|
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 |