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| Status |
Public on Dec 13, 2023 |
| Title |
pgEpiSC_low |
| Sample type |
SRA |
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| Source name |
Pig pre-gastrulation epiblast stem cells (pig pgEpiSCs)
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| Organism |
Sus scrofa |
| Characteristics |
developmental stage: E10 embryonic epiblast
tissue: Embryonic epiblast
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
A modified Smart-seq2 protocol (Gao et al., 2018; Wang et al., 2018)
Single cell was transferred into prepared lysis buffer contained an 8bp barcode. Then, the first-strand cDNA was reversed-synthesized and amplified in a reverse transcription (RT) mixture containing 4U RNase inhibitor, 100U SuperScript II reverse transcriptase (Invitrogen, Cat. 18064071), 1 mM dNTPs (TAKARA, Cat. 4019), 60 mM MgCl2, 3 µM RT primer with 10 µM TSO primer. After PCR incubation, the product was purified by 0.8×AMPure XP beads (Beckman, Cat. A63882). Biotin PCR was carried out and enriched. The single cell RNA-seq library was constructed according to the KAPA Hyper Prep Kits with PCR Library Amplication/Illumina series (KAPA, KK8054).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw reads from scRNA-seq were split by 8 bp cell barcodes located on the Read 2 allowed 2 mismatches, besides, the 8pb unique molecular identifiers(UMIs) located on the Read 2 were switched to the identifier line of paired Read 1.
Then the Read 1 were processed to remove the template switch oligo (TSO) primer, low quality bases and polyA sequence. The trimmed reads were aligned against Ensembl Sus scrofa reference genome (Sscrofa11.1, GCA_000003025.6) using STAR software (version 2.7.1a) with default parameters.
The aligned reads were further assigned to the ensemble gene annotations (Sus_scrofa.Sscrofa11.1.98) using featureCounts (version 1.6.4). Gene expression levels were estimated by counting the UMIs located the genes after deduplication by UMI-tools, next yielded an expression matrix consisting of UMI counts for each cell and gene.
Genome_build: Suscrofa.11.1
Supplementary_files_format_and_content: tab-delimited text files include the mean values of CPM values for each cell type.
Supplementary_files_format_and_content: tab-delimited text files include the variance of CPM values for each cell type.
Supplementary_files_format_and_content: Barcode information for single cell libraries
Supplementary_files_format_and_content: cell-level raw counts
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| Submission date |
Mar 02, 2021 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Jianyong Han |
| E-mail(s) |
[email protected]
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| Organization name |
China Agricultural University
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| Department |
State Key Laboratory of Agrobiotechnology
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| Lab |
Han lab
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| Street address |
2rd, Yuanmingyuan West Road
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| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL22918 |
| Series (2) |
| GSE168106 |
Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines [single-cell RNA-seq] |
| GSE168107 |
Generation and Characterization of Stable Pig Pre-gastrulation Epiblast Stem Cell Lines |
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| Relations |
| BioSample |
SAMN18125059 |
| SRA |
SRX10224159 |
| 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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