|
| Status |
Public on Jan 08, 2024 |
| Title |
X2_106 |
| Sample type |
SRA |
| |
|
| Source name |
intestinal stromal cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: intestinal stromal cells
population: X2
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
No growth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorting from intestinal biopsy cell suspensions, freshly isolated.
Bulk seq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
bulk RNA-seq
2_106Aligned.sortedByCoord.out.bam
subreadCounts.txt
|
| Data processing |
Indexed cDNA libraries were normalized, combined and the pools sequenced on the Illumina Nextseq 550 for a 75-cycle v2.5 sequencing generating 75bp single-end reads.
Bcl files were converted and demultiplexed to fastq using the bcl2fastq v2.20.0.422 program. STAR v2.5.2b was used to index the human reference genome (hg38/GRCh38) and align the resulting fastq files.
Mapped reads were then counted in annotated exons using featureCounts v1.5.1.
The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR package and its general linear models pipeline.
For the gene expression analysis genes that had 1 count per million in 3 or more samples were used and normalized using TMM normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: subreadCounts.txt: Count Matrix
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Jan 08, 2024 |
| Contact name |
Indranil Sinha |
| Organization name |
Stockholm University
|
| Department |
Department of Molecular Biosciences
|
| Lab |
Visa Lab
|
| Street address |
The Wenner-Gren Institute
|
| City |
Stockholm |
| State/province |
106 91 |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE171582 |
Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF |
|
| Relations |
| BioSample |
SAMN18640432 |
| SRA |
SRX10525269 |
