|
| Status |
Public on Jun 22, 2022 |
| Title |
EP_1 |
| Sample type |
SRA |
| |
|
| Source name |
nascent hematopoietic cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: caudal half
cell type: nascent hematopoietic cells
Stage: Embryonic day 10.5
strain: C57BL/6
genotype: Hlf-tdTomato knock-in
markers: Hlf-tdTomato+c-Kit+CD45-
|
| Treatment protocol |
Single-cell suspensions were prepared by treating tissues with collagenase [0.125% in PBS/10% fetal calf serum (FCS)/1% penicillin/streptomycin] for 1 h at 37°C. Hematopoietic fractions were isolated by cell sorter.
|
| Growth protocol |
Mice were housed in a specific-pathogen free animal facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis buffer containing 100 cells was directly used for cDNA synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
mRNA profile generated by deep sequencing using Illumina Next-Seq 500.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2.
Transcripts per kilobase million (TPM) were calculated by StringTie.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
|
| |
|
| Submission date |
Mar 02, 2021 |
| Last update date |
Jun 24, 2022 |
| Contact name |
Tomomasa Yokomizo |
| E-mail(s) |
tomoyokomizo@gmail.com
|
| Organization name |
Kumamoto University
|
| Street address |
2-2-1 Honjo, Chuo-ku
|
| City |
Kumamoto |
| ZIP/Postal code |
860-0811 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE168054 |
Transcriptome analysis of nascent hematopoietic cells II |
|
| Relations |
| BioSample |
SAMN18106893 |
| SRA |
SRX10206417 |
