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| Status |
Public on Jun 27, 2018 |
| Title |
WildType_DRIP-seq_INP |
| Sample type |
SRA |
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| Source name |
yeast cells genomic DNA
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: WRBb-9D
genotype: MATa ade2-1 bar1-delta can1-100 his3-11,15 leu2-3,112 RRM3::FLAG::KAN trp1-1 ura3::URA3/GPD-Tk(7x)
cell cycle stage: asynchronous
antibody: none
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| Growth protocol |
Yeast cell were grown in YPAD medium at 30ºC to mid-log phase.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DRIP protocol was performed as described in García-Pichardo et al. 2017. Briefly, harvested cells were treated to obtain spheroplasts, genomic DNA was extracted and spooled to purify it. Fragmentation was obtained with a cocktail of restriction enzymes. A fraction of the sample was separated as input control and the rest was immunoprecipitated using S9.6 monoclonal antibody. Both immunoprecipitated (IP) and input (INP) samples were subjected to a round of whole genome amplification using a GenomePlex® Complete Whole Genome Amplification Kit from Merck, following manufacturers specifications.
Library was prepared to obtain a fragment size of 200bp according to manufacturer’s protocol for the Ion Torrent PGM (Publication Part Number 4473623 Revision Date 14 November 2011 (Rev. A)). Samples were analyzed for size, integrity and contamination with Bionalyzer and High Sensitivity DNA analysis Kit at the Genomics service in CABIMER. Run was performed in Ion 316™ Chip v2. Barcodes were added in the library preparation step in order to pool them before loading the chip.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Ion Torrent PGM |
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| Data processing |
Library strategy: DRIP-Seq
Read quality testing and filtering (trimming of adapters and barcodes, filtering of non-template reads, polyclonal reads, and low-quality/uncertain calls) was performed using the Torrent Suite™ software 4.4.3.
Alignment was performed to reference genome S. cerevisiae sacCer3 (64-1-1_20110203), using the TMAP algorithm (the Torrent Mapping Alignment Program for Ion torrent) present in the Torrent suit software 4.4.3.
Duplicate reads (same start and end coordinates) were removed using SAMtools v1.7.
Read count normalization and bigwig preparation was performed using scripts available from El Hage et al. (2014).
Peak identification was performed using MACS2 2.1.1.20160309 analyzing the enrichment of IP (treatment) over the input (control), assuming a Poisson distribution (bdgcmp command) to later on perform a peak call (bdgpeakcall) with parameters (cutoff: 0.05, min length: 200 bp and max. gap 150 bp).
Genome_build: sacCer3
Supplementary_files_format_and_content: Intergenic scaled bigwig files were processed adapting the procedure described at El Hage et al. (2014). LogFE scaled bigwig file was created from these scaled bw using MACS2, as well as the bed file.
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| Submission date |
Apr 24, 2018 |
| Last update date |
Jun 29, 2018 |
| Contact name |
Andrés Aguilera |
| Organization name |
CABIMER, Universidad de Sevilla
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| Department |
Genome BIology
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| Lab |
Genome Instability & Cancer
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| Street address |
Av. Américo Vespucio 24
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| City |
Seville |
| ZIP/Postal code |
41092 |
| Country |
Spain |
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| Platform ID |
GPL16028 |
| Series (1) |
| GSE113580 |
Yra1-bound R loops cause orientation-independent transcription-replication collisions and telomere instability |
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| Relations |
| BioSample |
SAMN08975548 |
| SRA |
SRX3990033 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3109275_WT_DRIP-seq_INP.scaled.bw |
2.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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