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Sample GSM7048711 Query DataSets for GSM7048711
Status Public on Feb 17, 2023
Title Mouse_Liver_Array_1_pool_c
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 SAMN33326046
SRA SRX19391855

Supplementary file Size Download File type/resource
GSM7048711_Mouse_Liver_Array_1_pool_c_barcodes.tsv.gz 133.8 Kb (ftp)(http) TSV
GSM7048711_Mouse_Liver_Array_1_pool_c_expression.mtx.gz 7.8 Mb (ftp)(http) MTX
GSM7048711_Mouse_Liver_Array_1_pool_c_features.tsv.gz 63.9 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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