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Sample GSM5857213

Query DataSets for GSM5857213

Status

Public on Jun 12, 2022

Title

MRT_hotair_nanopore_25s

Sample type

SRA

Source name

in vitro transcribed HOTAIR RNA

Organism

synthetic construct

Characteristics

experiment goal: cDNA length measurement
reverse transcriptase: MarathonRT, 25 sec extension
molecule: in vitro transcribed HOTAIR RNA

Extracted molecule

other

Extraction protocol

cDNA was prepared using gene-specific RT primers. For nanopore sequencing, the cDNA was first converted to double-stranded DNA, and then Oxford Nanopore Ligation Sequencing Kit and Native Barcoding were used to construct the libraries. For Illumina TruSeq, Illumina TruSeq forward primer and indexed reverse primers were used to build the libraries.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

MinION

Data processing

For nanopore sequencing, Guppy (v2.2.3) was used for base calling, Porechop (v0.2.4) for adapter removal, and ngmlr (v0.2.7) for alignment. Customized Python scripts were used for data analysis.
For Illumina TruSeq, cutadapt (v1.9.1) was used for adapter removal, HISAT2 (v2.1.0) used for alignment, and RTEventsCounter.py used for data analysis

Submission date

Feb 02, 2022

Last update date

Jun 12, 2022

Contact name

Li-Tao Guo

E-mail(s)

li-tao.guo@yale.edu

Organization name

Yale University

Street address

260 Whitney Ave