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Status |
Public on Feb 17, 2023 |
Title |
Sorted LT-HSC 15405 |
Sample type |
SRA |
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Source name |
Primary
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Organism |
Mus musculus |
Characteristics |
cell line: Primary cell type: LT-HSC genotype: Tnfrsf11aCre; Spi1f/f developmental stage: E14.5
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 2000 |
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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
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Submission date |
Feb 16, 2023 |
Last update date |
Feb 17, 2023 |
Contact name |
Amir Hossein Kayvanjoo |
E-mail(s) |
kayvanjoo@uni-bonn.de
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Organization name |
LIMES Institute
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Street address |
Carl-Troll-Straße 31
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City |
Bonn |
ZIP/Postal code |
53115 |
Country |
Germany |
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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 |
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Relations |
BioSample |
SAMN33325592 |
SRA |
SRX19391572 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7048699_15405_abundance.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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