|
| Status |
Public on Apr 01, 2014 |
| Title |
RNAseq_LEC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Dermal lymphatic endothelium
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Dermal lymphatic endothelial cells
cell line: LEC
|
| Treatment protocol |
When indicated, 1 µM doxycyclin (dox) and 500 µM phosphonoformic acid (PFA) were added to the culture medium for 72 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 1x10^7 cells using RNABee (AMSBIO cat. Cs-104B) following the manufacturer guidelines. Polyadenylated RNA was isolated from the total fraction using Oligotex mRNA kit (Qiagen cat. 70022). The resulting mRNA was partially fragmented by alkaline hydrolysis with sodium carbonate to ,150 nt segments on average, and then fragments between 40–100 nt were isolated from gel.
Libraries for RNA-seq were prepared using the Ribo-Zero magnetic and the ART-seq kits following the manufacturer recommendations (Epicentre, MRZH11124 and RPHMR12126).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIPseq: reads were aligned to the hg19 genome assembly using Bowtie2 (v2.1.0, default parameters)
ChIPseq: peaks were called using MACS 1.4.2 using the default parameters except when otherwise specified (see Samples section)
RNAseq: reads were aligned to the hg19 genome assembly using TopHat2 (v2.0.8b, default parameters)
RNAseq: gene expression analysis was performed with the Cufflinks/Cuffdiff package v2.1.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq: peak calling output files from the MACS program (tab-delimited text format). Contain peak genomic location, tag abundance and peak score (p-value, FDR)
Supplementary_files_format_and_content: RNAseq: output files from Cufflinks and Cuffdiff (tab-delimited format) that include FPKM values, gene expression ratios (LEC219 vs LEC) and statistical analysis (scores) for all hg19-annotated genes
|
| |
|
| Submission date |
Mar 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
ALEXANDRE MERCIER |
| Organization name |
NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH
|
| Department |
INFECTIOUS DISEASES
|
| Lab |
DON GANEM
|
| Street address |
5300 CHIRON WAY
|
| City |
EMERYVILLE |
| State/province |
CA |
| ZIP/Postal code |
94608 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE56144 |
Site-Specific Association with Host and Viral Chromatin by KSHV LANA and its Reversal during Lytic Reactivation |
|
| Relations |
| BioSample |
SAMN02711784 |
| SRA |
SRX503353 |
