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| Status |
Public on Jun 04, 2020 |
| Title |
PDIS9063-235 |
| Sample type |
SRA |
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| Source name |
129/CAST hybrid mESC
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| Organism |
Mus musculus |
| Characteristics |
strain background: 129/CAST hybrid F1
cell type: Embryonic stem cell
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| Growth protocol |
The hybrid mouse ES cell line F1-21.6 (129Sv-Cast/EiJ, female), a kind gift from Prof. Joost Gribnau, were grown on either Laminin-511 (LN511, BioLamina, Stockholm, Sweden) in Std medium (15% fetal bovine serum [FBS] [Gibco], 0.1 mM β-mercaptoethanol [Wako Pure Chemicals, Osaka, Japan], 1000U/ml of leukemia inhibitory factor [LIF, Wako Pure Chemicals, Osaka, Japan]). This cell line was previously described in (Jonkers et al., 2009).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were collected in 1 μL of cell lysis buffer (1 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher), and RNase-free water (TaKaRa)) in a 96-well PCR plate (BIOplastics). The cell lysates were denatured at 70 °C for 90 s and held at 4 °C until the next step. To eliminate genomic DNA contamination, 1 µL of genomic DNA digestion mix (0.5× PrimeScript Buffer, 0.2 U of DNase I Amplification Grade, 1: 5 000 000 ERCC RNA Spike-In Mix I (Thermo Fisher) in RNase-free water) was added to 1 µL of the denatured sample. The mixtures were agitated for 30 s at 2000 rpm using a ThermoMixer C at 4 °C, incubated in a C1000 thermal cycler at 30 °C for 5 min and held at 4 °C until the next step.
Library preparation for single-cell RamDA-Seq was performed as described previously (Hayashi et al., 2018).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PDIS9063-235_TAGCGCTC-GCGTAAGA_L004
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| Data processing |
library strategy: RamDA-seq (random displacement amplification sequencing)
129 and CAST genomes by incorporating SNPs and indels into reference genome and transcriptome was created by Seqnature (Munger et al., 2014).
Bowtie (version 1.1.2) was used to align scRamDA-seq reads against the diploid transcriptome with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: ASEcount_G1_129.txt and ASEcount_G1_CAST.txt include read count data derived from 129 and CAST alleles, respectively, for each cell.
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| Submission date |
Jun 12, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
itoshi.nikaido@riken.jp
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| Organization name |
RIKEN
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| Department |
Center for Biosystems Dynamics Research
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| Lab |
Laboratory for Bioinformatics Research
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| Street address |
2-1 Hirosawa
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| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE132589 |
Allele-specific mRNA expression analysis in 129/CAST hybrid mESCs by single-cell full-length total RNA-sequencing |
| GSE132593 |
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN12037257 |
| SRA |
SRX6047831 |
| 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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