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SRX10021309: GSM5064745: KARR-seq F123 in vivo G3 Rep 1; Mus musculus; OTHER
1 ILLUMINA (Illumina NovaSeq 6000) run: 37.2M spots, 3.1G bases, 1.2Gb downloads

Submitted by: NCBI (GEO)
Study: KARR-seq reveals principles of high-order ribonucleoprotein structure assembly
show Abstracthide Abstract
We designed KARR-seq, which reveals RNA-RNA interactions transcriptome-wide. The frequency of KARR-seq chimeras accurately reveals the physical distances between RNAs in vivo. Using KARR-seq, we systematically analyzed celullar effect on RNA-RNA interactions. Overall design: KARR-seq were performed in difference cell lines under normal or treatment conditions. Treatments include knocking down selective RBPs, adding tranlation inhibitors, adding arsenite stress, etc. KARR-seq for in vitro refolded RNA and intact nuclei were also perfromed.
Sample: KARR-seq F123 in vivo G3 Rep 1
SAMN17792690 • SRS8196618 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: Resuspend cell pellets in 410 µL 25 mM K3BO3, with 50 µL 10% SDS, 30 µL proteinase K, 10 µL RNase inhibitor. The mixture was shaken at 55 ˚C for 2 h and was subjected to phenol-chloroform extraction and ethanol precipitation. Extracted RNA were used for enrichment, end repair, and proximity ligation. Libraries were conctructed by using the SMARTer Stranded Total RNA-seq kit v2 – pico input mammalian.
Experiment attributes:
GEO Accession: GSM5064745
Links:
Runs: 1 run, 37.2M spots, 3.1G bases, 1.2Gb
Run# of Spots# of BasesSizePublished
SRR1362828137,196,1073.1G1.2Gb2023-12-07

ID:
13148723

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