|
| Status |
Public on Jun 16, 2020 |
| Title |
RBFOX2 1100nM |
| Sample type |
SRA |
| |
|
| Source name |
predesigned sequence library using 3' UTRs from H. sapiens/M. musculus
|
| Organism |
synthetic construct |
| Characteristics |
protein concentration: RBFOX2 1100nM
|
| Treatment protocol |
Recombinantly-expressed, tagged RBFOX2 RRM was incubated at varied concentrations with 250nM synthetic RNA oligonucleotide library to equilibrium (1h 4C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RBP:RNA:bead complexes were pulled down with a magnet and washed gently 2X. RNA was eluted by two incubations with biotin for 30m at RT. RNA eluate was purified with Ampure beads.
RNA was reverse transcribed. The cDNA was amplified for 6-16 cycles and gel-purified to produce the final library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3' UTR 110-nt synthetic oligonucleotides
|
| Data processing |
Reads were aligned to the designed library.
Perfectly-mapping reads only were assigned to each oligonucleotide.
Only oligonucleotides with 100 or more attributable reads in the input RNA library were considered for further analyses.
Genome_build: 3' UTR nsRBNS library: hg19, mm9
Supplementary_files_format_and_content: Each processed data file contains the perfectly mapping reads attributable to each oligonucleotide in that sample.
|
| |
|
| Submission date |
Jun 15, 2020 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Bridget E Begg |
| E-mail(s) |
bebegg@mit.edu
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Biology
|
| Lab |
Burge Lab
|
| Street address |
31 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL19604 |
| Series (1) |
| GSE152510 |
Concentration-dependent regulation by Rbfox enabled by motifs of intermediate affinity |
|
| Relations |
| BioSample |
SAMN15239049 |
| SRA |
SRX8550192 |
