|
| Status |
Public on Jul 23, 2019 |
| Title |
meg-3(ax3055) meg-4(ax4311) JH3673 mixed population on NA22 bacteria replicate 1-sRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Whole worm, mixed population on NA22
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/genotype: meg-3(ax3055) meg-4(ax4311) JH3673
growth: on NA22
tissue: whole worm
group: mixed population
|
| Treatment protocol |
RNA for sRNAseq libraries was treated with 5’ polyphosphatase. RNA for mRNAseq libraries was treated with the RiboZero Gold Epedemiology Kit and supplemented with the ERCC Spike-in.
|
| Growth protocol |
Starvation synchronized or mixed population. Grown on either NA22 or HT115 bacteria with L4440 vector 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/TruSeq RNA Library Preparation Kit.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
smRNA-Seq
N2_meg34_strain3_mixed_NA22_smRNA_ID.txt
|
| Data processing |
Adapters were trimmed with Cutadapt for sRNAseq. This step was omitted for mRNAseq.
Reads were aligned with Bowtie2 for sRNAseq and HiSat2 for mRNAseq.
Read alignments were counted with HTSeq-count for both sRNAseq and mRNAseq.
Normalized read counts were obtained with DEseq2 for both sRNAseq and mRNAseq.
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) |
| GSE134628 |
meg-3 meg-4 upregulate endogenous sRNAs targeting RNAi genes and downregulate their mRNAs |
| GSE134638 |
P granules protect RNA interference genes from silencing by piRNAs |
|
| Relations |
| BioSample |
SAMN12335125 |
| SRA |
SRX6483172 |
