|
| Status |
Public on Jun 26, 2019 |
| Title |
EpiSC7_p7_onMEF_160309 |
| Sample type |
SRA |
| |
|
| Source name |
EpiSC
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL6
cell type: epiblast stem cell
|
| Treatment protocol |
For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).
|
| Growth protocol |
MEFs (mouse embryonic fibroblasts) were isolated from 12.5-day-old embryos from C57BL6 mice and cultured in D-MEM supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as described (Tesar et al. 2007).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
Library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Biological replicate 2 of 3.
Miura_FileName: EpiSC7_p7_onMEF_160309
Miura_Project ID: P242_14_1
Miura_MEMO: RNA_EpiSC7_p7_onMEF160309
processed data file: gene_fpkm.xlsx
|
| Data processing |
Before mapping, trimming the adaptor sequence and removing the low quality base reads were performed by Cutadapt version 1.4.1 (Martin, 2011) and Fastx_tool kit version 0.0.14 (https://github.com/agordon/fastx_toolkit). After this, fastq file was aligned to the mouse genome (UCSC mm9) by HISAT2 version 2.0.4 (Sirén et al., 2014). Mapped reads were quantified against the annotated UCSC transcriptome for mm9 to calculate FPKM (Fragments per kilobase per million mapped fragments) values using the Cuffdiff program of the Cufflinks package version 2.2.1 (Trapnell et al., 2012).
Genome_build: UCSC mm9 (MGSCv37)
Supplementary_files_format_and_content: gene_fpkm.xlsx: Excel file includes FPKM values.
|
| |
|
| Submission date |
May 02, 2018 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Ichiro Hiratani |
| E-mail(s) |
ichiro.hiratani@riken.jp
|
| Phone |
+81-78-306-3179
|
| Organization name |
RIKEN
|
| Department |
Center for Developmental Biology
|
| Lab |
Laboratory for Developmental Epigenetics
|
| Street address |
2-2-3 Minatojima-minamimachi, Chuo-ku
|
| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE113983 |
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [RNA-seq] |
| GSE113985 |
Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization |
|
| Relations |
| BioSample |
SAMN09015566 |
| SRA |
SRX4026235 |
