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Sample GSM4748613 Query DataSets for GSM4748613
Status Public on Aug 01, 2021
Title f5C_spikein_70C_DMSO
Sample type SRA
 
Source name Spike-In RNA oligos
Organism synthetic construct
Characteristics genotype: n/a
cell line: n/a
cell type: n/a
rna population: Spike-In RNA oligo
Extracted molecule total RNA
Extraction protocol Libraries were prepared according to Illumina's instructions
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 5fC_calibration_curve.xlsx, 5fC_SpikeIn_context.xlsx
Data processing Basecalls performed using CASAVA version 1.4
Low-quality and adapter-containing reads were trimmed from Spike-In oligos raw sequencing data using trim-galore package in single-end mode. Reads shorter than 50 bp were removed.
We used fastx_collapser in FASTX-toolkit to collapse identical sequences in a fastq file into a single sequence, which was used to remove duplicated reads from PCR amplification.
For the reason of In-line barcode design in the Spike-In libraries, First 5bp bases and last 11bp bases were cut from the collapsed reads.
The modified reads were finally used to calculate mutation rates based on different sequence context and generate the calibration curve.
Genome_build: Spike-In sequence
Supplementary_files_format_and_content: xlsx/calibration curve&Spike-In context
Library strategy: f5C-seq
 
Submission date Aug 26, 2020
Last update date Aug 01, 2021
Contact name Ruitu Lyu
E-mail(s) lvruitu@uchicago.edu
Organization name The University of Chicago
Department Chemistry
Lab Chuan He
Street address 929 E 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL26526
Series (1)
GSE156933 A Quantitative Sequencing Method for 5-Formylcytosine in RNA
Relations
BioSample SAMN15914525
SRA SRX9014802

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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