title: Sample 62
organism: Mus musculus
description: 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.
attributes.tag: ENA first public
attributes.value: 2016-04-13
attributes.tag: ENA last update
attributes.value: 2016-04-12
attributes.tag: External Id
attributes.value: SAMEA3927853
attributes.tag: INSDC center alias
attributes.value: EMBL-European Bioinformatics Institute & Wellcome Trust Sanger Institute
attributes.tag: INSDC center name
attributes.value: EMBL-European Bioinformatics Institute & Wellcome Trust Sanger Institute
attributes.tag: INSDC first public
attributes.value: 2016-04-13T17:04:35Z
attributes.tag: INSDC last update
attributes.value: 2016-04-12T21:08:48Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-4619:Sample 62
attributes.tag: age
attributes.value: 6 to 12
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: CD4-positive,CD3-positive,CD62L-negative
attributes.tag: common name
attributes.value: house mouse
attributes.tag: infect
attributes.value: Nippostrongylus Brasiliensis
attributes.tag: sample name
attributes.value: E-MTAB-4619:Sample 62
attributes.tag: sex
attributes.value: female
attributes.tag: single cell id
attributes.value: 62
attributes.tag: single cell well quality
attributes.value: OK
attributes.tag: strain
attributes.value: C57BL/6
attributes.tag: tissue
attributes.value: lung