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| Status |
Public on Apr 04, 2024 |
| Title |
GD3- Bgal- 3 |
| Sample type |
SRA |
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| Source name |
Lungs
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lungs
strain: C57BL/6
Sex: Male
treatment: Bleomycin
markers: GD3- Bgal-
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| Treatment protocol |
Four 9-week-old pathogen-free male C57BL/6 mice (Charles River) were treated with intratracheal instillation of 50 µl of phosphate-buffered saline (PBS) or bleomycin (2.5 U.kg−1, Sigma-Aldrich). After 28 days the lungs were recovered and dissociated by Dispase (Corning), collagenase A, and DNase I (Roche) digestion for 30 min at 37°C. The cells were filtrated, recovered in DMEM 10% FBS and incubated with Bafilomycin A1 100nM (Sigma-Aldrich, ref#196000) for 1 hour at 37°, 5% CO2. Then they were stained for SA-β-Galactosidase with a Senescence Assay Kit (abcam, ref#ab228562) following the manufacturer’s protocol. The cells were then stained with directly AF647 coupled antibody directed against GD3 for 30 min at 4°C after saturation with Fc-Block anti-CD16/CD32 antibodies (clone 2.4G2) for 15 min on ice. They were incubated with DAPI as a viability marker for 10min.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the Single Cell RNA Purification Kit (Norgen, ref#48200) following manufacturer’s instructions.
The library was prepared from 3 000pg of total RNA with SMART-Seq Stranded Mammalian Single Cell kit (Takara/Clontech, 634470) according to manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
3_GD3negbGalneg
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| Data processing |
The primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool.
Sequence alignment was done on the mouse genome (GRCm38) with STAR1 (v2.7.3a).
Gene expression was quantified using Salmon2 (V1.4) and the annotation of known genes from genecode vM25.
We normalized gene expression using Transcripts Per Million (TPM) by normalizing each gene length by the total read counts. RNA-seq quality control was evaluated by considering total number of reads, alignment and duplication rate.
Assembly: GRCm38
Supplementary files format and content: Counts and TPM
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| Submission date |
Apr 01, 2024 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Julien Cherfils-Vicini |
| E-mail(s) |
julien.cherfils@univ-cotedazur.fr
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| Organization name |
IRCAN - CNRS - INSERM
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| Street address |
28 Avenue de Valombrose
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| City |
Nice |
| ZIP/Postal code |
06107 |
| Country |
France |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE262926 |
Micro bulk sequencing on murine Bleomycin-induced fibrotic lungs sorted on SA-β-Gal and GD3 |
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| Relations |
| BioSample |
SAMN40707700 |
| SRA |
SRX24116052 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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