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| Status |
Public on Nov 28, 2018 |
| Title |
400-2 |
| Sample type |
SRA |
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| Source name |
C. elegans RNA
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| Organism |
Caenorhabditis elegans |
| Characteristics |
ir treatment: 400Gy
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| 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).
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| 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
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
gene_exp.xls
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| Data processing |
Illumina Bcl2FastQÂ 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
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| Submission date |
Nov 27, 2018 |
| Last update date |
Nov 28, 2018 |
| Contact name |
Youqin Xu |
| E-mail(s) |
582428099@qq.com
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| Organization name |
Southern Medical University
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| Street address |
No.1023-1063, Shatai Road South, Baiyun District
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| City |
GuangZhou |
| ZIP/Postal code |
510515 |
| Country |
China |
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| Platform ID |
GPL18245 |
| Series (1) |
| GSE122996 |
High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans |
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| Relations |
| BioSample |
SAMN10485262 |
| SRA |
SRX5065909 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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