|
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 |