|
| Status |
Public on Aug 18, 2020 |
| Title |
ce_hermaphrodite_whole_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
grown on lawn of Esherichia coli (op50)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: him-8
genotype: him-8(me4)IV
developmental stage: young adult
tissue: whole body
|
| Treatment protocol |
S. carpocapsae IJs were cultured with Xenorhabdus nematophila and collected at the IJ or young adult stage. C. elegans strain him-8 young adults were grown on Escherichia coli (op50) and collected at young adult stage. C.elegans strain N2 dauers were starved for 16 weeks at 25° C, confirmed phenotypically and collected.
|
| Growth protocol |
For S.carpocapse as described in Serra L, Chang DZ, Macchietto M, et al. Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq. Bio-protocol. 2018;8(4). doi:10.21769/BioProtoc.2729. For C.elegans as described in Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974;77(1):71-94. http://www.ncbi.nlm.nih.gov/pubmed/4366476.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PolyA RNA unstranded, paired-end, read_length= 43 bp
|
| Data processing |
Unstranded, paired-end 43 bp RNA-seq reads for each worm were mapped to the S. carpocapsae genome using Bowtie 1.0.0 with the following options: -X 1500 -a -m 200 --S -- seedlen 25 -n 2 --offrate 1 -p 64 -v 3 (Langmead et al. 2009). After Bowtie, gene expression was quantified with RSEM with the following options: rsem-calculate-expression -- bam -- paired-end. Gene expression for S. carpocapsae were performed as previously described (Lu et al. 2017) and reported in Transcripts Per Million (TPM). We used counts for differential gene expression analysis.
The Transcript per million (TPM) generated by rsem-calculate-expression for S. carpocapsae samples were normalized according to groups using the R package limma (Ritchie et al., 2015) because samples were collected, processed and sequenced in different batches.
|
| |
|
| Submission date |
Aug 17, 2020 |
| Last update date |
Aug 18, 2020 |
| Contact name |
Ali Mortazavi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and cell biology
|
| Lab |
Mortazavi
|
| Street address |
2300 Biological Sciences 3
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE156356 |
Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans |
|
| Relations |
| BioSample |
SAMN15832738 |
| SRA |
SRX8957167 |
