|
| Status |
Public on Jan 30, 2019 |
| Title |
zip-3 (gk3164) fed with control RNAi, biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
zip-3 (gk3164) fed with control RNAi
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole organism
genotype: zip-3(gk3164)
age: L4
|
| Treatment protocol |
Worms were fed with either control RNAi or spg-7 RNAi
|
| Growth protocol |
Wildtype, atfs-1(tm4919) and zip-3(gk3164) worms were synchronized by bleaching, raised to L4 on NGM plates seeded with control RNAi or spg-7 RNAi and then harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNA STAT reagent (Tel-Test Inc) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the C. Elegans genome (WBcel235) using STAR (version 2.5.3a) with the following parameter (--outFilterType BySJout \ --outFilterMultimapNmax 20 \ --alignSJoverhangMin 8 \ --alignSJDBoverhangMin 1 \ --outFilterMismatchNmax 999 \ --outFilterMismatchNoverReadLmax 0.04 \ --alignIntronMin 20 \ --alignIntronMax 1000000 \ --alignMatesGapMax 1000000 \)
featureCounts (subread-1.5.2) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) was used for differential gene expression analysis
Genome_build: WBcel235 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/)
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from featureCounts for each sample
|
| |
|
| Submission date |
Apr 13, 2018 |
| Last update date |
Jan 30, 2019 |
| Contact name |
Cole Haynes |
| Organization name |
U Mass Medical School
|
| Street address |
364 Plantation Street, 425
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL24892 |
| Series (1) |
| GSE113136 |
Differential expression analysis of wildtype, atfs-1(tm4919) and zip-3(gk3164) mutant with next generation sequencing |
|
| Relations |
| BioSample |
SAMN08930209 |
| SRA |
SRX3934462 |
