|
| Status |
Public on Jul 05, 2019 |
| Title |
LMD_niche_p1 |
| Sample type |
SRA |
| |
|
| Source name |
HPC niche
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Tissue
subject: Patient 1
|
| Treatment protocol |
Liver tissue samples were dissociated, after which the single cell suspension was incubated with Hoechst, Hoechst+verapamil or TROP-2 or EpCAM fluorophore-coupled antibody. SP, EpCAM+ and TROP-2+ populations were extracted with FACS. Frozen, chresyl violet stained sections were used for LMD isolation of HPCs and niche.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Plus Micro Kit
TruSeq LT Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HPCs and their surrounding niche
|
| Data processing |
Each fastq file was trimmed and filtered to remove adaptors, polyN nucleotides and low quality sequences and subsequently confirmed by performing a second quality control.
All reads were mapped by Tophat2 on the homo sapiens genome h19.
Transcript compilation was performed using Cufflinks with homo sapiens hg19 UCSC transcript annotation.
Differential expression was calculated by Cuffdiff and subsequently we converted FPKM to TPM (median gene expression) using RStudio.
The data were further analysed with IPA (Inguinity Pathway Analysis) and Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: commapoint-delimited csv file include TPM values for each gene and each sample
|
| |
|
| Submission date |
Aug 15, 2017 |
| Last update date |
Jul 05, 2019 |
| Contact name |
Stefaan Verhulst |
| E-mail(s) |
[email protected]
|
| Phone |
+3224774413
|
| Organization name |
Vrije Universiteit Brussel
|
| Department |
BMWE
|
| Lab |
Liver cell biology research group
|
| Street address |
Laarbeeklaan 103, D022
|
| City |
Brussels |
| ZIP/Postal code |
1090 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE102683 |
RNA sequencing based comparative analysis of human hepatic progenitor cells and their niche from alcoholic steatohepatitis livers |
|
| Relations |
| BioSample |
SAMN07509226 |
| SRA |
SRX3095191 |
