|
| Status |
Public on Jun 01, 2019 |
| Title |
smn-1(ok355) rep1 |
| Sample type |
SRA |
| |
|
| Source name |
worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: smn-1(ok355)
developmental stage: day 2 post the L1 larval stage at 20C
|
| Treatment protocol |
Animals were washed with M9 three times and left in M9 for three hours to remove intestinal bacteria.
|
| Growth protocol |
Mutants or wild-type animals were synchronized by bleaching and allowed to grow for 2 days post the L1 larval stage at 20℃.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted using TRI Reagent Solution according to manufacturer’s instructions (Invitrogen).
mRNA was enriched with oligo(dT) beads. RNA libraries were prepared using standard illumina protocols.The constructed libraries were sequenced as 150 bp paired-ends on Illumina platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base-calling was performed using CASAVA software.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows: 1) Remove the adaptor-polluted reads (Reads containing more than 5 adaptor-polluted bases were regarded as adaptor-polluted reads and would be filtered out). 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads. 3) Remove reads with number of N bases accounting for more than 5 %. As for paired-end sequencing data, both reads would be filtered out if any read of the paired-end reads are adaptor-polluted.
Bowtie/Bowtie2 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
Fragments Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was calculated to estimate the expression level of genes in each sample.
Genome_build: WBcel235
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Sep 21, 2018 |
| Last update date |
Jun 03, 2019 |
| Contact name |
Long Ma |
| E-mail(s) |
malong@sklmg.edu.cn
|
| Organization name |
Central South University
|
| Street address |
110 Xiangya Road, Kaifu District
|
| City |
Changsha |
| ZIP/Postal code |
410008 |
| Country |
China |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE120335 |
Defective expression of mitochondrial, histone and vesicle genes in a C. elegans SMA model |
|
| Relations |
| BioSample |
SAMN10105951 |
| SRA |
SRX4730253 |
