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Status |
Public on Apr 01, 2020 |
Title |
scRNA-seq-E16.5 |
Sample type |
SRA |
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|
Source name |
Female primordial germ cells
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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.
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|
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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
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|
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Submission date |
Apr 23, 2019 |
Last update date |
Apr 01, 2020 |
Contact name |
Qingyuan Sun |
E-mail(s) |
sunqy@ioz.ac.cn
|
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 |
|
Relations |
BioSample |
SAMN11483249 |
SRA |
SRX5726252 |