Sample 200
Mus musculus
Protocols: Three small (5-10 μm) C1 Single-Cell Auto Prep IFC chips (Fluidigm) were primed and 5,000 cells were sorted directly into the chip. To allow estimation of technical variability, 1 μl of 1:4000 dilution ERCC (External RNA Controls Consortium) spike-in mix (Ambion, Life Technologies) was added to the lysis reagent. Cell capture sites were visually inspected one by one using a microscope. C57BL/6 female mice were subcutaneously injected with 100ul (300/500 live third stage Nippostrongylus Brasiliensis larvae per dose), over two sites. Mediastinal lymph nodes, mesenteric lymph nodes, and lungs were taken from infected mice, 5 days after infection. Cells were isolated from mediastinal lymph nodes and mesenteric lymph nodes, by smashing the tissue though 70μm cell strainer. Lungs were incubated in collagenase D (0.72mg/ml, Amersham, Bucks, UK) for 30min, smashed though 70μm cell strainer, and suspended in RBC lysis buffer (eBioscience Ltd). Single cells were then stained with CD3e-APC-cy7, CD4-PE-Cy7 and CD62L-Violet-BV510 for 30 minutes on ice and then were washed. Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech). Sequencing libraries were prepared using Nextera XT DNA Sample Preparation kit with 96 indices (Illumina), according to the protocol supplied by Fluidigm.
ENA first public
2016-04-13
ENA last update
2016-04-12
External Id
SAMEA3927991
INSDC center alias
EMBL-European Bioinformatics Institute & Wellcome Trust Sanger Institute
INSDC center name
EMBL-European Bioinformatics Institute & Wellcome Trust Sanger Institute
INSDC first public
2016-04-13T17:04:36Z
INSDC last update
2016-04-12T21:08:53Z
INSDC status
public
Submitter Id
E-MTAB-4619:Sample 200
age
6 to 12
broker name
ArrayExpress
cell type
CD4-positive,CD3-positive,CD62L-negative
common name
house mouse
infect
Nippostrongylus Brasiliensis
sample name
E-MTAB-4619:Sample 200
sex
female
single cell id
200
single cell well quality
multiple cells
strain
C57BL/6
tissue
mesenteric lymph nodes