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| Status |
Public on Sep 25, 2020 |
| Title |
xrn1_A |
| Sample type |
SRA |
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| Source name |
yeast cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: xrn1[delta]::KanMX
parental strain: BY4741
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| Treatment protocol |
2 independent biological replicates
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| Growth protocol |
Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment (as in PMID: 23295673).
Starting from total RNA, poly(A) RNA is reverse transcribed using a biotinylated adapter containing an anchored oligo-dT primer. After second strand synthesis, fragments are captured by streptavidin beads, end-repaired, adenylated, and ligated to a second adapter. The library was prepared using oligos that allows the sequencing into the poly(A) tail (from the body of the cDNA) (Internal protocol in PMID: 23295673). Stringent library size selection (200bp was performed).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base-calling was performed using Illumina CASAVA pipeline and standard parameters (February 2011).
Filtering and trimming of adapters and low quality bases from reads wit Trimmomatic: 1) standard Illumina adapter removal and then removal of the barcodes at the 5’ end of reads (7 first bases), 2) removal of the P7 adapter in 3’ end after the polyA tail, 3) trimming of bases in 3’ that fall below a certain quality threshold (minumim quality).
Removal of polyA tails and downstream sequences with PRINSEQ and the options: min_gc 20, trim_right 16, min_len 20, trim_tail_right 5 out_format 3.
Mapping to the reference genome with Bowtie2, with default parameters.
Genome_build: Saccharomyces cerevisiae R64-1-1
Supplementary_files_format_and_content: Reads were collapsed to the last 3´nucleotide in bedGraph
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| Submission date |
Sep 24, 2020 |
| Last update date |
Sep 25, 2020 |
| Contact name |
Vicent Pelechano |
| E-mail(s) |
vicente.pelechano.garcia@ki.se
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| Organization name |
ScilifeLab - Karolinska Institutet
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| Department |
MTC
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| Street address |
Nobels väg 16
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| City |
Solna |
| ZIP/Postal code |
SE-17177 |
| Country |
Sweden |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE158548 |
Polyadenylation site mapping of xrn1∆ in Sacchromyces cerevisiae |
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| Relations |
| BioSample |
SAMN16261115 |
| SRA |
SRX9187634 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4802673_xrn1_A_Forward.bedgraph.gz |
1.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM4802673_xrn1_A_Reverse.bedgraph.gz |
1.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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