|
| Status |
Public on Feb 20, 2024 |
| Title |
embryo_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Bos taurus |
| Characteristics |
developmental stage: multiplexed sample: Morula and blastocyst
age: multiplexed sample: 6.0,7.0,8.0,9.0 day after fertilization
treatment: wildtype
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Polyadenylated RNAs were captured and reverse transcribed with an Oligo(dT) primer
In brief, single cells were incubated at 72 °C for 3 min with lysis mixture. Reverse transcription and PCR pre-amplification were carried out with SuperScript II (Invitrogen) and KAPA HiFi HotStart ReadyMix (KAPA Biosystems). After PCR amplification , the samples with different barcodes were mixed together and then purified with DNA Clean&Concentrator-5 (Zymo Research). The cDNAs of single cells were added with biotinylated index and purified using beads (Vazyme). The cDNAs were sheared into approximately 300 bp fragments using sonication (Covaries). The fragmented cDNAs were enriche by Dynabeads ® MyOne TM Streptavidin C1 (Invitrogen). Adaptor ligation and final library were conducted by NEBNext Library Quant Kit (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
210811D
Cell metadata included in file on series record named "metadata.txt".
|
| Data processing |
Reads were trimmed by Trimgalore to remove the bases with low quality and adapter sequences
The trimmed reads were align to ARS-UCD1.2 by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized by Seurat
Assembly: ARS-UCD1.2
Supplementary files format and content: text files include normalized counts calculated by Seurat for each sample
|
| |
|
| Submission date |
Aug 01, 2023 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Bingjie Hu |
| E-mail(s) |
hubingjie110@126.com
|
| Organization name |
Zhejiang University
|
| Street address |
Yuhangtang Rd, Hangzhou, Zhejiang , China
|
| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE239782 |
Principles of the Earliest Lineage Specification and X Chromosome Dosage Compensation in Bovine Early Embryos |
|
| Relations |
| BioSample |
SAMN36795542 |
| SRA |
SRX21218672 |
