|
| Status |
Public on Apr 17, 2014 |
| Title |
C.remanei male rep 1 DNAseq |
| Sample type |
SRA |
| |
|
| Source name |
whole worms
|
| Organism |
Caenorhabditis remanei |
| Characteristics |
strain: PB4641
developmental stage: young adult
|
| Treatment protocol |
Worms were hand picked into 1X M9. Worms were washed 3 times by settling with TE. Worms were suspended in 100uL TE and stored at -80C until DNA isolation.
|
| Growth protocol |
Worms were synchronized by bleaching gravid adults grown on plates at 20C temperature. Embryos were hatched overnight and starved as L1s. L1s were plated and grown to indicated stage at 20C temperature.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
staging protocol: 50 -100 young adults were hand picked from mixed stage plates.
400uL of Worm Lysis Buffer (0.1M TrisHCl; 0.1M NaCl; 50mM EDTA; 1.25%SDS) was added before sonicating to obtain chromatin fragments of majority size of between 200 and 800 bp.
Isolate DNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
DNA seq reads were aligned to genome version WS228 with Bowtie version 0.12.7 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
DNA seq bam files were sorted and used to generate bedgraph files (bedtools version 2.15.0)
RNA seq reads were aligned to genome version WS228 with tophat version 2.0.0
Using RNAseq bam files, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.0.2 using default parameters supplying gene annotations for WS228.
Genome_build: WS228
|
| |
|
| Submission date |
Dec 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah Elizabeth Albritton |
| Organization name |
New York University
|
| Department |
Biology
|
| Lab |
Ercan
|
| Street address |
100 Washington Square East 1009 Silver Center
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003-6688 |
| Country |
USA |
| |
|
| Platform ID |
GPL16141 |
| Series (1) |
| GSE53144 |
Male and Female DNA and RNA sequencing in several nematode species |
|
| Relations |
| BioSample |
SAMN02484497 |
| SRA |
SRX397070 |
