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Sample GSM7048701 Query DataSets for GSM7048701
Status Public on Feb 17, 2023
Title Sorted LT-HSC 15409
Sample type SRA
 
Source name Primary
Organism Mus musculus
Characteristics cell line: Primary
cell type: LT-HSC
genotype: Tnfrsf11aCre; Spi1f/f
developmental stage: E14.5
Extracted molecule total RNA
Extraction protocol RNA was extracted using the miRNeasy micro kit (Qiagen) and quantified via RNA assay on a tape station 4200 system (Agilent)
RNA was used as an input for library generation via SmartSeq 2 (SS2) RNA library production protocol as previously described (Picelli et al., 2014)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Samples were demultiplexed and fastq files were generated using bcl2fastq2 v2.20 before alignment and quantification using Kallisto v0.44.0 based on the Gencode (mm10, GRCm38) vM16 (Ensembl 91) reference genomes.
Sequencing results from the experiments were pseudoaligned using the Kallisto tool set
The final count matrix is free of GM, Rik, LOC, and sex genes.
Assembly: mm10
Supplementary files format and content: tab-separted value files, comma-separted value file for the final proccessed counts
 
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 GPL30172
Series (2)
GSE225442 Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi [bulkRNA-seq]
GSE225444 Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi
Relations
BioSample SAMN33325590
SRA SRX19391574

Supplementary file Size Download File type/resource
GSM7048701_15409_abundance.tsv.gz 1.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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