|
Status |
Public on Mar 16, 2015 |
Title |
PAN02EXO |
Sample type |
SRA |
|
|
Source name |
Primary culture (Life technologies)
|
Organism |
Homo sapiens |
Characteristics |
cell type: Human Kupffer cells treatment: Treatment with PAN02 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 |
PAN02exo
|
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 |
SAMN03407282 |
SRA |
SRX956335 |