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| Status |
Public on Sep 27, 2018 |
| Title |
GER024_10x |
| Sample type |
SRA |
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| Source name |
forelimb upper arm blastema 38 dpa
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| Organism |
Ambystoma mexicanum |
| Characteristics |
cre line: Prrx1:Cre-ER
sc-rna-seq method: 10X Genomics
tissue: uninjured upper arm section
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| Treatment protocol |
FACS enrichment for connective tissue cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
CT enrichment was performed through FACS and cDNA generation was performed using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
Sequencing libraries were generated using ChromiumTM Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Table_S9.csv
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| Data processing |
"freeIbis" was used for C1 and SmartSeq2 sample data as an efficient basecaller with calibrated quality scores for Illumina sequencers. (Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.) Cellranger, version 2.0.0, as part of the 10x Genomics analysis pipeline was used to call bases for 10x experiments.
"leeHom" was used to trim adapters and merge Illumina sequencing reads for C1 and SmartSeq2 sample data. (Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to trim adapters for 10x experiments.
"deML" was used for robust demultiplexing of Illumina sequences for C1 and SmartSeq2 sample data using a likelihood-based approach. (Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.) Cellranger, version 2.0.0, of the 10x Genomics analysis pipeline was used to demultiplex reads.
Reads were aligned against the axolotl transcriptome (www.axolotl-omics.org, Download: 2015-07-29) using kallisto (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) for C1 and SmartSeq 2 sample data or using STAR (Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.) implemented in 10x' cell ranger software, version 2.0.0, for 10x data.
Transcript Per Million (TPM) values were computed using kallisto for C1 and SmartSeq2 samples. (Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.) Cellranger, version 2.0.0, implemented in the 10x Genomics analysis pipeline was used to obtain bam alignment files and gene count (UMI) matrices.
Gene expression values of different isoforms of the same gene were summed using custom Perl scripts.
Genome_build: Axolotl transcriptome (Am_2.2)
Supplementary_files_format_and_content: Master data frame including cell ID, cell type, timepoint, gene ID, and TPM values for each single cell.
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| Submission date |
Jun 19, 2018 |
| Last update date |
Sep 27, 2018 |
| Contact name |
Tobias Gerber |
| E-mail(s) |
tobias.gerber@embl.de
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| Organization name |
MPI for Evolutionary Anthropology
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| Department |
Genetics
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| Lab |
Barbara Treutlein
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| Street address |
Deutscher Platz 6
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| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
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| Platform ID |
GPL22800 |
| Series (1) |
| GSE106269 |
Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration |
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| Relations |
| BioSample |
SAMN09458855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3206458_GER024_10x_barcodes.tsv.gz |
3.7 Kb |
(ftp)(http) |
TSV |
| GSM3206458_GER024_10x_genes.tsv.gz |
627.6 Kb |
(ftp)(http) |
TSV |
| GSM3206458_GER024_10x_matrix.mtx.gz |
5.2 Mb |
(ftp)(http) |
MTX |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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