|
| Status |
Public on Nov 26, 2018 |
| Title |
Bound RNA in APEX2-NES cells |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
genotype/variation: T-Rex stable line inducibly expressing V5-APEX2-NES
|
| Treatment protocol |
16 hours of 4SU labeling and Dox induction, BP addition for 30 min followed by Proximity biotinylation
|
| Growth protocol |
Cells were grown and routinely passaged in DMEM supplemented with 10% FCS and 1% pen/strip, and selective agent as required.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina without rRNA depletion
Cells were extracted in RIPA buffer, RNA was isolated by Phenol-Chloroform extraction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
2016_RNAseqTotalAndBound.xlsx
2017_RNAseq_TotalAndBound.xlsx
|
| Data processing |
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat (for RNA seq) or PARalyzer (for RBP footprints)
RNAseq reads and RPKM values per gene were generated by RNAcounter
Genome_build: hg19
Supplementary_files_format_and_content: RNAcounter / PARalyzer output files
|
| |
|
| Submission date |
Feb 08, 2018 |
| Last update date |
Nov 26, 2018 |
| Contact name |
Daniel Benhalevy |
| E-mail(s) |
benhalevyd@tauex.tau.ac.il
|
| Organization name |
Tel-Aviv University
|
| Department |
Shmunis School of Biomedicine and Cancer Research
|
| Lab |
Lab for Cellular RNA Biology
|
| Street address |
Tel Aviv University, Green Bldg. Room 205
|
| City |
Tel Aviv |
| ZIP/Postal code |
6997801 |
| Country |
Israel |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE110380 |
Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale |
|
| Relations |
| BioSample |
SAMN08507253 |
| SRA |
SRX3675315 |
