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Sample GSM3525908 Query DataSets for GSM3525908
Status Public on Jun 30, 2020
Title BCG_D19_HSPC_BM_D0
Sample type SRA
 
Source name bone marrow
Organism Homo sapiens
Characteristics tissue: bone marrow
cell type: HSPC
timepoint: D0
condition: BCG
donor: D19
Extracted molecule polyA RNA
Extraction protocol total RNA was isolated from FACS-sorted populations using Qiazol (QIAGEN GmbH, Germany) and the miRNeasy Micro Kit (QIAGEN GmbH, Germany).
libraries were constructed from 1ng total RNA following the QIAseq FX Single Cell RNA Library Kit protocol (QIAGEN GmbH, Germany).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description BCG_BM_cirovic_counts.txt
Data processing raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to human reference transcriptome hg38 from UCSC and transcript abundance quantified using kallisto (v0.440) with default parameters.
abundance measurements were imported into R using tximport (v1.8.0).
for further filtering transcripts were removed not matching HGNC gene symbols, read sum lower than 10 across all samples or corresponding antisense, LINC or pseudogenes.
filtered data was imported into the DESeq2 package (v1.20.0) in R to generated a normalized expression table.
Genome_build: hg38
Supplementary_files_format_and_content: normalised expression table from DESeq2 containing all samples.
 
Submission date Dec 20, 2018
Last update date Jun 30, 2020
Contact name Branko Cirovic
Organization name LIMES
Lab Myeloid Cell Biology
Street address Carl-Troll Str 31
City Bonn
ZIP/Postal code 53111
Country Germany
 
Platform ID GPL18460
Series (2)
GSE124218 Human Bacille Calmette-Guérin vaccination elicits trained immunity via the hematopoietic progenitor compartment [bone marrow]
GSE124220 Human Bacille Calmette-Guérin vaccination elicits trained immunity via the hematopoietic progenitor compartment
Relations
BioSample SAMN10621172
SRA SRX5171603

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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