|
| Status |
Public on Jun 01, 2022 |
| Title |
MTCHC01_monolayer_3 |
| Sample type |
SRA |
| |
|
| Source name |
MTCHC01 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: cholangiocarcinoma
cell line: MTCHC01
growth type: monolayer
replicate: 3
|
| Growth protocol |
The cells were grown for 10 days in anchoring-independent conditions with selective serum-free Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium supplemented with 1X B27 supplement minus vitamin A , human recombinant epidermal growth factor (hrEGF) (20 ng/ml), and bFGF (20 ng/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. Depletion of mammalian and mitochondrial rRNA was performed with the RiboGone – Mammalian kit according to manufacturer's instructions
Paired-end RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MCO_46
|
| Data processing |
base calling with bcl2fastq 2.20.0.422
read cleaning with fastp (v0.20.0): fastp -A -q 30 -u 50 -l 70 -y -w 20 -i raw/r1_raw -I raw/r2_raw -o pre/r1_prep -O pre/r2_prep -h pre/log.html -j /dev/null
read mapping with salmon (v0.14.1): salmon quant -p 22 --numGibbsSamples 500 -i genome -l A -1 r1_prep -2 r2_prep --validateMappings -o mapped
data collection: R (v3.6.3) Bioconductor tximport (v1.14.2)
analysis package: R Bioconductor DESeq2 (v2_1.26.0)
Genome_build: Homo sapiens GRCh38.p13
Supplementary_files_format_and_content: transcript and gene abundance tables both as R saved file and tab-separated txt file
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Matteo Ramazzotti |
| E-mail(s) |
matteo.ramazzotti@unifi.it
|
| Organization name |
University of Florence
|
| Department |
Experimental and Clinical Biomedical Sciences
|
| Street address |
viale Morgagni 50
|
| City |
Firenze |
| ZIP/Postal code |
50134 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE162845 |
Next generation sequencing of human cholangiocarcinoma cells and associated stem-like component |
|
| Relations |
| BioSample |
SAMN17026548 |
| SRA |
SRX9649182 |
