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Sample GSM2989391 Query DataSets for GSM2989391
Status Public on Nov 26, 2018
Title RBPs footprints 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 Preadenylated, barcoded 3┬┤adapter oligonucleotide was ligated followed by ligation of a 5┬┤adapter. Ligation products were reverse transcribed and amplified by PCR.
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 Pooled_LongAndShortFootprintsAnalysis.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 SAMN08507256
SRA SRX3675319

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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