|
Status |
Public on Feb 17, 2023 |
Title |
Mouse_Liver_Array_3_pool_a |
Sample type |
SRA |
|
|
Source name |
Fetal liver
|
Organism |
Mus musculus |
Characteristics |
cell type: CD11+F4/80+ tissue: Fetal liver strain: C57BL/10 developmental stage: E14.5
|
Extracted molecule |
total RNA |
Extraction protocol |
The fetal liver was collected from wild-type mouse embryos. The collected tissues were digested for 20 min at 37 °C in a digestion solution. The cell suspensions were centrifuged and the supernatants were removed. The pellets were resuspended, washed and stained for 25 min. Finally, the pellet was resuspended in FACS buffer. The CD11blow/+ F4/80+ cells were sorted into microtubes containing FACS buffer. Seq-Well arrays were prepared as described by Gierahn et al. (Gierahn, Wadsworth et al. 2017). Seq-Well libraries were generated as described by Gierahn, Wadsworth et al. 2017 and Hughes, Wadsworth et al. 2020.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Seq-Well
|
Data processing |
Fastq files from Seq-Well were loaded into a snakemake-based data pre-processing pipeline (version 0.31, available at https://github.com/Hoohm/dropSeqPipe) STAR alignment within the pipeline was performed using the murine GENCODE reference genome and transcriptome mm10 release vM16 Supplementary files format and content: Tab-separated values files and matrix files
|
|
|
Submission date |
Feb 16, 2023 |
Last update date |
Feb 17, 2023 |
Contact name |
Amir Hossein Kayvanjoo |
E-mail(s) |
kayvanjoo@uni-bonn.de
|
Organization name |
LIMES Institute
|
Street address |
Carl-Troll-Straße 31
|
City |
Bonn |
ZIP/Postal code |
53115 |
Country |
Germany |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE225443 |
Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi [scRNA-seq] |
GSE225444 |
Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi |
|
Relations |
BioSample |
SAMN33326042 |
SRA |
SRX19391859 |