|
| Status |
Public on Sep 30, 2022 |
| Title |
MMNK-1_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
immortalized cholangiocyte cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MMNK-1
rrid: CVCL_M266
cell type: immortalized cholangiocyte cell lines
|
| Treatment protocol |
none
|
| Growth protocol |
Cell lines were growth at 5% CO2 and 37C in difference base medium with 2 mM L-glutamin from Gibco (The detail are as follows:MCF7 (Eagle), MMNK-1 (Ham-F12), T-47D (RPMI-1640), ZR-75-1 (RPMI-1640)). Then medium were supplemented with 10% FBS (Biochrom) and 1% Penicillin-Streptomycin(Gibco). Culture medium were change every 2-3 days. Then split cell lines at ratio 1:3 to 1:6 using 0.25% trypsin/EDTA (Gibco) when culture reach confluent. All cell lines were tested mycoplasma before perform an experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from cell lines byTrizol reagent (Invitrogen). RNA purification using Ambion RNA isolation kit (Invitrogen) and perform on-column DNA treatement using PureLink DNase set (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SO_6831_MMNK1
|
| Data processing |
Transcriptome sequencing was performed using Illumina Hiseq2000 (Illumina, San Diego, CA) with 150x2 paired-end chemistry reads and sequencing at depth 20-25 million reads per sample.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The STAR (v2.5.3a) was used to align reads to human reference genome (hg19 release).
Other pipelines were used including sambamba (v0.6.6) for sorting the BAM files, samtools (v1.6): for indexing the BAM files, fastp (v0.19.4) for the read trimming and QC and subread (v1.6.2) for the gene/isoform quantification.
The expression levels for each gene were normalized to transcripts per million (TPM) to facilitate the comparison of transcript levels among samples.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.
|
| |
|
| Submission date |
Jan 14, 2019 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Somponnat Sampattavanich |
| E-mail(s) |
somponnat.sam@mahidol.edu
|
| Organization name |
Faculty of Medicine Siriraj Hospital, Mahidol University
|
| Department |
Department of Pharmacology
|
| Lab |
Siriraj Laboratory for Systems Pharmacology
|
| Street address |
2 Wanglang Road
|
| City |
Bangkoknoi |
| State/province |
Bangkok |
| ZIP/Postal code |
10700 |
| Country |
Thailand |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE125034 |
Basal transcriptomic profiling of immortalized cholangiocyte and breast cancer cell lines. |
|
| Relations |
| BioSample |
SAMN10740305 |
| SRA |
SRX5246900 |
