 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 26, 2024 |
| Title |
pHPC_CY153F_E58FL |
| Sample type |
SRA |
| |
|
| Source name |
fetal liver
|
| Organism |
Macaca fascicularis |
| Characteristics |
tissue: fetal liver
cell type: pHPC
developmental stage: Early 2nd trimester
Sex: female
treatment: fresh
|
| Growth protocol |
The cynomolgus macaque breeding ,manipulation of embryo, pregnancy check, cesarean section and sample collection were performed at Research Center for Animal Life Science, Shiga University of Medical Science.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Freshly isolated or frozen-thawed MACS-enriched CD34+ samples, derived from fetal liver, fetal bone marrow, and adult bone marrow, were stained with antibodies that had been validated for binding to cynomolgus protein. The cells were FACS-enriched to collect the target population and then loaded onto each channel of a Chromium chip. This was followed by GEM generation and RT reaction according to the 10X genomics manufacturer's protocol.
Library preparation (10X Genomics, Chromium Next GEM Single Cell 5’ Reagent Kits v.2, Chromium Next GEM Single Cell 5’ HT Reagent Kits v.2) were performed following the manufacturer’s instructions, with PCR cycle for cDNA amplification were adjusted based on FACS sorted cell counts.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw files were processed with the “mkfastq” command in Cell Ranger (v. 7.0.0) and mapped to the cynomolgus monkey reference genome MFA1912RKSv2 with “count” command with default setting.
Assembly: MFA1912RKSv2
Supplementary files format and content: Cell ranger output
|
| |
|
| Submission date |
Mar 21, 2024 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Ryo Yamamoto |
| E-mail(s) |
lab.r.yamamoto@gmail.com
|
| Organization name |
Kyoto Univerisity
|
| Department |
ASHBi
|
| Lab |
Ryo Yamamoto Lab
|
| Street address |
Yoshidakonoecho, Sakyo-ku
|
| City |
Japan |
| State/province |
Kyoto |
| ZIP/Postal code |
6068501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL28212 |
| Series (1) |
| GSE262140 |
Atlas of Cynomolgus Macaque Hematopoiesis |
|
| Relations |
| BioSample |
SAMN40557609 |
| SRA |
SRX24004977 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8158464_pHPC_CY153F_E58FL_barcodes.tsv.gz |
43.6 Kb |
(ftp)(http) |
TSV |
| GSM8158464_pHPC_CY153F_E58FL_features.tsv.gz |
251.7 Kb |
(ftp)(http) |
TSV |
| GSM8158464_pHPC_CY153F_E58FL_matrix.mtx.gz |
90.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
