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Sample GSM3490381 Query DataSets for GSM3490381
Status Public on Nov 28, 2018
Title 0-2
Sample type SRA
Source name C. elegans RNA
Organism Caenorhabditis elegans
Characteristics ir treatment: 0Gy
Treatment protocol Approximately 1000 age-synchronized young adult hermaphrodites (24 h post the L4 larval stage) were irradiated with 0 Gy, 200 Gy and 400 Gy of X-rays using a 600C/D linear accelerator (Varian, USA).
Growth protocol C. elegans were provided by South China Agricultural University, Guangzhou, Guangdong, China. NGM medium containing 0.3% NaCl, 0.25% peptone, 1.7% agar and 1 M KH2PO4-K2HPO4 solution buffer was used to culture C. elegans according to the standard protocol
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 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description gene_exp.xls
Data processing Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000002985.6_WBcel235 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCF_000002985.6_WBcel235
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample
Submission date Nov 27, 2018
Last update date Nov 28, 2018
Contact name Youqin Xu
Organization name Southern Medical University
Street address No.1023-1063, Shatai Road South, Baiyun District
City GuangZhou
ZIP/Postal code 510515
Country China
Platform ID GPL18245
Series (1)
GSE122996 High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans
BioSample SAMN10485267
SRA SRX5065905

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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