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| Status |
Public on May 11, 2016 |
| Title |
ZZY10330 rep1 |
| Sample type |
SRA |
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| Source name |
whole worm
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| Organism |
Caenorhabditis nigoni |
| Characteristics |
strain: ZZY10330
Stage: young adult male
genotype/variation: Mostly C. nigoni genome, with X chromosome syntenic region replaced by C. briggsae X chromosome (from 16.4 M to the end)
phenotype: sterile
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| Extracted molecule |
total RNA |
| Extraction protocol |
300 young adult males were picked for mRNA extraction for each sample for C. briggsae (AF16), C. nigoni (JU1421), ZZY10307 and ZZY10330 with three replicates each. For collection of ZZY10307 and ZZY10330 young adult males, fertile females that carry the introgression were mated with JU1421 males. The male progeny that carry the introgression as judged by the expression of cbr-myo-2::GFP were picked under a fluorescence microscope for mRNA extraction. Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s instructions. Illumina’s TruSeq Stranded mRNA Library Preparation Kit was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Illumina MiSeq with v2 chemistry and software MCS v2.3.0.3 used for basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic, then mapped to to C. briggsae genome (cb4) using CLC genomic workbench 8.0. The genome sequence and gene GFF annotation files were obtained from WormBase (WS250). The cutoff for C. nigoni reads are at least 85% similarity and 80% length while for C. birggsae reads, the cutoff are 90% similarity and 85% length. To de novo annotate putative TEs, RepeatMolder was run with the genome of C. nigoni (cn1, this study) and C. briggsae genome (cb4) as an input, respectively using default parameters. The consensus sequences of TEs produced were used as input to RepeatMasker to annotate all the possible TE loci over the two genomes. RMblast was used in the two annotation pipelines to align genome sequence against possible TEs. For the TE quantification, we mapped all reads from mRNAs against the consensus sequences of as described above using CLC genomic workbench 8.0, with a cutoff of at least 75% similarity and 75 % length.
The unique reads mapped to each genes/TEs were then counted with CLC genomic workbench 8.0. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with R package edgeR.
Genome_build: cb4
Supplementary_files_format_and_content: tab-delimited text files include unique reads mapped values for each sample
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| Submission date |
Dec 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Runsheng Li |
| E-mail(s) |
runsheng.lee@gmail.com
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| Phone |
0085255174247
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| Organization name |
City University of Hong Kong
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| Lab |
Room 2-502, 5/F, Block 2, To Yuen Building
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| Street address |
To Yuen Building, 31 To Yuen Street, City University of Hong Kong
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| City |
Hong Kong |
| ZIP/Postal code |
00852 |
| Country |
Hong Kong |
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| Platform ID |
GPL21276 |
| Series (1) |
| GSE76306 |
Analysis of Hybrid Incompatability between C nigoni and C briggsae by mRNA sequencing |
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| Relations |
| BioSample |
SAMN04365169 |
| SRA |
SRX1500350 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1980043_ZZY10330_1_TE.txt.gz |
3.6 Kb |
(ftp)(http) |
TXT |
| GSM1980043_ZZY10330_1_gene.txt.gz |
80.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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