title: do7635
organism: Mus musculus castaneus
description: Protocols: Cells were purified from spleen in two different sub-species of mice (C57BL/6 and CAST/EiJ; all male animals) using EASY cell strainer (30 μm, Greiner BioOne), cell separation media (lympholyte, #CL5035) and the CD4+ CD62L+ T Cell Isolation Kit II (Miltenyi Biotec, #130-093-227). We use a microfluidics-based approach (5-10 μm Auto Prep Integrated Fluidic Circuit - IFC, Fluidigm, San Francisco, CA) to capture single cells and the C1 Single cell Auto Prep System (Fluidigm) to prepare single-cell RNA-Seq libraries CD4+ T cells. Purified cells were directly loaded into the microfluidics (naive CD4+ T cells) or were stimulated on 96 round-plates coated with anti-CD3ε and anti-CD28 for 3 hours (activated CD4+ T cells). cDNAs were made on-chip (Fluidigm C1, 5-10um IFC) with Clontech SMARTer Ultra Low RNA kit. ERCC spike-in RNA (Ambion) (1 µL diluted at 1:50,000) was added to the C1 lysis mix. Sequencing libraries were prepared using Illumina Nextera XT kit (Illumina) using the recommendation in the Fluidigm protocol (# PN 100-7168 K1).
attributes.tag: ENA first public
attributes.value: 2016-07-21
attributes.tag: ENA last update
attributes.value: 2016-07-11
attributes.tag: External Id
attributes.value: SAMEA4073259
attributes.tag: INSDC center alias
attributes.value: EMBL-EBI
attributes.tag: INSDC center name
attributes.value: EMBL-EBI
attributes.tag: INSDC first public
attributes.value: 2016-07-21T17:08:49Z
attributes.tag: INSDC last update
attributes.value: 2016-07-11T13:31:53Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-4888:do7635
attributes.tag: age
attributes.value: 22.3
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: naive thymus-derived CD4-positive, alpha-beta T cell
attributes.tag: common name
attributes.value: southeastern Asian house mouse
attributes.tag: individual
attributes.value: CAST old 1
attributes.tag: sample name
attributes.value: E-MTAB-4888:do7635
attributes.tag: sex
attributes.value: male
attributes.tag: single cell id
attributes.value: do7635
attributes.tag: single cell well quality
attributes.value: multiple cells
attributes.tag: strain
attributes.value: CAST/EiJ
attributes.tag: sub_species
attributes.value: castaneus