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| Status |
Public on Aug 01, 2023 |
| Title |
wild-type, replicate 2 |
| Sample type |
SRA |
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| Source name |
Whole worm
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole worm
strain: N2 - wild-type
Stage: 1-day-old adult
temperature: 20°C
fraction: Whole worm lysate
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| Growth protocol |
50,000 synchronized adult animals (~68 h at 20 °C after L1 arrest) were collected, in biological triplicates.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms were resuspended in 1 ml Trizol reagent and freeze-thawed on dry ice followed by vortexing. RNA isolation was performed by chloroform extraction and isopropanol precipitation.
RNA samples were normalized to 7.5μg per 10μL, followed by polyA selection using the Dynabead mRNA Purification Kit. 100ng of polyA selected mRNA samples were treated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manual, using NEBNext multiplex oligos for Illumina.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
mRNA libraries sequenced on the Illumina NextSeq2000 100-cycle (SE 75-bp reads) platform.
Adapter sequences were trimmed using Trimmomatic (version 0.39)
Reads were mapped to the C. elegans genome, WS258, using HISAT2 (version 2.2.1)
Mapped reads for genomic features were counted using featureCounts which is part of the Subread package (version 2.0.1)
Assembly: WS258
Supplementary files format and content: Processed data files are tab-delimited text files including total reads mapping to each gene generated by featureCounts.
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| Submission date |
Jul 26, 2023 |
| Last update date |
Aug 01, 2023 |
| Contact name |
Carolyn Marie Phillips |
| E-mail(s) |
cphil@usc.edu
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| Organization name |
University of Southern California
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| Department |
Biological Sciences
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| Lab |
Phillips
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| Street address |
1050 Childs Way, RRI 201
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL32326 |
| Series (2) |
| GSE239286 |
Germ granule association drives small RNA specificity for a nuclear Argonaute protein [mRNA-seq] |
| GSE239291 |
Germ granule association drives small RNA specificity for a nuclear Argonaute protein |
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| Relations |
| BioSample |
SAMN36714632 |
| SRA |
SRX21162802 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7662632_38_N2-mRNA-2_S2.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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