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Sample GSM7770905 Query DataSets for GSM7770905
Status Public on Nov 01, 2023
Title eCLIP, IP, Control 3
Sample type SRA
Source name Kidney
Organism Mus musculus
Characteristics tissue: Kidney
genotype: control
Extracted molecule other
Extraction protocol Clipseq: snap-frozen kidneys in liquid nitrogen were pulverized using a mortar and pestle, UV-crosslinked, and lysed to immunoprecipitate miRNA-mRNA-argonaute2 (Ago2) complexes with anti-Ago2. The bound RNAs in the Ago2 immunoprecipitants were further trimmed with RNA exonuclease (RNase A) and then treated with T4 polynucleotide kinase (3’ phosphatase minus) to encourage ligation between miRNA and mRNA, and then T4 RNA ligase 1 was applied to the donor of ligase RNA with 5'phosphate and the 3’OH end of the RNA acceptor in the immunoprecipitants. The resultant chimeric reads were processed for highthroughput RNA sequencing.
We followed method described by Van Nostrand et al.
Library strategy RIP-Seq
Library source other
Library selection other
Instrument model Illumina NextSeq 500
Description IP3_437_S7
Data processing library strategy: eCLIP
The adapter sequences in the raw data were trimmed using Cutadapt, and STAR was utilized for aligning paired-end (for total RNA) or single-end (for small RNA and Clipseq) sequences to the mouse genome (mm39) and quantification.
Clipseq: PCR duplicates were removed for aligned reads (non-chimeric reads) using umi-tools, and Ago2 binding site peaks were identified using CLIPper. The clusters identified in the Ago2-immunoprecipitant are then normalized against a paired input sample.
Assembly: mm39
Supplementary files format and content: Clipseq: Bigwig peaks
Submission date Sep 09, 2023
Last update date Nov 01, 2023
Contact name Sang-Ho Kwon
Phone 706-721-0379
Organization name Augusta Univeristy
Department Cellular Biology and Anatomy
Street address 1120 15th Street
City Augusta
State/province Georgia
ZIP/Postal code 30912
Country USA
Platform ID GPL19057
Series (2)
GSE242806 MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease [CLIP-seq]
GSE242809 MicroRNA-mediated attenuation of branched-chain amino acid catabolism promotes ferroptosis in chronic kidney disease.
BioSample SAMN37341363
SRA SRX21712256

Supplementary file Size Download File type/resource 17.5 Mb (ftp)(http) BW 17.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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