|
| Status |
Public on Mar 16, 2015 |
| Title |
CTCEXO |
| Sample type |
SRA |
| |
|
| Source name |
Primary culture (Life technologies)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Kupffer cells
treatment: Treatment with normal pancreas exosomes
|
| Treatment protocol |
Cells were treated in 6 wells plates with 5ug/mL of exosomes every other day for 14 days
|
| Growth protocol |
RPMI + 10% exosome free FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CTLexo
|
| Data processing |
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Number of raw counts was calculated using the htseq-count script in the HTSeq package v0.6.1 with parameters "--stranded=no --mode=union --minaqual=10"; Genes with statistically significant changes in expression were selected by using the edgeR package v3.8.2.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files including gene name, RefSeq id, raw counts and normalized counts of each sample, for each gene
|
| |
|
| Submission date |
Mar 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
David Lyden |
| E-mail(s) |
dcl2001@med.cornell.edu
|
| Organization name |
Weill Medical College of Cornell University
|
| Department |
Departments of Pediatrics, Cell & Developmental Biology
|
| Street address |
413 E. 69th St., 12th Floor, BB-1251
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE66876 |
Pancreatic cancer exosomes induce pre-metastatic niche formation in the liver |
|
| Relations |
| BioSample |
SAMN03407247 |
| SRA |
SRX956334 |
