|
| Status |
Public on Feb 16, 2018 |
| Title |
LM3-Z3 |
| Sample type |
SRA |
| |
|
| Source name |
Unfixed Fresh Frozen Human Liver
|
| Organism |
Homo sapiens |
| Characteristics |
patient: LM3
zone: Z3
gender: Female
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Unfixed fresh frozen liver tissue embedded in OCT compound were cryo-cut followed by tissue collection via Laser Captured Microdissection methods. The RNA was extracted with RNeasy Micro Kit (QIAGEN).
1ng of RNA per sample was subjected to first-stranded cDNA synthesis followed by PCR amplification (11 cycles) using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Then, the amplified cDNA was used for the establishement of libraries using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls generated on Nextseq 500 by RTA v2
Raw data files in FASTQ format was analyzed with Partek Flow v4
FASTQ files were trimmed with Quality Score method
Trimmed reads were mapped with Star 2.4.1d to human hg38 genome build with Gencode v23 as guidance
Mapped reads were quantificed to Gencode v23 uisng Partek E/M method
Quantified reads were normalized by Upper Quartile method
Normalized reads were analzyed for differentially expression using Partek's Gene Specific Analysis method
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file includes normalized read counts (upper quartile normalization with offset 1) for genes in all samples
|
| |
|
| Submission date |
Jul 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Meng Li |
| Organization name |
University of Southern California
|
| Street address |
2003 Zonal Avenue
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089-0110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE83990 |
Zone dependent distinctive gene expression profile of the normal human liver tissue |
|
| Relations |
| BioSample |
SAMN05356954 |
| SRA |
SRX1896807 |
