|
| Status |
Public on Sep 08, 2010 |
| Title |
Normal tail tissue, specimen "G2_1-2" |
| Sample type |
SRA |
| |
|
| Source name |
Tail from adult fish
|
| Organism |
Danio rerio |
| Characteristics |
strain: Zebrafish TAB strain
age: 8-24 month
tissue: Tail
tumor type: n/a
|
| Growth protocol |
Fish were kept according to standard conditions described in: The Zebrafish Book: A Guide for the Laboratory use of Zebrafish (Danio rerio), Monte Westerfield - 1995 - Univ. of Oregon Press
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples for sequencing with the Illumina Genome Analyzer IIx system were prepared from the same batches of genomic DNA used for array-CGH, according to published methods (Quail MA, et al.(2008, PMID:19034268); Bentley DR, et al. (2008, PMID:18987734); Quail MA, etal. (2009, PMID: 19582764)). All the enzymes used in the preparation were from New England Biolabs, and the oligonucleotides were synthesized by Eurofins MWG Operon. Oligonucleotide sequences (ATTGGC; GATCTG; TCAAGT; CTGATC; AAGCTA; GTAGCC; TACAAG; CGTGAT; ACATCG; GCCTAA; TGGTCA; CACTGT) were added to the 3' end of the Illumina adaptors used for the paired-end library preparation in order to serve as barcodes so that multiple samples could be sequenced in the same reaction.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
raw file comprises 3 runs.
raw file run tags in fastq file: sp733 / sp741 / sp746
|
| Data processing |
Raw data generation: Sequencing was performed on an Illumina GAIIx Sequencer using Sequence Control Software v2.6.26. Sequences were processed with either Bustard.py (OLB 1.6.0) or GERALD.pl (CASAVA 1.6.0), downloaded from the Illumina website (http://www.illumina.com/software/genome_analyzer_software.ilmn), with a produced read length of 41 nucleotides. FASTQ sequence files were split into sample-specific subsets according to a barcode strategy and then barcodes were trimmed from the sequences using the applications fastx_barcode_splitter.pl and fastx_trimmer from the fastx_toolkit- 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/ ) package. Illumina sequence qualities were converted to Sanger sequence qualities using the MAQ application fq_all2std.pl (http://maq.sourceforge.net/qual.shtml ).
Processed data generation: Sequences were aligned to chromosomes in the zebrafish Zv8/danRer6 assembly using bwa0.5.7. Unassembled "scaffold" and "NA" fragments were not included in the alignment target. Alignments with quality scores of 10 or greater were extracted from the resulting SAM files, and counts were obtained for the number of reads aligning to consecutive, adjacent 100KB physical windows along the genome. Note that this data is not yet rescaled or normalized!
see readme.txt on the Series record for additional details
|
| |
|
| Submission date |
Aug 25, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Sebastian Hoersch |
| Organization name |
Massachusetts Institute of Technology
|
| Department |
David H. Koch Institute for Integrative Cancer Research at MIT
|
| Lab |
Bioinformatics and Computing Core
|
| Street address |
77 Massachusetts Avenue (E18-366)
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02474 |
| Country |
USA |
| |
|
| Platform ID |
GPL9319 |
| Series (1) |
| GSE23666 |
Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers |
|
| Relations |
| SRA |
SRX026697 |
| BioSample |
SAMN00113240 |
