Mus musculus
Protocols: Thymi from Foxn1cre x ROSA26TdTOMATO mice were enzymaticaly digested, cells were MACS enriched for CD11c+ fraction. Dendritic cells were then FACS sorted (BD influx sorter) as Gr-1-CD11c+TdTOMATO+. Sufficient cell concentration (2900 cells/ul in both samples) and viability (96% in both samples) were ascertained using a TC20 Automated Cell Counter (Bio-Rad). Cell identification was accomplished with cell barcodes and low-expression cells filtering using UMI-tools. We supplied following cell barcode and UMI extraction expression: '(?P<discard_1>.{0,5})(?P<cell_1>.{6})(?P<discard_2>TAGCCATCGCATTGC){s<=2}(?P<cell_2>.{6})(?P<discard_3>TACCTCTGAGCTGAA){s<=2}(?P<cell_3>.{6})(?P<discard_4>ACG)(?P<umi_1>.{8})(?P<discard_5>GAC)(?P<discard_6>T{0,6})'. After investigating the cell quality asessment, we selected 202 cells in sample DC1 and 218 cells in sample DC2 for further analysis. Cell specific gene expression was quantified using featureCounts after deduplication of per-gene assigned read counts by UMIs with UMI-tools. UMI-tools tutorial github page: https://github.com/CGATOxford/UMI-tools/blob/master/doc/Single_cell_tutorial.md We used Illumina Bio-Rad SureCell WTA 3' Library Prep Kit for the ddSEQ System for mRNA extraction and library construction. We used Illumina Bio-Rad SureCell WTA 3' Library Prep Kit for the ddSEQ System for mRNA extraction and library construction. Lengths and offsets of cell barcodes and umis is proprietary information of the platform manufacturers, additionally offsets of cell barcodes and umis in reads are relative to the first base.
ENA-FIRST-PUBLIC
2020-03-20T17:05:12Z
ENA-LAST-UPDATE
2019-06-17T15:57:44Z
External Id
SAMEA5721581
INSDC center name
Service Laboratory of Functional Genomics and Bioinformatics Institute of Molecular Genetics of the ASCR, v. v. i.
INSDC first public
2020-03-20T17:05:12Z
INSDC last update
2019-06-17T15:57:44Z
INSDC status
public
Submitter Id
E-MTAB-8028:DC1
age
3 to 6
broker name
ArrayExpress
cell type
dendritic cell
common name
house mouse
developmental stage
adult
genotype
Foxn1cre x ROSA26TdTOMATO
individual
1
inferred cell type
thymic dendritic cell subtype 1
organism part
thymus
phenotype
Gr-1-CD11c+TdTOMATO+
sample name
E-MTAB-8028:DC1
scientific_name
Mus musculus
sex
female
strain
C57BL/6J