|
| Status |
Public on Jul 29, 2024 |
| Title |
UNK 100vertRBNS, 100nM, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
in vitro large scale binding experiment
|
| Organisms |
Pan troglodytes; Homo sapiens |
| Characteristics |
cell type: UNK 100vertRBNS
|
| 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 |
SAMN40626348 |
| SRA |
SRX24072147 |
