|
| Status |
Public on Sep 20, 2023 |
| Title |
Mixed scRNA-seq Trichoplax adhaerens and Cladtertia collaboinventa 1 clicktags |
| Sample type |
SRA |
| |
|
| Source name |
Whole adult specimens
|
| Organisms |
Trichoplax adhaerens; Hoilungia sp. H23 |
| Characteristics |
tissue: Whole adult specimens
genotype: Wild type
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were fixed using the ACME protocol (10.1186/s13059-021-02302-5), FACS sorted, and processed with the 10X Genomics Chromium Single Cell 3' scRNAseq v3.1 kit.
Adult specimens were fixed, dissociated and pooled before sorting single-cells for scRNAseq. The same procedure was followed for chromatin profiling experiments, except that cells were used fresh for ATAC-seq and fixed with 1% formaldehyde (10 min) for ChIP-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cladtertia collaboinventa
Clicktags to demultiplex single-cells from H1 and H23. See Readme_ClickTag_demultiplexing.xlsx for details.
Tadh.umimatrix.cell_annotations.tsv
Tadh.umimatrix.genes.tsv
Tadh.umimatrix.mtx.gz
HoiH23.umimatrix.cell_annotations.tsv
HoiH23.umimatrix.genes.tsv
HoiH23.umimatrix.mtx.gz
|
| Data processing |
scRNA-seq: We used CellRanger 6.1.1 (10X Genomics) to map reads and count unique molecular identifiers (UMIs) per gene per cell. We used the --force-cells flat to set a constant number of 20,000 per experiment (well in excess of the expected number cells for each case, as we intended to remove non-cells from the dataset using our own procedure; see below). We used whole gene bodies to guide the mapping of reads to the genome (--transcriptome flag). We also extended gene ranges to include proximal scRNA-seq peaks located downstream of each gene (in the region 5 kbp downstream of each gene, or less if another gene was closer to that peak). For details on clicktag barcode demultiplexing see Readme_ClickTag_demultiplexing.xlsx file.
ATAC-seq: Reads were mapped using bwa 0.7.17, using the mem algorithm. The resulting BAM files were filtered using the alignmentSieve utility from the deeptools 3.5.1 package, in order to filter out weak alignments (with minimum mapping quality or MAPQ = 30) and shifting the left and right ends of reads according to usual ATAC specifications (+4/−5 bp in the positive and negative strands, activated with the --ATACshift flag in deeptools). Duplicated reads were removed using biobambam2 2.0.87, and the resulting alignments were coordinate-sorted with the same tool. Then, we concatenated all the ATAC-seq libraries for each species. bigWig files were generated with deepTools v3.5.2 bamCoverage function.
ChIP-seq: The ChIP-seq libraries corresponding to H3K4me2 and H3K4me3 were mapped to their corresponding species with bwa mem, using the same procedure as described for ATAC-seq (except for the adjustment of read end coordinates specific to ATAC libraries).
Assembly: Trichoplax adhaerens: GCA_000150275.1
Assembly: Trichoplax sp. H2: GCA_003344405.1
Assembly: Hoilungia honkgongensis: https://bitbucket.org/molpalmuc/hoilungia-genome/src/master/
Assembly: Cladtertia collaboinventa: https://www.frontiersin.org/articles/10.3389/fevo.2022.1016357/full
Supplementary files format and content: For ATAC-seq and ChIP-seq: bigWig coverage files (bw extension)
Supplementary files format and content: For scRNA_seq: TSV file with CellIDs and associated metadata (in the same order as in the UMI matrix)
Supplementary files format and content: For scRNA_seq: TSV file with gene names associated to the UMI matrix
Supplementary files format and content: For scRNA_seq: MTX file containin gene x cell UMI counts
|
| |
|
| Submission date |
Jun 09, 2023 |
| Last update date |
Sep 20, 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 |
GPL33479 |
| Series (1) |
| GSE234601 |
Stepwise emergence of the neuronal gene expression program in early animal evolution |
|
| Relations |
| BioSample |
SAMN35687527 |
| SRA |
SRX20648971 |
