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Status |
Public on Jun 12, 2022 |
Title |
MRT_hotair_nanopore_25s |
Sample type |
SRA |
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Source name |
in vitro transcribed HOTAIR RNA
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Organism |
synthetic construct |
Characteristics |
experiment goal: cDNA length measurement reverse transcriptase: MarathonRT, 25 sec extension molecule: in vitro transcribed HOTAIR RNA
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
MinION |
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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
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Submission date |
Feb 02, 2022 |
Last update date |
Jun 12, 2022 |
Contact name |
Li-Tao Guo |
E-mail(s) |
li-tao.guo@yale.edu
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Organization name |
Yale University
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Street address |
260 Whitney Ave
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City |
New Haven |
State/province |
Connecticut |
ZIP/Postal code |
06511 |
Country |
USA |
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Platform ID |
GPL25738 |
Series (1) |
GSE195979 |
Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules |
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Relations |
BioSample |
SAMN25599255 |
SRA |
SRX14023580 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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