|
| Status |
Public on Jul 23, 2019 |
| Title |
meg-3(ax3055) meg-4(ax3052) JH3475 fed HT115-pos-1(400nt) young mother replicate 1-sRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Whole worm, young mother
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/genotype: meg-3(ax3055) meg-4(ax3052) JH3475
tissue: whole worm
group: young mother
rna treatment: 5’ Polyphosphatase treated
|
| Treatment protocol |
RNA was either treated or not treated with 5’ polyphosphatase.
|
| Growth protocol |
Starvation synchronized. Grown on HT115 bacteria expressing pos-1 dsRNA at 20 C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol and Zymo RNA purification kit. TRIzol and Zymo RNA Concentrator
TruSeq Small RNA Library Preparation Kit.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
N2_meg34_1_pos1phos_smRNA_ID.txt
|
| Data processing |
Adapters were trimmed with Cutadapt.
Reads were aligned with Bowtie2
Read alignments were counted with HTseq-count
Normalized read counts were obtained with DEseq2
Genome browser views were obtained with IGV
Genome_build: ce10
Supplementary_files_format_and_content: Tab delimited .txt files with log2FCs, q-values, RPMs, etc.
|
| |
|
| Submission date |
Jul 22, 2019 |
| Last update date |
Jul 23, 2019 |
| Contact name |
Geraldine Seydoux |
| E-mail(s) |
gseydoux@jhmi.edu
|
| Organization name |
JHU School of Medicine
|
| Department |
Molecular Biology and Genetics
|
| Street address |
725 North Wolfe Street, PCTB 706
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (2) |
| GSE134627 |
meg-3 meg-4 mutants are defective in exogenous RNAi signal amplification |
| GSE134638 |
P granules protect RNA interference genes from silencing by piRNAs |
|
| Relations |
| BioSample |
SAMN12335097 |
| SRA |
SRX6483148 |
