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Sample GSM2236754 Query DataSets for GSM2236754
Status Public on Feb 10, 2017
Title In vitro degradation of randomized RNA substrate_16549
Sample type SRA
 
Source name synthetic RNA oligo NNNN-3´
Organism synthetic construct
Characteristics sample group: 10 min treatment with FLAG-dmDis3l2
molecule subtype: synthetic randomized RNA NNNN3´
Extracted molecule total RNA
Extraction protocol 10 min treatment with FLAG-dmDis3l2, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description 30-40 nt size selection
Data processing The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1). The random 4mers on the 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). Sequences with exact 4nt length were counted and the reads per million for each 4mer was calculated.
library strategy: synthetic RNA seq
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TXT (RPM): tab separated text containing 4mer and it's RPM (read per million); TXT (SEQCNT) tab separated text file containing alignment position, feature, tail statistics and count; XLSX: Excel file containing summary statistics (length, nt count, nt count from 3' to 5')
 
Submission date Jul 15, 2016
Last update date May 15, 2019
Contact name Thomas Rainer Burkard
E-mail(s) thomas.burkard@imba.oeaw.ac.at
Organization name IMBA
Street address Dr. Bohrgasse 7
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platform ID GPL19604
Series (1)
GSE84466 Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila
Relations
BioSample SAMN05407999
SRA SRX1951556

Supplementary file Size Download File type/resource
GSM2236754_16549.rpm.txt.gz 3.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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