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Sample GSM4318946 Query DataSets for GSM4318946
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
Reanalysis of GSM2599701
BioSample SAMN14126930
SRA SRX7740729

Supplementary file Size Download File type/resource
GSM4318946_Cao_et_al_2017_reprocessed_Packer_Zhu_2019.cell_metadata.tsv.gz 1.7 Mb (ftp)(http) TSV
GSM4318946_Cao_et_al_2017_reprocessed_Packer_Zhu_2019.gene_metadata.tsv.gz 164.8 Kb (ftp)(http) TSV 52.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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