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Sample GSM7349554 Query DataSets for GSM7349554
Status Public on Jan 31, 2024
Title MCP-SECURE rAPOBEC1 (R33A/K34A)_Replicate-2
Sample type SRA
 
Source name Kidney
Organism Homo sapiens
Characteristics tissue: Kidney
cell line: HEK293XT
cell type: immortalized cell line
rbp-rbe fusion: MCP-SECURE rAPOBEC1 (R33A/K34A)
replicate: 2
treatment: doxycycline-induced expression
Extracted molecule total RNA
Extraction protocol Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Nextera XT DNA Library Preparation Kit (Illumina, Cat # FC-131-2002 or Cat # FC-131-1024)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing remove adapter with Cutadapt
align to genome using bowtie2 or bwa-mem
generate count tables along reporter sequence using Pysamstats
Assembly: 12X MS2 stem-loop reporter mRNA
Supplementary files format and content: pysamstats tables that contain the read counts for RNA bases at each position along the reporter mRNA sequence
 
Submission date May 15, 2023
Last update date Jan 31, 2024
Contact name Brian Yee
E-mail(s) brian.alan.yee@gmail.com
Organization name UCSD
Department Health
Lab Yeo
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL15520
Series (2)
GSE232513 Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1)
GSE232520 Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies
Relations
BioSample SAMN35084893
SRA SRX20341231

Supplementary file Size Download File type/resource
GSM7349554_B2_S12.pysam.tsv.gz 59.3 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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