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Sample GSM1707564 Query DataSets for GSM1707564
Status Public on Mar 07, 2016
Title SRSF2_iCLIP_mm9_Rep3
Sample type SRA
 
Source name P19
Organism Mus musculus
Characteristics cell line: P19 embryonal carcinoma cell line
fusion protein expression: SRSF2-GFP
antibody: anti-EGFP (D. Drechsel, MPI-CBG)
barcode sequence: CCGG
Treatment protocol Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.
Growth protocol Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody (D. Drechsel, MPI-CBG).
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was separated into 3 size fractions by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonukelotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description processed data file: mSRSF2_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF2_iCLIP_all_mm9_iCLIP_tag_clusters.bed
Data processing Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tags for individual replicates or combined replicates (3-6 replicates).
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tag clusters from combined replicates.
 
Submission date Jun 09, 2015
Last update date May 15, 2019
Contact name Michaela Müller-McNicoll
E-mail(s) [email protected]
Phone +49 69 798 42079
Organization name Goethe University Frankfurt
Department Institute for Cell Biology and Neuroscience
Lab RNA Regulation Group
Street address Max-von-Laue-Str. 13
City Frankfurt am Main
ZIP/Postal code 60438
Country Germany
 
Platform ID GPL13112
Series (2)
GSE69689 Transcriptome-wide mapping of RNA:protein interactions of seven SR proteins and NXF1 in P19 cells by iCLIP
GSE69734 SR protein family in P19 cells
Relations
BioSample SAMN03766044
SRA SRX1054342

Supplementary file Size Download File type/resource
GSM1707564_mSRSF2_Rep3_mm9_iCLIP_tags.bed.gz 85.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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