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Sample GSM3205172 Query DataSets for GSM3205172
Status Public on Sep 27, 2018
Title axo8.C1A
Sample type SRA
 
Source name forelimb upper arm blastema 11 dpa
Organism Ambystoma mexicanum
Characteristics cre line: Prrx1:Cre-ER
sc-rna-seq method: Fluidigm C1
development stage: blastema 11 dpa
Treatment protocol FACS enrichment for connective tissue cells
Extracted molecule total RNA
Extraction protocol Single cell isolation and cDNA generation using Fluidigm C1 platform with reagents provided by Fluidigm as well as the SMARTer v2 Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000.
Libraries were prepared using Illumina Nextera XT kit according to illumina's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Table_S7.csv
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.
 
Submission date Jun 19, 2018
Last update date Sep 27, 2018
Contact name Tobias Gerber
E-mail(s) tobias.gerber@embl.de
Organization name EMBL Heidelberg
Department Developmental Biology
Lab Detlev Arendt
Street address Meyerhofstr. 1
City Heidelberg
ZIP/Postal code 69117
Country Germany
 
Platform ID GPL22800
Series (1)
GSE106269 Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration
Relations
BioSample SAMN09457492
SRA SRX4241363

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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