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Sample GSM8173295 Query DataSets for GSM8173295
Status Public on Apr 04, 2024
Title Caenorhabditis elegans,20℃,middle adult,rep3
Sample type SRA
 
Source name middle stage ADF
Organism Caenorhabditis elegans
Characteristics tissue: whole body
tissue: middle stage ADF
age: adult
cell type: hermaphrodite
genotype: WT
treatment: M9
Treatment protocol For the corresponding stages of worms, administer alternate day fasting (ADF) for a period of seven days, followed by the collection of a large number of nematodes for RNA extraction.
Growth protocol Harvest worms and collect eggs simultaneously. The eggs were cultured in M9 and incubated at 20℃ until L1.
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 04, 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)
GSE262666 RNA-seq analysis of the young stage ADF, middle stage ADF, and the control worms
Relations
BioSample SAMN40634841
SRA SRX24083321

Supplementary file Size Download File type/resource
GSM8173295_E2_3_fpkm.txt.gz 265.3 Kb (ftp)(http) TXT
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Raw data are available in SRA

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