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Sample GSM3733922 Query DataSets for GSM3733922
Status Public on Apr 01, 2020
Title scRNA-seq-E16.5
Sample type SRA
Source name Female primordial germ cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Fetal ovaries
age: Embryonic day 16.5
Extracted molecule polyA RNA
Extraction protocol RNA were prepared for sequencing
Female primordial germ cells at different timepoints were harvested and resuspended at 1 × 106 cells per milliliter in 1 × PBS with 0.04% BSA. Then, cell suspensions (300-1000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Library and Gel Bead Kit V2 (10x Genomics, 120237). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads (Invitrogen, 37002D). Single-cell RNA-seq libraries were prepared using Single Cell 3' Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description PGC.txt
Data processing We checked the quality of raw sequencing data by FastQC software. The read2 fastq sequence was trimmed by FASTX-Toolkit. We used 10x genomics cellranger count pipeline 2.0.0 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were merged together by cellranger aggr pipeline and normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations
Submission date Apr 23, 2019
Last update date Apr 01, 2020
Contact name Qingyuan Sun
Phone 8601064807050
Organization name Institute of Zoology, Chinese Academy of Sciences
Department State Key Laboratory of Stem Cell and Reproductive Biology
Street address Beichen West Rd., Chaoyang
City Beijing
State/province Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL24247
Series (1)
GSE130212 The single cell transcriptional landscape of female primordial germ cell differentiation
BioSample SAMN11483249
SRA SRX5726252

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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