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Sample GSM5602259 Query DataSets for GSM5602259
Status Public on Jan 30, 2022
Title T1Wt3d_DP_R2
Sample type SRA
 
Source name Blastema cells
Organism Ambystoma mexicanum
Characteristics animal line: Hoxa13:Cherry transgenic line
treatment: Cells transfected with Tig1wt construct
isolation: Dissociation and FACS isolation at 3 days post- transfection
Treatment protocol Forelimb were amputated and electroporated with Tig1-t2A-GFP or Tig1P155Amut-t2A-GFP constructs-containing plasmids when the hoxa13:Cherry+ domain was visible; Blastema tissue was collected at 3 or 8 days post-electroporation.
Extracted molecule total RNA
Extraction protocol Samples were collecte, dissociated with LiberaseTM and immediated isolated by FACs sorting based on double positive (Ch+GFP+) or single channel fluorescence (CH+). cDNA library preparation was performed using 300 cells per sample.
RNAseq was based on Smart-seq2 sensitive full-length transcriptome profiling and modified from Picelli et. al., 2013 (Picelli et al., 2013).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Basecalls were done with Illumina bcl2fastq version 2.19.1.
Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
Reads were aligned to the axolotl reference genome AmexG_v6.0-DD using the aligner STAR (v2.7.6a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters: -a AmexG_v6_DD/AmexG_v6_DD.gtf -s 0 -o genecount/bfx1392.AmexG_v6_DD.eAmexG_v6_DD.txt -Q 1).
Genome_build: AmexG_v6.0-DD
Supplementary_files_format_and_content: bfx1392.AmexG_v6_DD.eAmexG_v6_DD.txt.gz is a tab separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the samples.
 
Submission date Sep 28, 2021
Last update date Jan 30, 2022
Contact name Maximina Yun
E-mail(s) maximina.yun@tu-dresden.de
Organization name TUD
Department CRTD
Lab YUN
Street address Fetscherstrasse 105
City Dresden
State/province Saxony
ZIP/Postal code 01307
Country Germany
 
Platform ID GPL24679
Series (1)
GSE184948 Tig1 regulates proximo-distal identity during salamander limb regeneration
Relations
BioSample SAMN21885947
SRA SRX12388699

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

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