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Sample GSM776820 Query DataSets for GSM776820
Status Public on Aug 12, 2011
Title Sleeping Beauty induced lymphoma (BfaI sample 118)
Sample type SRA
 
Source name LYMPHOMA LIVER
Organism Mus musculus
Characteristics strain: mixed C57Bl6/129S5SvEvBrd
mouse id#: 117235
transposon: Sleeping beauty
Extracted molecule genomic DNA
Extraction protocol Isolation of gDNA and ligation-mediated amplification of regions flanking retroviral insertions after endonucelase digestion or acoustic shearing of gDNA. Subsequently, barcoded PCR products were pooled and sequenced on a 454 GS_FLX system according to the manufacturers protocol.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model 454 GS FLX
 
Description Barcode sequence: TAGTATCAGC
BfaI sample 118
Processed data file: Insertions_Bfa.bed
Processed data file build: NCBI m37
Original raw file name: Pool15.BfaI.sff
library strategy = barcode; library selection = LIGATION MEDIATED PCR
Data processing Sequence reads are mapped to NCBI m37 using BLAT, sorted on barcode and processed using custom made algortihms as described in the associated manuscript. All scripts available on request. The export.txt files contain a summary of all unique integration sites. Per integration site 1 read ID is shown together with the cumulative number of sequence reads (depth), without specifying the individual read IDs per integrations site.
 
Submission date Aug 10, 2011
Last update date May 15, 2019
Contact name Jos Jonkers
E-mail(s) j.jonkers@nki.nl, m.koudijs@nki.nl
Phone +31 20 5122000
Organization name Netherlands Cancer Institute
Department Molecular Biology
Lab Jonkers lab
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platform ID GPL9273
Series (1)
GSE22657 High-throughput semi-quantitative analysis of insertional mutations in heterogeneous tumors
Relations
SRA SRX097941
BioSample SAMN00722318

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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