title: Lung single cell 1229

description: lung single cell 1229


title: Lung single cell 1251

status: Public on Dec 06 2017

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: lung single cell 1251

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using STAR (version STAR_2.4.2a) and the count matrix shows the individual counts aligning to each gene per cell. In order to compare the gene expression counts between different cells, the total gene counts for each cell was normalized to 500,000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
We used different transgenic mouse reporter lines with fluorescent expression in different populations of vascular cells, Cldn5(BAC)eGFP mice that strongly labels lung endothelial cells, mice positive for Pdgfrb(BAC)eGFP and NG2dsRed.  We chose to focus our efforts to adult mice 12 to 15 weeks old in order to primarily define fully differentiated and quiescent vascular cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: lung

tag: age

value: adult mice 12 to 15 weeks old

tag: genotype

value: Pdgfrb(BAC)eGFP


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description: lung single cell 13


title: Brain astrocyte single cell 249

description: processed data file header: Brain.VSMC3_P18

source_name: Brain

extract_protocol:
We used transgenic mouse reporter line (SM22-Cre;Rosa26-stop-tdTomato). We chosed to focus our efforts to adult mice brain cells and we chose a methodology based on fluorescence-activated cell sorting (FACS) into 384-well plates followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: brain

value: adult mice


title: Brain astrocyte single cell 237

description: processed data file header: Brain.VSMC3_N11


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description: processed data file header: Brain.VSMC3_O11


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description: processed data file header: Brain.VSMC3_M17


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description: processed data file header: Brain.VSMC3_N24


title: Brain astrocyte single cell 236

description: processed data file header: Brain.VSMC3_M6


title: Lung single cell 5

description: lung single cell 5


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description: processed data file header: Brain.VSMC3_M15


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description: processed data file header: Brain.VSMC3_L16


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description: processed data file header: Brain.VSMC3_L11


title: Brain astrocyte single cell 250

description: processed data file header: Brain.VSMC3_P19


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description: processed data file header: Brain.VSMC3_L10


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description: processed data file header: Brain.VSMC3_P11


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description: processed data file header: Brain.VSMC3_K9


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description: processed data file header: Brain.VSMC3_K5


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description: processed data file header: Brain.VSMC3_K17


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description: processed data file header: Brain.VSMC3_J22


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description: processed data file header: Brain.VSMC3_I1


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description: processed data file header: Brain.VSMC3_I11


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description: processed data file header: Brain.VSMC3_L3


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description: processed data file header: Brain.VSMC3_I6


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description: processed data file header: Brain.VSMC3_H23


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description: processed data file header: Brain.VSMC3_H1


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description: processed data file header: Brain.VSMC3_G8


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description: processed data file header: Brain.VSMC3_G3


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description: processed data file header: Brain.VSMC3_G5


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description: processed data file header: Brain.VSMC3_G2


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description: processed data file header: Brain.VSMC3_H15


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description: processed data file header: Brain.VSMC3_G12


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description: processed data file header: Brain.VSMC3_F15


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description: processed data file header: Brain.VSMC3_H10


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description: processed data file header: Brain.VSMC3_F8


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description: processed data file header: Brain.VSMC3_C5


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description: processed data file header: Brain.VSMC3_C12


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description: processed data file header: Brain.VSMC3_B16


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description: processed data file header: Brain.VSMC3_E15


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description: processed data file header: Brain.VSMC3_C11


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description: processed data file header: Brain.VSMC3_G22


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description: processed data file header: Brain.VSMC3_A23


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description: processed data file header: Brain.VSMC3_A1


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description: processed data file header: Brain.VSMC3_A2


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description: processed data file header: Brain.VSMC3_A22


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description: processed data file header: Brain.VSMC3_F13


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description: processed data file header: Brain.VSMC3_F14


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description: processed data file header: Brain.VSMC3_A19


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description: processed data file header: Brain.VSMC3_A13


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description: processed data file header: Brain.VSMC2_P6


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description: processed data file header: Brain.VSMC3_A10


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description: processed data file header: Brain.VSMC3_B7


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description: processed data file header: Brain.VSMC2_P8


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description: processed data file header: Brain.VSMC2_P5


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description: processed data file header: Brain.VSMC2_P20


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description: processed data file header: Brain.VSMC2_P22


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description: processed data file header: Brain.VSMC2_P17


title: Brain astrocyte single cell 151

description: processed data file header: Brain.VSMC2_O24


title: Brain astrocyte single cell 152

description: processed data file header: Brain.VSMC2_O2


title: Brain astrocyte single cell 150

description: processed data file header: Brain.VSMC2_O22


title: Brain astrocyte single cell 156

description: processed data file header: Brain.VSMC2_P18


title: Brain astrocyte single cell 147

description: processed data file header: Brain.VSMC2_N8


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description: processed data file header: Brain.VSMC2_O1


title: Brain astrocyte single cell 145

description: processed data file header: Brain.VSMC2_N3


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description: processed data file header: Brain.VSMC3_A18


title: Brain astrocyte single cell 143

description: processed data file header: Brain.VSMC2_N23


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description: processed data file header: Brain.VSMC2_N21


title: Brain astrocyte single cell 146

description: processed data file header: Brain.VSMC2_N7


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description: processed data file header: Brain.VSMC2_N17


title: Brain astrocyte single cell 140

description: processed data file header: Brain.VSMC2_N1


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description: processed data file header: Brain.VSMC2_N20


title: Brain astrocyte single cell 137

description: processed data file header: Brain.VSMC2_N14


title: Brain astrocyte single cell 134

description: processed data file header: Brain.VSMC2_N10


title: Brain astrocyte single cell 138

description: processed data file header: Brain.VSMC2_N16


title: Brain astrocyte single cell 159

description: processed data file header: Brain.VSMC2_P4


title: Brain astrocyte single cell 132

description: processed data file header: Brain.VSMC2_M7


title: Brain astrocyte single cell 133

description: processed data file header: Brain.VSMC2_M8


title: Brain astrocyte single cell 153

description: processed data file header: Brain.VSMC2_O6


title: Brain astrocyte single cell 130

description: processed data file header: Brain.VSMC2_M5


title: Brain astrocyte single cell 154

description: processed data file header: Brain.VSMC2_P11


title: Brain astrocyte single cell 129

description: processed data file header: Brain.VSMC2_M3


title: Brain astrocyte single cell 125

description: processed data file header: Brain.VSMC2_M21


title: Brain astrocyte single cell 148

description: processed data file header: Brain.VSMC2_O10


title: Brain astrocyte single cell 128

description: processed data file header: Brain.VSMC2_M24


title: Brain astrocyte single cell 127

description: processed data file header: Brain.VSMC2_M23


title: Brain astrocyte single cell 135

description: processed data file header: Brain.VSMC2_N11


title: Brain astrocyte single cell 123

description: processed data file header: Brain.VSMC2_M17


title: Brain astrocyte single cell 124

description: processed data file header: Brain.VSMC2_M1


title: Brain astrocyte single cell 144

description: processed data file header: Brain.VSMC2_N2


title: Brain astrocyte single cell 120

description: processed data file header: Brain.VSMC2_M10


title: Brain astrocyte single cell 131

description: processed data file header: Brain.VSMC2_M6


title: Brain astrocyte single cell 122

description: processed data file header: Brain.VSMC2_M16


title: Brain astrocyte single cell 118

description: processed data file header: Brain.VSMC2_L5


title: Brain astrocyte single cell 117

description: processed data file header: Brain.VSMC2_L2


title: Brain astrocyte single cell 115

description: processed data file header: Brain.VSMC2_L22


title: Brain astrocyte single cell 116

description: processed data file header: Brain.VSMC2_L24


title: Brain astrocyte single cell 119

description: processed data file header: Brain.VSMC2_L9


title: Brain astrocyte single cell 114

description: processed data file header: Brain.VSMC2_L21


title: Brain astrocyte single cell 136

description: processed data file header: Brain.VSMC2_N13


title: Brain astrocyte single cell 113

description: processed data file header: Brain.VSMC2_L1


title: Brain astrocyte single cell 112

description: processed data file header: Brain.VSMC2_L19


title: Brain astrocyte single cell 111

description: processed data file header: Brain.VSMC2_L18


title: Brain astrocyte single cell 110

description: processed data file header: Brain.VSMC2_L17


title: Brain astrocyte single cell 108

description: processed data file header: Brain.VSMC2_L11


title: Brain astrocyte single cell 106

description: processed data file header: Brain.VSMC2_K9


title: Brain astrocyte single cell 109

description: processed data file header: Brain.VSMC2_L12


title: Brain astrocyte single cell 105

description: processed data file header: Brain.VSMC2_K8


title: Brain astrocyte single cell 104

description: processed data file header: Brain.VSMC2_K4


title: Brain astrocyte single cell 107

description: processed data file header: Brain.VSMC2_L10


title: Brain astrocyte single cell 103

description: processed data file header: Brain.VSMC2_K21


title: Brain astrocyte single cell 102

description: processed data file header: Brain.VSMC2_K20


title: Brain astrocyte single cell 101

description: processed data file header: Brain.VSMC2_K15


title: Brain astrocyte single cell 98

description: processed data file header: Brain.VSMC2_J8


title: Brain astrocyte single cell 100

description: processed data file header: Brain.VSMC2_K12


title: Brain astrocyte single cell 121

description: processed data file header: Brain.VSMC2_M14


title: Brain astrocyte single cell 96

description: processed data file header: Brain.VSMC2_J21


title: Brain astrocyte single cell 95

description: processed data file header: Brain.VSMC2_J1


title: Brain astrocyte single cell 93

description: processed data file header: Brain.VSMC2_J18


title: Brain astrocyte single cell 94

description: processed data file header: Brain.VSMC2_J19


title: Brain astrocyte single cell 92

description: processed data file header: Brain.VSMC2_J12


title: Brain astrocyte single cell 91

description: processed data file header: Brain.VSMC2_I9


title: Brain astrocyte single cell 88

description: processed data file header: Brain.VSMC2_I16


title: Brain astrocyte single cell 89

description: processed data file header: Brain.VSMC2_I20


title: Brain astrocyte single cell 90

description: processed data file header: Brain.VSMC2_I4


title: Brain astrocyte single cell 87

description: processed data file header: Brain.VSMC2_I15


title: Brain astrocyte single cell 86

description: processed data file header: Brain.VSMC2_I14


title: Brain astrocyte single cell 85

description: processed data file header: Brain.VSMC2_I13


title: Brain astrocyte single cell 84

description: processed data file header: Brain.VSMC2_H9


title: Brain astrocyte single cell 83

description: processed data file header: Brain.VSMC2_H7


title: Brain astrocyte single cell 82

description: processed data file header: Brain.VSMC2_H20


title: Brain astrocyte single cell 78

description: processed data file header: Brain.VSMC2_H13


title: Brain astrocyte single cell 81

description: processed data file header: Brain.VSMC2_H1


title: Brain astrocyte single cell 80

description: processed data file header: Brain.VSMC2_H16


title: Brain astrocyte single cell 76

description: processed data file header: Brain.VSMC2_G7


title: Brain astrocyte single cell 77

description: processed data file header: Brain.VSMC2_H11


title: Brain astrocyte single cell 75

description: processed data file header: Brain.VSMC2_G6


title: Brain astrocyte single cell 99

description: processed data file header: Brain.VSMC2_K10


title: Brain astrocyte single cell 73

description: processed data file header: Brain.VSMC2_G4


title: Brain astrocyte single cell 74

description: processed data file header: Brain.VSMC2_G5


title: Brain astrocyte single cell 97

description: processed data file header: Brain.VSMC2_J24