|
| Status |
Public on May 05, 2020 |
| Title |
L69 |
| Sample type |
SRA |
| |
|
| Source name |
Day5 collected cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8-10 weeks
tissue: Spleen
cell type: Day5 collected cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh isolated cells were transferred directly into cell lysis buffer and the reverse transcription and template swithc steps were performed following the Smart-seq2 protocol
The cDNA libraries were prepared for sequencing using a KAPA Hyper Prep Kit for Illumina
Modified Smart-seq2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
3' ends mRNA
|
| Data processing |
Raw reads were separated by specific cell barcode information attached in read 2 (R2) of the pair-ended reads.UMI information was aligned to the corresponding read 1 (R1),which was then trimmed to remove the template switch oligo (TSO) and ployA tail sequences;we also trimmed the reads with adaptor contaminants and low-quality bases (N> 10%)
The clean reads were aligned to the mm10 mouse transcriptome (UCSC) using TopHat (verson 2.0.12).Mapping reads were then counted using htseq-count in the HTSeq package. Based on the UMI information,duplicated transcripts with the same UMI sequences of each gene were removed.
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.
|
| |
|
| Submission date |
Jul 02, 2018 |
| Last update date |
May 05, 2020 |
| Contact name |
Caiying Zhu |
| E-mail(s) |
zhucaiying@ihcams.ac.cn
|
| Phone |
13622053408
|
| Organization name |
Institute of Hematology & Blood Diseases Hospital
|
| Street address |
NO. 288 Nanjing Road, Heping District, Tianjin
|
| City |
Tianjin |
| ZIP/Postal code |
300020 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE116530 |
Differentiation of transplanted haematopoietic stem cells tracked by single-cell transcriptomic analysis |
|
| Relations |
| BioSample |
SAMN09534292 |
| SRA |
SRX4334631 |
