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Sample GSM8171707 Query DataSets for GSM8171707
Status Public on Jul 29, 2024
Title 100vertRBNS input
Sample type SRA
 
Source name in vitro large scale binding experiment, input
Organisms Pan troglodytes; Homo sapiens
Characteristics cell type: 100vertRBNS input
Extracted molecule total RNA
Extraction protocol Bound RNA was eluted from streptavidin magnetic beads in 4 mM biotin (nsRBNS) or 0.1% SDS with 0.3 mg/mL proteinase K (100vertRBNS). RNA was concentrated via phenol-chloroform extraction
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Reads were trimmed using fastx_toolkit before mapping with STAR to generate counts
Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: Custom genome (see supplementary files)
Supplementary files format and content: tab-delimited text file includes enrichment values for each sample
 
Submission date Mar 27, 2024
Last update date Jul 29, 2024
Contact name Daniel Dominguez
Organization name UNC Chapel Hill
Department Pharmacology
Lab Dominguez Lab
Street address 120 Mason farm
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL34340
Series (1)
GSE262560 Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro
Relations
BioSample SAMN40626347
SRA SRX24072148

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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