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Sample GSM8172212 Query DataSets for GSM8172212
Status Public on Apr 01, 2024
Title Caenorhabditis elegans,20℃, after feeding 5mM tryptophan for 36 hours in L4 period, rep1
Sample type SRA
 
Source name whole body
Organism Caenorhabditis elegans
Characteristics tissue: whole body
age: young adult
cell type: hermaphrodite
genotype: WT
treatment: 5mM tryptophan was fed for 36 hours from the L4 period
Treatment protocol At L4 period, the experimental group worms are fed 5 mM tryptophan for 36 h.
Growth protocol Synchronize the worms, culture the collected eggs in M9 and incubate to L1 at 20 °C, transfer to NGM plates and feed to the L4 stage.
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.7 software used for base-calling
Sequenced reads were trimmed for adaptor sequence. and masked for low-complexity or low-quality sequence. then mapped to WBcel235 whole genome using bowtie v0.12.2 with parameters
The transcript abundances for each sample was estimated with StringTie(1.3.3)
The FPKM value for gene and transcript level was calculated through a protocol from Chepelev et al., Nucleic Acids Research,2009.
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of expression gene.
 
Submission date Mar 27, 2024
Last update date Apr 01, 2024
Contact name Shanqing Zheng
E-mail(s) zhengshanqing@henu.edu.cn
Phone +8637122892869
Organization name Henan university
Street address 1 Jinming Avenue North, Longting District, School of Basic Medical Sciences, Henan University
City Kaifeng
ZIP/Postal code 475004
Country China
 
Platform ID GPL13657
Series (1)
GSE262600 RNA-seq analysis of young adult fed 5mM tryptophan and control worms
Relations
BioSample SAMN40630724
SRA SRX24078245

Supplementary file Size Download File type/resource
GSM8172212_Trp_1_fpkm.txt.gz 258.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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