|
| Status |
Public on Dec 11, 2023 |
| Title |
Xenoturbella_adult_scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Adult specimen
|
| Organism |
Xenoturbella bocki |
| Characteristics |
stage/cell type: Adult specimen
strain: Wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
.MARS-seq was performed as described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4). All 42 plates (a total of 15,960 single cell libraries) were prepared using the same conditions and reagents. Using a Bravo automated liquid handling platform (Agilent), mRNA was reverse transcribed into cDNA using the lysis oligonucleotide containing unique molecular identifiers (UMIs) and cell barcodes. Residual, unused oligonucleotides were removed by treatment with Exonuclease I (NEB). cDNAs were pooled and linearly amplified using T7 in vitro transcription. The resulting RNA was fragmented and ligated to an oligo containing the pool barcode and Illumina sequences, using T4 ssDNA:RNA ligase. RNA was reverse transcribed into DNA and PCR-amplified with 17 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read_1 files were mapped into Xenoturbella genome using STARR, using default parameters.
Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Keren-Shaul et al. 2019 (10.1038/s41596-019-0164-4).
Pipeline can be found: http://compgenomics.weizmann.ac.il/tanay/?page_id=672
Xenoturbella_MARS_gene_intervals.txt: Gene intervals used to quantify single-cell expression (UMIs) in MARS-seq pipeline.
Xenoturbella_proteins.fasta: Protein models used in this study.
Xenoturbella_sc_cell_tpye_assignments.txt: Assignment of single-cell IDs to cell type classification generated in this study.
Xboc_plus_bacteria_and_ERCC.fasta: Genome used to quantify single-cell expression (UMIs) in MARS-seq pipeline.
|
| |
|
| Submission date |
Aug 16, 2022 |
| Last update date |
Dec 11, 2023 |
| Contact name |
Arnau Sebe-Pedros |
| E-mail(s) |
arnau.sebe@crg.es
|
| Organization name |
Centre for Genomic Regulation
|
| Department |
Systems Biology
|
| Lab |
Sebe-Pedros lab
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL32575 |
| Series (1) |
| GSE211408 |
Single cell atlas of Xenoturbella bocki highlights the limited cell-type complexity of a non-vertebrate deuterostome lineage |
|
| Relations |
| BioSample |
SAMN30351716 |
| SRA |
SRX17107717 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6469642_Xboc_plus_bacteria_and_ERCC.fasta.gz |
31.6 Mb |
(ftp)(http) |
FASTA |
| GSM6469642_Xenoturbella_MARS_gene_intervals.txt.gz |
164.7 Kb |
(ftp)(http) |
TXT |
| GSM6469642_Xenoturbella_metacell_UMI_counts.tsv.gz |
636.8 Kb |
(ftp)(http) |
TSV |
| GSM6469642_Xenoturbella_metacell_gene_expression.tsv.gz |
972.3 Kb |
(ftp)(http) |
TSV |
| GSM6469642_Xenoturbella_proteins.fasta.gz |
3.5 Mb |
(ftp)(http) |
FASTA |
| GSM6469642_Xenoturbella_sc_cell_tpye_assignments.txt.gz |
40.2 Kb |
(ftp)(http) |
TXT |
| GSM6469642_Xenoturbella_sc_expression.tsv.gz |
7.1 Mb |
(ftp)(http) |
TSV |
| GSM6469642_Xenoturbella_sc_mc_assignments.tsv.gz |
41.0 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
