|
| Status |
Public on Dec 17, 2015 |
| Title |
set1_6_2 |
| Sample type |
SRA |
| |
|
| Source name |
Wholeworm Tissue
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
tissue: whole worm
replicate: 2
RNAi treatment: set1
days exposed to rnai: 6
|
| Treatment protocol |
dsRNA-containing food for RNAi treatment was generated as previously described (Gurley et al., 2008); briefly, cloned genes were transformed into bacterial strain Ht115, induced to express dsRNA with 1mM (final) IPTG, incubated with shaking at 37C for 2 hours, then pelleted, rinsed, and mixed with calf liver paste for ingestion. set1 was treated with RNAi for 6 and 9 days. and mll1/2 was treated with RNAi for 9 and 12 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
To isolate stem cells, we used a well-established method to isolate planarian stem cells by Hoechst blue staining and flow cytometry. Sorted cells were homogenized in Trizol reagent and RNA was isolated per the manufacturer-supplied protocol. Isolated RNA from whole worm tissue was treated with RNase-free DNase on QIagen RNeasy columns and eluted in nuclease-free water.
500ng-1μg RNA per whole worm sample or 100ng of sorted cell RNA was used for generation of RNAseq libraries using the Illumina TruSeq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rpkm_set1_WW.txt
|
| Data processing |
Base calls were performed using CASAVA-1.8.2
Reads were aligned using bowtie with the following parameters: --best --strata -v 2 -m 5 against transcriptome smed_20140614 defined in GEO submission: GSE72389
Read counts to genes were tallied from the SAM files with a custom script. RPKM values were generated using the rpkm function from the edgeR library from Bioconductor in R.
Genome_build: Schmidtea_mediterranea_3.1
Supplementary_files_format_and_content: rpkm.txt files contain tab-delimited RPKM values for each sample.
|
| |
|
| Submission date |
Oct 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex Daniel Chitsazan |
| E-mail(s) |
chitsazanalex@gmail.com
|
| Phone |
5039169064
|
| Organization name |
Oregon Health and Science University
|
| Street address |
2720 S Moody Ave
|
| City |
Happy Valley |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL20150 |
| Series (2) |
| GSE74054 |
Set1 and MLL1/2 target distinct sets of functionally different genomic loci in vivo: An in depth RNA-seq analysis of H3K4me3 targets in vivo and upon Set1 and mll1 knockdown |
| GSE74169 |
Set1 and MLL1/2 target distinct sets of functionally different genomic loci in vivo |
|
| Relations |
| BioSample |
SAMN04168072 |
| SRA |
SRX1338168 |
