|
| Status |
Public on Jan 05, 2022 |
| Title |
wild-type normal condition (OP50)_1 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: wild-type (bristol)
treatment: normal condition
developmental period: L4
|
| Treatment protocol |
L4 wroms were washed off plates by M9 and clean up 3 times by M9, then transfer to slow-killing plate (SK) with OP50 or P.A14, and maintained at 20℃ for 2 hrs before samples collection. SK plate were seeded with OP50 or P.A14 48 hrs before use, and maintained at 37℃, 24 hrs before use, plates were moved to 20 ℃.
|
| Growth protocol |
Worms were fed on OP50 (normal food) on nematode growth medium (NGM) at 20℃ until L4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted by Trizol reagent and chloroform extraction.
1)mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA (For total RNA extracted from human whole blood, globin mRNA are depleted ); 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB; 6) Sequencing on DNBSEQ platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
raw sequencing data was aligned to C. elegans genome reference (ce11) by HISAT2 (version 2.1.0) with default settings
duplicated reads or reads with low mapping quality (<30) were removed using samtools version 1.9
the filtered reads were counted at the gene level using featureCount version 1.6.3
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files containing gene expression counts
|
| |
|
| Submission date |
Jan 02, 2022 |
| Last update date |
Jan 06, 2022 |
| Contact name |
Guan Jialiang |
| E-mail(s) |
guanjialiang@pku.edu.cn
|
| Phone |
18800192720
|
| Organization name |
Peking University
|
| Street address |
China, Beijing, Haidian district, Peking University, 1000871
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL30091 |
| Series (1) |
| GSE192901 |
Transcriptome sequencing of bristol strain (wild-type), metl-9 KO strain and metl-9 mutation strain upon P.aeruginosa infection |
|
| Relations |
| BioSample |
SAMN24579322 |
| SRA |
SRX13578338 |
