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Sample GSM2236753 Query DataSets for GSM2236753
Status Public on Feb 10, 2017
Title In vitro degradation of randomized RNA substrate_16548
Sample type SRA
Source name synthetic RNA oligo NNNN-3´
Organism synthetic construct
Characteristics sample group: 2 min sec treatment with FLAG-dmDis3l2
molecule subtype: synthetic randomized RNA NNNN3´
Extracted molecule total RNA
Extraction protocol 2 min sec 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
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
BioSample SAMN05407998
SRA SRX1951555

Supplementary file Size Download File type/resource
GSM2236753_16548.rpm.txt.gz 3.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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