|
| 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 |
