|
| Status |
Public on Jun 30, 2020 |
| Title |
BCG_D10_HSPC_BM_D90 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell type: HSPC
timepoint: D90
condition: BCG
donor: D10
|
| 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 |
SAMN10621160 |
| SRA |
SRX5171584 |
