|
| Status |
Public on Feb 19, 2020 |
| Title |
c.elegans cells (L2 stage) [re-analysis] |
| Sample type |
SRA |
| |
|
| Source name |
whole c.elegans (L2 stage)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: C. elegans strain (RW12139 stIs11435(unc-120::H1-Wcherry;unc-119(+));unc-119(tm4063)) carrying an integrated Punc-120::mCherry gene in a wild type background was used
developmental stage: L2
|
| Treatment protocol |
For c.elegans, a synchronized L2 population was obtained by two cycles of bleaching gravid adults to isolate fertilized eggs allowing the eggs to hatch in the absence of food to generate a population of starved L1 animals.
|
| Growth protocol |
All cultured cell lines were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
All cell lines were trypsinized, spun down at 300xg for 5 min (4°C). and washed once in 1X PBS. L2 stage worms were disscociated with SDS-DTT solution and pronase to generate single cell suspension. Detailed protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."
library construction protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sciRNAseq with c.elegans cells (during sorting, polyploid c.elegans cells were exlcuded)
|
| Data processing |
Data was processed using the 10X Genomics CellRanger pipeline, mapping to a modified version of the reference transcriptome from WormBase version 260 (WS260). Our modifications to the refrence transcriptome consisted of extending the 3' UTR of transcripts by 0-500 bp (see Methods section of paper).
Genome_build: WS260
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, lineage, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.
|
| |
|
| Submission date |
Feb 18, 2020 |
| Last update date |
Feb 19, 2020 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
|
| Department |
Biology
|
| Lab |
Junhyong Kim
|
| Street address |
433 S University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE126954 |
A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution |
|
| Relations |
| Reanalysis of |
GSM2599701 |
| BioSample |
SAMN14126930 |
| SRA |
SRX7740729 |
