 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 20, 2024 |
| Title |
cow.sc.esc.1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryos & Embryonic epiblast
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Embryos & Embryonic epiblast
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For STRT-seq, a modified Smart-seq2 protocol (Gao et al., 2018; Wang et al., 2018)
For STRT-seq, 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
all_counts.txt
|
| Data processing |
For STRT-seq, 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 to the Bos_taurus.ARS_UCD1.2 reference genomes. The unique molecular identifier (UMI) counts using kallisto (v-0.46.0)
Assembly:Bos_taurus.ARS_UCD1.2
Supplementary files format and content: txt
|
| |
|
| Submission date |
Feb 20, 2024 |
| Last update date |
Oct 20, 2024 |
| Contact name |
Jianyong Han |
| E-mail(s) |
hanjy@cau.edu.cn
|
| Organization name |
China Agricultural University
|
| Department |
State Key Laboratory of Agrobiotechnology
|
| Lab |
Han lab
|
| Street address |
2rd, Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL24230 |
| Series (1) |
| GSE256201 |
Investigating alterations in bovine embryonic pluripotency through scRNA-seq and establishing robust Formative stem cell lines |
|
| Relations |
| BioSample |
SAMN40002378 |
| SRA |
SRX23672049 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
