NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2087321 Query DataSets for GSM2087321
Status Public on Sep 05, 2016
Title DCKO iCLIP
Sample type SRA
 
Source name thymus
Organism Mus musculus
Characteristics cell type: total naive thymocytes
genotype: DCKO
strain: C57BL/6JBabr
Treatment protocol Intact cells were irradiated with UV-light (300 mJ/cm2, Stratalinker 2400)
Extracted molecule total RNA
Extraction protocol Cells were lysed and ZFP36L1-RNA complexes were pulled down with Brf1/2 antibody using protein A Dynabeads. RNA-protein complexes were run on an SDS-PAGE gel, transfered to nitrocellulose and visualised by radiolabelling a proportion of the immunoprecipitated material. Correctly sized complexes were cut out of the membrane and used to generate libraries.
Wild-type cDNA libraries from two independent experiments and a DCKO cDNA library from one experiment were prepared using the RCLIP primers indicated and sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing). RCLIP primers used for RNA reverse transcription included a barcode at the 5’end with three known bases and four random nucleotides
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: iCLIP-Seq
Libaries were sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing)
Basecalling was done using Illumina default pipeline
Sample demultiplexing was performed by identification of the 3 known bases of the 7 bases barcode introduced in the 5’ end of the read by the RCLIP primer. The remaining four random bases were used to remove PCR duplicate reads
Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome GRCm38 using Bowtie
Identification of highly significant ZFP36L1 binding sites was performed using iCount to assign a FDR to each crosslink site. Data generated by having sequenced the same sample on two lanes (sample 2 and sample 3) was merged during iCOUNT processing.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated text file includes output from iCOUNT pipeline
 
Submission date Mar 14, 2016
Last update date May 15, 2019
Contact name Martin Turner
E-mail(s) martin.turner@babraham.ac.uk
Organization name Babraham Institute
Department Lymphocyte Signalling and Development
Lab Dr. Martin Turner
Street address Babraham Hall
City Cambridge
ZIP/Postal code CB22 3AT
Country United Kingdom
 
Platform ID GPL13112
Series (2)
GSE79178 Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice. [iCLIP]
GSE79179 Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice
Relations
BioSample SAMN04549424
SRA SRX1630327

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap