|
| Status |
Public on Oct 04, 2012 |
| Title |
KC167 PE CNV Replicate 1 extraction1_seq1 aliquote 1 |
| Sample type |
SRA |
| |
|
| Source name |
KC_PE_CNV_1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Kc167
tissue: embryo-derived cell-line
developmental stage: late embryonic stage
genotype: se/e
Sex: Female
|
| Growth protocol |
The general growth protocol for growing Drosophila cell lines in culture.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation from Drosophila cell lines. RNAse-treated cellular extract is treated with ethanol in order to precipitate DNA.
Generation of a genomic library suitable for Illumina sequencing.Generation of a genomic library suitable for Illumina sequencing. The procedure starts with random shearing of genomic DNA with sonication followed by Illumina-developed sample preparation protocol.
|
| |
|
| Library strategy |
WGS |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina HS Paired End:DM:1 protocol. Load sample onto flow cell at a (usually ~24 pM, variable) concentration and run on an HiSeq2000 with the paired-end module. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald. Processed data are obtained using following parameters: read length is 50 Bowtie alignment:DM:1 protocol. For paired end CNV:Using the default setting, Bowtie2 was used to align paired sequenced reads to the reference genome. Single end HiSeq RepliSeq:Bowtie was used to align sequenced reads to the reference genome, with the following parameters:--phred33-quals -p 6 -n 2 -l 20 -m 1 -k 1 -S -y --best --strata Processed data are obtained using following parameters: genome version is 5.1 CNV Paired End Analysis:DM:1 protocol. Read pairs deemed by Bowtie2 to be concordantly aligned, containing those that contain a positive insert length, were used to determine the genomic coverage at each base. The coverage between replicates were summed, and RPKM was then determined in 1000 bp non-overlapping windows.
|
| |
|
| Submission date |
Oct 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
DCC modENCODE |
| E-mail(s) |
[email protected]
|
| Phone |
416-673-8579
|
| Organization name |
Ontario Institute for Cancer Research
|
| Lab |
modENCODE DCC
|
| Street address |
MaRS Centre, South Tower, 101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
|
| Relations |
| SRA |
SRX193620 |
| BioSample |
SAMN01761203 |
