|
Status |
Public on Jan 05, 2022 |
Title |
metl-9 KO normal condition (OP50)_2 |
Sample type |
SRA |
|
|
Source name |
whole animal
|
Organism |
Caenorhabditis elegans |
Characteristics |
genotype: metl-9 KO 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
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|
|
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 |
SAMN24579317 |
SRA |
SRX13578343 |