|
| Status |
Public on Oct 17, 2017 |
| Title |
TEM Day4 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Donor_1 TEM Day4
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HepLPCs
culture condition: in the transition and expansion medium (Passage 1, 4 days)
ethnicity: Asian
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the hg38 genome assembly using Hisat2(version:2.0.4).
Gene abundance measurements were generationed and normalized using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
|
| |
|
| Submission date |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
yan hexin |
| E-mail(s) |
hexinyw@163.com
|
| Organization name |
Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine
|
| Street address |
No. 1630 East Road
|
| City |
shanghai |
| ZIP/Postal code |
200120 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE105019 |
Gene expression analysis of human liver progenitor-like cells in culture |
|
| Relations |
| BioSample |
SAMN07789047 |
| SRA |
SRX3287578 |
