|
| Status |
Public on Jun 07, 2021 |
| Title |
alh-4_ko_mutant_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
alh-4_ko_mutant_whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4
strain: Bristol N2 with alh-4 deletion (hj221)
genotype: alh-4(-)
tissue: Whole body
|
| Treatment protocol |
No treatment
|
| Growth protocol |
C. elegans strains were synchronized, fed with E. coli OP50 and grown to L4 stage on standard Nematode Growth Medium (NGM) plates at 20℃ using standard protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Worms were havested freshly and snap freezed with dry ice before being lysed for library preparation
RNA libraries were prepared for sequencing using the Smart-seq2 Protocol adapted for worm RNA-seq (DOI: 10.21769/bioprotoc.2729) with the following modifications: the number of worms for each replicate and the reagent for worm lysis were scaled up by 10 fold and the worms were broken with a mini-pestle in a 1.5ml disposable tube on ice instead of cutting.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ko_mutant_rep1_S4
|
| Data processing |
Illumina bcl2fastq v2.19 with default parameters was used for basecalling to generate demultiplexed FASTQ files.
To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:20:20 MINLEN:20’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009).
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Illumina ce10 iGenome annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: ce10
Supplementary_files_format_and_content: Matrix table with FPKM value for every gene and every sample
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Jun 07, 2021 |
| Contact name |
Ho Yi Mak |
| E-mail(s) |
[email protected]
|
| Organization name |
The Hong Kong University of Science and Technology
|
| Department |
Division of Life Science
|
| Lab |
Mak Lab
|
| Street address |
Clear Water Bay
|
| City |
Hong Kong |
| ZIP/Postal code |
NA |
| Country |
China |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE162792 |
Nuclear receptor NHR-49 promotes peroxisome proliferation to compensate for aldehyde dehydrogenase deficiency in C. elegans |
|
| Relations |
| BioSample |
SAMN17016181 |
| SRA |
SRX9641625 |
