|
| Status |
Public on Apr 08, 2016 |
| Title |
Wildtype head X2 single cell 40 |
| Sample type |
SRA |
| |
|
| Source name |
Wildtype animal heads
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
strain: Asexual CIW4
facs gate: X2
treatment: Amputation fragment
tissue: heads
sample type: single cell
|
| Treatment protocol |
Cells from the heads of 30 animals were FACS sorted to obtain 96 single X1s and 72 single X2s and cDNA was prepared from poly-A+ mRNA for each cell using Smartseq2 and deep sequenced to a depth of 5M reads, as illustrated in Figure 1A of the manuscript. cDNA from two X1 and 1 X2 bulk tube controls of 200 cells each was prepared using the same protocol and sequenced to a depth of 10-20M reads each.
|
| Growth protocol |
The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver. Organisms were starved for 1 week prior to tissue collection.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
All samples were prepared using the Smartseq2 protocol and the Nextera XT DNA library preparation kit from Illumina.
Illumina V4 chemistry and reagents
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
X2.59
|
| 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 BioProject 215411 using the program Bowtie2 version 2.2.4. Raw counts were extracted from resulting SAM files and normalized using DESeq2.
The 1000 most highly variable transcripts across the single cell data were extracted based on mean and coefficient of variation values. The expression values for these transcripts in each cell were log transformed with a small pseudo-counts (+ 0.001) and used for heirarchical clustering and t-distributed stocastic neighbor embedding. Cell groups were defined by producing a dendrogram of the heirarchical clustering results and cutting the tree into 10 groups.
Genome_build: NCBI BioProject PRJNA215411 SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: [Molinaro_NCBI_rawcounts.txt] Raw counts values for each sample for each transcript are listed. Only transcripts that were detected in at least one sample are listed. [Molinaro_NCBI_normalizedcounts.txt] single cell DESeq2-normalized counts.
|
| |
|
| Submission date |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bret J Pearson |
| E-mail(s) |
pearsobr@ohsu.edu
|
| Organization name |
Oregon Health and Science University
|
| Department |
Pediatrics
|
| Lab |
Pearson
|
| Street address |
3181 SW Sam Jackson Park Rd., BRB Room 305
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL20150 |
| Series (1) |
| GSE79866 |
In silico lineage tracing through single cell transcriptomes identifies a neural stem cell population in planarians |
|
| Relations |
| BioSample |
SAMN04604912 |
| SRA |
SRX1677154 |
