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Sample GSM5505018 Query DataSets for GSM5505018
Status Public on May 11, 2022
Title scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_24
Sample type SRA
Source name Primordial germ cells
Organism Mus musculus
Characteristics cell type: Primordial germ cells
strain: C57BL/6;129S1/SvlmJ
developmental stage: E12.5
genotype: Eed -/-
gender: Male
Growth protocol Control and ECKO male and female embryos were obtained from crosses between OG; Eedfl/fl (Lengner et al., 2007; Yu et al., 2009) homozygous females and BC; Eedf/l+ heterozygous males (Ohinata et al., 2005) at E10.5, E11.5 and E13.5. Embryos were staged by the detection of a vaginal plug on the morning after time-mating pairs were established E0.5.
Extracted molecule polyA RNA
Extraction protocol Female E12.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Single Cell RNA sequencing libraries were prepared according to the Smart Seq 2 single cell sequencing protocol (Picelli et al., 2014). The RNA was converted to cDNA in each well using Superscript II (Invitrogen). The cDNA was amplified in each well using a KAPA HiFI HotStart polymerase (KAPA Biosystems) in a PCR run for 18 cycles. cDNA was tagged via the Nextera Tagmentation kit (Illumina) using libraries A and C (Illumina). Indexed cDNA was pooled and run on a 2% agarose gel and the smear between 200-500 bp was extracted. Gel extract was cleaned with the Qiagen Gel Extraction Kit (Qiagen) and sent for sequencing.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description MattLowe5704_male_counts.txt
Data processing The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2. CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.
Submission date Aug 05, 2021
Last update date May 11, 2022
Contact name Pao-Yang Chen
Organization name Academia Sinica
Department Institute of Plant and Microbial Biology
Lab Pao-Yang Chen
Street address 128 Sec. 2, Academia Rd, Nankang,
City Taipei
ZIP/Postal code 115
Country Taiwan
Platform ID GPL24247
Series (1)
GSE139413 EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad
BioSample SAMN20603950
SRA SRX11664896

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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