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| Status |
Public on Oct 29, 2024 |
| Title |
Undifferentiated_PGC_rep2 |
| Sample type |
SRA |
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| Source name |
Primordial germ cells
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| Organism |
Gallus gallus |
| Characteristics |
cell line: Primordial germ cells
cell type: Undifferentiated_PGC
treatment: Cultured
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| Treatment protocol |
The adherent (somatic differentiated) PGCs were enriched by removal of the suspension (undifferentiated) PGCs by aspiration and continued proliferation for an additional two–three weeks.
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| Growth protocol |
Chicken PGCs were isolated from blood of chicken embryos at Hamburger and Hamilton stage (HH) 16 to 16+. The PGCs were maintained in the KnockOut DMEM supplemented with 1% chicken serum, 1 × B-27, 2 mM GlutaMAX™, 1 × nucleosides, 1 × MEM Non-Essential Amino Acids Solution (NEAA), 1 × antibiotic–antimycotic mixed stock solution, 0.5 mM monothioglycerol, 1 mM sodium pyruvate, 1 unit/mL heparin, 10 ng/mL human FGF2, 0.2 μM H1152, and 0.2 μM Blebbistatin.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
1 μg of total RNA was purified using FastGene™ RNA Premium kit (NIPPON Genetics Co. Ltd., Tokyo, Japan) from each PGC line.
mRNA was enriched from the total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), and cDNA libraries were constructed using SMARTer® Stranded RNA-Seq Kit (TaKaRa Bio, Kusatsu, Japan) and MGIEasy Universal Library Conversion Kit (MGI, Shenzhen, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
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| Description |
PGC_PGC.2
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| Data processing |
The quality of the row sequence reads was assessed using FastQC (ver. 0.11.9).
The raw reads were trimmed and quality filtered using Trimmomatic (ver. 0.39) as well as Trim Galore (ver. 0.6.6) with Cutadapt (ver. 3.1) software then mapped to the chicken genome (GRCg6a) using STAR (ver. 2.7.3a).
Reads were counted using RSEM (ver.1.3.1).
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text files include TPM values for each sample.
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| Submission date |
Oct 22, 2024 |
| Last update date |
Oct 29, 2024 |
| Contact name |
Kennosuke Ichikawa |
| Organization name |
The University of Edinburgh
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| Department |
The Roslin Institute
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| Street address |
Easter Bush Campus
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| City |
Midlothian |
| ZIP/Postal code |
EH25 9RG |
| Country |
United Kingdom |
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| Platform ID |
GPL31227 |
| Series (1) |
| GSE280091 |
A cell-matrix interaction regulates the undifferentiated state and self-renewal capacity of avian primordial germ cells |
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| Relations |
| BioSample |
SAMN44383723 |
| SRA |
SRX26458766 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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