|
| Status |
Public on Apr 01, 2022 |
| Title |
blmp1_rep_3 |
| Sample type |
SRA |
| |
|
| Source name |
young adult animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: blmp-1(s71)
developmental stage: young adult animal
|
| Growth protocol |
Embryos were isolated by bleach treatment and synchronized L1 were grown on NGM plates to the young adult stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Invitrogen TRIzol Reagent
Library construction was created using TruSeq RNA Sample Preparation Kits (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Transcriptome sequence reads were initially quality and adaptor trimmed using Trimmomatic (v0.36; parameter used: ILLUMINACLIPTruSeq2-PE.fa:2:40:12:8:true LEADING:10 TRAILING:10 SLIDINGWINDOW:3:15 MINLEN:34)
Pair-end reads were mapped to C. elegans reference with HISAT2 (v2.1.0)
Read counts of individual genes were obtained using featureCounts (v1.6.3)
Differential expressions between wild type and blmp-1 mutant strain were determined with DESeq2 (v1.22.0; padj < 0.05 and FDR > 2)
Genome_build: Wormbase (WS267)
Supplementary_files_format_and_content: CPM and TPM of genes were listed in csv file
|
| |
|
| Submission date |
Jul 04, 2021 |
| Last update date |
Apr 03, 2022 |
| Contact name |
Yi-Chun Wu |
| E-mail(s) |
yichun@ntu.edu.tw
|
| Organization name |
National Taiwan University
|
| Department |
Institute of Molecular and Cellular Biology
|
| Street address |
No. 1 Sec. 4 Roosevelt Road
|
| City |
Taipei |
| ZIP/Postal code |
10617 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL15716 |
| Series (1) |
| GSE179411 |
RNA-seq analysis of wild-type and blmp-1(s71) young adult mutant |
|
| Relations |
| BioSample |
SAMN20056938 |
| SRA |
SRX11349173 |
