|
| Status |
Public on Sep 01, 2014 |
| Title |
Chimera_F19b3 |
| Sample type |
SRA |
| |
|
| Source name |
Humanized mouse liver
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: Liver tissue
injury: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver were homogenized in trizol. The aqueous layer was alcohol precipitated and cleaned up on Qiagen Rneasy Mini columns with on column DNAse digestion
2ug total RNA was prepared with the Illumina Truseq RNA sample prep kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling performed by CASAVA
Alignment was performed with Bowtie version 0.12.7 set to allow no mismatches. I trimmed the first 4 bases from each read and aligned to the next 44 bases. Only tags with unique alignments were counted.
Tags counts were compiled into a matrix using custom R-scripts
Genome_build: A custom transcriptome of 42 NCBI Refseq genes was used
Supplementary_files_format_and_content: tab-delimited text files include unique mapped reads for each sample and gene
|
| |
|
| Submission date |
Jun 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Branden Tarlow |
| E-mail(s) |
btarlow@gmail.com
|
| Phone |
(503) 494-6889
|
| Organization name |
Oregon Health & Science University
|
| Department |
Pediatrics
|
| Lab |
Markus Grompe, MD
|
| Street address |
3181 SW Sam Jackson Park Road
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL16512 |
| Series (1) |
| GSE58679 |
Human hepatocyte metaplasia in injured humanized mouse livers |
|
| Relations |
| BioSample |
SAMN02867595 |
| SRA |
SRX612496 |
