|
| Status |
Public on Jan 03, 2014 |
| Title |
Myc_FIbro3 |
| Sample type |
SRA |
| |
|
| Source name |
SV40-transformed tail fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: c-myc25xI;RosaI-SceI-GR
activation protocol: none
cell type: SV40-transformed tail fibroblasts
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in the presence of proteinaseK, and genomic DNA was Ethanol-precipitated, then resuspended. Genomic DNA was sonicated to fragment size 200-500bp.
HTGTS libraries were constructed with the adapter-PCR method as described in Chiarle et al., Cell, 2011. Libraries were prepared for sequencing with MiSeq Illumina kit MS-102-2003, according to instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: HTGTS
Standard basecalling formats for Miseq reads
Paired end reads required trimming and stitching using ea-utilsv1.1.2 (http://code.google.com/p/ea-utils) followed by CD-HITv4.5 (Li & Godzik, Bioinformatics 2006) to remove 100% duplicates
Miseq reads are aligned using Blat (Kent, Genome Research 2002). Reads containing artifacts or duplicate junctions were removed.
For alignment of reads from IgH B and T cell libraries, the reference genome was modified to delete the Smu region (chr12:114661018-114664694) and include an I-SceI site target (sequence: TCGAGGTCGAAATAGGGATAACAGGGTAATAATTATTACCCTGTTATCCCTAAATCGACCCTAGTGGGGGCGCCAAGTTAGCTTGGCTGGACGTAAACTCCTCTTCAGACCTAATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTATTGAATATGATCGGAATTCCTCGACATCGATGCATCGATGCATCGATGCATCGATGTCGAGT) at position chr12:114661018
For alignment of reads from c-myc B cell libraries, the reference genome was modified to include an I-SceI site target (sequence: GATCGAATTCGTCGACCGCCGCTAATTCCGATCATATTCAATAACCCTTAATATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCCCTCGAGGAATTCTGCAGATTAGGGATAACAGGGTAATAATTATTACCCTGTTATCCCTAATCCATCACACTGGCGGCCC) at position chr15:61914629
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files containing filtered unique junctions and including the following information: sequence ID (Qname); blat score (score); beginning (Qstart) and end (Qend) nucleotide position within the read of alignment; orientation of junction (strand); chromosome (Tname) and position (Tstart and Tend) of alignment to the genome build; the entire read sequence (raw) including stitched paired end reads; and the RefGene feature the alignment is associated with (Genes; NA=no annotation)
|
| |
|
| Submission date |
Jan 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Frederick Alt |
| Organization name |
Boston Children's Hospital
|
| Department |
Program in Cellular and Molecular Medicine
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE53755 |
Long-range joining of intra-chromosomal DNA double-strand breaks |
|
| Relations |
| BioSample |
SAMN02566797 |
| SRA |
SRX403893 |
