|
| Status |
Public on Oct 19, 2021 |
| Title |
AGD1289 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
1000 young adult worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: AGD1289
Stage: young adult
|
| Treatment protocol |
Standard growth conditions. Temperature: 20 degrees Celsius.
|
| Growth protocol |
Worms were age-synchobized by treatment with alkaline hypochlorite solution, according to standard procedures. 1000 L1 worms were plated on 9 cm NGM plate per genotype. Nematodes were harvested at the young adult stage about 50h post L1 plating. £ biological replicates were collected for each genotype.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by standard Trizol extraction techniques.
Libraries were made using either NEBNext mRNA Second Strand Synthesis Module (E6111) followed by NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB-E7645) or NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NE7490) as per manufacturers protocols using half reactions. 13 Cycles of amplification was used for library enrichment; quality and size distribution of the the libraries was ascertained by running on a Bioanalyzer High Sensitivity DNA Chip (Agilent 5067-4626) and concentration was determined using KAPA Library Quantification Kit (KK4824). Libraries were sequenced on an Illumina HiSeq 2500 system by the Babraham Sequencing Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
lane6353_2-N2
|
| Data processing |
Standard Illumina Pipeline Processing
FASTQ reads quality trimmed with Trim Galore v0.4.4 using Cutadapt v1.15
Mapped with HISAT2 (v2.1.0)
Differential gene expression performed with SeqMonk and DESeq2.
Genome_build: WBCel235 / WBCel235.75 splice sites
Supplementary_files_format_and_content: Excel file comprising 2 worksheets: DEgenes_per_replicate – output from SeqMonk giving a log10 normalised quantitation of each gene using the SeqMonk “RNA-Seq quantitation pipeline”. The worksheet lists each gene, genomic location and quantitation value. log2FC_average_AGD1289_vs_WT – gives the average log2-fold change of each gene between conditions and P-value as determined by DESeq2 and SeqMonk. The table lists the gene name, genomic location and quantitation values for each gene.
|
| |
|
| Submission date |
Feb 11, 2020 |
| Last update date |
Oct 19, 2021 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
|
| Organization name |
MRC Laboratory of Molecular Biology
|
| Department |
Cell Biology
|
| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE145123 |
Neuronal HSF-1 activity coordinates fat desaturation across tissues in C. elegans via TGF-b/BMP signalling |
|
| Relations |
| BioSample |
SAMN14085333 |
| SRA |
SRX7709075 |
