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Sample GSM896525 Query DataSets for GSM896525
Status Public on Jul 23, 2012
Title N21-HD-r1
Sample type SRA
Source name Random oligo, 21 nucleotides
Organism synthetic construct
Characteristics adapters: HD
length: 21
molecule: Random oligo, 21 nucleotides
Extracted molecule total RNA
Extraction protocol For N9 RNA and N21 RNA cloning for NGS approximately 3 and 100 pmoles of oligonucleotide were used respectively. Library preparation was based on the Illumina small RNA v1.5 sample preparation guide. RNA was ligated to the pre-adenylated 3' adapter (custom synthesised by Bioo Scientific) with T4 Rnl2 truncated ligase (NEB). The ligated fragment was then ligated to the 5' adapter (Dharmacon) using T4 Rnl1. For Illumina protocol recommended adapter sequences were used. For HD protocol four degenerate nucleotides (with uniform probability distribution) were added both to the 5' end of the 3' adapter and to the 3 end of the 5' adapter. The ligated fragment was then reverse transcribed using the SRA RT primer followed by 8-14 cycles of PCR. The PCR products were size fractionated by polyacrylamide gel electrophoresis (8% PAGE). A band corresponding to approximately 100bp was gel purified and sent for NGS sequencing on a Illumina Genome Analyzer IIx with 50 nt read length (Baseclear).
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina Genome Analyzer II
Description Random oligo, 21 nucleotides, HD protocol, replicate 1
Data processing 3' adapter was trimmed, reads summarized after adapter trimming
Submission date Mar 15, 2012
Last update date May 15, 2019
Contact name Helio Pais
Organization name University of Oxford
Department Weatherall Institute of Molecular Medicine
Street address Jonh Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL9423
Series (1)
GSE36540 Sequencing random oligonucleotides using standard GA II protocol
SRA SRX129974
BioSample SAMN00828818

Supplementary file Size Download File type/resource
GSM896525_N21-HD-r1.csv.gz 65.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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