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| Status |
Public on Nov 28, 2023 |
| Title |
Zmat3 -/- 4 |
| Sample type |
SRA |
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| Source name |
thymus
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| Organism |
Mus musculus |
| Characteristics |
tissue: thymus
cell type: thymocytes
genotype: Zmat3 KO
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from thymocytes using the miRNeasy Micro Kit (Qiagen) according to the manufacturer's protocol, including a DNase digestion step. An input of total 100 ng total RNA for each sample was indexed separately using the TruSeq RNA Prep Kit v2 (Illumina).
Each library was quantified using the Agilent Tapestation. The indexed libraries were pooled and diluted to 750 pM for paired end sequencing (2 x 116 cycles) on the NextSeq 2000 instrument using the P3 200 cycle High Output Kit (Illumina) according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de- multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Raw FASTQ files were processed, and quality control performed using the nf-core/rnaseq (v. 3.10.1). Reads were pseudo-aligned and quantified using the Salmon option.
We filtered out genes: i) with obsolete Entrez Gene IDs, ii) ribosomal RNA (rRNA), iii) non-protein coding immunoglobulin genes iv) the Xist gene and v) genes that are on chromosome Y. Next, we filtered out lowly expressed genes by discarding those that did not show a minimum reliable level of expression of 20 counts per million reads of the smallest library size, in at least all the samples of the smallest group.
The DESeq2 package (v. 1.40.0) was used for the differential expression analysis. We adjusted for the sex as a batch effect correction and surrogate variables were calculated with SVA.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files incudes raw counts for each sample
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| Submission date |
Nov 27, 2023 |
| Last update date |
Nov 28, 2023 |
| Contact name |
Gerard Romero |
| E-mail(s) |
grspianus1999@gmail.com
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| Organization name |
Universitat Pompeu Fabra
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| Department |
Dpt of Medicine and Life Sciences, Universitat Pompeu Fabra (MELIS/UPF)
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| Street address |
Doctor Aiguader, 88
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| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08003 |
| Country |
Spain |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE248747 |
Combined absence of Trp53 target genes Zmat3, Puma and p21 cause a high incidence of cancer in mice |
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| Relations |
| SRA |
SRX22600070 |
| BioSample |
SAMN38351323 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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