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| Status |
Public on Mar 17, 2023 |
| Title |
ag49+52VT_E15.5_MS257_024 |
| Sample type |
SRA |
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| Source name |
15XRi-AGVT#7
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| Organism |
Macaca fascicularis |
| Characteristics |
cell line: 15XRi-AGVT#7
cell type: PGCLC
tag: TFAP2C-EGFP, DDX4-tdTomato
genotype: wildtype
treatment: aggregate culture with mouse ovarian somatic cells at E15.5
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA extraction from 5000-20000 cells were carried out using Nucleospin RNA XS extraction kit (Takara, 740902).
cDNA synthesis was performed as described previously (Nakamura et al, 2015). Briefly, 0.2ng/µL of V1(dT)24 sequence was annealed to the 3’ end of the 1ng of total RNA by incubation at 70ºC for 90 seconds. Reverse transcription was performed by adding 133U/µL of SuperScript III (Invitrogen, 1089075) and serial incubation at 50ºC for 5 min and at 70ºC for 10 min. The residual primers were excised by treating with 0.5U/µL of Exonuclease I (Takara, 2650A) at 37ºC for 30 min followed by 80ºC for 25 min. Poly-A was added to the 3’ end of the cDNA by incubating at 37ºC 15 min and 70ºC for 10 min in the presence of 3mM dATPs (GE Healthcare, 28-4065-01) and 0.75U/µL terminal nucleotidyl transferase (TdT, Invitrogen, 10533-065). For cDNA amplification, the cDNA was applied to thermal cycling in the presence of 0.62 µM of V3(dT)24 and V1(dT)24, 0.05U/µL Ex Taq HS (Takara, RR006).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ag49+52 AG-VT+
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| Data processing |
All read data were processed with cutadapt v1.18 and mapped with Tophat2 v2.1.1/bowtie2 v2.3.4.1 as described previously (Nakamura et.al.).
Read counts per genes were calculated using HTseq v0.11.0.
For allelic expression analysis, read data were re-mapped using masked MacFas5.0 reference, as described above.
Mapped BAM files were processed with SNPsplit and masked MacFas5.0 reference to split into paternal and maternal allele
Read counts per genes were calculated using HTseq for both BAM, separately.
Assembly: macFas5.0 or GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample
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| Submission date |
Oct 20, 2022 |
| Last update date |
Mar 17, 2023 |
| Contact name |
Yukihiro Yabuta |
| E-mail(s) |
yabyab@anat2.med.kyoto-u.ac.jp
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| Organization name |
Kyoto University, Graduate school of medicine
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| Department |
Anatomy and Cell Biology
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| Street address |
Yoshida-Konoe-cho, Sakyo-ku
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| City |
Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| Platform ID |
GPL22523 |
| Series (2) |
| GSE216205 |
Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys (RNA-Seq II) |
| GSE216206 |
Induction of fetal meiotic oocytes from embryonic stem cells in cynomolgus monkeys |
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| Relations |
| BioSample |
SAMN31389091 |
| SRA |
SRX17968285 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6661537_Expression_MS257_024_macFas5_HTSeq_count.txt.gz |
537.8 Kb |
(ftp)(http) |
TXT |
| GSM6661537_Expression_MS257_024_macFas5_maternal_HTSeq_count.txt.gz |
514.6 Kb |
(ftp)(http) |
TXT |
| GSM6661537_Expression_MS257_024_macFas5_paternal_HTSeq_count.txt.gz |
514.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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