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Sample GSM3001091 Query DataSets for GSM3001091
Status Public on Jun 04, 2020
Title Infected-hLEC-3
Sample type SRA
 
Source name primary human lymphatic endothelial cell
Organism Homo sapiens
Characteristics cell type: primary human lymphatic endothelial cell
treatment: Mycobacterium tuberculosis infected
Treatment protocol Mtb cultures were grown to exponential phase before being used to infect hLECs at MOI of 10 for 5 hours. Cells were washed free of Mtb with PBS and cultured for 48h with gentamicin.
Growth protocol Primary hLEC were cultured up to 5 passages in complete endothelial cell medium
Extracted molecule total RNA
Extraction protocol Cells were lysed with TRIzol and total RNA was extracted using Direct-zol RNA miniprep kit
RNA-Seq libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Trimmomatic v0.36
STAR v2.5.2a
RSEM v1.2.29
DESeq2 v1.18.1
Genome_build: GRCh38 release 88
 
Submission date Feb 13, 2018
Last update date Mar 29, 2023
Contact name Rachel Lai
E-mail(s) rachel.lai@imperial.ac.uk
Organization name Imperial College London
Department Infectious Disease
Street address Du Cane Road
City London
ZIP/Postal code W12 0NN
Country United Kingdom
 
Platform ID GPL16791
Series (1)
GSE110564 Mycobacterium tuberculosis cording in lymphatic endothelial cells (hLEC)
Relations
BioSample SAMN08529091
SRA SRX3691940

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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