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Sample GSM3878434 Query DataSets for GSM3878434
Status Public on Jun 04, 2020
Title PDIS9063-333
Sample type SRA
 
Source name 129/CAST hybrid mESC
Organism Mus musculus
Characteristics strain background: 129/CAST hybrid F1
cell type: Embryonic stem cell
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).
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description PDIS9063-333_CCTAAGAC-GCGTAAGA_L005
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.
 
Submission date Jun 12, 2019
Last update date Jun 04, 2020
Contact name Itoshi NIKAIDO
E-mail(s) itoshi.nikaido@riken.jp
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Bioinformatics Research
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
 
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
Relations
BioSample SAMN12037757
SRA SRX6047500

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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