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| Status |
Public on Sep 15, 2023 |
| Title |
A1-2_PGCLC_d6 |
| Sample type |
SRA |
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| Source name |
BVSC-iPSC
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| Organism |
Mus musculus |
| Characteristics |
cell line: BVSC-iPSC
cell type: BVSC-iPSC-derived day 6 PGCLC
treatment: Day 6 PGCLCs positive for both Blimp1-Venus and Stella-ECFP were collected
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| Extracted molecule |
total RNA |
| Extraction protocol |
To prepare pooled PGCs, E12.5 female embryonic gonads were harvested from inbred C57BL/6J fetuses. PGCs, positive for both SSEA1 and integrin β3, were collected using a FACSAria III (BD Bioscience). D6 PGCLCs derived from a BVSC-iPSC line were also collected at day 8 of the culture by following the same protocol as the start of the IVD culture. Four replicates of respective PGC and PGCLC pools, consisting of 30,000 to 340,000 cells, were prepared from independent experiments. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including removal of genomic DNA. The RNA quality was determined by 2200 TapeStation (Agilent Technologies). All samples had a RIN value of greater than 8.
Extracted RNA was prepared for sequencing using the TruSeq Stranded mRNA (Illumina) following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 (Illumina), with sequencing depth of 20 million reads per sample and sequencing configuration of single-end 100 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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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 |
GPL24247 |
| Series (2) |
| GSE223478 |
Comprehensive comparison of female germ cell development in vitro and in vivo identifies epigenetic gene regulation crucial for oocyte development and embryonic competence [bulk RNA-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 |
SAMN32875213 |
| SRA |
SRX19141691 |
| 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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