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Sample GSM821480 Query DataSets for GSM821480
Status Public on Oct 25, 2011
Title sampling retroviral library
Sample type SRA
Source name haploid mouse ES cells
Organism Mus musculus
Characteristics cell type: haploid mouse ES cells
retrovirus used: reFlipROSAß-Geo(Cre)
selection: G418
transfection batch: FS6
Treatment protocol selection was performed with G418 or ricinus communis
Growth protocol ES cells were grown in standard ES cell medium
Extracted molecule genomic DNA
Extraction protocol inverse PCR: In brief, genomic DNA preparations were digested using DpnII or MseI, purified using the QIAquick Gel Extraction Kit, and fragments ligated at a concentration of 3µg/ml over night. The ligase was then heat inactivated and rings were re-digested in ligase buffer using the enzymes NheI and PvuII. Linearized fragments were purified using the QIAquick Gel Extraction Kit and subjected to PCR using Accuprime Taq polymerase (Invitrogen), primers FS Solexa upstream and FS Solexa downstream, and a BioRad Thermal Cycler. The program of 95ºC for 30 sec, 60ºC for 30 sec, and 68ºC for 105 sec was repeated 36 times. Amplicons were loaded on agarose gels, eluted and subjected to deep sequencing using an Illumina Genome Analyzer and primer FS flowcell. The following iPCR primers were used: upstream primer AATGATACGGCGACCACCGAGATCGCCAGTCCTCCGATTGA downstream primer CAAGCAGAAGACGGCATACGAGTTCCTATTCCGAAGTTCCTATTCTCTA flowcell sequencing primer TGATTGACTACCCGTCAGCGGGGGTCTTTCA
Library strategy OTHER
Library source genomic
Library selection PCR
Instrument model Illumina Genome Analyzer IIx
Description sampling retroviral library
Data processing Illumina GA Pipeline RTA 1.8.7; reads were mapped to the mouse mm9 genome using bowtie 0.12.5
Submission date Oct 24, 2011
Last update date May 15, 2019
Contact name Ulrich Elling
Organization name IMBA
Lab Penninger
Street address Dr. Bohr-Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
Platform ID GPL11002
Series (1)
GSE33184 Retroviral mutagenesis in haploid ES cells
SRA SRX104121
BioSample SAMN00749868

Supplementary file Size Download File type/resource
GSM821480_ricinus_mapping.txt.gz 43.2 Mb (ftp)(http) TXT
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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