sequencing, the DNA is primer‐extended and ligated with a second sequencing adaptor. After gel‐purification and PCR, the amplified library is ready for high‐throughput sequencing
For complete protocol see: Rhee & Pugh (2012) curr. Protoc. Mol. Biol. Chapter 21:Unit 21.24. doi: 10.1002/0471142727.mb2124s100
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
yeast cells grown in YPD
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| Data processing |
Peconic Bioinf Guide (http://www.peconicgenomics.com/CHIP-exo%20services.html)
tab files were converted to wig file using a custom script
Genome_build: saccharomyces_cerevisiae_R56-1-1_20070407 (http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/)
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| Submission date |
Feb 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gal Haimovich |
| E-mail(s) |
[email protected]
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| Organization name |
Weizmann Institute of Science
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| Department |
Dept. Molecular Genetics
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| Lab |
Jeffrey Gerst
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| Street address |
Belfer bldg. 416
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE44312 |
Gene expression is a circular process |
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| Relations |
| SRA |
SRX237128 |
| BioSample |
SAMN01920615 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1082952_Lsm1.roman.unstranded.wig.gz |
96.6 Kb |
(ftp)(http) |
WIG |
| GSM1082952_Lsm1_P120-101_y754_-_YPD_-_XO121.combined.added.tab.gz |
119.3 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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