|
| Status |
Public on May 05, 2024 |
| Title |
LO-iMAC-FA-2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver organoid
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver organoid
agent: iMAC-FA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA). The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, Böblingen, Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using STAR version 2.6.1d
TPM were calculated by using Salmon (version 1.6.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Dayeon Gil |
| E-mail(s) |
gilje@korea.kr
|
| Phone |
+82-43-249-2527
|
| Organization name |
Korea national institute of health
|
| Department |
Division of intractable disease research
|
| Street address |
202 Osongsaengmyung 2-ro, Heungdeok-gu
|
| City |
Cheongju-si |
| State/province |
Chungcheongbuk-do |
| ZIP/Postal code |
28160 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE229596 |
Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression [RNA-Seq] |
| GSE229609 |
Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression |
|
| Relations |
| SRA |
SRX19950677 |
| BioSample |
SAMN34164256 |
