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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 01, 2023 |
| Title |
eCLIP, IP, Control 2 |
| Sample type |
SRA |
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| Source name |
Kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: Kidney
genotype: control
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| 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.
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| Library strategy |
RIP-Seq |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
IP2_435_S6
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| 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
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| Submission date |
Sep 09, 2023 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Sang-Ho Kwon |
| E-mail(s) |
kkwon@augusta.edu
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| Phone |
706-721-0379
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| Organization name |
Augusta Univeristy
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| Department |
Cellular Biology and Anatomy
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| Street address |
1120 15th Street
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| City |
Augusta |
| State/province |
Georgia |
| ZIP/Postal code |
30912 |
| Country |
USA |
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| 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. |
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| Relations |
| BioSample |
SAMN37341364 |
| SRA |
SRX21712255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7770904_IP2_435_S6_R1_001.CombinedID.merged.r2.norm.neg.bw |
20.6 Mb |
(ftp)(http) |
BW |
| GSM7770904_IP2_435_S6_R1_001.CombinedID.merged.r2.norm.pos.bw |
21.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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