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| Status |
Public on Sep 15, 2023 |
| Title |
A2-4 |
| Sample type |
SRA |
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| Source name |
GRO derived from BVSC-iPSC
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| Organism |
Mus musculus |
| Characteristics |
cell type: GRO derived from BVSC-iPSC
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Each GRO and FGO derived from BVSC-iPSCs, E12.5 gonads, 6 dpp follicles and in vivo samples was dissociated from follicular somatic cells using 30G needles, followed by treatment with Accumax (Innovative Cell Technologies) for 5 min and by pipetting to remove somatic cells completely. The zona pellucida of each GRO and FGO was removed by acid tyrode’s solution (Merck) and samples were individually washed in PBS supplemented with 0.01% PVA (PBS-PVA) and lysed in the lysis buffer composed of 0.09% Triton-X 100, 2 U SUPERase IN RNase inhibitor (Invitrogen, AM2694), 2.5 μM Oligo-dT primer (Microsynth AG), dNTP mix (2.5 mM each, Promega), ERCC RNA Spike-In Mix (1 : 3.2 x 107, Thermo Fischer Scientific 4456740) in individual tubes of a 8-well strip, then immediately frozen on the dry ice and kept at -80C for longer storage.
RNA sequencing libraries for single oocytes were prepared according to the Smartseq2 protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-Seq datasets were aligned to a custom genome containing the Mus musculus genome assembly (GRCm38/mm10 Dec. 2011) and ERCC92 sequences using STAR (Dobin et al., 2013) with parameters "-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000", allowing multimappers with up to 300 matches in the genome and choosing positions for multimappers randomly
A random transcript isoform for each gene was chosen from Bioconductor annotation package TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.2.2) and exonic genomic regions for the random transcript isoforms for each gene were used in further analyses.
Expression quantification for selected exonic genomic regions was done using QuasR R package (Gaidatzis et al., 2015) selecting only uniquely mapped reads (mapqMin=255).
Assembly: mm10
Supplementary files format and content: CSV file contatining read count table for exonic regions of each gene (column ENTREZID), total length of genomic regions for each gene (column width) and each single oocyte.
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| Submission date |
Jan 23, 2023 |
| Last update date |
Sep 15, 2023 |
| Contact name |
Antoine Peters |
| E-mail(s) |
Antoine.Peters@fmi.ch
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| Organization name |
Friedrich Miescher Institute
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE223477 |
Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence [scRNA-seq] |
| GSE223479 |
Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence |
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| Relations |
| BioSample |
SAMN32875439 |
| SRA |
SRX19141764 |
| 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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