title: Pax7 lineage - E14.5b4_57

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_59

status: Public on Apr 12 2022

type: SRA

city: Hong Kong

first: Angela

last: Wu

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description:
ss2_filtered_count.csv
E14.5_b4_1

library_source: transcriptomic

data_processing:
Smart-seq2 samples basecalling were performed using bcl2fastq2; 10x samples were performed using bcl2fastq.
Smart-seq2 samples were quantified using kallisto 0.44.0, summarized using tximport in R; 10x samples were aligned using STAR and matrices were generated with cellranger count
Both datasets were loaded in R environment as Seurat object and filtered for poor quality reads.
Genome_build: mm10
Supplementary_files_format_and_content: csv containing raw counts

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic cells

extract_protocol:
YFP+ signals reporting Pax7-lineage cells were FACS sorted. Additional sorting with antibody labeling were done for bulk samples regarding surface marker studies.
Sequencing libraries for single-cell samples were constructed using Smart-seq2 protocol or 10x protocol. Smart-seq2 was also applied to bulk samples.

treatment_protocol: The progeny Pax7-expressing cells during early developmental stage were traced by injecting a single dose of TMX (75 µg/g body weight) intraperitoneally into the pregnant mice at E9.5 to initiate Cre-Lox recombination in Pax7-expressing cells. Embryos were harvested later at E12.5, E14.5, and E16.5.

tag: tissue

value: embryonic cells

tag: method

tag: sequencng type

value: Single-cell

tag: time point

tag: plate batch

value: Plate 6

tag: sequence batch

value: Batch 4

tag: medium

tag: marker


title: Pax7 lineage - E14.5b4_60

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_61

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_50

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_56

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_51

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_52

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_55

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_48

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_53

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_46

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_49

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_54

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_45

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_44

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_42

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_47

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_43

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_39

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_40

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_41

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_35

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_38

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_37

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_34

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_36

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_58

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_33

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_31

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_32

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_30

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_28

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_27

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_24

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_25

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_19

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_18

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_23

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_21

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_26

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_20

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_16

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_17

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_22

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_15

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_13

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_14

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_12

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_6

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_11

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_7

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_9

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_10

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_5

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_63

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_29

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_4

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_2

description:
ss2_filtered_count.csv
E14.5_b4_9


title: Pax7 lineage - E14.5b4_8

description:
ss2_filtered_count.csv
E14.5_b4_1


title: Pax7 lineage - E14.5b4_1

description:
ss2_filtered_count.csv
E14.5_b4_9


title: Pax7 lineage - E14.5b3_95

description:
ss2_filtered_count.csv
E14.5_b3_9

value: Plate 5


title: Pax7 lineage - E14.5b3_93

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b3_94

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b3_96

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b3_91

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b3_89

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_92

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b3_85

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_86

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_84

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_87

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_83

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_82

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_81

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_78

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_74

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_76

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_75

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_77

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_79

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_80

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_73

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_71

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_72

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_88

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_70

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_90

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b3_69

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_68

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_67

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_62

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_66

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_63

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_64

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_59

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_60

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_65

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_57

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_55

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_58

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_61

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_53

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_56

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_54

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_49

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_50

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_46

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_47

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_51

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_52

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_48

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_45

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_41

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_42

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_43

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_44

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_39

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_40

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_38

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_37

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_36

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_35

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_34

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_33

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_32

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_30

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_28

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_29

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_26

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_25

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_20

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_21

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_24

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_18

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_17

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_16

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_14

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_13

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_15

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_12

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_10

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_31

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b4_3

description:
ss2_filtered_count.csv
E14.5_b4_9


title: Pax7 lineage - E14.5b3_7

description:
ss2_filtered_count.csv
E14.5_b3_7


title: Pax7 lineage - E14.5b3_8

description:
ss2_filtered_count.csv
E14.5_b3_8


title: Pax7 lineage - E14.5b3_4

description:
ss2_filtered_count.csv
E14.5_b3_4


title: Pax7 lineage - E14.5b3_6

description:
ss2_filtered_count.csv
E14.5_b3_6


title: Pax7 lineage - E14.5b3_23

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_5

description:
ss2_filtered_count.csv
E14.5_b3_5


title: Pax7 lineage - E14.5b3_19

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b3_3

description:
ss2_filtered_count.csv
E14.5_b3_3


title: Pax7 lineage - E14.5b3_27

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_22

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b3_1

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b2_94

description:
ss2_filtered_count.csv
E14.5_b2_1

value: Plate 4

value: Batch 3


title: Pax7 lineage - E14.5b3_2

description:
ss2_filtered_count.csv
E14.5_b3_2


title: Pax7 lineage - E14.5b2_92

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_95

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_90

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_93

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b3_11

description:
ss2_filtered_count.csv
E14.5_b3_1


title: Pax7 lineage - E14.5b2_85

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_84

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_83

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_82

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_86

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b3_9

description:
ss2_filtered_count.csv
E14.5_b3_9


title: Pax7 lineage - E14.5b2_77

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_73

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_80

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_91

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_74

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_81

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_76

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_75

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_71

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_96

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_88

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_72

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_89

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_66

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_70

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_65

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_64

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_69

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_63

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_67

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_87

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_62

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_79

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_61

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_78

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_60

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_59

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_58

description:
ss2_filtered_count.csv
E14.5_b2_1


title: SCA1- Mouse 4 transplanted (dsRED+)

city: Boston

first: Aaron

middle: L.

last: Moye

state: MA

address: 1 Blackfan Circle

department: Stem Cell Program

country: USA

institute: Boston Children's Hospital

description:
Transplantated cells from a nude mouse after transplantation of SCA1- organoid cells
SL15

data_processing:
10X Genomics Cell Ranger 3.1.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz  for each library.

source_name: Lung epithelial cells from a bleomycin pre-treated nude mouse with organoid transplantation

extract_protocol:
Lungs from untreated or organoid transplanted mice were extracted, single cell suspensions generated, and native or transplanted (dsRed+) cells were collected using FACS. Cells from organoid co-cultures were also collected. Cells were encapsulated and libraries generated using the 10X Genomics Single Cell 3' pipeline. Pooled libraries were sequenced using an Illumina NextSeq500.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 2 or 3

treatment_protocol: Cells from organoid co-cultures were delivered intratracheally into murine lungs after pre-treatment with bleomycin. Native SCA1+ cells were collected from untreated mice.

tag: cell type

value: DAPI- CD31- CD45- EPCAM+ dsRED+


title: SCA1+ Mouse 2 transplanted (dsRED+)

description:
Transplantated cells from a nude mouse after transplantation of SCA1+ organoid cells
SL8


title: SCA1+ Organoid co-culture 1

description:
SCA1+ murine lung epithelial organoids co-cultured with lung stromal cells
SL9

source_name: Lung organoid co-cultures

value: dsRED+


title: SCA1+ Organoid co-culture 2

description:
SCA1+ murine lung epithelial organoids co-cultured with lung stromal cells
SL10


title: SCA1- Mouse 3 native (dsRED-)

description:
Native cells from a nude mouse after transplantation of SCA1- organoid cells
SL12

value: DAPI- CD31- CD45- EPCAM+ SCA1-


title: SCA1- Mouse 4 native (dsRED-)

description:
Native cells from a nude mouse after transplantation of SCA1- organoid cells
SL14


title: SCA1+ Mouse 1 native (no injury)

description:
SCA1+ murine lung epithelial cells
IW1

source_name: Lung epithelial cells from an uninjured C57/BL6 mouse

value: DAPI- CD31- CD45- EPCAM+ SCA1+


title: SCA1- Organoid co-culture 1

description:
SCA1- murine lung epithelial organoids co-cultured with lung stromal cells
SL5


title: Pax7 lineage - E14.5b2_68

description:
ss2_filtered_count.csv
E14.5_b2_1


title: FGF10+ ADU_rep1

city: La Jolla

first: Helen

last: Makarenkova

state: CA

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

description: Mouse injected with tamoxifen (0.1 mg per g of weight) at P57/58 and sacrified at P60

data_processing:
Libraries were then sequenced on an Illumina NextSeq500 sequencer
The reads were trimmed for the adapter sequences using cutadapt 1.18
The trimmed reads were mapped to the mouse reference genome (ENSEMBL build GRCm38 r91) using the STAR aligner 2.5.2a
Gene abundance was estimated with python 2.7.11, and HTSeq 0.11.0
Final gene counts of all samples including raw counts, normalized counts and the differential gene expression analyses was performed using R 3.5.1, and DESeq2 1.20.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SMG FGF10+ cells

extract_protocol:
Sorted cells were pelleted and resuspended with 700 µL Qiazol lysis reagent (#79306, Qiagen). RNA was isolated with the miRNeasy Micro Kit (#217084, Qiagen), according to the manufacturer’s instructions.
Total RNA was extracted, and multiplexed libraries were prepared and validated using the Agilent BioAnalyzer, normalized and pooled for sequencing. One nanogram total RNA from each sample was used to prepare sequencing libraries using the SMART-Seq HT (Takara) library prep kit following manufacturer recommended protocol.

tag: strain

value: SMG

tag: genotype

value: Fgf10CreERT2:Rosa26Tomato fl/fl

tag: age

value: post natal day 60


title: SCA1+ Mouse 2 native (no injury)

description:
SCA1+ murine lung epithelial cells
IW3


title: SCA1+ Mouse 1 transplanted (dsRED+)

description:
Transplantated cells from a nude mouse after transplantation of SCA1+ organoid cells
SL7


title: SCA1- Mouse 2 native (dsRED-)

description:
Native cells from a nude mouse after transplantation of SCA1- organoid cells
SL3


title: SCA1- Mouse 1 transplanted (dsRED+)

description:
Transplantated cells from a nude mouse after transplantation of SCA1- organoid cells
SL2


title: FGF10+ PUP_rep1

description: Mouse injected with tamoxifen (0.1 mg per g of weight) at P4/5 and sacrified at P7

value: post natal day 7


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_DMEM_rep3

description:
bulk_filtered_count.csv
n_Thy1+_3 in processed data

value: Bulk

value: DMEM


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_DMEM_rep3

description:
bulk_filtered_count.csv
n_Thy1-_3 in processed data

value: embryonic cells


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_rep2

description:
bulk_filtered_count.csv
e2_Thy1- in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_DMEM_rep2

description:
bulk_filtered_count.csv
n_Thy1+_2 in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_DMEM_rep1

description:
bulk_filtered_count.csv
n_Thy1-_1 in processed data


title: SCA1+ Mouse 3 native (no injury)

description:
SCA1+ murine lung epithelial cells
IW5


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_DMEM_rep1

description:
bulk_filtered_count.csv
n_Thy1+_1 in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_DMEM_rep2

description:
bulk_filtered_count.csv
n_Thy1-_2 in processed data


title: FGF10+ ADU_rep2


title: Pax7 lineage - bulk_Pdgfra-/Cd36+_rep1

description:
bulk_filtered_count.csv
e1_Cd36+ in processed data


title: SCA1+ Organoid co-culture 3

description:
SCA1+ murine lung epithelial organoids co-cultured with lung stromal cells
SL11


title: SCA1- Organoid co-culture 2

description:
SCA1- murine lung epithelial organoids co-cultured with lung stromal cells
SL6


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_rep1

description:
bulk_filtered_count.csv
e1_Thy1- in processed data


title: FGF10+ PUP_rep2


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_rep2

description:
bulk_filtered_count.csv
e2_Thy1+ in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_ADM_rep3

description:
bulk_filtered_count.csv
a_Thy1+_3 in processed data

value: ADM


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_ADM_rep1

description:
bulk_filtered_count.csv
a_Thy1+_1 in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_ADM_rep2

description:
bulk_filtered_count.csv
a_Thy1+_2 in processed data


title: Pax7 lineage - bulk_Pdgfra-/Cd36+_rep2

description:
bulk_filtered_count.csv
e2_Cd36+ in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1+_rep1

description:
bulk_filtered_count.csv
e1_Thy1+ in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_ADM_rep3

description:
bulk_filtered_count.csv
a_Thy1-_3 in processed data


title: Pax7 lineage - E16.5

description:
10x_filtered_count.csv
Appended with -3 in processed data

value: Single-cell


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_ADM_rep1

description:
bulk_filtered_count.csv
a_Thy1-_1 in processed data


title: Pax7 lineage - bulk_Pdgfra+/Thy1-_ADM_rep2

description:
bulk_filtered_count.csv
a_Thy1-_2 in processed data


title: Pax7 lineage - E16.5b4_94

description:
ss2_filtered_count.csv
E16.5_b4_3

value: Plate 13

value: Batch 6


title: Pax7 lineage - E16.5b4_96

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_91

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_95

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_93

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_88

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_82

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_92

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_90

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E12.5

description:
10x_filtered_count.csv
Appended with -1 in processed data


title: Pax7 lineage - E16.5b4_89

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_85

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_78

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_87

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_84

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_83

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_86

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_79

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_80

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_81

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E14.5

description:
10x_filtered_count.csv
Appended with -2 in processed data


title: Pax7 lineage - E16.5b4_73

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_77

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_71

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_74

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_70

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_75

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_68

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_65

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_64

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_67

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_63

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_61

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_58

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_66

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_59

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_62

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_56

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_76

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_55

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_57

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_53

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_49

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_52

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_50

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_46

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_54

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_72

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_51

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_48

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_69

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_47

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_45

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_44

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_43

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_41

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_60

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_42

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_40

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_39

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_38

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_35

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_33

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_34

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_36

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_37

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_29

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_32

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_31

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_27

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_26

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_30

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_23

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_19

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_20

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_28

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_21

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_25

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_17

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_16

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_18

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_15

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_24

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_14

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_12

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_11

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_13

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_10

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_8

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_22

description:
ss2_filtered_count.csv
E16.5_b4_3


title: Pax7 lineage - E16.5b4_6

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_5

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_4

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_2

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b3_96

description:
ss2_filtered_count.csv
E16.5_b3_2

value: Plate 12


title: Pax7 lineage - E16.5b4_3

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b4_1

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b3_93

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_94

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_95

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_90

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_91

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_92

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_87

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_85

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_88

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_84

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_82

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_81

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_80

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_89

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_83

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b4_7

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b3_79

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_78

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b4_9

description:
ss2_filtered_count.csv
E16.5_b4_2


title: Pax7 lineage - E16.5b3_77

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_76

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_72

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_75

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_86

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_73

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_74

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_71

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_67

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_70

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_68

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_66

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_65

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_63

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_64

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_62

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_60

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_61

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_57

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_59

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_55

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_58

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_54

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_53

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_56

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_50

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_51

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_52

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_49

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_47

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_48

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_69

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_46

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_45

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_42

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_41

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_44

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_40

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_35

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_39

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_38

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_34

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_37

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_31

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_33

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_30

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_32

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_26

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_28

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_29

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_27

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_24

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_25

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_23

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_19

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_43

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_18

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_20

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_22

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_21

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_14

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_16

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_15

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_17

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_13

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_36

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_12

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_9

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_11

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_10

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_8

description:
ss2_filtered_count.csv
E16.5_b3_2


title: Pax7 lineage - E16.5b3_6

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b3_7

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b3_5

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b3_4

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b3_2

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b3_3

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b2_96

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b3_1

description:
ss2_filtered_count.csv
E16.5_b3_1


title: Pax7 lineage - E16.5b2_94

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_93

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_92

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_91

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_88

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_87

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_85

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_84

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_82

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_83

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_90

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_81

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_80

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_89

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_79

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_95

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_86

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_76

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_74

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_75

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_78

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_73

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_71

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_69

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_68

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_67

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_66

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_65

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_63

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_62

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_61

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_60

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_59

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_58

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_57

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_77

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_54

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_51

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_52

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_49

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_50

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_70

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_46

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_44

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_45

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_48

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_47

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_43

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_42

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_40

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_64

description:
ss2_filtered_count.csv
E16.5_b2_1


title: CDseq_U2OS_oxidized_Ts_EndoIII&NEIL1

city: Grand Rapids

first: Gerd

middle: P.

last: Pfeifer

state: Michigan

address: 333 Bostwick Ave. NE.

department: Center for Epigenetics

institute: Van Andel Research Institute

library_source: genomic

data_processing:
Library strategy: circle-damage-seq
Fastq files containing sequencing reads were trimmed from the 3’ end to 2x80 nucleotide length using Trim_Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned to the hg19 reference genome using BWA-MEM with default parameters.
Duplicate alignments were marked and removed with the ‘removeDups’ SAMBLASTER option.
Only divergently aligned pairs of reads with a single nucleotide gap between reads were selected by selecting SAM records with TLEN of 3 and saved as bam files for downstream analyses. TLEN=3 represents divergently aligned reads with 1 nucleotide between mates.
To visualize the reads, bam files were visualized using the Integrative Genomics Viewer version 2.8.9. The tracks were displayed with a ‘view as pairs’ option to show pairs together with a line joining the ends.
Genome_build: hg19
Supplementary_files_format_and_content: Chromosome name, start position, stop position, and inferred strand (+/-) for all selected read pair loci were written to a BED file.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human bone osteosarcoma

growth_protocol: Human skin fibroblasts cells (HDF, ATCC PCS-201-012) and human osteosarcoma cells (U2OS, ATCC HTB-96) were cultured in the Fibroblast Growth Kit (ATCC, Cat. PCS-201-041) supplemented with 2% fetal bovine serum (FBS) and in DMEM/high glucose supplemented with 10% FBS, respectively, at 37°C in a 5% CO2 standard incubator.

extract_protocol:
Genomic DNAs were isolated using Quick-DNA Miniprep Plus Kit (Zymo Research; Irvine, CA) according to the manufacturer’s instruction manual.
Genomic DNAs were framgmeted to an averge length of 300 bp and circuliarized with T4 DNA ligase at 16°C overnight. Non-circularized linear DNAs were removed with Plasmid-Safe ATP-Dependent DNAse treatment. To generate DNA double-strand breaks at 8-oxo-dG lesions, the circularized DNAs were treated with Fpg and APE1 followed by S1 nuclease to create double-strand breaks with ligatable ends. To generate double-strand breaks at oxidized thymines, the circularized DNA was initially treated with EndoIII, NEIL1 or EndoIII & NEIL1 followed by EndoIV (NEB) treatment, and then S1 nuclease to create double-strand breaks with ligatable ends. A-tailed with Klenow fragment exo- (NEB) and then adaptors were ligated with NEBNext Ultra II Ligation Master Mix and followed by incubation with USER enzyme (NEB). The purified DNA libraries were amplified by PCR with NEBNext Ultra II Q5 Master mix and NEBNext i5 and i7 primers and used for DNA sequencing.

treatment_protocol: To induce 8-oxo-dGs, HDF cells were washed with 1x PBS and treated in PBS with diluted H2O2 solution to final concentration 5 mM and 10 mM for 30 min at 37°C in a 5% CO2 incubator. To induce oxidized thymines, 1 x 107 of U2OS cells were washed with 1x PBS and treated with 40 mM KMnO4 for 70 sec at 37°C in the solution with the following components: 15 mM Tris-HCl, pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, and 300 mM sucrose. The reaction was quenched by treatment 50 mM EDTA, 0.7 M beta-mercaptoethanol, 1% SDS, and 40 μg/ml RNase for 1 hour at 37°C.

tag: cell line

tag: treatment

value: 10 mM of KMnO4

tag: repair enzyme

value: EndoIII & NEIL1


title: Pax7 lineage - E16.5b2_56

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_55

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_53

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_37

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_36

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_39

description:
ss2_filtered_count.csv
E16.5_b2_1


title: CDseq_HDF_8oxodG_10mM

source_name: Human skin fibroblasts

value: HDF

value: 10 mM of H2O2

value: Fpg


title: CDseq_U2OS_oxidized_Ts_NT


title: Pax7 lineage - E16.5b2_35

description:
ss2_filtered_count.csv
E16.5_b2_1


title: CDseq_U2OS_oxidized_Ts_NEIL1


title: Pax7 lineage - E16.5b2_34

description:
ss2_filtered_count.csv
E16.5_b2_1


title: CDseq_HDF_8oxodG_5mM

value: 5 mM of H2O2


title: Pax7 lineage - E16.5b2_33

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell70 [B7]

city: Kyoto

first: Ratklao

last: Siriwach

address: Sakyo-ku, Shogoin Kawahara-cho

department: Department of Drug Discovery Medicine

country: Japan

institute: Kyoto University Graduate School of Medicine

description: W0059_C1WTA_DEAN_B7_TAAGGCGA-AAGGAGTA_L008

data_processing:
Illumina Casava  software used for basecalling.
Raw read sequence quality were evaluated using FastQC (v0.11.8) and adaptor sequence were trimmed using Cutadapt (v2.3)
Reads were mapped to the reference genome (hg38) together with annotation files for GENCODE.v30 using STAR (v2.7.0f)
A raw count matrix was generated with featureCounts (v1.6.4)
If the same sample have two split fastq files (refering to file name 001 and 002), the raw count reads were summed up.
Data were filtered using the following specifications; cells with total counts of less than 500,000, total number of expressed genes less than 2,000, a percentage of counts in mitochondrial genes more than 30%, and genes expressed in less than 2 cells were excluded.
Raw counts were normalized by library size and then log-transformed
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene of filtering samples

growth_protocol: NHEKs were seeded into 24-welled plated in concentration of 5x104 cells per well for 24 h. Growth factors were removed and cultured medium was changed to low calcium concentration (60 μM) medium for 2 days.

extract_protocol:
single cell suspension of 300 cells/μl from either vehicle control or LPA stimulation was prepared and loaded onto  a the 96-well microfluidic chip (17-25μm-diameter) for single cell capture using the Microfluidic C1 Autoprep System Fluidigm. The capturing efficiency was evaluated on a microscope and only single cells were subjected to library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols  using Nextera XT DNA Library Preparation Kit. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 10μM Oleoyl-L-α-lysophosphatidic acid  together with calcium (final concentration 1.2 mM) were then added into the cell culture in the presence of 30 ng/ml IL-4. Cells were continuously cultivated for 3 days at 37 ºC in a humidified incubator with 5% CO2.

value: Normal Human Epidermal Keratinocytes (NHEKs)


title: NHEKs_1.2mMCa+10μMLPA_Cell71 [B8]

description: W0059_C1WTA_DEAN_B8_TAAGGCGA-CTAAGCCT_L008


title: CDseq_U2OS_oxidized_Ts_EndoIII

value: EndoIII


title: Pax7 lineage - E16.5b2_31

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_32

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell72 [B9]

description: W0059_C1WTA_DEAN_B9_CGTACTAG-GCGTAAGA_L008


title: Pax7 lineage - E16.5b2_27

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_41

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_30

description:
ss2_filtered_count.csv
E16.5_b2_1


title: CDseq_HDF_8oxodG_10mM_540M


title: Pax7 lineage - E16.5b2_28

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_24

description:
ss2_filtered_count.csv
E16.5_b2_1


title: CDseq_HDF_8oxodG_NT


title: Pax7 lineage - E16.5b2_38

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_25

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell63 [B67]

description: W0059_C1WTA_DEAN_B67_GCTACGCT-TATCCTCT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell66 [B6]

description: W0059_C1WTA_DEAN_B6_TAAGGCGA-ACTGCATA_L008


title: Pax7 lineage - E16.5b2_23

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_26

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell65 [B69]

description: W0059_C1WTA_DEAN_B69_GCTACGCT-GTAAGGAG_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell67 [B70]

description: W0059_C1WTA_DEAN_B70_GCTACGCT-ACTGCATA_L008


title: Pax7 lineage - E16.5b2_72

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell62 [B66]

description: W0059_C1WTA_DEAN_B66_GCTACGCT-CTCTCTAT_L008


title: Pax7 lineage - E16.5b2_29

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_21

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell61 [B65]

description: W0059_C1WTA_DEAN_B65_GCTACGCT-GCGTAAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell68 [B71]

description: W0059_C1WTA_DEAN_B71_GCTACGCT-AAGGAGTA_L008


title: Pax7 lineage - E16.5b2_22

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell69 [B72]

description: W0059_C1WTA_DEAN_B72_GCTACGCT-CTAAGCCT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell59 [B63]

description: W0059_C1WTA_DEAN_B63_CAGAGAGG-AAGGAGTA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell58 [B62]

description: W0059_C1WTA_DEAN_B62_CAGAGAGG-ACTGCATA_L008


title: Pax7 lineage - E16.5b2_18

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_19

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell60 [B64]

description: W0059_C1WTA_DEAN_B64_CAGAGAGG-CTAAGCCT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell64 [B68]

description: W0059_C1WTA_DEAN_B68_GCTACGCT-AGAGTAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell57 [B61]

description: W0059_C1WTA_DEAN_B61_CAGAGAGG-GTAAGGAG_L008


title: Pax7 lineage - E16.5b2_17

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_16

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell55 [B5]

description: W0059_C1WTA_DEAN_B5_TAAGGCGA-GTAAGGAG_L008


title: Pax7 lineage - E16.5b2_15

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell54 [B59]

description: W0059_C1WTA_DEAN_B59_CAGAGAGG-TATCCTCT_L008


title: Pax7 lineage - E16.5b2_13

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_14

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell53 [B58]

description: W0059_C1WTA_DEAN_B58_CAGAGAGG-CTCTCTAT_L008


title: Pax7 lineage - E16.5b2_11

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell51 [B56]

description: W0059_C1WTA_DEAN_B56_CTCTCTAC-CTAAGCCT_L008


title: Pax7 lineage - E16.5b2_12

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell52 [B57]

description: W0059_C1WTA_DEAN_B57_CAGAGAGG-GCGTAAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell50 [B55]

description: W0059_C1WTA_DEAN_B55_CTCTCTAC-AAGGAGTA_L008


title: Pax7 lineage - E16.5b2_20

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_9

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_10

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell48 [B53]

description: W0059_C1WTA_DEAN_B53_CTCTCTAC-GTAAGGAG_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell49 [B54]

description: W0059_C1WTA_DEAN_B54_CTCTCTAC-ACTGCATA_L008


title: Pax7 lineage - E16.5b2_8

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell47 [B52]

description: W0059_C1WTA_DEAN_B52_CTCTCTAC-AGAGTAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell46 [B51]

description: W0059_C1WTA_DEAN_B51_CTCTCTAC-TATCCTCT_L008


title: Pax7 lineage - E16.5b2_7

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell56 [B60]

description: W0059_C1WTA_DEAN_B60_CAGAGAGG-AGAGTAGA_L008


title: Pax7 lineage - E16.5b2_5

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E16.5b2_6

description:
ss2_filtered_count.csv
E16.5_b2_1


title: Pax7 lineage - E14.5b2_57

description:
ss2_filtered_count.csv
E14.5_b2_1

value: Plate 4

value: Batch 3


title: Pax7 lineage - E16.5b2_4

description:
ss2_filtered_count.csv
E16.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell43 [B49]

description: W0059_C1WTA_DEAN_B49_CTCTCTAC-GCGTAAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell44 [B4]

description: W0059_C1WTA_DEAN_B4_TAAGGCGA-AGAGTAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell42 [B48]

description: W0059_C1WTA_DEAN_B48_TAGGCATG-CTAAGCCT_L008


title: Pax7 lineage - E14.5b2_56

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_55

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell39 [B45]

description: W0059_C1WTA_DEAN_B45_TAGGCATG-GTAAGGAG_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell41 [B47]

description: W0059_C1WTA_DEAN_B47_TAGGCATG-AAGGAGTA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell40 [B46]

description: W0059_C1WTA_DEAN_B46_TAGGCATG-ACTGCATA_L008


title: Pax7 lineage - E14.5b2_54

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell38 [B44]

description: W0059_C1WTA_DEAN_B44_TAGGCATG-AGAGTAGA_L008


title: Pax7 lineage - E14.5b2_52

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell37 [B43]

description: W0059_C1WTA_DEAN_B43_TAGGCATG-TATCCTCT_L008


title: Pax7 lineage - E14.5b2_53

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell35 [B41]

description: W0059_C1WTA_DEAN_B41_TAGGCATG-GCGTAAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell36 [B42]

description: W0059_C1WTA_DEAN_B42_TAGGCATG-CTCTCTAT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell45 [B50]

description: W0059_C1WTA_DEAN_B50_CTCTCTAC-CTCTCTAT_L008


title: Pax7 lineage - E14.5b2_51

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_50

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell34 [B40]

description: W0059_C1WTA_DEAN_B40_GGACTCCT-CTAAGCCT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell32 [B39]

description: W0059_C1WTA_DEAN_B39_GGACTCCT-AAGGAGTA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell33 [B3]

description: W0059_C1WTA_DEAN_B3_TAAGGCGA-TATCCTCT_L008


title: Pax7 lineage - E14.5b2_47

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_48

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_49

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell31 [B38]

description: W0059_C1WTA_DEAN_B38_GGACTCCT-ACTGCATA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell30 [B37]

description: W0059_C1WTA_DEAN_B37_GGACTCCT-GTAAGGAG_L008


title: Pax7 lineage - E14.5b2_46

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_45

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_43

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_42

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell28 [B35]

description: W0059_C1WTA_DEAN_B35_GGACTCCT-TATCCTCT_L008


title: Pax7 lineage - E14.5b2_44

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell27 [B34]

description: W0059_C1WTA_DEAN_B34_GGACTCCT-CTCTCTAT_L008


title: Pax7 lineage - E14.5b2_41

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell26 [B33]

description: W0059_C1WTA_DEAN_B33_GGACTCCT-GCGTAAGA_L008


title: Pax7 lineage - E14.5b2_40

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_38

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_39

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell24 [B31]

description: W0059_C1WTA_DEAN_B31_TCCTGAGC-AAGGAGTA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell23 [B30]

description: W0059_C1WTA_DEAN_B30_TCCTGAGC-ACTGCATA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell25 [B32]

description: W0059_C1WTA_DEAN_B32_TCCTGAGC-CTAAGCCT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell22 [B2]

description: W0059_C1WTA_DEAN_B2_TAAGGCGA-CTCTCTAT_L008


title: Pax7 lineage - E14.5b2_37

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell21 [B29]

description: W0059_C1WTA_DEAN_B29_TCCTGAGC-GTAAGGAG_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell20 [B28]

description: W0059_C1WTA_DEAN_B28_TCCTGAGC-AGAGTAGA_L008


title: Pax7 lineage - E14.5b2_35

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell18 [B26]

description: W0059_C1WTA_DEAN_B26_TCCTGAGC-CTCTCTAT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell29 [B36]

description: W0059_C1WTA_DEAN_B36_GGACTCCT-AGAGTAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell19 [B27]

description: W0059_C1WTA_DEAN_B27_TCCTGAGC-TATCCTCT_L008


title: Pax7 lineage - E14.5b2_31

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell16 [B24]

description: W0059_C1WTA_DEAN_B24_AGGCAGAA-CTAAGCCT_L008


title: Pax7 lineage - E14.5b2_30

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell15 [B23]

description: W0059_C1WTA_DEAN_B23_AGGCAGAA-AAGGAGTA_L008


title: Pax7 lineage - E14.5b2_33

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_28

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell14 [B22]

description: W0059_C1WTA_DEAN_B22_AGGCAGAA-ACTGCATA_L008


title: Pax7 lineage - E14.5b2_29

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell13 [B21]

description: W0059_C1WTA_DEAN_B21_AGGCAGAA-GTAAGGAG_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell12 [B20]

description: W0059_C1WTA_DEAN_B20_AGGCAGAA-AGAGTAGA_L008


title: Pax7 lineage - E14.5b2_27

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell11 [B1]

description: W0059_C1WTA_DEAN_B1_TAAGGCGA-GCGTAAGA_L008


title: Pax7 lineage - E14.5b2_36

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell10 [B19]

description: W0059_C1WTA_DEAN_B19_AGGCAGAA-TATCCTCT_L008


title: Pax7 lineage - E14.5b2_26

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_34

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell9 [B18]

description: W0059_C1WTA_DEAN_B18_AGGCAGAA-CTCTCTAT_L008


title: Pax7 lineage - E14.5b2_25

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_24

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell17 [B25]

description: W0059_C1WTA_DEAN_B25_TCCTGAGC-GCGTAAGA_L008


title: Pax7 lineage - E14.5b2_32

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_23

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell8 [B17]

description: W0059_C1WTA_DEAN_B17_AGGCAGAA-GCGTAAGA_L008


title: Pax7 lineage - E14.5b2_20

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_21

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell7 [B16]

description: W0059_C1WTA_DEAN_B16_CGTACTAG-CTAAGCCT_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell5 [B14]

description: W0059_C1WTA_DEAN_B14_CGTACTAG-ACTGCATA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell6 [B15]

description: W0059_C1WTA_DEAN_B15_CGTACTAG-AAGGAGTA_L008


title: Pax7 lineage - E14.5b2_19

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell2 [B11]

description: W0059_C1WTA_DEAN_B11_CGTACTAG-TATCCTCT_L008


title: Pax7 lineage - E14.5b2_17

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_16

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_18

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa+10μMLPA_Cell3 [B12]

description: W0059_C1WTA_DEAN_B12_CGTACTAG-AGAGTAGA_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell4 [B13]

description: W0059_C1WTA_DEAN_B13_CGTACTAG-GTAAGGAG_L008


title: NHEKs_1.2mMCa+10μMLPA_Cell1 [B10]

description: W0059_C1WTA_DEAN_B10_CGTACTAG-CTCTCTAT_L008


title: NHEKs_1.2mMCa_Cell71 [A8]

description: W0059_C1WTA_DEAN_A8_TAAGGCGA-CTAAGCCT_L007


title: Pax7 lineage - E14.5b2_13

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_15

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_14

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa_Cell72 [A9]

description: W0059_C1WTA_DEAN_A9_CGTACTAG-GCGTAAGA_L007


title: NHEKs_1.2mMCa_Cell69 [A72]

description: W0059_C1WTA_DEAN_A72_GCTACGCT-CTAAGCCT_L007


title: NHEKs_1.2mMCa_Cell70 [A7]

description: W0059_C1WTA_DEAN_A7_TAAGGCGA-AAGGAGTA_L007


title: NHEKs_1.2mMCa_Cell66 [A6]

description: W0059_C1WTA_DEAN_A6_TAAGGCGA-ACTGCATA_L007


title: NHEKs_1.2mMCa_Cell68 [A71]

description: W0059_C1WTA_DEAN_A71_GCTACGCT-AAGGAGTA_L007


title: Pax7 lineage - E14.5b2_9

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_10

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_22

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_8

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_7

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_5

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_6

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa_Cell65 [A69]

description: W0059_C1WTA_DEAN_A69_GCTACGCT-GTAAGGAG_L007


title: Pax7 lineage - E14.5b2_11

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa_Cell62 [A66]

description: W0059_C1WTA_DEAN_A66_GCTACGCT-CTCTCTAT_L007


title: Pax7 lineage - E14.5b2_2

description:
ss2_filtered_count.csv
E14.5_b2_9


title: NHEKs_1.2mMCa_Cell64 [A68]

description: W0059_C1WTA_DEAN_A68_GCTACGCT-AGAGTAGA_L007


title: NHEKs_1.2mMCa_Cell63 [A67]

description: W0059_C1WTA_DEAN_A67_GCTACGCT-TATCCTCT_L007


title: NHEKs_1.2mMCa_Cell60 [A64]

description: W0059_C1WTA_DEAN_A64_CAGAGAGG-CTAAGCCT_L007


title: Pax7 lineage - E14.5b2_4

description:
ss2_filtered_count.csv
E14.5_b2_1


title: NHEKs_1.2mMCa_Cell59 [A63]

description: W0059_C1WTA_DEAN_A63_CAGAGAGG-AAGGAGTA_L007


title: NHEKs_1.2mMCa_Cell58 [A62]

description: W0059_C1WTA_DEAN_A62_CAGAGAGG-ACTGCATA_L007


title: NHEKs_1.2mMCa_Cell61 [A65]

description: W0059_C1WTA_DEAN_A65_GCTACGCT-GCGTAAGA_L007


title: Pax7 lineage - E14.5b2_12

description:
ss2_filtered_count.csv
E14.5_b2_1


title: Pax7 lineage - E14.5b2_1

description:
ss2_filtered_count.csv
E14.5_b2_9


title: NHEKs_1.2mMCa_Cell56 [A60]

description: W0059_C1WTA_DEAN_A60_CAGAGAGG-AGAGTAGA_L007


title: Pax7 lineage - E14.5b1_96

description:
ss2_filtered_count.csv
E14.5_b1_9

value: Plate 3


title: NHEKs_1.2mMCa_Cell55 [A5]

description: W0059_C1WTA_DEAN_A5_TAAGGCGA-GTAAGGAG_L007


title: Pax7 lineage - E14.5b1_94

description:
ss2_filtered_count.csv
E14.5_b1_9

value: embryonic cells


title: NHEKs_1.2mMCa_Cell57 [A61]

description: W0059_C1WTA_DEAN_A61_CAGAGAGG-GTAAGGAG_L007


title: Pax7 lineage - E14.5b1_95

description:
ss2_filtered_count.csv
E14.5_b1_9


title: Pax7 lineage - E14.5b1_93

description:
ss2_filtered_count.csv
E14.5_b1_9


title: NHEKs_1.2mMCa_Cell52 [A57]

description: W0059_C1WTA_DEAN_A57_CAGAGAGG-GCGTAAGA_L007


title: NHEKs_1.2mMCa_Cell67 [A70]

description: W0059_C1WTA_DEAN_A70_GCTACGCT-ACTGCATA_L007


title: Pax7 lineage - E14.5b2_3

description:
ss2_filtered_count.csv
E14.5_b2_9


title: Pax7 lineage - E14.5b1_91

description:
ss2_filtered_count.csv
E14.5_b1_9


title: NHEKs_1.2mMCa_Cell53 [A58]

description: W0059_C1WTA_DEAN_A58_CAGAGAGG-CTCTCTAT_L007


title: Pax7 lineage - E14.5b1_87

description:
ss2_filtered_count.csv
E14.5_b1_8


title: Pax7 lineage - E14.5b1_89

description:
ss2_filtered_count.csv
E14.5_b1_8


title: NHEKs_1.2mMCa_Cell51 [A56]

description: W0059_C1WTA_DEAN_A56_CTCTCTAC-CTAAGCCT_L007


title: NHEKs_1.2mMCa_Cell50 [A55]

description: W0059_C1WTA_DEAN_A55_CTCTCTAC-AAGGAGTA_L007


title: NHEKs_1.2mMCa_Cell47 [A52]

description: W0059_C1WTA_DEAN_A52_CTCTCTAC-AGAGTAGA_L007


title: Pax7 lineage - E14.5b1_88

description:
ss2_filtered_count.csv
E14.5_b1_8


title: Pax7 lineage - E14.5b1_86

description:
ss2_filtered_count.csv
E14.5_b1_8


title: NHEKs_1.2mMCa_Cell49 [A54]

description: W0059_C1WTA_DEAN_A54_CTCTCTAC-ACTGCATA_L007


title: Pax7 lineage - E14.5b1_90

description:
ss2_filtered_count.csv
E14.5_b1_9


title: Pax7 lineage - E14.5b1_85

description:
ss2_filtered_count.csv
E14.5_b1_8


title: Pax7 lineage - E14.5b1_92

description:
ss2_filtered_count.csv
E14.5_b1_9


title: NHEKs_1.2mMCa_Cell48 [A53]

description: W0059_C1WTA_DEAN_A53_CTCTCTAC-GTAAGGAG_L007


title: Pax7 lineage - E14.5b1_84

description:
ss2_filtered_count.csv
E14.5_b1_8


title: NHEKs_1.2mMCa_Cell46 [A51]

description: W0059_C1WTA_DEAN_A51_CTCTCTAC-TATCCTCT_L007


title: NHEKs_1.2mMCa_Cell44 [A4]

description: W0059_C1WTA_DEAN_A4_TAAGGCGA-AGAGTAGA_L007


title: NHEKs_1.2mMCa_Cell54 [A59]

description: W0059_C1WTA_DEAN_A59_CAGAGAGG-TATCCTCT_L007


title: NHEKs_1.2mMCa_Cell45 [A50]

description: W0059_C1WTA_DEAN_A50_CTCTCTAC-CTCTCTAT_L007


title: Pax7 lineage - E14.5b1_83

description:
ss2_filtered_count.csv
E14.5_b1_8


title: NHEKs_1.2mMCa_Cell41 [A47]

description: W0059_C1WTA_DEAN_A47_TAGGCATG-AAGGAGTA_L007


title: NHEKs_1.2mMCa_Cell43 [A49]

description: W0059_C1WTA_DEAN_A49_CTCTCTAC-GCGTAAGA_L007


title: Pax7 lineage - E14.5b1_80

description:
ss2_filtered_count.csv
E14.5_b1_8


title: Pax7 lineage - E14.5b1_79

description:
ss2_filtered_count.csv
E14.5_b1_7


title: Pax7 lineage - E14.5b1_82

description:
ss2_filtered_count.csv
E14.5_b1_8


title: Pax7 lineage - E14.5b1_81

description:
ss2_filtered_count.csv
E14.5_b1_8


title: NHEKs_1.2mMCa_Cell40 [A46]

description: W0059_C1WTA_DEAN_A46_TAGGCATG-ACTGCATA_L007


title: Pax7 lineage - E14.5b1_77

description:
ss2_filtered_count.csv
E14.5_b1_7


title: NHEKs_1.2mMCa_Cell39 [A45]

description: W0059_C1WTA_DEAN_A45_TAGGCATG-GTAAGGAG_L007


title: NHEKs_1.2mMCa_Cell42 [A48]

description: W0059_C1WTA_DEAN_A48_TAGGCATG-CTAAGCCT_L007


title: Pax7 lineage - E14.5b1_78

description:
ss2_filtered_count.csv
E14.5_b1_7


title: NHEKs_1.2mMCa_Cell37 [A43]

description: W0059_C1WTA_DEAN_A43_TAGGCATG-TATCCTCT_L007


title: NHEKs_1.2mMCa_Cell38 [A44]

description: W0059_C1WTA_DEAN_A44_TAGGCATG-AGAGTAGA_L007


title: NHEKs_1.2mMCa_Cell34 [A40]

description: W0059_C1WTA_DEAN_A40_GGACTCCT-CTAAGCCT_L007


title: NHEKs_1.2mMCa_Cell36 [A42]

description: W0059_C1WTA_DEAN_A42_TAGGCATG-CTCTCTAT_L007


title: Pax7 lineage - E14.5b1_73

description:
ss2_filtered_count.csv
E14.5_b1_7


title: NHEKs_1.2mMCa_Cell35 [A41]

description: W0059_C1WTA_DEAN_A41_TAGGCATG-GCGTAAGA_L007


title: Pax7 lineage - E14.5b1_74

description:
ss2_filtered_count.csv
E14.5_b1_7


title: NHEKs_1.2mMCa_Cell32 [A39]

description: W0059_C1WTA_DEAN_A39_GGACTCCT-AAGGAGTA_L007


title: Pax7 lineage - E14.5b1_75

description:
ss2_filtered_count.csv
E14.5_b1_7


title: Pax7 lineage - E14.5b1_72

description:
ss2_filtered_count.csv
E14.5_b1_7


title: Pax7 lineage - E14.5b1_70

description:
ss2_filtered_count.csv
E14.5_b1_7


title: Pax7 lineage - E14.5b1_71

description:
ss2_filtered_count.csv
E14.5_b1_7


title: Pax7 lineage - E14.5b1_69

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell31 [A38]

description: W0059_C1WTA_DEAN_A38_GGACTCCT-ACTGCATA_L007


title: NHEKs_1.2mMCa_Cell30 [A37]

description: W0059_C1WTA_DEAN_A37_GGACTCCT-GTAAGGAG_L007


title: NHEKs_1.2mMCa_Cell29 [A36]

description: W0059_C1WTA_DEAN_A36_GGACTCCT-AGAGTAGA_L007


title: Pax7 lineage - E14.5b1_67

description:
ss2_filtered_count.csv
E14.5_b1_6


title: Pax7 lineage - E14.5b1_76

description:
ss2_filtered_count.csv
E14.5_b1_7


title: Pax7 lineage - E14.5b1_68

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell28 [A35]

description: W0059_C1WTA_DEAN_A35_GGACTCCT-TATCCTCT_L007


title: NHEKs_1.2mMCa_Cell27 [A34]

description: W0059_C1WTA_DEAN_A34_GGACTCCT-CTCTCTAT_L007


title: Pax7 lineage - E14.5b1_66

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell26 [A33]

description: W0059_C1WTA_DEAN_A33_GGACTCCT-GCGTAAGA_L007


title: Pax7 lineage - E14.5b1_64

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell33 [A3]

description: W0059_C1WTA_DEAN_A3_TAAGGCGA-TATCCTCT_L007


title: Pax7 lineage - E14.5b1_65

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell25 [A32]

description: W0059_C1WTA_DEAN_A32_TCCTGAGC-CTAAGCCT_L007


title: Pax7 lineage - E14.5b1_63

description:
ss2_filtered_count.csv
E14.5_b1_6


title: Pax7 lineage - E14.5b1_62

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell24 [A31]

description: W0059_C1WTA_DEAN_A31_TCCTGAGC-AAGGAGTA_L007


title: NHEKs_1.2mMCa_Cell23 [A30]

description: W0059_C1WTA_DEAN_A30_TCCTGAGC-ACTGCATA_L007


title: NHEKs_1.2mMCa_Cell22 [A2]

description: W0059_C1WTA_DEAN_A2_TAAGGCGA-CTCTCTAT_L007


title: NHEKs_1.2mMCa_Cell21 [A29]

description: W0059_C1WTA_DEAN_A29_TCCTGAGC-GTAAGGAG_L007


title: Pax7 lineage - E14.5b1_61

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell19 [A27]

description: W0059_C1WTA_DEAN_A27_TCCTGAGC-TATCCTCT_L007


title: Pax7 lineage - E14.5b1_59

description:
ss2_filtered_count.csv
E14.5_b1_5


title: Pax7 lineage - E14.5b1_60

description:
ss2_filtered_count.csv
E14.5_b1_6


title: NHEKs_1.2mMCa_Cell20 [A28]

description: W0059_C1WTA_DEAN_A28_TCCTGAGC-AGAGTAGA_L007


title: Pax7 lineage - E14.5b1_56

description:
ss2_filtered_count.csv
E14.5_b1_5


title: Pax7 lineage - E14.5b1_58

description:
ss2_filtered_count.csv
E14.5_b1_5


title: Pax7 lineage - E14.5b1_57

description:
ss2_filtered_count.csv
E14.5_b1_5


title: NHEKs_1.2mMCa_Cell18 [A26]

description: W0059_C1WTA_DEAN_A26_TCCTGAGC-CTCTCTAT_L007


title: NHEKs_1.2mMCa_Cell17 [A25]

description: W0059_C1WTA_DEAN_A25_TCCTGAGC-GCGTAAGA_L007


title: Pax7 lineage - E14.5b1_55

description:
ss2_filtered_count.csv
E14.5_b1_5


title: NHEKs_1.2mMCa_Cell16 [A24]

description: W0059_C1WTA_DEAN_A24_AGGCAGAA-CTAAGCCT_L007


title: NHEKs_1.2mMCa_Cell15 [A23]

description: W0059_C1WTA_DEAN_A23_AGGCAGAA-AAGGAGTA_L007


title: Pax7 lineage - E14.5b1_53

description:
ss2_filtered_count.csv
E14.5_b1_5


title: NHEKs_1.2mMCa_Cell14 [A22]

description: W0059_C1WTA_DEAN_A22_AGGCAGAA-ACTGCATA_L007


title: Pax7 lineage - E14.5b1_52

description:
ss2_filtered_count.csv
E14.5_b1_5


title: 16_Tumour

type: protein

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description: GeoMx DSP Ncounter

data_processing: Ncounter data was exported and normalised by RUVseq. Differential expression was performed between primary and metastatic samples

label: DNA barcode

molecule: protein

source_name: FFPE Resected Tumour

extract_protocol: Commercial HNSCC TMA was analysed by GeoMX DSP. Antibody incubations and Ncounter readout were performed as per standardised Nanostring GeoMX DSP protocol

value: FFPE Resected Tumour

tag: type

value: Primary Only

tag: followup(days)

tag: current status

value: ALIVE


title: 17_Tumour

description: GeoMx DSP Ncounter

tag: tissue


title: 15_Tumour

description: GeoMx DSP Ncounter


title: NHEKs_1.2mMCa_Cell13 [A21]

description: W0059_C1WTA_DEAN_A21_AGGCAGAA-GTAAGGAG_L007


title: 15_Stroma

description: GeoMx DSP Ncounter


title: 16_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_50

description:
ss2_filtered_count.csv
E14.5_b1_5

tag: method

tag: sequencng type

value: Single-cell


title: Pax7 lineage - E14.5b1_51

description:
ss2_filtered_count.csv
E14.5_b1_5

tag: time point

tag: plate batch


title: NHEKs_1.2mMCa_Cell12 [A20]

description: W0059_C1WTA_DEAN_A20_AGGCAGAA-AGAGTAGA_L007


title: NHEKs_1.2mMCa_Cell10 [A19]

description: W0059_C1WTA_DEAN_A19_AGGCAGAA-TATCCTCT_L007


title: 19_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_49

description:
ss2_filtered_count.csv
E14.5_b1_4

tag: sequence batch

tag: medium


title: 17_Stroma

description: GeoMx DSP Ncounter


title: 18_Stroma

description: GeoMx DSP Ncounter

value: Nodal Met Only


title: 18_Tumour

description: GeoMx DSP Ncounter


title: NHEKs_1.2mMCa_Cell11 [A1]

description: W0059_C1WTA_DEAN_A1_TAAGGCGA-GCGTAAGA_L007

tag: cell type


title: NHEKs_1.2mMCa_Cell9 [A18]

description: W0059_C1WTA_DEAN_A18_AGGCAGAA-CTCTCTAT_L007


title: 20_Stroma

description: GeoMx DSP Ncounter


title: 20_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_48

description:
ss2_filtered_count.csv
E14.5_b1_4

tag: marker


title: 19_Tumour

description: GeoMx DSP Ncounter


title: 21_Stroma

description: GeoMx DSP Ncounter


title: 21_Tumour

description: GeoMx DSP Ncounter


title: NHEKs_1.2mMCa_Cell8 [A17]

description: W0059_C1WTA_DEAN_A17_AGGCAGAA-GCGTAAGA_L007


title: Pax7 lineage - E14.5b1_54

description:
ss2_filtered_count.csv
E14.5_b1_5


title: Pax7 lineage - E14.5b1_47

description:
ss2_filtered_count.csv
E14.5_b1_4


title: Pax7 lineage - E14.5b1_46

description:
ss2_filtered_count.csv
E14.5_b1_4


title: NHEKs_1.2mMCa_Cell7 [A16]

description: W0059_C1WTA_DEAN_A16_CGTACTAG-CTAAGCCT_L007


title: 22_Tumour

description: GeoMx DSP Ncounter

value: DEATH


title: 23_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_45

description:
ss2_filtered_count.csv
E14.5_b1_4


title: Pax7 lineage - E14.5b1_44

description:
ss2_filtered_count.csv
E14.5_b1_4


title: NHEKs_1.2mMCa_Cell6 [A15]

description: W0059_C1WTA_DEAN_A15_CGTACTAG-AAGGAGTA_L007


title: NHEKs_1.2mMCa_Cell5 [A14]

description: W0059_C1WTA_DEAN_A14_CGTACTAG-ACTGCATA_L007


title: 24_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_43

description:
ss2_filtered_count.csv
E14.5_b1_4


title: 24_Stroma

description: GeoMx DSP Ncounter


title: NHEKs_1.2mMCa_Cell4 [A13]

description: W0059_C1WTA_DEAN_A13_CGTACTAG-GTAAGGAG_L007


title: Pax7 lineage - E14.5b1_41

description:
ss2_filtered_count.csv
E14.5_b1_4


title: 27_Tumour

description: GeoMx DSP Ncounter


title: 25_Stroma

description: GeoMx DSP Ncounter


title: 28_Tumour

description: GeoMx DSP Ncounter


title: 22_Stroma

description: GeoMx DSP Ncounter


title: 25_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_40

description:
ss2_filtered_count.csv
E14.5_b1_4


title: NHEKs_1.2mMCa_Cell1 [A10]

description: W0059_C1WTA_DEAN_A10_CGTACTAG-CTCTCTAT_L007


title: 29_Tumour

description: GeoMx DSP Ncounter


title: 28_Stroma

description: GeoMx DSP Ncounter


title: 23_Stroma

description: GeoMx DSP Ncounter


title: 29_Stroma

description: GeoMx DSP Ncounter


title: A375_CRTC3KO2_FSK

first: Jelena

last: Ostojic

address: 10010 N Torrey Pines Road

department: PBL-M

institute: Salk Institute for Biological Studies

data_processing:
High-throughput sequencing was performed on the HiSeq 2500 system (Illumina) at a run configuration of single read 50 bases.
Image analysis and base calling were done with Illumina CASAVA-1.8.2.on HiSeq 2500 system and sequenced reads were quality-tested using FASTQC.
FASTQ files were aligned to the mouse mm10 genome builds using STAR.
Raw counts and differential expression analyses were preformed using HOMER (analyzeRepeats.pl with options –raw -count exons -condenseGenes; getDiffExpression.pl using DESeq2)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw exon counts for every gene and every sample.

source_name: A375 human melanoma cell line

growth_protocol: Cells were grown to 70% confluency on 10cm dishes.

extract_protocol:
Cels were collected in Trizol reagent for Trizol-chloroform RNA extraction. RNA extracts were further purified and DNAse treated by using RNAeasy Qiagen columns (DNAse 79254, Qiagen). 1µg RNA was used for further analysis.
TruSeq stranded mRNA Sample Preparation Kit v2 (RS-122-2001) was used according to Illumina protocols.

treatment_protocol: Cells were treated with DMSO or 1µM FSK for 1h.

value: Forskolin, 1h

tag: genotype

value: CRTC3 -/-


title: Pax7 lineage - E14.5b1_42

description:
ss2_filtered_count.csv
E14.5_b1_4


title: Pax7 lineage - E14.5b1_38

description:
ss2_filtered_count.csv
E14.5_b1_3


title: NHEKs_1.2mMCa_Cell3 [A12]

description: W0059_C1WTA_DEAN_A12_CGTACTAG-AGAGTAGA_L007


title: A375_CRTC3KO1_FSK


title: 26_Tumour

description: GeoMx DSP Ncounter


title: 30_Tumour

description: GeoMx DSP Ncounter


title: 30_Stroma

description: GeoMx DSP Ncounter


title: NHEKs_1.2mMCa_Cell2 [A11]

description: W0059_C1WTA_DEAN_A11_CGTACTAG-TATCCTCT_L007


title: 31_Tumour

description: GeoMx DSP Ncounter


title: 26_Stroma

description: GeoMx DSP Ncounter


title: 27_Stroma

description: GeoMx DSP Ncounter


title: 31_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_36

description:
ss2_filtered_count.csv
E14.5_b1_3


title: A375_CTRL1_FSK

value: Wild-type


title: 32_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_35

description:
ss2_filtered_count.csv
E14.5_b1_3


title: Pax7 lineage - E14.5b1_39

description:
ss2_filtered_count.csv
E14.5_b1_3


title: 33_Stroma

description: GeoMx DSP Ncounter


title: 32_Stroma

description: GeoMx DSP Ncounter


title: A375_CRTC3KO2_DMSO

value: DMSO (vehicle), 1h


title: 34_Tumour

description: GeoMx DSP Ncounter


title: A375_CRTC3KO1_DMSO


title: 34_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_33

description:
ss2_filtered_count.csv
E14.5_b1_3


title: Pax7 lineage - E14.5b1_32

description:
ss2_filtered_count.csv
E14.5_b1_3


title: 36_Tumour

description: GeoMx DSP Ncounter


title: 35_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_37

description:
ss2_filtered_count.csv
E14.5_b1_3


title: A375_CTRL1_DMSO


title: A375_CTRL2_FSK


title: A375_CTRL2_DMSO


title: CD45+ TILs [G5_T1]

city: Lausanne

first: Jesus

last: Corria-Osorio

state: Vaud

address: Chemin des Boveresses 155

department: Department of Fundamental Oncology

country: Switzerland

institute: Ludwig Institute for Cancer Research. Lausanne Branch. UNIL

library_source: transcriptomic single cell

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina) and primary data analysis performed with Cell Ranger (version 2.2.0) and aligning to the GRC38 genome build and genome annotation release 94 from Ensembl.
Assembly: GRCm38
Supplementary files format and content: QC filtered cell ranger output consists of gene by barcode (cell) count matrices in sparse matrix market format (mtx) and corresponding row and column annotation in *genes.tsv and *barcode.tsv files

source_name: Tumor infiltrating immune cells

extract_protocol:
RNA from snap frozen tissue biopsies was extracted using the RNA easy kit (Qiagen, Hilden, Germany). RNA quality was assessed using the Fragment Analyzer (Advances Analytical Technologies Inc., Ankeny, USA). RNA-seq libraries were prepared from 250 ng of total RNA. The RNA samples were depleted for ribosomal RNAs with the Illumina TruSeq Stranded Total RNA Gold kit. Ribosomal-RNA depleted RNA was then converted in cDNA and amplified with the kit Nugen Ovation® RNA-Seq System V2. It was used to generate sequencing libraries with the Illumina TruSeq DNA Nano kit.
A Chromium Next GEM Chip G (10X genomics) was loaded with the appropriate number of cells, and the sequencing libraries prepared with the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 following the manufacturer’s recommendations. Briefly, an emulsion encapsulating single cells, reverse transcription reagents and cell barcoding oligonucleotides was generated. After the actual reverse transcription step, the emulsion was broken, and double stranded cDNA generated and amplified in a bulk reaction.
For 5’ gene expression library this cDNA was fragmented, ligated to a sequencing adaptor, and PCR amplified. For V(D)J library preparation, a similar approach was followed except that 2 steps of PCR based V(D)J target enrichment were performed prior to fragmentation.  Libraries were quantified by a fluorimetric method and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 140 to 165 pM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 PE Cluster Kit reagents. Sequencing was performed on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents according to 10X Genomics recommendations (26 cycles read1, 8 cycles i7 index read, and 91 cycles read2).

tag: strain

value: CD45+ Tumor infiltrating immune cells were sorted, which includes the following populations:CD8+ T cells, CD4+ T cells, NK cells, NKT and Myeloid cells

value: Non-Treated (G5)


title: 33_Tumour

description: GeoMx DSP Ncounter


title: 37_Stroma

description: GeoMx DSP Ncounter


title: 36_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_31

description:
ss2_filtered_count.csv
E14.5_b1_3


title: 37_Tumour

description: GeoMx DSP Ncounter


title: 35_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_30

description:
ss2_filtered_count.csv
E14.5_b1_3


title: 38_Tumour

description: GeoMx DSP Ncounter


title: CD45+ TILs [G4_T3]

value: PD1d/2V/33-secreting OT1 (G4)


title: 39_Stroma

description: GeoMx DSP Ncounter


title: 38_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_34

description:
ss2_filtered_count.csv
E14.5_b1_3


title: CD45+ TILs [G4_T2]


title: Pax7 lineage - E14.5b1_29

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 40_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_28

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 40_Stroma

description: GeoMx DSP Ncounter


title: 41_Tumour

description: GeoMx DSP Ncounter

value: Matched Nodal-Met


title: CD45+ TILs [G4_T1]


title: Pax7 lineage - E14.5b1_27

description:
ss2_filtered_count.csv
E14.5_b1_2

value: Batch 3


title: 41_Stroma

description: GeoMx DSP Ncounter


title: CD45+ TILs [G3_T2]

value: PD1d/33-secreting OT1 (G3)


title: Pax7 lineage - E14.5b1_25

description:
ss2_filtered_count.csv
E14.5_b1_2

value: embryonic cells

value: Plate 3


title: 39_Tumour

description: GeoMx DSP Ncounter

value: FFPE Resected Tumour


title: CD45+ TILs [G2_T2]

value: PD1d/IL2V-secreting OT1 (G2)


title: Pax7 lineage - E14.5b1_24

description:
ss2_filtered_count.csv
E14.5_b1_2

value: Single-cell


title: 43_Tumour

description: GeoMx DSP Ncounter

value: Nodal Met Only


title: Pax7 lineage - E14.5b1_23

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 42_Tumour

description: GeoMx DSP Ncounter

value: Matched Primary

value: ALIVE


title: 43_Stroma

description: GeoMx DSP Ncounter

value: DEATH


title: 42_Stroma

description: GeoMx DSP Ncounter


title: CD45+ TILs [G1_T2]

value: Treated with ACT using Untransduced OT1 T cells (G1)


title: CD45+ TILs [G1_T1]


title: Pax7 lineage - E14.5b1_22

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 44_Tumour

description: GeoMx DSP Ncounter


title: RNA-seq data of Rattus replicate 1

city: Chengdu

first: Mengnan

last: He

address: Huimin road 211#

country: China

institute: Sichuan Agriculture University

description:
rat_quant_TPM.txt
ployA
PE125
Specific

data_processing:
RNA sequencing reads were aligned to reference genomes applying the STAR (2.6.0c) (Dobin, A. et al.).
Transcript quantification was conducted with kallisto (0.44.0) (Bray, N. L. et al.)
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

organism: Rattus norvegicus

source_name: Rat Liver Fibroblasts

growth_protocol: Most of the fibroblasts were grown in Dulbecco's Modified Eagle Medium (DMEM, 11995-065, Gibco) containing 10% Fetal Bovine Serum (FBS, 10099-141, Gibco) and 1× penicillin/streptomycin (P/S, 15140-122, Gibco), incubated at 37 °C in 5% CO2.

extract_protocol:
total RNA  of each cell sample was extracted by using the Trizol  (Invitrogen).
We used an rRNA depletion protocol (Epicentre Ribo-zero™ rRNA Removal Kit, Epicentre, USA) or  mRNA capture protocol (Oligo (dT) magnetic beads, Promega, USA) coupled with the strand specific or non-specific RNA-seq library protocol  for each sample.

value: Fibroblasts

tag: tissue source

value: Liver

tag: age

value: unknown


title: 44_Stroma

description: GeoMx DSP Ncounter


title: 46_Tumour

description: GeoMx DSP Ncounter


title: 46_Stroma

description: GeoMx DSP Ncounter


title: Hi-C data of Rattus replicate 1

data_processing:
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Hiclib.
TADs were identified using DomainCaller
Compartment A/B identification at 20-Kb was performed by using A-B index value which represented the comparative likelihood of a sequence interacting with A or B (100-Kb) as described previously (Rowley, M. J. et al. ). Bins at 20-Kb with positive values (more association with A at 100-Kb) were called as A compartments, while 20-Kb bins with negative values (more association with B at 100-Kb) were called as B compartments. These positive or negative values were termed as A-B index values.
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

extract_protocol:
Briefly, about 20 to 25 million cells were crosslinked with 2% formaldehyde for 10 min at room temperature (20–25 °C), then used glycine to quench the formaldehyde in a final concentration of 0.25 M at room temperature for 5 min, and subsequently on ice for 15 min.
Dilution Hi-C was performed as a previous study (Lieberman-Aiden, E. et al. ). Nuclei were permeabilized by a Dounce homogenizer in the presence of cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1× protease inhibitor solution). DNA was digested with 400 units of HindⅢ, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume (8 mL). After reversal of cross-links, ligated DNA was puriﬁed and prepped for Illumina sequencing.


title: 45_Tumour

description: GeoMx DSP Ncounter


title: 47_Tumour

description: GeoMx DSP Ncounter


title: 47_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_26

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 48_Tumour

description: GeoMx DSP Ncounter


title: 48_Stroma

description: GeoMx DSP Ncounter


title: 45_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_19

description:
ss2_filtered_count.csv
E14.5_b1_1


title: Pax7 lineage - E14.5b1_20

description:
ss2_filtered_count.csv
E14.5_b1_2


title: Pax7 lineage - E14.5b1_17

description:
ss2_filtered_count.csv
E14.5_b1_1


title: Pax7 lineage - E14.5b1_18

description:
ss2_filtered_count.csv
E14.5_b1_1


title: 50_Tumour

description: GeoMx DSP Ncounter


title: 49_Tumour

description: GeoMx DSP Ncounter


title: 49_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_21

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 52_Tumour

description: GeoMx DSP Ncounter


title: 50_Stroma

description: GeoMx DSP Ncounter


title: 38

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Homo sapiens (hsa, TXID: 9606)
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)
Assembly: GRCh38.p12

source_name: Gel-filtrated platelets

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Cat. 217004).
Libraries were prepared using the CleanTag small RNA library preparation kit (Cat. L-3206-24, TriLink Biotechnologies).

tag: sample type

value: Cell pellet

tag: platelet activation

value: basal

tag: donor


title: 40

value: Supernatant

value: stimulated


title: 35

source_name: Washed platelets


title: 34

source_name: PPP

value: Plasma


title: 37


title: 33

source_name: PRP


title: Pax7 lineage - E14.5b1_15

description:
ss2_filtered_count.csv
E14.5_b1_1

value: embryonic cells

value: Plate 3

value: Batch 3


title: Pax7 lineage - E14.5b1_16

description:
ss2_filtered_count.csv
E14.5_b1_1

value: Single-cell


title: 32

source_name: Buffy coat


title: 51_Tumour

description: GeoMx DSP Ncounter

value: FFPE Resected Tumour

tag: type

value: Nodal Met Only

tag: followup(days)

tag: current status


title: 51_Stroma

description: GeoMx DSP Ncounter

tag: tissue

value: ALIVE


title: Pax7 lineage - E14.5b1_14

description:
ss2_filtered_count.csv
E14.5_b1_1

tag: method

tag: sequencng type

tag: time point


title: 53_Tumour

description: GeoMx DSP Ncounter

value: Matched Nodal-Met

value: DEATH


title: 53_Stroma

description: GeoMx DSP Ncounter


title: 52_Stroma

description: GeoMx DSP Ncounter


title: 31

source_name: Erythrocytes


title: 54_Stroma

description: GeoMx DSP Ncounter

value: Matched Primary


title: 55_Stroma

description: GeoMx DSP Ncounter


title: 55_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_13

description:
ss2_filtered_count.csv
E14.5_b1_1

source_name: Mouse embryonic cells

tag: plate batch

tag: sequence batch

tag: medium


title: 56_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_12

description:
ss2_filtered_count.csv
E14.5_b1_1

tag: marker


title: 30


title: 28


title: Pax7 lineage - E14.5b1_10

description:
ss2_filtered_count.csv
E14.5_b1_1


title: Pax7 lineage - E14.5b1_9

description:
ss2_filtered_count.csv
E14.5_b1_9


title: 58_Tumour

description: GeoMx DSP Ncounter


title: 57_Stroma

description: GeoMx DSP Ncounter

value: Primary Only


title: 57_Tumour

description: GeoMx DSP Ncounter


title: 56_Stroma

description: GeoMx DSP Ncounter


title: 54_Tumour

description: GeoMx DSP Ncounter


title: 60_Stroma

description: GeoMx DSP Ncounter


title: 60_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_8

description:
ss2_filtered_count.csv
E14.5_b1_8


title: 58_Stroma

description: GeoMx DSP Ncounter


title: 59_Stroma

description: GeoMx DSP Ncounter


title: 61_Tumour

description: GeoMx DSP Ncounter


title: 24


title: Pax7 lineage - E14.5b1_7

description:
ss2_filtered_count.csv
E14.5_b1_7


title: 23


title: 62_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_6

description:
ss2_filtered_count.csv
E14.5_b1_6


title: 22


title: 62_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_11

description:
ss2_filtered_count.csv
E14.5_b1_1


title: 61_Stroma

description: GeoMx DSP Ncounter


title: 27


title: 63_Tumour

description: GeoMx DSP Ncounter


title: 21


title: 25


title: 59_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_5

description:
ss2_filtered_count.csv
E14.5_b1_5


title: 63_Stroma

description: GeoMx DSP Ncounter


title: 64_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_4

description:
ss2_filtered_count.csv
E14.5_b1_4


title: 64_Tumour

description: GeoMx DSP Ncounter


title: 20


title: 18


title: Pax7 lineage - E14.5b1_3

description:
ss2_filtered_count.csv
E14.5_b1_3


title: 65_Tumour

description: GeoMx DSP Ncounter


title: 17


title: Pax7 lineage - E14.5b1_2

description:
ss2_filtered_count.csv
E14.5_b1_2


title: 65_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E14.5b1_1

description:
ss2_filtered_count.csv
E14.5_b1_1


title: 15


title: 66_Tumour

description: GeoMx DSP Ncounter


title: 67_Tumour

description: GeoMx DSP Ncounter


title: 14


title: 67_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_96

description:
ss2_filtered_count.csv
E12.5_b2_9

value: Plate 2

value: Batch 2


title: Pax7 lineage - E12.5b2_95

description:
ss2_filtered_count.csv
E12.5_b2_9


title: 1_Stroma

description: GeoMx DSP Ncounter


title: 68_Stroma

description: GeoMx DSP Ncounter


title: 68_Tumour

description: GeoMx DSP Ncounter


title: 13


title: 12

value: Cell pellet


title: Pax7 lineage - E12.5b2_93

description:
ss2_filtered_count.csv
E12.5_b2_9


title: 2_Stroma

description: GeoMx DSP Ncounter


title: 1_Tumour

description: GeoMx DSP Ncounter


title: 3_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_92

description:
ss2_filtered_count.csv
E12.5_b2_9


title: 2_Tumour

description: GeoMx DSP Ncounter


title: 3_Tumour

description: GeoMx DSP Ncounter


title: 4_Tumour

description: GeoMx DSP Ncounter


title: 11


title: 8

value: basal


title: 66_Stroma

description: GeoMx DSP Ncounter