|
| Status |
Public on Dec 31, 2020 |
| Title |
single cell RNA-low 3 |
| Sample type |
SRA |
| |
|
| Source name |
planarian whole body
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
facs gate: RNA-low
sample type: single cell
treatment: Hoechst/pyronin Y stain & FACS
tissue: sorted cells
strain: Asexual CIW4
|
| Treatment protocol |
Animals were dissociated by douncing in cold CMF + 1% BSA and cells were stained with Hoechst and pyrnonin Y prior to FACS.
|
| Growth protocol |
The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bulk samples were RNA extracted in Trizol reagent.
Bulk samples were library prepped using Illumina's Truseq Library kits. Single cell samples were prepped using the Smart-seq2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-low_scRNAseq_data.xlsx
|
| Data processing |
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Trimmed reads (3' 15 bp) were aligned to the transcriptome associated with NCBI BioProject PRJNA215411 using the program Bowtie2. Raw counts were extracted from resulting SAM files.
For bulk samples, raw counts were normalized to the number of mapped reads to calculate Reads Per Million (RPM) prior to analysis. For single cell samples, raw counts were log2 normalized with a small pseudocount of +1 prior to analysis.
Genome_build: NCBI BioProject 215411, SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Excel tab delimited. Raw counts.
|
| |
|
| Submission date |
Sep 11, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Alyssa M Molinaro |
| Organization name |
University of Toronto
|
| Department |
Molecular Genetics
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21689 |
| Series (1) |
| GSE157860 |
Identification of TOR-responsive slow-cycling neoblasts in planarians |
|
| Relations |
| BioSample |
SAMN16114277 |
| SRA |
SRX9108997 |
