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Sample GSM2409861 Query DataSets for GSM2409861
Status Public on Mar 20, 2017
Title Rrp6-HTP_Rrp44-exo_2
Sample type SRA
Source name BY4741-Rrp6-HTP_Rrp44-exo_2
Organism Saccharomyces cerevisiae
Characteristics cleavage site: HISx6-TEV proteas cleavage site-protA
strain: BY4741
tagged protein: Rrp6-HTP
Treatment protocol Protein-RNA complexes were stabilised by in-vivo UV crosslinking.
Growth protocol S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.
Extracted molecule total RNA
Extraction protocol UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiniSeq
Description barcode: NNNCTAGC
Data processing Library strategy: CRAC-seq
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using from pyCRAC package
Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign version 2.07.00 and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gtf format
Submission date Nov 29, 2016
Last update date May 15, 2019
Contact name Clementine Delan-Forino
Phone 01316507093
Organization name University of Edinburgh - WTCCB
Lab Tollervey lab
Street address Michael Swann Building 5.1, King's Buildings, Mayfield Road
City Edinburgh
ZIP/Postal code EH9 3JR
Country United Kingdom
Platform ID GPL22715
Series (1)
GSE90647 Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex
BioSample SAMN06067894
SRA SRX2589412

Supplementary file Size Download File type/resource
GSM2409861_Rrp6-HTP_Rrp44-exo_2.gtf.gz 1.9 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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