title: 3mix-FACS, 3mix-FACS-plate2_87

description:
3mix-FACS-plate2_87
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_86

status: Public on Dec 15 2022

type: SRA

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

description:
3mix-FACS-plate2_86
3mix_RNA_expression.txt

library_source: transcriptomic

data_processing:
Basecalls performed by Illumina MiSeq or Hiseq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq or using bcl2fastq for Illumina Hiseq resultes
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA molecules per cell for each gene is listed (cells which were not filtered out are shown).

molecule: total RNA

organism: Mus musculus

source_name: Cell line mixture of murine T cell, murine leukemia cell, and murine hematopoietic progenitor cell

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Murine T cells, leukemia cells, hematopoietic progenitor cells, and PBMCs were isolated by ALPS or FACS

tag: strain

tag: cell type

value: hematopoietic progenitor cell

tag: isolation method

value: FACS


title: 3mix-FACS, 3mix-FACS-plate2_85

description:
3mix-FACS-plate2_85
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_82

description:
3mix-FACS-plate2_82
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_84

description:
3mix-FACS-plate2_84
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_83

description:
3mix-FACS-plate2_83
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_81

description:
3mix-FACS-plate2_81
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_88

description:
3mix-FACS-plate2_88
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_80

description:
3mix-FACS-plate2_80
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_77

description:
3mix-FACS-plate2_77
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_75

description:
3mix-FACS-plate2_75
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_76

description:
3mix-FACS-plate2_76
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_96

description:
3mix-FACS-plate2_96
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_74

description:
3mix-FACS-plate2_74
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_73

description:
3mix-FACS-plate2_73
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_93

description:
3mix-FACS-plate2_93
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_78

description:
3mix-FACS-plate2_78
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_72

description:
3mix-FACS-plate2_72
3mix_RNA_expression.txt

value: T cell


title: 3mix-FACS, 3mix-FACS-plate2_70

description:
3mix-FACS-plate2_70
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_71

description:
3mix-FACS-plate2_71
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_68

description:
3mix-FACS-plate2_68
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_69

description:
3mix-FACS-plate2_69
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_67

description:
3mix-FACS-plate2_67
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_64

description:
3mix-FACS-plate2_64
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_63

description:
3mix-FACS-plate2_63
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_89

description:
3mix-FACS-plate2_89
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_65

description:
3mix-FACS-plate2_65
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_62

description:
3mix-FACS-plate2_62
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_66

description:
3mix-FACS-plate2_66
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_79

description:
3mix-FACS-plate2_79
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_59

description:
3mix-FACS-plate2_59
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_60

description:
3mix-FACS-plate2_60
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_57

description:
3mix-FACS-plate2_57
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_56

description:
3mix-FACS-plate2_56
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_54

description:
3mix-FACS-plate2_54
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_55

description:
3mix-FACS-plate2_55
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_53

description:
3mix-FACS-plate2_53
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_58

description:
3mix-FACS-plate2_58
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_52

description:
3mix-FACS-plate2_52
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_51

description:
3mix-FACS-plate2_51
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_50

description:
3mix-FACS-plate2_50
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_49

description:
3mix-FACS-plate2_49
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_46

description:
3mix-FACS-plate2_46
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_43

description:
3mix-FACS-plate2_43
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_47

description:
3mix-FACS-plate2_47
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_48

description:
3mix-FACS-plate2_48
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_41

description:
3mix-FACS-plate2_41
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_39

description:
3mix-FACS-plate2_39
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_38

description:
3mix-FACS-plate2_38
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_40

description:
3mix-FACS-plate2_40
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_44

description:
3mix-FACS-plate2_44
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_45

description:
3mix-FACS-plate2_45
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_61

description:
3mix-FACS-plate2_61
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_42

description:
3mix-FACS-plate2_42
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_37

description:
3mix-FACS-plate2_37
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_34

description:
3mix-FACS-plate2_34
3mix_RNA_expression.txt

value: leukemia cell


title: 3mix-FACS, 3mix-FACS-plate2_33

description:
3mix-FACS-plate2_33
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_36

description:
3mix-FACS-plate2_36
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_32

description:
3mix-FACS-plate2_32
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_35

description:
3mix-FACS-plate2_35
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_30

description:
3mix-FACS-plate2_30
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_31

description:
3mix-FACS-plate2_31
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_29

description:
3mix-FACS-plate2_29
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_28

description:
3mix-FACS-plate2_28
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_26

description:
3mix-FACS-plate2_26
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_27

description:
3mix-FACS-plate2_27
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_25

description:
3mix-FACS-plate2_25
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_22

description:
3mix-FACS-plate2_22
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_20

description:
3mix-FACS-plate2_20
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_21

description:
3mix-FACS-plate2_21
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_19

description:
3mix-FACS-plate2_19
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_18

description:
3mix-FACS-plate2_18
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_17

description:
3mix-FACS-plate2_17
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_15

description:
3mix-FACS-plate2_15
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_13

description:
3mix-FACS-plate2_13
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_12

description:
3mix-FACS-plate2_12
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_14

description:
3mix-FACS-plate2_14
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_11

description:
3mix-FACS-plate2_11
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_10

description:
3mix-FACS-plate2_10
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_9

description:
3mix-FACS-plate2_9
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_8

description:
3mix-FACS-plate2_8
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_2

description:
3mix-FACS-plate2_2
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_4

description:
3mix-FACS-plate2_4
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_5

description:
3mix-FACS-plate2_5
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_6

description:
3mix-FACS-plate2_6
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_3

description:
3mix-FACS-plate2_3
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_96

description:
3mix-FACS-plate1_96
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_24

description:
3mix-FACS-plate2_24
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_92

description:
3mix-FACS-plate1_92
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_7

description:
3mix-FACS-plate2_7
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_93

description:
3mix-FACS-plate1_93
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_91

description:
3mix-FACS-plate1_91
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_23

description:
3mix-FACS-plate2_23
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_95

description:
3mix-FACS-plate1_95
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_90

description:
3mix-FACS-plate1_90
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_16

description:
3mix-FACS-plate2_16
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_89

description:
3mix-FACS-plate1_89
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_87

description:
3mix-FACS-plate1_87
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_88

description:
3mix-FACS-plate1_88
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_86

description:
3mix-FACS-plate1_86
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_84

description:
3mix-FACS-plate1_84
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate2_1

description:
3mix-FACS-plate2_1
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_83

description:
3mix-FACS-plate1_83
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_81

description:
3mix-FACS-plate1_81
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_80

description:
3mix-FACS-plate1_80
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_78

description:
3mix-FACS-plate1_78
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_79

description:
3mix-FACS-plate1_79
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_82

description:
3mix-FACS-plate1_82
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_94

description:
3mix-FACS-plate1_94
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_74

description:
3mix-FACS-plate1_74
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_73

description:
3mix-FACS-plate1_73
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_65

description:
3mix-FACS-plate1_65
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_75

description:
3mix-FACS-plate1_75
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_68

description:
3mix-FACS-plate1_68
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_70

description:
3mix-FACS-plate1_70
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_71

description:
3mix-FACS-plate1_71
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_67

description:
3mix-FACS-plate1_67
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_64

description:
3mix-FACS-plate1_64
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_72

description:
3mix-FACS-plate1_72
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_66

description:
3mix-FACS-plate1_66
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_85

description:
3mix-FACS-plate1_85
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_60

description:
3mix-FACS-plate1_60
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_58

description:
3mix-FACS-plate1_58
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_59

description:
3mix-FACS-plate1_59
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_62

description:
3mix-FACS-plate1_62
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_63

description:
3mix-FACS-plate1_63
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_57

description:
3mix-FACS-plate1_57
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_56

description:
3mix-FACS-plate1_56
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_77

description:
3mix-FACS-plate1_77
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_54

description:
3mix-FACS-plate1_54
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_53

description:
3mix-FACS-plate1_53
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_52

description:
3mix-FACS-plate1_52
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_61

description:
3mix-FACS-plate1_61
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_50

description:
3mix-FACS-plate1_50
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_76

description:
3mix-FACS-plate1_76
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_51

description:
3mix-FACS-plate1_51
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_69

description:
3mix-FACS-plate1_69
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_49

description:
3mix-FACS-plate1_49
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_55

description:
3mix-FACS-plate1_55
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_47

description:
3mix-FACS-plate1_47
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_48

description:
3mix-FACS-plate1_48
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_45

description:
3mix-FACS-plate1_45
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_46

description:
3mix-FACS-plate1_46
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_43

description:
3mix-FACS-plate1_43
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_44

description:
3mix-FACS-plate1_44
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_39

description:
3mix-FACS-plate1_39
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_40

description:
3mix-FACS-plate1_40
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_37

description:
3mix-FACS-plate1_37
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_41

description:
3mix-FACS-plate1_41
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_38

description:
3mix-FACS-plate1_38
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_32

description:
3mix-FACS-plate1_32
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_36

description:
3mix-FACS-plate1_36
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_33

description:
3mix-FACS-plate1_33
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_35

description:
3mix-FACS-plate1_35
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_34

description:
3mix-FACS-plate1_34
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_28

description:
3mix-FACS-plate1_28
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_26

description:
3mix-FACS-plate1_26
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_22

description:
3mix-FACS-plate1_22
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_21

description:
3mix-FACS-plate1_21
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_24

description:
3mix-FACS-plate1_24
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_23

description:
3mix-FACS-plate1_23
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_29

description:
3mix-FACS-plate1_29
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_25

description:
3mix-FACS-plate1_25
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_20

description:
3mix-FACS-plate1_20
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_42

description:
3mix-FACS-plate1_42
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_19

description:
3mix-FACS-plate1_19
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_14

description:
3mix-FACS-plate1_14
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_15

description:
3mix-FACS-plate1_15
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_18

description:
3mix-FACS-plate1_18
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_13

description:
3mix-FACS-plate1_13
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_11

description:
3mix-FACS-plate1_11
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_16

description:
3mix-FACS-plate1_16
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_30

description:
3mix-FACS-plate1_30
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_9

description:
3mix-FACS-plate1_9
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_8

description:
3mix-FACS-plate1_8
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_10

description:
3mix-FACS-plate1_10
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_6

description:
3mix-FACS-plate1_6
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_31

description:
3mix-FACS-plate1_31
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_7

description:
3mix-FACS-plate1_7
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_4

description:
3mix-FACS-plate1_4
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_12

description:
3mix-FACS-plate1_12
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_27

description:
3mix-FACS-plate1_27
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_5

description:
3mix-FACS-plate1_5
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_3

description:
3mix-FACS-plate1_3
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_2

description:
3mix-FACS-plate1_2
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_1

description:
3mix-FACS-plate1_1
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_93

description:
3mix-target-plate4_93
3mix_RNA_expression.txt

value: ALPS


title: 3mix-target, 3mix-target-plate4_96

description:
3mix-target-plate4_96
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_94

description:
3mix-target-plate4_94
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_92

description:
3mix-target-plate4_92
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_95

description:
3mix-target-plate4_95
3mix_RNA_expression.txt


title: 3mix-FACS, 3mix-FACS-plate1_17

description:
3mix-FACS-plate1_17
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_91

description:
3mix-target-plate4_91
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_90

description:
3mix-target-plate4_90
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_89

description:
3mix-target-plate4_89
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_88

description:
3mix-target-plate4_88
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_87

description:
3mix-target-plate4_87
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_86

description:
3mix-target-plate4_86
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_83

description:
3mix-target-plate4_83
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_80

description:
3mix-target-plate4_80
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_84

description:
3mix-target-plate4_84
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_82

description:
3mix-target-plate4_82
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_78

description:
3mix-target-plate4_78
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_74

description:
3mix-target-plate4_74
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_77

description:
3mix-target-plate4_77
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_75

description:
3mix-target-plate4_75
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_73

description:
3mix-target-plate4_73
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_72

description:
3mix-target-plate4_72
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_71

description:
3mix-target-plate4_71
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_76

description:
3mix-target-plate4_76
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_81

description:
3mix-target-plate4_81
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_68

description:
3mix-target-plate4_68
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_70

description:
3mix-target-plate4_70
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_67

description:
3mix-target-plate4_67
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_64

description:
3mix-target-plate4_64
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_65

description:
3mix-target-plate4_65
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_62

description:
3mix-target-plate4_62
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_63

description:
3mix-target-plate4_63
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_61

description:
3mix-target-plate4_61
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_60

description:
3mix-target-plate4_60
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_59

description:
3mix-target-plate4_59
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_57

description:
3mix-target-plate4_57
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_85

description:
3mix-target-plate4_85
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_58

description:
3mix-target-plate4_58
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_79

description:
3mix-target-plate4_79
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_56

description:
3mix-target-plate4_56
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_55

description:
3mix-target-plate4_55
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_52

description:
3mix-target-plate4_52
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_51

description:
3mix-target-plate4_51
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_50

description:
3mix-target-plate4_50
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_69

description:
3mix-target-plate4_69
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_48

description:
3mix-target-plate4_48
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_47

description:
3mix-target-plate4_47
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_49

description:
3mix-target-plate4_49
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_46

description:
3mix-target-plate4_46
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_43

description:
3mix-target-plate4_43
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_44

description:
3mix-target-plate4_44
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_45

description:
3mix-target-plate4_45
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_66

description:
3mix-target-plate4_66
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_40

description:
3mix-target-plate4_40
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_39

description:
3mix-target-plate4_39
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_38

description:
3mix-target-plate4_38
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_42

description:
3mix-target-plate4_42
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_34

description:
3mix-target-plate4_34
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_35

description:
3mix-target-plate4_35
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_36

description:
3mix-target-plate4_36
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_54

description:
3mix-target-plate4_54
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_33

description:
3mix-target-plate4_33
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_53

description:
3mix-target-plate4_53
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_28

description:
3mix-target-plate4_28
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_30

description:
3mix-target-plate4_30
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_29

description:
3mix-target-plate4_29
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_26

description:
3mix-target-plate4_26
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_27

description:
3mix-target-plate4_27
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_37

description:
3mix-target-plate4_37
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_32

description:
3mix-target-plate4_32
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_25

description:
3mix-target-plate4_25
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_23

description:
3mix-target-plate4_23
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_41

description:
3mix-target-plate4_41
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_16

description:
3mix-target-plate4_16
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_19

description:
3mix-target-plate4_19
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_18

description:
3mix-target-plate4_18
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_15

description:
3mix-target-plate4_15
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_31

description:
3mix-target-plate4_31
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_21

description:
3mix-target-plate4_21
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_17

description:
3mix-target-plate4_17
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_20

description:
3mix-target-plate4_20
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_14

description:
3mix-target-plate4_14
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_11

description:
3mix-target-plate4_11
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_8

description:
3mix-target-plate4_8
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_7

description:
3mix-target-plate4_7
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_6

description:
3mix-target-plate4_6
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_5

description:
3mix-target-plate4_5
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_10

description:
3mix-target-plate4_10
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_9

description:
3mix-target-plate4_9
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_13

description:
3mix-target-plate4_13
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_4

description:
3mix-target-plate4_4
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_2

description:
3mix-target-plate4_2
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_3

description:
3mix-target-plate4_3
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_24

description:
3mix-target-plate4_24
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_1

description:
3mix-target-plate4_1
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_22

description:
3mix-target-plate4_22
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_95

description:
3mix-target-plate3_95
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_92

description:
3mix-target-plate3_92
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_93

description:
3mix-target-plate3_93
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_94

description:
3mix-target-plate3_94
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_87

description:
3mix-target-plate3_87
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_91

description:
3mix-target-plate3_91
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate4_12

description:
3mix-target-plate4_12
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_86

description:
3mix-target-plate3_86
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_85

description:
3mix-target-plate3_85
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_90

description:
3mix-target-plate3_90
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_84

description:
3mix-target-plate3_84
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_89

description:
3mix-target-plate3_89
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_83

description:
3mix-target-plate3_83
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_88

description:
3mix-target-plate3_88
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_82

description:
3mix-target-plate3_82
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_79

description:
3mix-target-plate3_79
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_78

description:
3mix-target-plate3_78
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_76

description:
3mix-target-plate3_76
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_77

description:
3mix-target-plate3_77
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_75

description:
3mix-target-plate3_75
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_80

description:
3mix-target-plate3_80
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_81

description:
3mix-target-plate3_81
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_96

description:
3mix-target-plate3_96
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_70

description:
3mix-target-plate3_70
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_74

description:
3mix-target-plate3_74
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_69

description:
3mix-target-plate3_69
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_72

description:
3mix-target-plate3_72
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_73

description:
3mix-target-plate3_73
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_68

description:
3mix-target-plate3_68
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_64

description:
3mix-target-plate3_64
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_66

description:
3mix-target-plate3_66
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_67

description:
3mix-target-plate3_67
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_65

description:
3mix-target-plate3_65
3mix_RNA_expression.txt


title: 3mix-target, 3mix-target-plate3_71

description:
3mix-target-plate3_71
3mix_RNA_expression.txt


title: lambda_4h_R2

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

country: USA

institute: UCLA

description:
RNAseq_counts_Wilder.csv
lambda3.4

data_processing:
Sequencing reads were aligned and mapped onto the mm10 genome with STAR v.2.5. Count tables were generated with featureCounts.
Assembly: mm10
Supplementary files format and content: count table in .csv format

extract_protocol:
RNA was collected from cells lysed in TRIzol Reagent (Fisher Scientific #15-596-018) and isolated using the Direct-zol RNA Extraction Kit (Zymo Research #R2052).
RNA libraries were generated using the KAPA Stranded mRNA-Sequencing Kit with KAPA mRNA Capture Beads (Roche #07962207001). Samples were enriched for poly(A)+ mRNA strands using mRNA Capture Beads. The captured mRNA was synthesized into complementary DNA (cDNA). cDNA libraries were ligated using Illumina TruSeq single index adapters (Roche #KK8700), amplified, and quantified using a Qubit dsDNA Broad Range Assay Kit (Life Technologies #Q32850) and a Qubit 2.0 fluorometer.

tag: cell line

value: type II alveolar epithelial

tag: genotype

value: WT

tag: treatment

value: IFN-lambda-3 100 ng/ml

tag: timepoint

value: 4 hours

tag: replicate

value: replicate 2


title: pulse_6h_R2

description:
RNAseq_counts_Wilder.csv
pulse.6

value: IFN-beta 10 U/ml

value: 6 hours


title: pulse_3h_R2

description:
RNAseq_counts_Wilder.csv
pulse.3

value: 3 hours


title: pulse_2h_R2

description:
RNAseq_counts_Wilder.csv
pulse.2

value: 2 hours


title: lambda_12h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.12

value: 12 hours


title: beta1_24h_R2

description:
RNAseq_counts_Wilder.csv
beta1.24

value: IFN-beta 1 U/ml

value: 24 hours


title: lambda_6h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.6


title: pulse_24h_R2

description:
RNAseq_counts_Wilder.csv
pulse.24


title: lambda_1h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.1

value: 1 hour


title: lambda_3h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.3


title: pulse_12h_R2

description:
RNAseq_counts_Wilder.csv
pulse.12


title: lambda_24h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.24


title: pulse_1h_R2

description:
RNAseq_counts_Wilder.csv
pulse.1


title: pulse_8h_R2

description:
RNAseq_counts_Wilder.csv
pulse.8

value: 8 hours


title: lambda_0.5h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.05

value: 0.5 hours


title: pulse_4h_R2

description:
RNAseq_counts_Wilder.csv
pulse.4


title: lambda_8h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.8


title: beta1_12h_R2

description:
RNAseq_counts_Wilder.csv
beta1.12


title: beta1_8h_R2

description:
RNAseq_counts_Wilder.csv
beta1.8


title: beta1_4h_R2

description:
RNAseq_counts_Wilder.csv
beta1.4


title: pulse_0.5h_R2

description:
RNAseq_counts_Wilder.csv
pulse.05


title: lambda_2h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.2


title: beta1_3h_R2

description:
RNAseq_counts_Wilder.csv
beta1.3


title: beta10_8h_R2

description:
RNAseq_counts_Wilder.csv
beta10.8


title: beta1_2h_R2

description:
RNAseq_counts_Wilder.csv
beta1.2


title: beta1_0.5h_R2

description:
RNAseq_counts_Wilder.csv
beta1.05


title: beta1_1h_R2

description:
RNAseq_counts_Wilder.csv
beta1.1


title: beta10_24h_R2

description:
RNAseq_counts_Wilder.csv
beta10.24


title: beta10_12h_R2

description:
RNAseq_counts_Wilder.csv
beta10.12


title: beta1_6h_R2

description:
RNAseq_counts_Wilder.csv
beta1.6


title: beta10_2h_R2

description:
RNAseq_counts_Wilder.csv
beta10.2


title: beta10_6h_R2

description:
RNAseq_counts_Wilder.csv
beta10.6


title: pulse_1h_r1

description:
RNAseq_counts_Wilder.csv
pulse1

value: replicate 1


title: pulse_0h_R2

description:
RNAseq_counts_Wilder.csv
pulse.0

value: Unstimulated


title: beta10_0h_R2

description:
RNAseq_counts_Wilder.csv
beta10.0

value: type II alveolar epithelial


title: beta1_0h_R2

description:
RNAseq_counts_Wilder.csv
beta1.0

value: WT


title: beta1_4h_R1

description:
RNAseq_counts_Wilder.csv
low4


title: pulse_4h_R1

description:
RNAseq_counts_Wilder.csv
pulse4


title: beta10_1h_R2

description:
RNAseq_counts_Wilder.csv
beta10.1


title: beta10_3h_R2

description:
RNAseq_counts_Wilder.csv
beta10.3


title: lambda_2h_R1

description:
RNAseq_counts_Wilder.csv
lambda2

value: IFN-lambda-3 100 ng/ml


title: lambda_12h_R1

description:
RNAseq_counts_Wilder.csv
lambda12


title: beta1_1h_R1

description:
RNAseq_counts_Wilder.csv
low1


title: lambda_8h_R1

description:
RNAseq_counts_Wilder.csv
lambda8


title: beta10_0.5h_R2

description:
RNAseq_counts_Wilder.csv
beta10.05


title: lambda_4h_R1

description:
RNAseq_counts_Wilder.csv
lambda4

value: 4 hours


title: beta10_4h_R2

description:
RNAseq_counts_Wilder.csv
beta10.4

value: replicate 2


title: lambda_0h_R1

description:
RNAseq_counts_Wilder.csv
lambda0


title: beta10_24h_R1

description:
RNAseq_counts_Wilder.csv
beta24

value: IFN-beta 10 U/ml


title: lambda_0h_R2

description:
RNAseq_counts_Wilder.csv
lambda3.0


title: lambda_1h_R1

description:
RNAseq_counts_Wilder.csv
lambda1


title: lambda_0.5h_R1

description:
RNAseq_counts_Wilder.csv
lambda05


title: beta10_12h_R1

description:
RNAseq_counts_Wilder.csv
beta12


title: beta10_1h_R1

description:
RNAseq_counts_Wilder.csv
beta1


title: beta10_4h_R1

description:
RNAseq_counts_Wilder.csv
beta4


title: beta10_2h_R1

description:
RNAseq_counts_Wilder.csv
beta2


title: beta10_36h_R1

description:
RNAseq_counts_Wilder.csv
beta36

value: 36 hours


title: beta10_8h_R1

description:
RNAseq_counts_Wilder.csv
beta8


title: lambda_36h_R1

description:
RNAseq_counts_Wilder.csv
lambda36


title: beta10_0.5h_R1

description:
RNAseq_counts_Wilder.csv
beta05


title: lambda_24h_R1

description:
RNAseq_counts_Wilder.csv
lambda24


title: LPD_40 (Sample 3)

city: Huddersfield

first: Patrick

middle: C

last: McHugh

address: Queensgate, Huddersfield

department: Pharmacy

country: United Kingdom

institute: University of Huddersfield

data_processing:
The original data obtained from the high throughput sequencing platforms were transformed into sequenced reads by base calling.
Reads were then filtered for adaptor contamination using cutadapt and filtered such that at least 90% of bases of each read had a quality score > 20.
The program Salmon was used for quantifying abundances of transcripts from RNA-sequencing data, or more generally of target sequences using high-throughput sequencing reads. The index for Mus_musculus.GRCm38.88_transcripts.fa was built in Salmon using the default parameters. The program Wasabi was used to prepare Salmon output for downstream processing by Sleuth. Bootstrapping of the quantification was performed iteratively for 100 rounds.
Resulting counts were then normalized through the transcripts per kilobase million (TPM) method. Differential expression analysis was carried out using the software package Sleuth (v0.30.0) using TPM normalized counts for each cell type.
Assembly: GRCm38.88_mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: C57Bl/6 ES cells- low protein diet

growth_protocol: Disaggregated cells deribed from the blastocysts were seeded onto fresh feeder layers on 96 well plates  C57BL/6 females (7-9 week) were mated naturally overnight with C57BL/6 males and plug positive

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 3 ug of total RNA was used for the construction of sequencing libraries.
The quality control and concentration of the library was assessed using Qubit 2.0, Agilent 2100 bioanalyzer and qRT-PCR. The qualified libraries were fed into Illumina sequencers after pooling according to their effective concentration and expected data volume.

treatment_protocol: C57BL/6 females (7-9 week) were mated naturally overnight with C57BL/6 males and plug positive females were housed individually the following morning and assigned randomly to either control normal protein diet (18% casein, NPD) or isocaloric low protein diet (9% casein, LPD) supplied by Special Dietary Services Ltd, UK, and fed ad libitum until embryonic day 3.5 (E3.5); diet composition has been described elsewhere (Watkins, Ursell et al. 2008).

tag: Sex

value: Male

value: ES Cells

value: Wild-type

value: Derived from mothers on low protein diet


title: LPD_1 (Sample 1)


title: beta10_0h_R1

description:
RNAseq_counts_Wilder.csv
beta0


title: LPD_4 (Sample 4)


title: NPD_15 (Sample 7)

source_name: C57Bl/6 ES cells- normal protein diet

value: Derived from mothers on normal protein diet


title: LPD_6 (Sample 5)


title: LPD_20 (Sample 2)


title: NPD_36 (Sample 9)


title: NPD_21 (Sample 8)


title: NPD_8 (Sample 6)


title: Dnmt3a KO, E7.5, ExE, 3 (RNA-seq)

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

data_processing:
bcl2fastq version 1.8.4 was used for demultiplexing
Assembly: GRCm38
Fastq sequence files were quality and adaptor trimmed with trim galore v0.4.2 using default parameters. RNAseq data was subjected to trimming with Trim Galore (v0.6.6, options '--clip_r1 8' to remove a nucleotide bias at the 5' end), and aligned to the GRCm38 mouse genome build, to which a ribosomal DNA sequence had been added (BK000964.1), using HISAT2 (v2.1.0, guided by gene models from Ensembl annotation release 90, options: --dta –no-softclip). Hits were again filtered to remove mappings with MAPQ scores <20.
Gene expression was quantitated using the RNA-seq quantitation pipeline in SeqMonk.  Differentially expressed genes were identified using DESeq2 in SeqMonk, with a minimum 1.5-fold change between KO and matched WT samples.
Supplementary files format and content: Tab-separated file (Annotated SeqMonk Probe report) where the first columns are information about the gene (name, strand, start, end, chromosome, …), and the remaining columns are the samples (log2RPM counts).

source_name: Extra-embryonic ectoderm

extract_protocol:
Natural timed matings between heterozygous females and males were used for Dnmt3l, Dnmt3a, Dnmt3b and Dnmt3a/3b KO strains to generate KO and WT embryos. E7.5 epiblast, extra-embryonic ectoderm (ExE) and ectoplacental cone (EPC) for each embryo were manually separated. Single E7.5 epiblast and ExE samples were individually frozen in 10µL of buffer RLT Plus (Qiagen) for RNA-seq or PBAT; the corresponding EPC was used for genotyping.  Samples were homogenized in 400µL of TRIzol (Invitrogen) and phase separated with 80µL of chloroform:isoamyl alcohol (Sigma), centrifuging at 4°C for 15 minutes.  The aqueous phase was combined with 1µL GlycoBlue and 300µL of cold isopropanol. The RNA was pelleted by centrifugation for 10 minutes at 4°C, washed once with 75% ethanol, dried and then resuspended in 5µL of ultra-pure water.  To each RNA sample, 20µL of lysis/binding buffer was immediately added, proceeding directly to a single round of oligo(dT)25 capture of mRNA, using Dynabeads mRNA DIRECT kit (Life Technologies), using previously described adaptations for low starting material. Using the SMARTer Stranded RNA-seq kit (Clontech), mRNA libraries were prepared as per the manufacturers’ instructions with 15 amplification cycles. Libraries were quantified using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification (KAPA). Libraries were multiplexed and sequenced using 50bp single-end on the Illumina HiSeq 2500 RapidRun.
Using the SMARTer Stranded RNA-seq kit (Clontech), mRNA libraries were prepared as per the manufacturers’ instructions with 15 amplification cycles. Libraries were quantified using the High DNA Sensitivity Bioanalyzer 2500 (Agilent) and Illumina library quantification (KAPA). Libraries were multiplexed and sequenced using 50bp single-end on the Illumina HiSeq 2500 RapidRun.

value: Extra-embryonic ectoderm

value: Dnmt3a KO

tag: age


title: Dnmt3a KO, E7.5, ExE, 2 (RNA-seq)


title: Dnmt3a KO, E7.5, ExE, 1 (RNA-seq)


title: NPD_51 (Sample 10)


title: Dnmt3b KO, E7.5, ExE, 3 (RNA-seq)

value: Dnmt3b KO


title: Dnmt3b KO, E7.5, ExE, 1 (RNA-seq)


title: Dnmt3b KO, E7.5, ExE, 4 (RNA-seq)


title: Dnmt3ab DKO, E7.5, ExE, 2 (RNA-seq)

value: Dnmt3a/Dnmt3b DKO


title: Dnmt3ab DKO, E7.5, ExE, 3 (RNA-seq)


title: Dnmt3ab DKO, E7.5, ExE, 1 (RNA-seq)


title: Dnmt3b WT, E7.5, ExE_1 (RNA-seq)

value: Wildtype


title: Dnmt3ab WT, E7.5, ExE, 1 (RNA-seq)


title: Dnmt3ab WT, E7.5, ExE, 2 (RNA-seq)


title: Dnmt3ab WT, E7.5, ExE, 3 (RNA-seq)


title: Dnmt3ab WT, E7.5, ExE, 4 (RNA-seq)


title: Dnmt3l KO, E7.5, ExE, 2 (RNA-seq)

value: Dnmt3l KO


title: Dnmt3l KO, E7.5, ExE, 1 (RNA-seq)


title: Dnmt3l KO, E7.5, ExE, 3 (RNA-seq)


title: Dnmt3l WT, E7.5, ExE, 3 (RNA-seq)


title: Islets WT3_1118

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Islets

extract_protocol: Islet were isolated, disrupted and lyzed in RLT buffer. RNA was harvested using RNeasy kit (Quiagen).

tag: tissue

value: Islets

value: 8 weeks old

value: wild type


title: Islets MUT1_1118

value: Ngn3-Cre; Ctnna1 flox/flox


title: Islets WT2_1118


title: Islets WT4_1118


title: Islets MUT4_1201


title: Islets MUT2_1118


title: Dnmt3l WT, E7.5, ExE, 2 (RNA-seq)


title: Cyclin D1 p53-/- Pineoblastoma p90 rep2_ChIP

city: Beirut

first: Pierre

last: Khoueiry

address: Bliss street

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

library_source: genomic

data_processing:
Quality check for raw sequencing reads was performed using FastQC v0.11.8
RNA-seq reads were aligned to mm10 genome assembly using hisat2 v2.1.0  with parameters --rna-strandness RF. ChIP-seq and ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 v2.3.4.1 with parameters  --very-sensitive –maxins 2000 –end-to-end. ATAC-seq aligned reads were shifted using alignment sieve from deeptools v3.5.0
RNA-seq bigwig files were generated using deeptools v3.5.0 and normalized using CPM. ATAC-seq and ChIP-seq bigwig files were generated using deeptools and normalized using RPGC method
ATAC-seq and ChiP-seq peaks were called using MACS2 v2.2.7.1 with parameters –nomodel -q 0.05
RNA-seq featurecounts matrix was generated using FeatureCounts v2.0.1 from SubRead package
Genome_build: mm10
Supplementary_files_format_and_content: processed data files include featureCounts file, bigwig files and narrowPeak files

molecule: genomic DNA

source_name: Pineal Gland

growth_protocol: Irbp-Cyclin D1 transgenic mice  were bred with p53 -/- mice and maintained in a mixed C57BL/6 × 129/Sv genetic background.

extract_protocol:
For RNA-seq, RNA was extracted from pineal gland tissues collected at day 10, 49 and 90 from Cyclin D1 p53-/- genotype using the RNeasy Plus Mini Kit. Tissues were harvested in RLT Plus Buffer. For ATAC-seq, tissues were homogenized in 1X Homogenization Buffer followed by disruption and nuclei were isolated and counted using Trypan blue staining. 50,000 nuclei were collected per condition. For ChIP-seq, tissues were cross-linked on rotator with 1% formaldehyde for 10 min at RT and subsequently quenched by 0.125M glycine at RT for 5 min with mild rocking. Cross-linked tissues were lysed on ice with cell lysis buffer (containing 1% SDS, 10mM EDTA, 50mM Tris, 1X Protease Inhibitor cocktail and PMSF) followed by nuclear lysis buffer (containing 10mM Tris, 1mM EDTA, 1% SDS, and 1X Prostease Inhibitors and PMSF) to release nuclear chromatin. DNA was then sonicated in nuclear lysis buffer into 200bp-700bp fragments using Diagenode Bioruptor.
ChIP-seq library preparation was performed using the Illumina Thruplex Rubicon kit. Sequencing was performed on the Illumina Novaseq S1 (2x50 Paired-end). ATAC-seq libraries were prepared by PCR amplification using  Nextera Index Kit (Illumina, no. 15055289) and the NEBNext High-Fidelity 2× PCR Master Mix (NEB, no. M0541L) with 4–6 cycles. Libraries were quantified by PicoGreenn DNA Quantification assay and sequenced on Illumina NovaSeq S2 using 2x50 paired-end reads in biological duplicate.  Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, Inc; San Diego, CA) with an input of 500ng of total RNA following the low sample procedure. Briefly, ribosomal RNA (rRNA) was depleted from total RNA and the remaining RNA purified, fragmented appropriately, and primed for cDNA synthesis. Blunt-ended cDNA was generated after first and second strand synthesis. Adenylation of the 3’ blunt-ends was followed by adapter ligation prior to the enrichment of the cDNA fragments. Final library quality control was carried out by evaluating the fragment size on a DNA1000 chip ran on a 2100 BioAnalyzer (Agilent; Santa Clara, CA). The concentration of each library was determined by quantitative PCR (qPCR) by the KAPA Library Quantification Kit for Next Generation Sequencing (KAPA Biosystems; Woburn, MA) prior to sequencing.  Libraries were normalized to 2 nmol/L in 10 mM Tris-Cl, pH8.5 with 0.1% Tween 20 then pooled evenly. The pooled libraries were denatured with 0.05N NaOH and diluted to 20 pmol/L. Cluster generation of the denatured libraries was performed according to the manufacturer’s specifications (Illumina, Inc; San Diego, CA) utilizing the HiSeq PE Cluster Kit v2 chemistry and flow cells. Libraries were clustered appropriately with a 1% PhiX spike-in. Sequencing-by-synthesis (SBS) was performed on a HiSeq2500 utilizing v2 chemistry with paired-end 101-bp reads resulting in an average of 58.9 million paired-end reads per sample. Sequence read data were processed and converted to FASTQ format for downstream analysis by Illumina BaseSpace analysis software, FASTQ Generation v1.0.0.

treatment_protocol: Animals were examined at least twice weekly and were euthanized at defined time points (P10, P49 and ~P90 corresponding to proliferating, premalignant and tumorigenic stages) or when obviously ill

tag: tissue type

value: Pineoblastoma Tissue

value: mixed C57BL/6 x 129/Sv

value: Postnatal day 90


title: Dnmt3b KO, E7.5, ExE, 2 (RNA-seq)


title: Islets WT1_1118


title: Cyclin D1 p53-/- Pineoblastoma p90 rep1_ChIP


title: Cyclin D1 p53-/- Pineoblastoma p49 rep1_ChIP

value: Postnatal day 49


title: Cyclin D1 p53-/- Pineoblastoma p49 rep2_ChIP


title: Cyclin D1 p53-/- Pineoblastoma p90 rep2_atac

description: ATAC-seq


title: Cyclin D1 p53-/- Pineoblastoma p90 rep1_atac

description: ATAC-seq


title: Cyclin D1 p53-/- Pineoblastoma p49 rep2_atac

description: ATAC-seq


title: Dnmt3l KO, E7.5, ExE, 4 (RNA-seq)


title: Cyclin D1 p53-/- Pineoblastoma p49 rep1_atac

description: ATAC-seq


title: Cyclin D1 p53-/- Pineoblastoma p10 rep2_atac

description: ATAC-seq

value: Postnatal day 10


title: Cyclin D1 p53-/- Pineoblastoma p10 rep1_atac

description: ATAC-seq


title: Cyclin D1 p53-/- Pineoblastoma p90 rep1_rna

description: RNA-seq


title: Cyclin D1 p53-/- Pineoblastoma p90 rep3_rna

description: RNA-seq


title: Cyclin D1 p53-/- Pineoblastoma p49 rep3_rna

description: RNA-seq


title: Dnmt3l WT, E7.5, ExE, 1 (RNA-seq)


title: Cyclin D1 p53-/- Pineoblastoma p49 rep1_rna

description: RNA-seq


title: Cyclin D1 p53-/- Pineoblastoma p49 rep2_rna

description: RNA-seq


title: Cyclin D1 p53-/- Pineoblastoma p10 rep1_rna

description: RNA-seq


title: Islets MUT3_1118


title: Cyclin D1 p53-/- Pineoblastoma p10 rep3_rna

description: RNA-seq


title: Cyclin D1 p53-/- Pineoblastoma p10 rep2_rna

description: RNA-seq


title: 3mix-timelapse, 3mix-timelapse-plate8_95

description:
3mix-timelapse-plate8_95
3mix_RNA_expression.txt

value: random selection

value: ALPS


title: 3mix-timelapse, 3mix-timelapse-plate8_90

description:
3mix-timelapse-plate8_90
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_93

description:
3mix-timelapse-plate8_93
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_86

description:
3mix-timelapse-plate8_86
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_89

description:
3mix-timelapse-plate8_89
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_85

description:
3mix-timelapse-plate8_85
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_92

description:
3mix-timelapse-plate8_92
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_91

description:
3mix-timelapse-plate8_91
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_84

description:
3mix-timelapse-plate8_84
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_87

description:
3mix-timelapse-plate8_87
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_88

description:
3mix-timelapse-plate8_88
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_80

description:
3mix-timelapse-plate8_80
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_81

description:
3mix-timelapse-plate8_81
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_82

description:
3mix-timelapse-plate8_82
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_77

description:
3mix-timelapse-plate8_77
3mix_RNA_expression.txt


title: Cyclin D1 p53-/- Pineoblastoma p90 rep2_rna

description: RNA-seq


title: 3mix-timelapse, 3mix-timelapse-plate8_75

description:
3mix-timelapse-plate8_75
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_79

description:
3mix-timelapse-plate8_79
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_78

description:
3mix-timelapse-plate8_78
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_76

description:
3mix-timelapse-plate8_76
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_72

description:
3mix-timelapse-plate8_72
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_94

description:
3mix-timelapse-plate8_94
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_96

description:
3mix-timelapse-plate8_96
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_74

description:
3mix-timelapse-plate8_74
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_73

description:
3mix-timelapse-plate8_73
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_70

description:
3mix-timelapse-plate8_70
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_71

description:
3mix-timelapse-plate8_71
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_69

description:
3mix-timelapse-plate8_69
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_63

description:
3mix-timelapse-plate8_63
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_65

description:
3mix-timelapse-plate8_65
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_67

description:
3mix-timelapse-plate8_67
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_83

description:
3mix-timelapse-plate8_83
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_62

description:
3mix-timelapse-plate8_62
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_66

description:
3mix-timelapse-plate8_66
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_61

description:
3mix-timelapse-plate8_61
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_64

description:
3mix-timelapse-plate8_64
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_60

description:
3mix-timelapse-plate8_60
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_59

description:
3mix-timelapse-plate8_59
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_57

description:
3mix-timelapse-plate8_57
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_55

description:
3mix-timelapse-plate8_55
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_56

description:
3mix-timelapse-plate8_56
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_54

description:
3mix-timelapse-plate8_54
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_58

description:
3mix-timelapse-plate8_58
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_52

description:
3mix-timelapse-plate8_52
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_53

description:
3mix-timelapse-plate8_53
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_51

description:
3mix-timelapse-plate8_51
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_49

description:
3mix-timelapse-plate8_49
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_50

description:
3mix-timelapse-plate8_50
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_46

description:
3mix-timelapse-plate8_46
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_48

description:
3mix-timelapse-plate8_48
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_44

description:
3mix-timelapse-plate8_44
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_45

description:
3mix-timelapse-plate8_45
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_41

description:
3mix-timelapse-plate8_41
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_68

description:
3mix-timelapse-plate8_68
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_42

description:
3mix-timelapse-plate8_42
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_43

description:
3mix-timelapse-plate8_43
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_40

description:
3mix-timelapse-plate8_40
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_39

description:
3mix-timelapse-plate8_39
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_36

description:
3mix-timelapse-plate8_36
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_34

description:
3mix-timelapse-plate8_34
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_38

description:
3mix-timelapse-plate8_38
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_35

description:
3mix-timelapse-plate8_35
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_30

description:
3mix-timelapse-plate8_30
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_37

description:
3mix-timelapse-plate8_37
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_32

description:
3mix-timelapse-plate8_32
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_26

description:
3mix-timelapse-plate8_26
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_24

description:
3mix-timelapse-plate8_24
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_27

description:
3mix-timelapse-plate8_27
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_25

description:
3mix-timelapse-plate8_25
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_28

description:
3mix-timelapse-plate8_28
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_29

description:
3mix-timelapse-plate8_29
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_47

description:
3mix-timelapse-plate8_47
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_22

description:
3mix-timelapse-plate8_22
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_21

description:
3mix-timelapse-plate8_21
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_18

description:
3mix-timelapse-plate8_18
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_19

description:
3mix-timelapse-plate8_19
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_16

description:
3mix-timelapse-plate8_16
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_17

description:
3mix-timelapse-plate8_17
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_14

description:
3mix-timelapse-plate8_14
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_20

description:
3mix-timelapse-plate8_20
3mix_RNA_expression.txt


title: TSD2

city: Hangzhou

first: zhaowei

last: cai

state: Zhejiang

address: Binwen road 548

department: Laboratory Animal Research Center

country: China

institute: zhejiang chinese medical university

data_processing:
Raw sequencing data were evaluated by FAST-QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), an online bioinformatics program used to characterize quality distributions of nucleotides, position-specific sequencing qualities, GC contents, the proportions of PCR duplication, and k-mer frequencies
Raw reads after quality control testing were then mapped to the reference pig genome version 10.2 (Sscrofa 10.2), using THISAT package
The normalized expression level of each gene was measured by Fragments Per Kilobase of exon per Million Reads (FPKM).
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt

organism: Sus scrofa

source_name: Liver tissue

extract_protocol:
Total RNA were isolated from each liver samples using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Sequencing libraries were prepared using a mRNASeqsample preparation kit (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: two miniature pig breeds fed either standard or a high-fat and high-cholesterol diet for 6 months

tag: breed

value: Chinese Tibetan Pigs

value: liver

value: 3–4 months old

value: TP fed a standard diet


title: TSD1


title: TSD3


title: 3mix-timelapse, 3mix-timelapse-plate8_15

description:
3mix-timelapse-plate8_15
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_31

description:
3mix-timelapse-plate8_31
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_33

description:
3mix-timelapse-plate8_33
3mix_RNA_expression.txt


title: THF3

value: TP fed a high-fat and high-cholesterol diet


title: 3mix-timelapse, 3mix-timelapse-plate8_13

description:
3mix-timelapse-plate8_13
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_12

description:
3mix-timelapse-plate8_12
3mix_RNA_expression.txt


title: THF2


title: 3mix-timelapse, 3mix-timelapse-plate8_10

description:
3mix-timelapse-plate8_10
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_23

description:
3mix-timelapse-plate8_23
3mix_RNA_expression.txt


title: THF1


title: 3mix-timelapse, 3mix-timelapse-plate8_11

description:
3mix-timelapse-plate8_11
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_9

description:
3mix-timelapse-plate8_9
3mix_RNA_expression.txt


title: WHF2

value: Chinese Wuzhishan Pigs

value: WZSP fed  a high-fat and high-cholesterol diet


title: 3mix-timelapse, 3mix-timelapse-plate8_8

description:
3mix-timelapse-plate8_8
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_7

description:
3mix-timelapse-plate8_7
3mix_RNA_expression.txt


title: WSD3

value: WZSP fed a standard diet


title: 3mix-timelapse, 3mix-timelapse-plate8_6

description:
3mix-timelapse-plate8_6
3mix_RNA_expression.txt


title: WSD2


title: WHF1


title: 3mix-timelapse, 3mix-timelapse-plate8_5

description:
3mix-timelapse-plate8_5
3mix_RNA_expression.txt


title: TIG120

type: genomic

city: San Francisco

first: Akira

last: Kunitomi

address: 1650 Owens Street

institute: The J. David Gladstone Institutes

description: Primary human dermal fibroblasts. This cell is the source cell of nOSKL_1, nOSKL_2, nOSKL_FF_1 and nOSKL_FF_2.

hyb_protocol: The Genomic DNA was hybridized onto the Infinium OmniExpress24 v1.3 DNA Analysis Kit (Illumina)

scan_protocol: Using Illumina iScan according to recommended scanner setting

data_processing: GenomeStudio (2.0.4)

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Human dermal fibroblasts

label_protocol: Standard Illumina Protocol

growth_protocol: Primed PSCs were maintained in StemFit AK02N medium (Ajinomoto) on laminin 511-E8 fragments (iMatrix-511, Nippi)-coated plates. Naive PSCs were cultured on iMEFs and maintained in t2iLGö medium. Feeder-free naive iPSCs were maintained on Matrigel (hESC-qualified, Corning)

extract_protocol: Genomic DNA were extracted from cell lysates using the AllPrep DNA/RNA Mini Kit (QIAGEN)

value: Human dermal fibroblasts


title: Primed_H9

description: Primed embryonic stem cells. This cell is the source cell of nH9.

source_name: Human embryonic stem cells

value: Primed embryonic stem cells


title: 3mix-timelapse, 3mix-timelapse-plate8_3

description:
3mix-timelapse-plate8_3
3mix_RNA_expression.txt


title: nOSKL_FF_2

description: Feeder-free naive induced pluripotent stem cells derived from human dermal fibroblasts

source_name: Human induced pluripotent stem cells

value: Naive induced pluripotent stem cells


title: CTL_PBMC_No1_day5

description: Primary periferal blood mononuclear cells. This cell is the source cell of nOSKL_3.

source_name: Human peripheral blood mononuclear cells


title: nOSKL_FF_1


title: CTL_PBMC_No4_day5

description: Primary periferal blood mononuclear cells. This cell is the source cell of nOSKL_4.

value: Human peripheral blood mononuclear cells


title: WHF3


title: 3mix-timelapse, 3mix-timelapse-plate8_1

description:
3mix-timelapse-plate8_1
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_96

description:
3mix-timelapse-plate7_96
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate8_2

description:
3mix-timelapse-plate8_2
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_95

description:
3mix-timelapse-plate7_95
3mix_RNA_expression.txt


title: nH9

description: Naive embryonic stem cells which were reset from the primed to naive state

value: Naive embryonic stem cells


title: nOSKL_4

description: Naive induced pluripotent stem cells derived from periferal blood mononuclear cells


title: 3mix-timelapse, 3mix-timelapse-plate7_92

description:
3mix-timelapse-plate7_92
3mix_RNA_expression.txt


title: nOSKL_2

description: Naive induced pluripotent stem cells derived from human dermal fibroblasts


title: nOSKL_3


title: 3mix-timelapse, 3mix-timelapse-plate7_89

description:
3mix-timelapse-plate7_89
3mix_RNA_expression.txt


title: nOSKL_1


title: 3mix-timelapse, 3mix-timelapse-plate7_90

description:
3mix-timelapse-plate7_90
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_91

description:
3mix-timelapse-plate7_91
3mix_RNA_expression.txt


title: Non-Atopic Mother 0285M

city: Denver

first: Sonia

middle: M

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 174

hyb_protocol: Genomic DNA was sheared, McrBC digested and gel fractionated before labeling and hybridization onto arrays covering 2.1M CpG sites according to CHARM protocol (Ladd-Acosta et al. 2010 PMID:20373514)

scan_protocol: Hybridized microarrays were scanned on an Agilent microarray scanner (Agilent, Santa Clara, CA) and images were processed in the Feature Extraction software (Agilent, Santa Clara, CA).

data_processing:
Probe-level estimates of percentage DNA methylation, known as methp values, were generated with the Charm v2.18.0 package in the R Statistical Computing language v2.15.1, using the options of quantile normalization for between-sample normalization and removing control probes and probes with a mean pmQuality measure lower than 75
Hauk_GEO_AtopicMothers_methp.txt: Percent methylation value represented as the normalized (range 0-1) log-ratio of the intensities observed in McrBC-treated and untreated channels (methp values).
Probe-level estimates of percentage DNA methylation, known as methp values, were generated with the Charm v2.18.0 package in the R Statistical Computing language v2.15.1, using the options of quantile normalization for between-sample normalization and removing control probes and probes with a mean pmQuality measure lower than 75. The Probabilistic Estimation of Expression Residual (PEER) (Stegle et al, 2012) method was applied to raw methp values to estimate hidden confounding factors, with the option batch_correct=4, using the peer v1.3 package in R and subtracted from the raw methp values. This dataset can then be directly used in linear mixed models with other clinical variables.
Hauk_GEO_AtopicMothers_methp_4PEERfactorsSubtracted.txt: Percent methylation value represented as the normalized log-ratio of the intensities observed in McrBC-treated and untreated channels, corrected for latent factors by subtracting the four PEER factors (range -1 to 1).

source_name: input fraction of DNA from whole blood

extract_protocol: Genomic DNA was obtained from maternal whole blood at a gestational age of >= 34 weeks with PAXgene DNA tubes according to the manufacturer's instructions (Qiagen, Hilden, Germany).

tag: dna fraction

value: input

tag: parental history of atopy (maternal or biparental)

value: Non-Atopic

tag: maternal age at delivery

tag: exposure during pregnancy to inside/outside smoking and or animals

value: Yes

tag: maternal ethnicity

value: cauc

tag: child ethnicity

value: mixed, other

tag: maternal exposure to insulin

tag: maternal exposure to folic acid in addition to dietary folate and folate in prenatal vitamins

source_name: Methyl-depleted fraction of DNA from whole blood

value: methyl-depleted


title: 3mix-timelapse, 3mix-timelapse-plate7_88

description:
3mix-timelapse-plate7_88
3mix_RNA_expression.txt

tag: strain

tag: cell type

value: random selection

tag: isolation method

value: ALPS


title: WSD1

value: liver

value: 3–4 months old

tag: treatment


title: 3mix-timelapse, 3mix-timelapse-plate8_4

description:
3mix-timelapse-plate8_4
3mix_RNA_expression.txt


title: Non-Atopic Mother 0283M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 173

label_protocol: Genomic DNA was sheared, McrBC digested and gel fractionated before labeling and hybridization onto arrays covering 2.1M CpG sites according to CHARM protocol (Ladd-Acosta et al. 2010 PMID:20373514)

value: No

value: hisp


title: 3mix-timelapse, 3mix-timelapse-plate7_87

description:
3mix-timelapse-plate7_87
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_86

description:
3mix-timelapse-plate7_86
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_85

description:
3mix-timelapse-plate7_85
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_84

description:
3mix-timelapse-plate7_84
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_94

description:
3mix-timelapse-plate7_94
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_82

description:
3mix-timelapse-plate7_82
3mix_RNA_expression.txt


title: Non-Atopic Mother 0275M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 169


title: 3mix-timelapse, 3mix-timelapse-plate7_93

description:
3mix-timelapse-plate7_93
3mix_RNA_expression.txt


title: Atopic Mother 0274M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 168

value: Atopic


title: 3mix-timelapse, 3mix-timelapse-plate7_83

description:
3mix-timelapse-plate7_83
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_81

description:
3mix-timelapse-plate7_81
3mix_RNA_expression.txt


title: Non-Atopic Mother 0277M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 170

value: othe


title: Atopic Mother 0270M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 166

value: AA


title: Atopic Mother 0279M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 171


title: Non-Atopic Mother 0268M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 165


title: Atopic Mother 0273M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 167


title: Atopic Mother 0266M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 163


title: Non-Atopic Mother 0281M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 172


title: 3mix-timelapse, 3mix-timelapse-plate7_78

description:
3mix-timelapse-plate7_78
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_76

description:
3mix-timelapse-plate7_76
3mix_RNA_expression.txt


title: Non-Atopic Mother 0264M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 161


title: Atopic Mother 0265M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 162


title: Non-Atopic Mother 0262M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 160


title: 3mix-timelapse, 3mix-timelapse-plate7_77

description:
3mix-timelapse-plate7_77
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_75

description:
3mix-timelapse-plate7_75
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_74

description:
3mix-timelapse-plate7_74
3mix_RNA_expression.txt


title: Non-Atopic Mother 0254M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 159


title: Atopic Mother 0250M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 158


title: 3mix-timelapse, 3mix-timelapse-plate7_73

description:
3mix-timelapse-plate7_73
3mix_RNA_expression.txt


title: Non-Atopic Mother 0249M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 157


title: 3mix-timelapse, 3mix-timelapse-plate7_72

description:
3mix-timelapse-plate7_72
3mix_RNA_expression.txt


title: Atopic Mother 0248M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 156


title: 3mix-timelapse, 3mix-timelapse-plate7_71

description:
3mix-timelapse-plate7_71
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_70

description:
3mix-timelapse-plate7_70
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_69

description:
3mix-timelapse-plate7_69
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_68

description:
3mix-timelapse-plate7_68
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_79

description:
3mix-timelapse-plate7_79
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_80

description:
3mix-timelapse-plate7_80
3mix_RNA_expression.txt


title: Atopic Mother 0246M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 155


title: 3mix-timelapse, 3mix-timelapse-plate7_67

description:
3mix-timelapse-plate7_67
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_66

description:
3mix-timelapse-plate7_66
3mix_RNA_expression.txt


title: Non-Atopic Mother 0241M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 151


title: Atopic Mother 0267M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 164


title: Atopic Mother 0244M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 153

value: asian


title: Atopic Mother 0242M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 152


title: Atopic Mother 0245M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 154


title: 3mix-timelapse, 3mix-timelapse-plate7_65

description:
3mix-timelapse-plate7_65
3mix_RNA_expression.txt


title: Atopic Mother 0239M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 150


title: Atopic Mother 0230M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 148


title: Atopic Mother 0238M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 149


title: 3mix-timelapse, 3mix-timelapse-plate7_63

description:
3mix-timelapse-plate7_63
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_61

description:
3mix-timelapse-plate7_61
3mix_RNA_expression.txt


title: Non-Atopic Mother 0226M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 145


title: Non-Atopic Mother 0229M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 147


title: Non-Atopic Mother 0228M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 146


title: Non-Atopic Mother 0223M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 144


title: 3mix-timelapse, 3mix-timelapse-plate7_59

description:
3mix-timelapse-plate7_59
3mix_RNA_expression.txt


title: Non-Atopic Mother 0222M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 143


title: 3mix-timelapse, 3mix-timelapse-plate7_58

description:
3mix-timelapse-plate7_58
3mix_RNA_expression.txt


title: Atopic Mother 0220M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 142


title: 3mix-timelapse, 3mix-timelapse-plate7_57

description:
3mix-timelapse-plate7_57
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_56

description:
3mix-timelapse-plate7_56
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_55

description:
3mix-timelapse-plate7_55
3mix_RNA_expression.txt


title: Non-Atopic Mother 0219M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 141


title: Non-Atopic Mother 0213M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 138


title: 3mix-timelapse, 3mix-timelapse-plate7_53

description:
3mix-timelapse-plate7_53
3mix_RNA_expression.txt


title: Atopic Mother 0216M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 139


title: Non-Atopic Mother 0212M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 137


title: Non-Atopic Mother 0217M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 140


title: 3mix-timelapse, 3mix-timelapse-plate7_64

description:
3mix-timelapse-plate7_64
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_51

description:
3mix-timelapse-plate7_51
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_52

description:
3mix-timelapse-plate7_52
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_62

description:
3mix-timelapse-plate7_62
3mix_RNA_expression.txt


title: Non-Atopic Mother 0211M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 136


title: 3mix-timelapse, 3mix-timelapse-plate7_49

description:
3mix-timelapse-plate7_49
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_50

description:
3mix-timelapse-plate7_50
3mix_RNA_expression.txt


title: Non-Atopic Mother 0208M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 134


title: Atopic Mother 0210M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 135


title: 3mix-timelapse, 3mix-timelapse-plate7_60

description:
3mix-timelapse-plate7_60
3mix_RNA_expression.txt


title: Atopic Mother 0205M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 132


title: Non-Atopic Mother 0204M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 131


title: 3mix-timelapse, 3mix-timelapse-plate7_46

description:
3mix-timelapse-plate7_46
3mix_RNA_expression.txt


title: Non-Atopic Mother 0202M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 130


title: 3mix-timelapse, 3mix-timelapse-plate7_44

description:
3mix-timelapse-plate7_44
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_45

description:
3mix-timelapse-plate7_45
3mix_RNA_expression.txt


title: Atopic Mother 0199M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 127


title: 3mix-timelapse, 3mix-timelapse-plate7_54

description:
3mix-timelapse-plate7_54
3mix_RNA_expression.txt


title: Non-Atopic Mother 0201M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 129


title: Atopic Mother 0200M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 128


title: 3mix-timelapse, 3mix-timelapse-plate7_43

description:
3mix-timelapse-plate7_43
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_41

description:
3mix-timelapse-plate7_41
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_39

description:
3mix-timelapse-plate7_39
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_42

description:
3mix-timelapse-plate7_42
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_37

description:
3mix-timelapse-plate7_37
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_48

description:
3mix-timelapse-plate7_48
3mix_RNA_expression.txt


title: Non-Atopic Mother 0196M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 126


title: 3mix-timelapse, 3mix-timelapse-plate7_36

description:
3mix-timelapse-plate7_36
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_38

description:
3mix-timelapse-plate7_38
3mix_RNA_expression.txt


title: Non-Atopic Mother 0193M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 124


title: Non-Atopic Mother 0191M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 122


title: 3mix-timelapse, 3mix-timelapse-plate7_35

description:
3mix-timelapse-plate7_35
3mix_RNA_expression.txt


title: Non-Atopic Mother 0207M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 133


title: Atopic Mother 0195M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 125


title: 3mix-timelapse, 3mix-timelapse-plate7_47

description:
3mix-timelapse-plate7_47
3mix_RNA_expression.txt


title: Non-Atopic Mother 0190M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 121


title: Atopic Mother 0188M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 119


title: Non-Atopic Mother 0184M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 118


title: Atopic Mother 0189M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 120


title: 3mix-timelapse, 3mix-timelapse-plate7_33

description:
3mix-timelapse-plate7_33
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_34

description:
3mix-timelapse-plate7_34
3mix_RNA_expression.txt


title: Atopic Mother 0183M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 117


title: Non-Atopic Mother 0179M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 116


title: 3mix-timelapse, 3mix-timelapse-plate7_30

description:
3mix-timelapse-plate7_30
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_32

description:
3mix-timelapse-plate7_32
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_31

description:
3mix-timelapse-plate7_31
3mix_RNA_expression.txt


title: Atopic Mother 0178M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 115


title: Non-Atopic Mother 0176M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 114


title: Non-Atopic Mother 0192M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 123


title: Atopic Mother 0174M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 113


title: 3mix-timelapse, 3mix-timelapse-plate7_28

description:
3mix-timelapse-plate7_28
3mix_RNA_expression.txt


title: Atopic Mother 0173M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 112


title: 3mix-timelapse, 3mix-timelapse-plate7_27

description:
3mix-timelapse-plate7_27
3mix_RNA_expression.txt


title: Atopic Mother 0172M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 111


title: 3mix-timelapse, 3mix-timelapse-plate7_26

description:
3mix-timelapse-plate7_26
3mix_RNA_expression.txt


title: Non-Atopic Mother 0171M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 110


title: Atopic Mother 0169M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 109


title: Atopic Mother 0168M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 108


title: 3mix-timelapse, 3mix-timelapse-plate7_25

description:
3mix-timelapse-plate7_25
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_24

description:
3mix-timelapse-plate7_24
3mix_RNA_expression.txt


title: Non-Atopic Mother 0164M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 106


title: 3mix-timelapse, 3mix-timelapse-plate7_22

description:
3mix-timelapse-plate7_22
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_23

description:
3mix-timelapse-plate7_23
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_21

description:
3mix-timelapse-plate7_21
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_20

description:
3mix-timelapse-plate7_20
3mix_RNA_expression.txt


title: Non-Atopic Mother 0163M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 105


title: Non-Atopic Mother 0162M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 104


title: 3mix-timelapse, 3mix-timelapse-plate7_19

description:
3mix-timelapse-plate7_19
3mix_RNA_expression.txt


title: Non-Atopic Mother 0161M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 103


title: Non-Atopic Mother 0160M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 102


title: 3mix-timelapse, 3mix-timelapse-plate7_17

description:
3mix-timelapse-plate7_17
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_18

description:
3mix-timelapse-plate7_18
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_29

description:
3mix-timelapse-plate7_29
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_16

description:
3mix-timelapse-plate7_16
3mix_RNA_expression.txt


title: Atopic Mother 0157M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 100


title: Non-Atopic Mother 0159M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 101


title: 3mix-timelapse, 3mix-timelapse-plate7_15

description:
3mix-timelapse-plate7_15
3mix_RNA_expression.txt


title: Non-Atopic Mother 0156M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 99


title: Atopic Mother 0154M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 98


title: 3mix-timelapse, 3mix-timelapse-plate7_14

description:
3mix-timelapse-plate7_14
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_13

description:
3mix-timelapse-plate7_13
3mix_RNA_expression.txt


title: Non-Atopic Mother 0167M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 107


title: Atopic Mother 0153M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 97


title: 3mix-timelapse, 3mix-timelapse-plate7_12

description:
3mix-timelapse-plate7_12
3mix_RNA_expression.txt


title: Non-Atopic Mother 0150M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 95


title: Atopic Mother 0152M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 96


title: Atopic Mother 0148M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 94


title: 3mix-timelapse, 3mix-timelapse-plate7_11

description:
3mix-timelapse-plate7_11
3mix_RNA_expression.txt


title: Non-Atopic Mother 0147M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 93


title: 3mix-timelapse, 3mix-timelapse-plate7_8

description:
3mix-timelapse-plate7_8
3mix_RNA_expression.txt


title: Non-Atopic Mother 0142M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 92


title: 3mix-timelapse, 3mix-timelapse-plate7_7

description:
3mix-timelapse-plate7_7
3mix_RNA_expression.txt


title: Non-Atopic Mother 0140M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 91


title: 3mix-timelapse, 3mix-timelapse-plate7_6

description:
3mix-timelapse-plate7_6
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_40

description:
3mix-timelapse-plate7_40
3mix_RNA_expression.txt


title: Non-Atopic Mother 0138M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 90


title: Atopic Mother 0136M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 89


title: 3mix-timelapse, 3mix-timelapse-plate7_4

description:
3mix-timelapse-plate7_4
3mix_RNA_expression.txt


title: Non-Atopic Mother 0134M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 88


title: 3mix-timelapse, 3mix-timelapse-plate7_3

description:
3mix-timelapse-plate7_3
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_2

description:
3mix-timelapse-plate7_2
3mix_RNA_expression.txt


title: Atopic Mother 0133M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 87


title: Atopic Mother 0132M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 86


title: Atopic Mother 0131M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 85


title: 3mix-timelapse, 3mix-timelapse-plate7_1

description:
3mix-timelapse-plate7_1
3mix_RNA_expression.txt


title: Non-Atopic Mother 0129M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 83


title: 3mix-timelapse, 3mix-timelapse-plate6_96

description:
3mix-timelapse-plate6_96
3mix_RNA_expression.txt


title: Atopic Mother 0128M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 82


title: 3mix-timelapse, 3mix-timelapse-plate6_95

description:
3mix-timelapse-plate6_95
3mix_RNA_expression.txt


title: Atopic Mother 0130M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 84


title: 3mix-timelapse, 3mix-timelapse-plate6_94

description:
3mix-timelapse-plate6_94
3mix_RNA_expression.txt


title: Non-Atopic Mother 0127M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 81


title: 3mix-timelapse, 3mix-timelapse-plate7_9

description:
3mix-timelapse-plate7_9
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_92

description:
3mix-timelapse-plate6_92
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_10

description:
3mix-timelapse-plate7_10
3mix_RNA_expression.txt


title: Non-Atopic Mother 0123M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 79


title: 3mix-timelapse, 3mix-timelapse-plate6_93

description:
3mix-timelapse-plate6_93
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_91

description:
3mix-timelapse-plate6_91
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_90

description:
3mix-timelapse-plate6_90
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_88

description:
3mix-timelapse-plate6_88
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate7_5

description:
3mix-timelapse-plate7_5
3mix_RNA_expression.txt


title: Non-Atopic Mother 0124M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 80


title: 3mix-timelapse, 3mix-timelapse-plate6_87

description:
3mix-timelapse-plate6_87
3mix_RNA_expression.txt


title: Atopic Mother 0119M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 76


title: Atopic Mother 0117M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 75


title: 3mix-timelapse, 3mix-timelapse-plate6_89

description:
3mix-timelapse-plate6_89
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_86

description:
3mix-timelapse-plate6_86
3mix_RNA_expression.txt


title: Atopic Mother 0116M

description:
CHARM  profile of whole blood of mother of infant with maternal or biparental history of atopy
Sample 74


title: 3mix-timelapse, 3mix-timelapse-plate6_85

description:
3mix-timelapse-plate6_85
3mix_RNA_expression.txt


title: Non-Atopic Mother 0115M

description:
CHARM  profile of whole blood of mother of infant with no parental history of atopy
Sample 73


title: 3mix-timelapse, 3mix-timelapse-plate6_84

description:
3mix-timelapse-plate6_84
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_83

description:
3mix-timelapse-plate6_83
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_81

description:
3mix-timelapse-plate6_81
3mix_RNA_expression.txt


title: 3mix-timelapse, 3mix-timelapse-plate6_80

description:
3mix-timelapse-plate6_80
3mix_RNA_expression.txt