title: HE8W_EVT4_sc11

description: mRNA with polyA tail


title: HE8W_EVT4_sc10

status: Public on Jul 24 2018

type: SRA

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

country: China

institute: Peking University

description: mRNA with polyA tail

library_source: transcriptomic

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Read 2 was used to obtain the cell barcodes to further split the reads according to the cell IDs (barcode) and the same time recorded the UMI sequences
Read 1 was picked in each cell and these raw reads were trimmed to remove TSO or polyA sequence
Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data
TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: TPM (transcripts-per-million mapped reads) data was calculated as the total UMIs for a genes to be divided by the sum of UMIs from each cell and then multiply by 1,000,000

molecule: total RNA

organism: Homo sapiens

source_name: Extravillous trophoblast of Week 8

extract_protocol:
Chrion were scraped from human  placenta and the remaining villi were collected and minced into small pieces. The tissue were digested with an enzyme cocktail (0.125% trypsin 0.04% Dnase and 0.05% type Ⅳcollagenase) for 8 min twice at 37 ℃. Cell suspension were collected by filtering the ezyme mixture with 70 μm cell strainer and the enzyme reaction were stopped by addition of 5% DMEM. cells were centrifuged at 1200 g at 4 ℃ on a percoll gradient (7 layers: 10%, 20%, 30%, 40%, 50%, 60% and 70%) and cells from 30% - 50% percoll gradient were collected and washed with DMEM. EVT and CTB were sorted with MACS with PE-conjucted HLA-G and CDH1 antibody combined with anti-PE beads,STB were purified with mouth pipette based on their big size from the cell population and the remaning HLA-G and CDH1 double negative cells were stromal cells. For isolation of EVT from the basal plate of the 24 w placenta, basal plate were scaped from the placenta, minced and  digested with the method as described above,finally 24 w EVT were purified by MACs with HLA-G antibody.
the single cells were picked into 2ul cell lysis buffer using mouse pipet, then the transcriptome was amplified by modified smart-seq2 protocol which added in barcode for each cell. the amplified cDNAs were sheared into 300bp  fragments, the 3' end of the cDNAs were enriched to build library with KAPA Hyper Prep Kits for Illumina

treatment_protocol: human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h

tag: cell type

value: Extravillous trophoblast

tag: cell population

value: HLA-G+

tag: Stage

value: Week 8


title: HE8W_EVT4_sc27

description: mRNA with polyA tail


title: HE8W_EVT3_sc81

description: mRNA with polyA tail


title: HE8W_EVT3_sc77

description: mRNA with polyA tail


title: HE8W_EVT3_sc78

description: mRNA with polyA tail


title: HE8W_EVT3_sc79

description: mRNA with polyA tail


title: HE8W_EVT3_sc75

description: mRNA with polyA tail


title: HE8W_EVT3_sc76

description: mRNA with polyA tail


title: HE8W_EVT3_sc74

description: mRNA with polyA tail


title: HE8W_EVT4_sc2

description: mRNA with polyA tail


title: HE8W_EVT4_sc16

description: mRNA with polyA tail


title: HE8W_EVT4_sc15

description: mRNA with polyA tail


title: HE8W_EVT3_sc72

description: mRNA with polyA tail


title: HE8W_EVT4_sc13

description: mRNA with polyA tail


title: HE8W_EVT3_sc71

description: mRNA with polyA tail


title: HE8W_EVT3_sc68

description: mRNA with polyA tail


title: HE8W_EVT3_sc69

description: mRNA with polyA tail


title: HE8W_EVT3_sc67

description: mRNA with polyA tail


title: HE8W_EVT3_sc65

description: mRNA with polyA tail


title: HE8W_EVT3_sc66

description: mRNA with polyA tail


title: HE8W_EVT3_sc64

description: mRNA with polyA tail


title: HE8W_EVT3_sc73

description: mRNA with polyA tail


title: HE8W_EVT3_sc63

description: mRNA with polyA tail


title: HE8W_EVT3_sc62

description: mRNA with polyA tail


title: HE8W_EVT3_sc70

description: mRNA with polyA tail


title: HE8W_EVT3_sc60

description: mRNA with polyA tail


title: HE8W_EVT3_sc61

description: mRNA with polyA tail


title: HE8W_EVT3_sc57

description: mRNA with polyA tail


title: HE8W_EVT3_sc56

description: mRNA with polyA tail


title: HE8W_EVT3_sc59

description: mRNA with polyA tail


title: HE8W_EVT3_sc54

description: mRNA with polyA tail


title: HE8W_EVT3_sc51

description: mRNA with polyA tail


title: HE8W_EVT3_sc58

description: mRNA with polyA tail


title: HE8W_EVT3_sc53

description: mRNA with polyA tail


title: HE8W_EVT3_sc50

description: mRNA with polyA tail


title: HE8W_EVT3_sc52

description: mRNA with polyA tail


title: HE8W_EVT3_sc80

description: mRNA with polyA tail


title: HE8W_EVT2_sc81

description: mRNA with polyA tail


title: HE8W_EVT2_sc78

description: mRNA with polyA tail


title: HE8W_EVT2_sc76

description: mRNA with polyA tail


title: HE8W_EVT2_sc75

description: mRNA with polyA tail


title: HE8W_EVT2_sc72

description: mRNA with polyA tail


title: HE8W_EVT2_sc73

description: mRNA with polyA tail


title: HE8W_EVT2_sc79

description: mRNA with polyA tail


title: HE8W_EVT2_sc70

description: mRNA with polyA tail


title: HE8W_EVT2_sc68

description: mRNA with polyA tail


title: HE8W_EVT2_sc77

description: mRNA with polyA tail


title: HE8W_EVT2_sc80

description: mRNA with polyA tail


title: HE8W_EVT3_sc55

description: mRNA with polyA tail


title: HE8W_EVT2_sc74

description: mRNA with polyA tail


title: HE8W_EVT2_sc71

description: mRNA with polyA tail


title: HE8W_EVT2_sc67

description: mRNA with polyA tail


title: HE8W_EVT4_sc12

description: mRNA with polyA tail


title: HE8W_EVT2_sc66

description: mRNA with polyA tail


title: HE8W_EVT2_sc60

description: mRNA with polyA tail


title: HE8W_EVT2_sc64

description: mRNA with polyA tail


title: HE8W_EVT2_sc65

description: mRNA with polyA tail


title: HE8W_EVT2_sc62

description: mRNA with polyA tail


title: HE8W_EVT2_sc63

description: mRNA with polyA tail


title: HE8W_EVT2_sc59

description: mRNA with polyA tail


title: HE8W_EVT2_sc56

description: mRNA with polyA tail


title: HE8W_EVT2_sc61

description: mRNA with polyA tail


title: HE8W_EVT2_sc55

description: mRNA with polyA tail


title: HE8W_EVT2_sc58

description: mRNA with polyA tail


title: HE8W_EVT2_sc54

description: mRNA with polyA tail


title: HE8W_EVT2_sc69

description: mRNA with polyA tail


title: HE8W_EVT2_sc51

description: mRNA with polyA tail


title: HE8W_EVT2_sc50

description: mRNA with polyA tail


title: HE8W_EVT2_sc52

description: mRNA with polyA tail


title: HE8W_STB_sc79

description: mRNA with polyA tail

source_name: Syncytiotrophoblast of Week 8

value: Syncytiotrophoblast


title: HE8W_STB_sc81

description: mRNA with polyA tail


title: HE8W_STB_sc80

description: mRNA with polyA tail


title: HE8W_STB_sc78

description: mRNA with polyA tail


title: HE8W_STB_sc76

description: mRNA with polyA tail


title: HE8W_STB_sc77

description: mRNA with polyA tail


title: HE8W_EVT2_sc57

description: mRNA with polyA tail


title: HE8W_STB_sc74

description: mRNA with polyA tail


title: HE8W_STB_sc73

description: mRNA with polyA tail


title: HE8W_STB_sc71

description: mRNA with polyA tail


title: HE8W_STB_sc68

description: mRNA with polyA tail


title: HE8W_STB_sc70

description: mRNA with polyA tail


title: HE8W_STB_sc69

description: mRNA with polyA tail


title: HE8W_EVT2_sc53

description: mRNA with polyA tail


title: HE8W_STB_sc67

description: mRNA with polyA tail


title: HE8W_STB_sc64

description: mRNA with polyA tail


title: HE8W_STB_sc63

description: mRNA with polyA tail


title: HE8W_STB_sc66

description: mRNA with polyA tail


title: HE8W_STB_sc59

description: mRNA with polyA tail


title: HE8W_STB_sc61

description: mRNA with polyA tail


title: HE8W_STB_sc60

description: mRNA with polyA tail


title: HE8W_STB_sc62

description: mRNA with polyA tail


title: HE8W_STB_sc58

description: mRNA with polyA tail


title: HE8W_STB_sc57

description: mRNA with polyA tail


title: HE8W_STB_sc55

description: mRNA with polyA tail


title: HE8W_STB_sc54

description: mRNA with polyA tail


title: HE8W_STB_sc56

description: mRNA with polyA tail


title: HE8W_STB_sc72

description: mRNA with polyA tail


title: HE8W_STB_sc52

description: mRNA with polyA tail


title: HE8W_STB_sc53

description: mRNA with polyA tail


title: HE8W_STB_sc75

description: mRNA with polyA tail


title: HE8W_EVT4_sc33

description: mRNA with polyA tail


title: HE8W_STB_sc65

description: mRNA with polyA tail


title: HE8W_STB_sc51

description: mRNA with polyA tail


title: HE8W_STB0_sc7

description: mRNA with polyA tail


title: HE8W_STB0_sc9

description: mRNA with polyA tail


title: HE8W_STB_sc50

description: mRNA with polyA tail


title: HE8W_STB0_sc8

description: mRNA with polyA tail


title: HE8W_STB0_sc6

description: mRNA with polyA tail


title: HE8W_STB0_sc5

description: mRNA with polyA tail


title: HE8W_STB0_sc32

description: mRNA with polyA tail


title: HE8W_STB0_sc4

description: mRNA with polyA tail


title: HE8W_STB0_sc3

description: mRNA with polyA tail


title: HE8W_STB0_sc28

description: mRNA with polyA tail


title: HE8W_STB0_sc30

description: mRNA with polyA tail


title: HE8W_STB0_sc29

description: mRNA with polyA tail


title: HE8W_STB0_sc31

description: mRNA with polyA tail


title: HE8W_STB0_sc27

description: mRNA with polyA tail


title: HE8W_STB0_sc25

description: mRNA with polyA tail


title: HE8W_STB0_sc26

description: mRNA with polyA tail


title: HE8W_STB0_sc23

description: mRNA with polyA tail


title: HE8W_STB0_sc24

description: mRNA with polyA tail


title: HE8W_STB0_sc2

description: mRNA with polyA tail


title: HE8W_STB0_sc21

description: mRNA with polyA tail


title: HE8W_STB0_sc20

description: mRNA with polyA tail


title: HE8W_STB0_sc22

description: mRNA with polyA tail


title: HE8W_STB0_sc19

description: mRNA with polyA tail


title: HE8W_STB0_sc18

description: mRNA with polyA tail


title: HE8W_STB0_sc16

description: mRNA with polyA tail


title: HE8W_STB0_sc17

description: mRNA with polyA tail


title: HE8W_STB0_sc15

description: mRNA with polyA tail


title: HE8W_STB0_sc14

description: mRNA with polyA tail


title: HE8W_STB0_sc13

description: mRNA with polyA tail


title: HE8W_STB0_sc12

description: mRNA with polyA tail


title: HE8W_STB0_sc1

description: mRNA with polyA tail


title: HE8W_STB0_sc11

description: mRNA with polyA tail


title: HE8W_STB0_sc10

description: mRNA with polyA tail


title: HE8W_CTB4_sc90

description: mRNA with polyA tail

source_name: Cytotrophoblast of Week 8

value: Cytotrophoblast


title: HE8W_CTB4_sc87

description: mRNA with polyA tail


title: HE8W_CTB4_sc86

description: mRNA with polyA tail


title: HE8W_CTB4_sc85

description: mRNA with polyA tail


title: HE8W_CTB4_sc88

description: mRNA with polyA tail


title: HE8W_CTB4_sc83

description: mRNA with polyA tail


title: HE8W_CTB4_sc82

description: mRNA with polyA tail


title: HE8W_CTB4_sc79

description: mRNA with polyA tail


title: HE8W_CTB4_sc77

description: mRNA with polyA tail


title: HE8W_CTB4_sc78

description: mRNA with polyA tail


title: HE8W_CTB4_sc84

description: mRNA with polyA tail


title: HE8W_CTB4_sc81

description: mRNA with polyA tail


title: HE8W_CTB4_sc75

description: mRNA with polyA tail


title: HE8W_CTB4_sc74

description: mRNA with polyA tail


title: HE8W_CTB4_sc73

description: mRNA with polyA tail


title: HE8W_CTB4_sc76

description: mRNA with polyA tail


title: HE8W_CTB4_sc72

description: mRNA with polyA tail


title: HE8W_CTB4_sc71

description: mRNA with polyA tail


title: HE8W_CTB4_sc68

description: mRNA with polyA tail


title: HE8W_CTB4_sc66

description: mRNA with polyA tail


title: HE8W_CTB4_sc69

description: mRNA with polyA tail


title: HE8W_CTB4_sc67

description: mRNA with polyA tail


title: HE8W_CTB4_sc89

description: mRNA with polyA tail


title: HE8W_CTB4_sc63

description: mRNA with polyA tail


title: HE8W_CTB4_sc61

description: mRNA with polyA tail


title: HE8W_CTB4_sc65

description: mRNA with polyA tail


title: HE8W_CTB4_sc70

description: mRNA with polyA tail


title: HE8W_CTB4_sc64

description: mRNA with polyA tail


title: HE8W_CTB4_sc80

description: mRNA with polyA tail


title: HE8W_CTB4_sc57

description: mRNA with polyA tail


title: HE8W_CTB4_sc56

description: mRNA with polyA tail


title: HE8W_EVT4_sc44

description: mRNA with polyA tail


title: HE8W_CTB4_sc59

description: mRNA with polyA tail


title: HE8W_CTB4_sc55

description: mRNA with polyA tail


title: HE8W_CTB4_sc52

description: mRNA with polyA tail


title: HE8W_CTB4_sc60

description: mRNA with polyA tail


title: HE8W_CTB4_sc54

description: mRNA with polyA tail


title: HE8W_CTB4_sc58

description: mRNA with polyA tail


title: HE8W_CTB4_sc50

description: mRNA with polyA tail


title: HE8W_CTB4_sc46

description: mRNA with polyA tail


title: HE8W_CTB4_sc47

description: mRNA with polyA tail


title: HE8W_CTB4_sc44

description: mRNA with polyA tail


title: HE8W_CTB4_sc45

description: mRNA with polyA tail


title: HE8W_CTB4_sc49

description: mRNA with polyA tail


title: HE8W_CTB3_sc89

description: mRNA with polyA tail


title: HE8W_CTB4_sc43

description: mRNA with polyA tail


title: HE8W_CTB3_sc9

description: mRNA with polyA tail


title: HE8W_CTB3_sc88

description: mRNA with polyA tail


title: HE8W_CTB3_sc87

description: mRNA with polyA tail


title: HE8W_CTB3_sc86

description: mRNA with polyA tail


title: HE8W_CTB3_sc84

description: mRNA with polyA tail


title: HE8W_CTB3_sc83

description: mRNA with polyA tail


title: HE8W_CTB3_sc82

description: mRNA with polyA tail


title: HE8W_CTB3_sc85

description: mRNA with polyA tail


title: HE8W_CTB4_sc51

description: mRNA with polyA tail


title: HE8W_CTB4_sc48

description: mRNA with polyA tail


title: HE8W_CTB3_sc81

description: mRNA with polyA tail


title: HE8W_CTB3_sc80

description: mRNA with polyA tail


title: HE8W_CTB3_sc8

description: mRNA with polyA tail


title: HE8W_CTB3_sc75

description: mRNA with polyA tail


title: HE8W_CTB3_sc77

description: mRNA with polyA tail


title: HE8W_CTB3_sc79

description: mRNA with polyA tail


title: HE8W_CTB3_sc78

description: mRNA with polyA tail


title: HE8W_CTB3_sc90

description: mRNA with polyA tail


title: HE8W_CTB3_sc76

description: mRNA with polyA tail


title: HE8W_CTB3_sc74

description: mRNA with polyA tail


title: HE8W_CTB3_sc73

description: mRNA with polyA tail


title: HE8W_CTB4_sc62

description: mRNA with polyA tail


title: HE8W_CTB3_sc70

description: mRNA with polyA tail


title: HE8W_CTB3_sc68

description: mRNA with polyA tail


title: HE8W_CTB3_sc67

description: mRNA with polyA tail


title: HE8W_CTB4_sc53

description: mRNA with polyA tail


title: HE8W_CTB3_sc66

description: mRNA with polyA tail


title: HE8W_CTB3_sc72

description: mRNA with polyA tail


title: HE8W_CTB3_sc6

description: mRNA with polyA tail


title: HE8W_CTB3_sc61

description: mRNA with polyA tail


title: HE8W_CTB3_sc62

description: mRNA with polyA tail


title: HE8W_CTB3_sc65

description: mRNA with polyA tail


title: HE8W_CTB3_sc59

description: mRNA with polyA tail


title: HE8W_CTB3_sc52

description: mRNA with polyA tail


title: HE8W_CTB3_sc54

description: mRNA with polyA tail


title: HE8W_CTB3_sc55

description: mRNA with polyA tail


title: HE8W_CTB3_sc56

description: mRNA with polyA tail


title: HE8W_CTB3_sc60

description: mRNA with polyA tail


title: HE8W_CTB3_sc49

description: mRNA with polyA tail


title: HE8W_CTB3_sc64

description: mRNA with polyA tail


title: HE8W_CTB3_sc7

description: mRNA with polyA tail


title: HE8W_CTB3_sc42

description: mRNA with polyA tail


title: HE8W_CTB3_sc48

description: mRNA with polyA tail


title: HE8W_CTB3_sc58

description: mRNA with polyA tail


title: HE8W_CTB3_sc5

description: mRNA with polyA tail


title: HE8W_CTB3_sc53

description: mRNA with polyA tail


title: HE8W_CTB3_sc51

description: mRNA with polyA tail


title: HE8W_CTB3_sc71

description: mRNA with polyA tail


title: HE8W_CTB3_sc40

description: mRNA with polyA tail


title: HE8W_CTB3_sc39

description: mRNA with polyA tail


title: HE8W_CTB3_sc41

description: mRNA with polyA tail


title: HE8W_CTB3_sc50

description: mRNA with polyA tail


title: HE8W_CTB3_sc47

description: mRNA with polyA tail


title: HE8W_CTB3_sc46

description: mRNA with polyA tail


title: HE8W_CTB3_sc37

description: mRNA with polyA tail


title: HE8W_CTB3_sc35

description: mRNA with polyA tail


title: HE8W_CTB3_sc45

description: mRNA with polyA tail


title: HE8W_CTB3_sc32

description: mRNA with polyA tail


title: HE8W_CTB3_sc63

description: mRNA with polyA tail


title: HE8W_CTB3_sc69

description: mRNA with polyA tail


title: HE8W_CTB3_sc4

description: mRNA with polyA tail


title: HE8W_CTB3_sc44

description: mRNA with polyA tail


title: HE8W_CTB3_sc43

description: mRNA with polyA tail


title: HE8W_CTB3_sc57

description: mRNA with polyA tail


title: HE8W_CTB3_sc29

description: mRNA with polyA tail


title: HE8W_CTB3_sc31

description: mRNA with polyA tail


title: HE8W_CTB3_sc27

description: mRNA with polyA tail


title: HE8W_CTB3_sc36

description: mRNA with polyA tail


title: HE8W_CTB3_sc38

description: mRNA with polyA tail


title: HE8W_CTB3_sc30

description: mRNA with polyA tail


title: HE8W_CTB3_sc28

description: mRNA with polyA tail


title: HE8W_CTB3_sc26

description: mRNA with polyA tail


title: HE8W_CTB3_sc22

description: mRNA with polyA tail


title: HE8W_CTB3_sc24

description: mRNA with polyA tail


title: HE8W_CTB3_sc20

description: mRNA with polyA tail


title: HE8W_CTB3_sc2

description: mRNA with polyA tail


title: HE8W_CTB3_sc19

description: mRNA with polyA tail


title: HE8W_CTB3_sc33

description: mRNA with polyA tail


title: HE8W_CTB3_sc21

description: mRNA with polyA tail


title: HE8W_CTB3_sc16

description: mRNA with polyA tail


title: HE8W_CTB3_sc17

description: mRNA with polyA tail


title: HE8W_CTB3_sc15

description: mRNA with polyA tail


title: HE8W_CTB3_sc3

description: mRNA with polyA tail


title: HE8W_CTB3_sc14

description: mRNA with polyA tail


title: HE8W_CTB3_sc12

description: mRNA with polyA tail


title: HE8W_CTB3_sc1

description: mRNA with polyA tail


title: HE8W_CTB3_sc13

description: mRNA with polyA tail


title: HE8W_CTB3_sc25

description: mRNA with polyA tail


title: HE8W_CTB2_sc90

description: mRNA with polyA tail


title: HE8W_CTB2_sc86

description: mRNA with polyA tail


title: HE8W_CTB2_sc89

description: mRNA with polyA tail


title: HE8W_CTB2_sc88

description: mRNA with polyA tail


title: HE8W_CTB2_sc9

description: mRNA with polyA tail


title: HE8W_CTB3_sc11

description: mRNA with polyA tail


title: HE8W_CTB2_sc84

description: mRNA with polyA tail


title: HE8W_CTB2_sc83

description: mRNA with polyA tail


title: HE8W_CTB2_sc82

description: mRNA with polyA tail


title: HE8W_CTB3_sc18

description: mRNA with polyA tail


title: HE8W_CTB2_sc85

description: mRNA with polyA tail


title: HE8W_CTB2_sc81

description: mRNA with polyA tail


title: HE8W_CTB2_sc8

description: mRNA with polyA tail


title: HE8W_CTB2_sc77

description: mRNA with polyA tail


title: HE8W_CTB2_sc78

description: mRNA with polyA tail


title: HE8W_CTB2_sc75

description: mRNA with polyA tail


title: HE8W_CTB2_sc87

description: mRNA with polyA tail


title: HE8W_CTB3_sc10

description: mRNA with polyA tail


title: HE8W_CTB2_sc73

description: mRNA with polyA tail


title: HE8W_CTB2_sc7

description: mRNA with polyA tail


title: HE8W_CTB2_sc74

description: mRNA with polyA tail


title: HE8W_CTB2_sc76

description: mRNA with polyA tail


title: HE8W_CTB2_sc79

description: mRNA with polyA tail


title: HE8W_CTB2_sc70

description: mRNA with polyA tail


title: HE8W_CTB2_sc66

description: mRNA with polyA tail


title: HE8W_CTB2_sc65

description: mRNA with polyA tail


title: HE8W_CTB2_sc68

description: mRNA with polyA tail


title: HE8W_CTB2_sc67

description: mRNA with polyA tail


title: HE8W_CTB2_sc69

description: mRNA with polyA tail


title: HE8W_CTB2_sc62

description: mRNA with polyA tail


title: HE8W_CTB2_sc61

description: mRNA with polyA tail


title: HE8W_CTB2_sc63

description: mRNA with polyA tail


title: HE8W_CTB2_sc59

description: mRNA with polyA tail


title: HE8W_CTB2_sc60

description: mRNA with polyA tail


title: HE8W_CTB2_sc64

description: mRNA with polyA tail


title: HE8W_CTB2_sc6

description: mRNA with polyA tail


title: HE8W_CTB2_sc58

description: mRNA with polyA tail


title: HE8W_CTB2_sc57

description: mRNA with polyA tail


title: HE8W_CTB2_sc54

description: mRNA with polyA tail


title: HE8W_CTB2_sc55

description: mRNA with polyA tail


title: HE8W_CTB2_sc80

description: mRNA with polyA tail


title: HE8W_CTB2_sc53

description: mRNA with polyA tail


title: HE8W_CTB2_sc56

description: mRNA with polyA tail


title: HE8W_CTB2_sc71

description: mRNA with polyA tail


title: HE8W_CTB2_sc50

description: mRNA with polyA tail


title: HE8W_CTB2_sc51

description: mRNA with polyA tail


title: HE8W_CTB2_sc49

description: mRNA with polyA tail


title: HE8W_CTB2_sc48

description: mRNA with polyA tail


title: HE8W_CTB2_sc46

description: mRNA with polyA tail


title: HE8W_CTB2_sc52

description: mRNA with polyA tail


title: HE8W_CTB2_sc47

description: mRNA with polyA tail


title: HE8W_CTB2_sc72

description: mRNA with polyA tail


title: HE8W_CTB2_sc40

description: mRNA with polyA tail


title: HE8W_CTB2_sc42

description: mRNA with polyA tail


title: HE8W_CTB2_sc41

description: mRNA with polyA tail


title: HE8W_CTB2_sc39

description: mRNA with polyA tail


title: HE8W_CTB2_sc43

description: mRNA with polyA tail


title: HE8W_CTB2_sc44

description: mRNA with polyA tail


title: HE8W_CTB2_sc5

description: mRNA with polyA tail


title: HE8W_CTB2_sc38

description: mRNA with polyA tail


title: HE8W_CTB2_sc36

description: mRNA with polyA tail


title: HE8W_CTB2_sc45

description: mRNA with polyA tail


title: HE8W_CTB2_sc32

description: mRNA with polyA tail


title: HE8W_CTB2_sc3

description: mRNA with polyA tail


title: HE8W_CTB2_sc33

description: mRNA with polyA tail


title: HE8W_CTB2_sc27

description: mRNA with polyA tail


title: HE8W_CTB2_sc4

description: mRNA with polyA tail


title: HE8W_CTB2_sc28

description: mRNA with polyA tail


title: HE8W_CTB2_sc30

description: mRNA with polyA tail


title: HE8W_CTB2_sc29

description: mRNA with polyA tail


title: HE8W_CTB2_sc31

description: mRNA with polyA tail


title: HE8W_CTB2_sc22

description: mRNA with polyA tail


title: HE8W_CTB2_sc26

description: mRNA with polyA tail


title: HE8W_CTB2_sc25

description: mRNA with polyA tail


title: HE8W_CTB2_sc24

description: mRNA with polyA tail


title: HE8W_CTB2_sc37

description: mRNA with polyA tail


title: HE8W_CTB2_sc19

description: mRNA with polyA tail


title: HE8W_CTB2_sc21

description: mRNA with polyA tail


title: HE8W_CTB2_sc20

description: mRNA with polyA tail


title: HE8W_CTB2_sc2

description: mRNA with polyA tail


title: HE8W_CTB2_sc35

description: mRNA with polyA tail


title: HE8W_CTB2_sc17

description: mRNA with polyA tail


title: HE8W_CTB2_sc15

description: mRNA with polyA tail


title: HE8W_CTB2_sc18

description: mRNA with polyA tail


title: HE8W_CTB2_sc16

description: mRNA with polyA tail


title: HE8W_CTB2_sc11

description: mRNA with polyA tail


title: HE8W_CTB2_sc1

description: mRNA with polyA tail


title: HE8W_CTB2_sc14

description: mRNA with polyA tail


title: HE8W_CTB0_sc5

description: mRNA with polyA tail


title: HE8W_CTB0_sc7

description: mRNA with polyA tail


title: HE8W_CTB0_sc8

description: mRNA with polyA tail


title: HE8W_CTB2_sc10

description: mRNA with polyA tail


title: HE8W_CTB0_sc9

description: mRNA with polyA tail


title: HE8W_CTB0_sc4

description: mRNA with polyA tail


title: HE8W_CTB0_sc21

description: mRNA with polyA tail


title: HE8W_CTB0_sc2

description: mRNA with polyA tail


title: HE8W_CTB0_sc19

description: mRNA with polyA tail


title: HE8W_CTB0_sc20

description: mRNA with polyA tail


title: HE8W_CTB0_sc23

description: mRNA with polyA tail


title: HE8W_CTB0_sc3

description: mRNA with polyA tail


title: HE8W_CTB0_sc24

description: mRNA with polyA tail


title: HE8W_CTB2_sc12

description: mRNA with polyA tail


title: HE8W_CTB0_sc17

description: mRNA with polyA tail


title: HE8W_CTB0_sc16

description: mRNA with polyA tail


title: HE8W_CTB0_sc14

description: mRNA with polyA tail


title: HE8W_CTB2_sc13

description: mRNA with polyA tail


title: HE8W_CTB0_sc13

description: mRNA with polyA tail


title: HE8W_CTB0_sc18

description: mRNA with polyA tail


title: HE8W_CTB0_sc15

description: mRNA with polyA tail


title: HE8W_CTB0_sc11

description: mRNA with polyA tail


title: HE24W_EVT5_sc9

description: mRNA with polyA tail

source_name: Extravillous trophoblast of Week 24

value: Week 24


title: HE8W_CTB0_sc6

description: mRNA with polyA tail


title: HE8W_CTB0_sc1

description: mRNA with polyA tail


title: HE8W_CTB0_sc10

description: mRNA with polyA tail


title: HE24W_EVT5_sc6

description: mRNA with polyA tail


title: HE24W_EVT5_sc8

description: mRNA with polyA tail


title: HE24W_EVT5_sc40

description: mRNA with polyA tail


title: HE8W_CTB0_sc22

description: mRNA with polyA tail


title: HE24W_EVT5_sc4

description: mRNA with polyA tail


title: HE24W_EVT5_sc39

description: mRNA with polyA tail


title: HE24W_EVT5_sc38

description: mRNA with polyA tail


title: HE24W_EVT5_sc37

description: mRNA with polyA tail


title: HE24W_EVT5_sc36

description: mRNA with polyA tail


title: HE24W_EVT5_sc3

description: mRNA with polyA tail


title: HE24W_EVT5_sc33

description: mRNA with polyA tail


title: HE24W_EVT5_sc35

description: mRNA with polyA tail


title: HE24W_EVT5_sc34

description: mRNA with polyA tail


title: HE24W_EVT5_sc31

description: mRNA with polyA tail


title: HE24W_EVT5_sc30

description: mRNA with polyA tail


title: HE8W_CTB0_sc12

description: mRNA with polyA tail


title: HE24W_EVT5_sc27

description: mRNA with polyA tail


title: HE24W_EVT5_sc32

description: mRNA with polyA tail


title: HE24W_EVT5_sc24

description: mRNA with polyA tail


title: HE24W_EVT5_sc26

description: mRNA with polyA tail


title: HE24W_EVT5_sc25

description: mRNA with polyA tail


title: HE24W_EVT5_sc23

description: mRNA with polyA tail


title: HE24W_EVT5_sc5

description: mRNA with polyA tail


title: HE24W_EVT5_sc2

description: mRNA with polyA tail


title: HE24W_EVT5_sc22

description: mRNA with polyA tail


title: HE24W_EVT5_sc19

description: mRNA with polyA tail


title: HE24W_EVT5_sc16

description: mRNA with polyA tail


title: HE24W_EVT5_sc17

description: mRNA with polyA tail


title: HE24W_EVT5_sc15

description: mRNA with polyA tail


title: HE24W_EVT5_sc21

description: mRNA with polyA tail


title: HE24W_EVT5_sc12

description: mRNA with polyA tail


title: HE24W_EVT5_sc1

description: mRNA with polyA tail


title: HE24W_EVT5_sc14

description: mRNA with polyA tail


title: HE24W_EVT5_sc18

description: mRNA with polyA tail


title: HE24W_EVT5_sc29

description: mRNA with polyA tail


title: HE24W_EVT5_sc13

description: mRNA with polyA tail


title: HE24W_EVT5_sc11

description: mRNA with polyA tail


title: HE24W_EVT5_sc28

description: mRNA with polyA tail


title: HE24W_EVT5_sc10

description: mRNA with polyA tail


title: HE24W_EVT4_sc8

description: mRNA with polyA tail


title: HE24W_EVT4_sc9

description: mRNA with polyA tail


title: HE24W_EVT4_sc7

description: mRNA with polyA tail


title: HE24W_EVT4_sc4

description: mRNA with polyA tail


title: HE24W_EVT4_sc6

description: mRNA with polyA tail


title: HE24W_EVT4_sc5

description: mRNA with polyA tail


title: HE24W_EVT5_sc20

description: mRNA with polyA tail


title: HE24W_EVT4_sc40

description: mRNA with polyA tail


title: HE24W_EVT4_sc38

description: mRNA with polyA tail


title: HE24W_EVT4_sc39

description: mRNA with polyA tail


title: HE24W_EVT4_sc37

description: mRNA with polyA tail


title: HE24W_EVT5_sc7

description: mRNA with polyA tail


title: HE24W_EVT4_sc36

description: mRNA with polyA tail


title: HE24W_EVT4_sc34

description: mRNA with polyA tail


title: HE24W_EVT4_sc33

description: mRNA with polyA tail


title: HE24W_EVT4_sc3

description: mRNA with polyA tail


title: HE24W_EVT4_sc35

description: mRNA with polyA tail


title: HE24W_EVT4_sc32

description: mRNA with polyA tail


title: HE24W_EVT4_sc31

description: mRNA with polyA tail


title: HE24W_EVT4_sc28

description: mRNA with polyA tail


title: HE24W_EVT4_sc27

description: mRNA with polyA tail


title: HE24W_EVT4_sc29

description: mRNA with polyA tail


title: HE24W_EVT4_sc25

description: mRNA with polyA tail


title: HE24W_EVT4_sc30

description: mRNA with polyA tail


title: HE24W_EVT4_sc23

description: mRNA with polyA tail


title: HE24W_EVT4_sc22

description: mRNA with polyA tail


title: HE24W_EVT4_sc24

description: mRNA with polyA tail


title: HE24W_EVT4_sc26

description: mRNA with polyA tail


title: HE24W_EVT4_sc21

description: mRNA with polyA tail


title: HE24W_EVT4_sc2

description: mRNA with polyA tail


title: HE24W_EVT4_sc20

description: mRNA with polyA tail


title: HE24W_EVT4_sc18

description: mRNA with polyA tail


title: HE24W_EVT4_sc16

description: mRNA with polyA tail


title: HE24W_EVT4_sc15

description: mRNA with polyA tail


title: HE24W_EVT4_sc19

description: mRNA with polyA tail


title: HE24W_EVT4_sc13

description: mRNA with polyA tail


title: HE24W_EVT4_sc12

description: mRNA with polyA tail


title: HE24W_EVT4_sc11

description: mRNA with polyA tail


title: HE24W_EVT4_sc10

description: mRNA with polyA tail


title: HE24W_EVT3_sc9

description: mRNA with polyA tail


title: HE24W_EVT3_sc8

description: mRNA with polyA tail


title: HE24W_EVT4_sc14

description: mRNA with polyA tail


title: HE24W_EVT3_sc7

description: mRNA with polyA tail


title: HE24W_EVT3_sc4

description: mRNA with polyA tail


title: HE24W_EVT3_sc5

description: mRNA with polyA tail


title: HE24W_EVT3_sc40

description: mRNA with polyA tail


title: HE24W_EVT3_sc39

description: mRNA with polyA tail


title: HE24W_EVT3_sc37

description: mRNA with polyA tail


title: HE24W_EVT3_sc34

description: mRNA with polyA tail


title: HE24W_EVT3_sc38

description: mRNA with polyA tail


title: HE24W_EVT3_sc33

description: mRNA with polyA tail


title: HE24W_EVT3_sc32

description: mRNA with polyA tail


title: HE24W_EVT3_sc35

description: mRNA with polyA tail


title: HE24W_EVT3_sc29

description: mRNA with polyA tail


title: HE24W_EVT4_sc1

description: mRNA with polyA tail


title: HE24W_EVT3_sc6

description: mRNA with polyA tail


title: HE24W_EVT3_sc31

description: mRNA with polyA tail


title: HE24W_EVT3_sc28

description: mRNA with polyA tail


title: HE24W_EVT3_sc30

description: mRNA with polyA tail


title: HE24W_EVT3_sc27

description: mRNA with polyA tail


title: HE24W_EVT3_sc26

description: mRNA with polyA tail


title: HE24W_EVT3_sc36

description: mRNA with polyA tail


title: HE24W_EVT3_sc23

description: mRNA with polyA tail


title: HE24W_EVT3_sc21

description: mRNA with polyA tail


title: HE24W_EVT3_sc25

description: mRNA with polyA tail


title: HE24W_EVT3_sc19

description: mRNA with polyA tail


title: HE24W_EVT3_sc18

description: mRNA with polyA tail


title: HE24W_EVT3_sc24

description: mRNA with polyA tail


title: HE24W_EVT3_sc2

description: mRNA with polyA tail


title: HE24W_EVT3_sc22

description: mRNA with polyA tail


title: HE24W_EVT3_sc20

description: mRNA with polyA tail


title: HE24W_EVT4_sc17

description: mRNA with polyA tail


title: HE24W_EVT3_sc3

description: mRNA with polyA tail


title: HE24W_EVT3_sc16

description: mRNA with polyA tail


title: HE24W_EVT3_sc15

description: mRNA with polyA tail


title: HE24W_EVT3_sc14

description: mRNA with polyA tail


title: HE24W_EVT3_sc13

description: mRNA with polyA tail


title: HE24W_EVT3_sc1

description: mRNA with polyA tail


title: HE24W_EVT2_sc9

description: mRNA with polyA tail


title: HE24W_EVT3_sc10

description: mRNA with polyA tail


title: HE24W_EVT3_sc12

description: mRNA with polyA tail


title: HE24W_EVT2_sc6

description: mRNA with polyA tail


title: HE24W_EVT2_sc5

description: mRNA with polyA tail


title: HE24W_EVT2_sc7

description: mRNA with polyA tail


title: HE24W_EVT2_sc40

description: mRNA with polyA tail


title: HE24W_EVT2_sc4

description: mRNA with polyA tail


title: HE24W_EVT2_sc37

description: mRNA with polyA tail


title: HE24W_EVT2_sc39

description: mRNA with polyA tail


title: HE24W_EVT3_sc17

description: mRNA with polyA tail


title: HE24W_EVT2_sc36

description: mRNA with polyA tail


title: HE24W_EVT2_sc38

description: mRNA with polyA tail


title: HE24W_EVT2_sc34

description: mRNA with polyA tail


title: HE24W_EVT2_sc33

description: mRNA with polyA tail


title: HE24W_EVT2_sc3

description: mRNA with polyA tail


title: HE24W_EVT2_sc30

description: mRNA with polyA tail


title: HE24W_EVT2_sc29

description: mRNA with polyA tail


title: HE24W_EVT2_sc27

description: mRNA with polyA tail


title: HE24W_EVT2_sc26

description: mRNA with polyA tail


title: HE24W_EVT2_sc28

description: mRNA with polyA tail


title: HE24W_EVT3_sc11

description: mRNA with polyA tail


title: HE24W_EVT2_sc8

description: mRNA with polyA tail


title: HE24W_EVT2_sc22

description: mRNA with polyA tail


title: HE24W_EVT2_sc23

description: mRNA with polyA tail


title: HE24W_EVT2_sc2

description: mRNA with polyA tail


title: HE24W_EVT2_sc19

description: mRNA with polyA tail


title: HE24W_EVT2_sc20

description: mRNA with polyA tail


title: HE24W_EVT2_sc18

description: mRNA with polyA tail


title: HE24W_EVT2_sc17

description: mRNA with polyA tail


title: HE24W_EVT2_sc35

description: mRNA with polyA tail


title: HE24W_EVT2_sc24

description: mRNA with polyA tail


title: HE24W_EVT2_sc21

description: mRNA with polyA tail


title: HE24W_EVT2_sc16

description: mRNA with polyA tail


title: HE24W_EVT2_sc15

description: mRNA with polyA tail


title: HE24W_EVT2_sc13

description: mRNA with polyA tail


title: HE24W_EVT2_sc31

description: mRNA with polyA tail


title: HE24W_EVT2_sc14

description: mRNA with polyA tail


title: HE24W_EVT2_sc32

description: mRNA with polyA tail


title: HE24W_EVT2_sc12

description: mRNA with polyA tail


title: HE24W_EVT2_sc10

description: mRNA with polyA tail


title: HE24W_EVT2_sc11

description: mRNA with polyA tail


title: HE24W_EVT2_sc1

description: mRNA with polyA tail


title: HE24W_EVT2_sc25

description: mRNA with polyA tail


title: HE24W_EVT1_sc9

description: mRNA with polyA tail


title: HE24W_EVT1_sc7

description: mRNA with polyA tail


title: HE24W_EVT1_sc5

description: mRNA with polyA tail


title: HE24W_EVT1_sc6

description: mRNA with polyA tail


title: HE24W_EVT1_sc39

description: mRNA with polyA tail


title: HE24W_EVT1_sc38

description: mRNA with polyA tail


title: HE24W_EVT1_sc4

description: mRNA with polyA tail


title: HE24W_EVT1_sc35

description: mRNA with polyA tail


title: HE24W_EVT1_sc29

description: mRNA with polyA tail


title: HE24W_EVT1_sc23

description: mRNA with polyA tail


title: HE24W_EVT1_sc8

description: mRNA with polyA tail


title: HE24W_EVT1_sc31

description: mRNA with polyA tail


title: HE24W_EVT1_sc33

description: mRNA with polyA tail


title: HE24W_EVT1_sc2

description: mRNA with polyA tail


title: HE24W_EVT1_sc32

description: mRNA with polyA tail


title: HE24W_EVT1_sc25

description: mRNA with polyA tail


title: HE24W_EVT1_sc28

description: mRNA with polyA tail


title: HE24W_EVT1_sc19

description: mRNA with polyA tail


title: HE24W_EVT1_sc30

description: mRNA with polyA tail


title: HE24W_EVT1_sc21

description: mRNA with polyA tail


title: HE24W_EVT1_sc24

description: mRNA with polyA tail


title: HE24W_EVT1_sc34

description: mRNA with polyA tail


title: HE24W_EVT1_sc40

description: mRNA with polyA tail


title: HE24W_EVT1_sc27

description: mRNA with polyA tail


title: HE24W_EVT1_sc22

description: mRNA with polyA tail


title: HE24W_EVT1_sc3

description: mRNA with polyA tail


title: HE24W_EVT1_sc20

description: mRNA with polyA tail


title: HE24W_EVT1_sc14

description: mRNA with polyA tail


title: HE24W_EVT1_sc12

description: mRNA with polyA tail


title: HE24W_EVT1_sc36

description: mRNA with polyA tail


title: HE24W_EVT1_sc37

description: mRNA with polyA tail


title: HE24W_EVT1_sc16

description: mRNA with polyA tail


title: HE24W_EVT1_sc17

description: mRNA with polyA tail


title: HE24W_EVT1_sc15

description: mRNA with polyA tail


title: HE24W_EVT1_sc18

description: mRNA with polyA tail


title: HE24W_EVT1_sc13

description: mRNA with polyA tail


title: HE24W_EVT1_sc26

description: mRNA with polyA tail


title: HE24W_EVT1_sc10

description: mRNA with polyA tail


title: HE24W_EVT1_sc11

description: mRNA with polyA tail


title: smRNA seq library of late oocytes from tdrd6a mut fish

city: mainz

first: lucas

last: kaaij

address: ackermannweg 4

department: RNA silencing

country: Germany

institute: IMB

data_processing:
1. Adapter trimming with cutadapt (-O 8 -m 26 -M 38 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
2. Low-quality read filtering with fastq_quality_filter ( -q 20 -p 100 -Q 33).
3. Duplicate reads were collapsed using the unique molecule identifiers (UMIs) added during library preparation (4 random bases at both the 5' and 3' end), using a custom bash script.
4. UMIs were trimmed with seqtk trimfq -b 4 -a 4
5. Reads with less than 15 nt in length were filtered out with seqtk seq -L 15
6. Mapping was done to Zebrafish (_Danio rerio_) genome assembly Zv9 with bowtie v0.12.8 (--tryhard --best --strata --chunkmbs 256 -v 1 -M 5).
7. Bigwig tracks normalized to the number of mapped reads were created using genomeCoverageBed -bg -split -scale (bedtools 2.25.0) followed by bedGraphToBigWig (Kent utilities).
8. Mapped reads (converted to bed with bamToBed) where intersected with the locations of transposable elements (LINE, SINE, LTR and DNA) downloaded from the UCSC genome browser (repeat masker track, Zv9) using bedtools intersect -a reads -b transposons -wa -wb -bed -f 1.0 -nonamecheck to keep both the read and the transposon information. The arguments -s/-S were also set to find reads mapping sense or antisense to the transposons. Results are in data file transposons_counts.txt.gz
Genome_build: Zv9
Supplementary_files_format_and_content: transposons_counts.txt.gz is a compressed tab-delimited file. Each line corresponds a read that overlaps and annotated transposon. The fields chr_re, start_re, end_re, repFamily, repName strand_re, and repClass represent the location and classification of the repeat elements as described in the RepeatMasker track of UCSC. Feature is whether they are DNA or RNA transposons, and readlength the length of the read that. Sample is the sample name, and Mapping whether teh reads mapped sense or antisense in relation to the transposon it maps to.
Supplementary_files_format_and_content: Files ending in .bw are bigwig tracks.

organism: Danio rerio

source_name: late oocytes from tdrd6a mut fish

extract_protocol:
RNA was extracted from ovary tissue, as indicated, by Trizol extraction.
Standard smRNA-seq library preperation

tag: tissue

value: late oocytes

tag: genotype

value: tdrd6a mutant


title: smRNA seq library of early oocytes from tdrd6a het fish

source_name: early oocytes from tdrd6a het fish

value: Early oocytes

value: tdrd6a heterozygote


title: OVCAR8 Input DNA

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

country: USA

institute: Indiana University

description: OVCAR8 Input DNA

library_source: genomic

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using Bowtie2 (v2.0.6)
Peak calling was accomplished using the Useq platform (v8.0.1).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include for each stated sample: chromosome, start, stop
Supplementary_files_format_and_content: bound regions (bed)

molecule: genomic DNA

source_name: OVCAR8 Ovarian cancer cell line

growth_protocol: HEYA8 and OVCAR8 cells were maintained in DMEM media (Mediatech-Cellgro) with 10% FBS, 100 U/ml Penicillin/Streptomycin

extract_protocol:
ChIP DNA was isolated as described in Hollenhorst et. al., Genes and Development, 2011
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

treatment_protocol: No Treatment

tag: cell line

tag: antibody

value: none, input


title: ETS1 knockdown in HEYA8 cells using shRNA replicate 3

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using TopHat2 (v2.0.7) running BowTie2 (v2.0.6) and Samtools (v.0.1.18) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The parameters used were -G -p 8
Differential expression of aligned reads was produced using Cufflinks (v2.1.1) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The three replicates for each shRNA PC3 cell line were combined for the differential expression analysis. The parameters used were -b -p 8 -u -L
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include for each combination of replicates: RPKM values, locus, status, log2(fold_change), test_stat, p-value, q-value, and significance

source_name: low grade serous ovarian carcinoma

growth_protocol: HEYA8 cells were maintained in DMEM media (Mediatech-Cellgro) with 10% FBS, 100 U/ml Penicillin/Streptomycin, and 5microgram/ml puromycin (for plasmid selection)

extract_protocol:
Total RNA was isolated from HEYA8 cells transduced with shRNA knockdown vector using the Rneasy mini kit (Qiagen) according to manufacturer's instruction
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol.Total RNA was DNAase treated with TURBO DNase (Invitrogen) The DNase treated RNA was polyA selected with oligo(dT) beads (Invitrogen). A Superscript III Reverse Transcriptase First-Strand Synthesis (Invitrogen) system was used to generate cDNA from the polyA selected RNA with random hexamer primers (Invitrogen). After first strand synthesis a second strand was generated using E. coli DNA ligase (New England BioLabs) and E. coli DNA polymerase I (New England BioLabs). The double stranded cDNAs were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

treatment_protocol: No treatment

tag: genotype/variation

value: ETS1 knockdown


title: ETS1 knockdown in HEYA8 cells using shRNA replicate 2


title: smRNA seq library of ovary from tdrd6a mut fish

source_name: Ovary from tdrd6a mut fish

value: whole ovary


title: Luciferase knockdown in HEYA8 cells using shRNA replicate 1

value: Luciferase knockdown


title: Luciferase knockdown in HEYA8 cells using shRNA replicate 2


title: OVCAR8 ETS1 ChIP

description: OVCAR8 ETS1 ChIP


title: HEYA8 ETS1 ChIP

description: HEYA8 ETS1 ChIP

source_name: HEYA8 Ovarian cancer cell line


title: smRNA seq library of ovary from tdrd6a het fish

source_name: Ovary from tdrd6a het fish


title: HEYA8 Input DNA

description: HEYA8 Input DNA


title: Input_1

data_processing:
Reads were mapped to Zv9 using tophat (trapnell et al, 2009)to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq (Anders et al, 2009)
Genome_build: zv9
Supplementary_files_format_and_content: The mRNA_counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.

source_name: Zebrafish Zygotes

growth_protocol: Zebrafish were maintained under standard conditions.

extract_protocol:
mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction
The RNA was extracted using chloroform and precipitated with iso-propanol. Ovation RNA-seq System V2 (NuGEN) library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.

tag: fraction

value: Input


title: smRNA seq library of late oocytes from tdrd6a hett fish

source_name: late oocytes from tdrd6a hett fish


title: Input_3


title: smRNA seq library of early oocytes from tdrd6a mut fish

source_name: early oocytes from tdrd6a mut fish

value: early oocytes


title: Tdrd6a_IP_2


title: Luciferase knockdown in HEYA8 cells using shRNA replicate 3


title: Input_2


title: Tdrd6a_IP_3


title: THB2-123-L (tau)

first: Salil

last: Sharma

state: Indiana

address: 702 North Walnut Grove Ave

department: Psychological & Brain Sciences

institute: Indiana University Bloomington

data_processing:
Single end sequencing reads were cleaned with quality filter, adapter cutter, and length filter, using ACGT101_miR_v4.2g from LC Sciences.
The cleaned reads were mapped to miRBase (miRBase v21) using Bowtie v1.1.1.
The un-mapped reads were mapped to multiple databases including mRNA (NCBI M_musculus/RNA build 03/04/2011), Rfam11, and genomic DNA (UCSC mm9), using Bowtie v1.1.1.
Novel miRNA candidates were identified from genome mapped reads based on the propensity of hairpin formation in corresponding genome positions, using ACGT101_miR_v4.2g from LC Sciences.
Data were normalized by dividing sequence counts of individual samples by corresponding normalization factors which are the median values of the ratios between specific sample counts and geometric mean counts of all samples.
Genome_build: UCSC mm9

organism: Mus musculus

source_name: hippocampus tissue

extract_protocol:
Hippocampus was removed and flah frozen. miRVana RNA extraction kit (part no. AM1560, ThermoFisher scientific) was used to extract total RNA. A small RNA library was generated from a customer sample using the Illumina Truseq™ Small RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

tag: age

value: 6 months

tag: animal model

value: rTg4510 mouse model of tauopathy

value: tau:positive, CamK:positive


title: THB2-125-R (tau)


title: Tdrd6a_IP_1


title: HE24W_EVT1_sc1

description: mRNA with polyA tail

value: Extravillous trophoblast

value: HLA-G+


title: THB1-2-L51 (tau)


title: THB2-120-LR (control)

value: tau:negative, CamK:negative


title: THB1-2-NO-49 (tau)


title: ETS1 knockdown in HEYA8 cells using shRNA replicate 1


title: 2L-186 (tau)

value: 2 months


title: R-184 (tau)


title: THB2-126-NO (control)


title: 2R-187 (control)


title: 2LS (tau)


title: L-183 (control)


title: L-178 (control)


title: THB9-R-RNA1_S4_R1_001 (tau)

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq 500.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 5 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Raw counts and normalized abundance measurement from edgeR

extract_protocol:
Hippocampus was removed and flah frozen. miRVana RNA extraction kit (part no. AM1560, ThermoFisher scientific) was used to extract total RNA. RNA was treated with DNase I to remove genomic DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit


title: THB1-L-RNA9_S3_R1_001 (control)


title: THB6-2R_S10_R1_001 (tau)


title: THB1-L_S8_R1 (control)


title: THB6-R_S9_R1_001 (control)


title: THB10-2R-RNA6_S1_R1_001 (control)


title: THB1-R-RNA8_S5_R1_001 (tau)


title: 142-IUE-5_S5_R1_001 (IUE)

source_name: cortex tissue

extract_protocol:
Cortex was removed and flah frozen. miRVana RNA extraction kit (part no. AM1560, ThermoFisher scientific) was used to extract total RNA. RNA was treated with DNase I to remove genomic DNA.
Illumina TruSeq Stranded mRNA Library Prep Kit

value: cortex

value: 1 month

value: Wildtype ICR mice

value: WT

tag: constructs

value: miR142-GFP plasmid DNA


title: THB6-2LR_S7_R1_001 (control)


title: THB9-LR-RNA7_S2_R1_001 (control)


title: 142-IUE-2_S4_R1_001 (IUE)


title: MIR142-IUE-3_S4_R1_001 (IUE)


title: TDTOM-CTRL-IUE-5_S2_R1_001 (control)

value: tdtomato plasmid DNA


title: 142-IUE-6_S6_R1_001 (IUE)


title: THB1-R_S12_R1_001 (tau)


title: TDTOM-CTRL-IUE-1_S1_R1_001 (control)


title: MIR142-IUE-1_S3_R1_001 (IUE)


title: TDTOM-IUE-2_S1_R1_001 (control)


title: THB4-2L_S11_R1_001 (tau)


title: TDTOM-IUE-6_S2_R1_001 (control)


title: mTEC-IV_rep2_wce

status: Public on Jul 23 2018

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Sorted cells enriched for mTEC-IV from murine thymus
processed data file:
H3K4me2-TEC-cluster-5-6-Combined_peaks-top-set.txt

data_processing:
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108).
findPeaks <input tag directory> -o <out file> -style histone -i <WCE tag directory>
IDR using from Qunhua Li and Anshul Kundaje method (Oct,2010)
Genome_build: mm9
Supplementary_files_format_and_content: merged peaks after IDR
Supplementary_files_format_and_content: Normalized read counts of merged peaks across all conditiones

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered, stained with Flow cytometry antibodies and cross linked with Formaldehyde.
High troughput ChIP, developed from the iChIP protocol (Lara-Astiaso, Weiner et al. Science 2014)

treatment_protocol: Mice were sacrified by CO2

tag: enrichment

value: Thymus

tag: strain

tag: chip antibody


title: mTEC-II_rep1_wce

description:
Sorted cells enriched for mTEC-II from murine thymus
processed data file:
H3K4me2-TEC-cluster-7-10-Combined_peaks-top-set.txt


title: mTEC-I_rep2_wce

description:
Sorted cells enriched for mTEC-I from murine thymus
processed data file:
H3K4me2-TEC-cluster-1-3-Combined_peaks-top-set.txt


title: mTEC-III_rep2_wce

description:
Sorted cells enriched for mTEC-III from murine thymus
processed data file:
H3K4me2-TEC-cluster-12-Combined_peaks-top-set.txt


title: mTEC-IV_rep1_wce


title: mTEC-II_rep2_wce


title: TDTOM-IUE-3_S3_R1_001 (control)


title: mTEC-I_rep1_wce


title: mTEC-IV_rep2_H3K4me2

value: Anti H3K4me2 -monoclonal antibody abcam ab3254


title: mTEC-III_rep2_H3K4me2


title: mTEC-II_rep2_H3K4me2


title: mTEC-II_rep1_H3K4me2


title: mTEC-III_rep1_wce


title: mTEC-I_rep2_H3K4me2


title: mTEC-III_rep1_H3K4me2


title: mTEC-IV_rep2_ATAC

description: Sorted cells enriched for mTEC-IV from murine thymus

data_processing:
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108).
findPeaks <input tag directory> -o <out file> -style factor -size 300
FDR in Homer peak creation (http://homer.ucsd.edu/homer/)
annotatePeaks.pl <merged peaks.bed> mm9 -d <list of tag directory> > ATAC-TEC_merged_annotated_peaks_counts.txt
Genome_build: mm9
Supplementary_files_format_and_content: sample pages include peak file, Normalized read counts of merged peaks across all conditions is available on series record.

extract_protocol:
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Tagmentated DNA was isolated and undergoes two cycles of PCR amplification with indexing Nextra primers


title: mTEC-III_rep2_ATAC

description: Sorted cells enriched for mTEC-III from murine thymus


title: mTEC-II_rep2_ATAC

description: Sorted cells enriched for mTEC-II from murine thymus


title: mTEC-III_rep1_ATAC


title: mTEC-I_rep2_ATAC

description: Sorted cells enriched for mTEC-I from murine thymus


title: mTEC-II_rep1_ATAC


title: mTEC-I_rep1_ATAC


title: AB2977

description:
Hpgds-tomato Intestine_mouse31
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each sample.  Meta data file associating each single cell with its amplification batch and index sorting readouts is available on the series record in the file "metadata.txt".

molecule: polyA RNA

source_name: Intestine

extract_protocol:
Thymus: Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Intestine: Murine small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

value: Intestine

tag: selection marker

value: Epcam+ Hpgds-tomato+

tag: treatment

value: untreated

tag: mouse age

value: 4-6 weeks


title: AB2980

description:
Hpgds-tomato Intestine_mouse32
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2978


title: AB2976


title: AB2979


title: AB2975


title: AB2973


title: AB2749

description:
Thymic-Sox9-GFP_mouse30
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

source_name: Thymus

value: CD45- Epcam+ Sox9-GFP+ L1cam+


title: AB2974


title: AB2748


title: mTEC-I_rep1_H3K4me2


title: mTEC-IV_rep1_ATAC


title: AB2736

description:
Thymic_Epithel_Pou2f_KO_mouse28
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

value: CD45- Epcam+


title: AB2737


title: AB2732


title: AB2672

description:
Thymic_Epithel_Pou2f_KO_mouse27
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2735


title: AB2734


title: AB2981


title: AB2671


title: mTEC-IV_rep1_H3K4me2


title: AB2669


title: AB2668


title: AB2667


title: AB2666


title: AB2665


title: AB2663


title: AB2661

description:
Thymic_Epithel_Pou2f_WT_mouse26
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2662


title: AB2664


title: AB2658


title: AB2659


title: AB2670


title: AB2733


title: AB2177

description:
Thymic_Epithel_E18.5_mouse25
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2174


title: AB2660


title: AB2173


title: AB2175


title: AB2172


title: AB2171

description:
Thymic_Epithel_E18.5_mouse24
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2162

description:
Thymic_Epithel_E14.5_mouse23
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2169


title: AB2167

description:
Thymic_Epithel_6d_mouse20
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.

value: 6 days


title: AB2161


title: AB2166


title: AB2157

description:
Thymic_Epithel_E14.5_mouse22
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2135

description:
Thymic_Epithel_E18.5_mouse21
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2159


title: AB2165


title: AB2133

description:
Thymic_Epithel_6d_mouse19
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2132


title: AB2131


title: AB2129


title: AB2127

description:
Thymic_Epithel_E14.5_mouse18
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2126


title: AB2738

description:
Thymic_Epithel_Pou2f_WT_mouse29
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1966

description:
AireKO_Thymic_Epithel_newMarkers_mouse16
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB2164


title: AB2124

description:
Thymic_Epithel_E14.5_mouse17
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1967


title: AB2158


title: AB1964


title: AB2160


title: AB1963


title: AB1962


title: AB1960


title: AB1957


title: AB1961


title: AB1753

description:
Thymic_Epithel_newMarkers_mouse14
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1792

description:
Thymic_Epithel_newMarkers_mouse15
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1795


title: AB1648

description:
Thymic_Epithel_newMarkers_mouse13
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1751


title: AB1959


title: AB1793


title: AB1646


title: AB2125


title: AB1649


title: AB1545

description:
Thymic_Epithel_newMarkers_mouse12
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1544


title: AB1647


title: AB1542

description:
Thymic_Epithel_newMarkers_mouse11
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1541


title: AB1546


title: AB1459

description:
Thymic_Epithel_newMarkers_mouse10
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1540


title: AB1958


title: AB1539


title: AB1458


title: AB833

description:
thymus_stroma_WT_mouse6
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1965


title: AB837


title: AB832


title: AB834


title: AB790

description:
thymus_stroma_WT_mouse4
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB835


title: AB1302

description:
thymus_stroma_WT_mouse7
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1398

description:
Thymic_Epithel_newMarkers_mouse9
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB752

description:
thymus_stroma_WT_mouse5
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1396

description:
Thymic_Epithel_newMarkers_mouse8
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB676

description:
thymus_stroma_WT_mouse3
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB1301


title: AB1395


title: AB731


title: AB730


title: AB677


title: AB674


title: AB591

description:
thymus_stroma_WT_mouse2
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB675


title: AB593

description:
thymus_stroma_WT_mouse1
paired-end sequencing. Read2 used to read cell and molecule barcodes only and this information was appended to the fastq entry header. Thus only Read1 was submitted.


title: AB592


title: AB594


title: AB595


title: AB590


title: E9.5_VPR_Pdx1-pos_1_25

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

description:
Sample 631
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz

data_processing:
Bulk-cell RNA-seq (Sample 001-016)
Sequencing reads were aligned to the Mus musculus reference genome GRCm38/mm10 using TopHat (v2.1.0) with parameter "-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2".
Reads aligned to genes were counted by HTSeq (v 0.6.0) with parameters "-f bam -r pos -s reverse -a 30".
Reads of biological replicates were pooled.
Gene expression levels were quantified as reads per kilobase of longest transcript per million mapped reads (RPKM).
Single-cell RNA-seq (Sample 023-541, 568-586, 607-631, 671-674)
Sequencing reads were aligned to the Mus musculus reference genome GRCm38/mm10 using TopHat (v2.1.0) with parameter "-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq".
Reads aligned to genes were counted by HTSeq (v 0.6.0) with parameters "-f bam -r pos -s no -a 30".
Gene expression levels were quantified as reads per kilobase of longest transcript per million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and RPKM values for each sample

source_name: Ventral Pdx1-expression region

growth_protocol: Undifferentiated NKX6.1-mCherry Mel-1 hESCs were maintained on mouse embryo fibroblast feeder layers in hESC media as previously described (Kennedy et al., 2007). For generation of NKX6.1+ pancreatic progenitors, a protocol described by (Nostro et al., 2015) was used. Differentiation was started when NKX6.1-mCherry Mel-1 hESCs reached 80% confluence. Briefly, after removal of hESC media, cultures were treated with RPMI media containing 100 ng/ml of hActivin A and 2 mM CHIR 99021 (Tocris) for 1 day (d0–d1). Cells were treated with RPMI containing 100 ng/ml of hActivin A and 5 ng/ml hbFGF for 2 days (d1–d3). At day 3 of differentiation, cultures were treated with stage 2 media consisting of serum-free differentiation (SFD) media 63 containing 50 ng/ml of hFGF10 and 3 ng/ml mWnt3a. At d6 of differentiation, the medium was changed to DMEM with 1% vol/vol B27 supplement (without vitamin A) (Life Technologies), ascorbic acid (50 mg/ml; Sigma), KAAD-cyclopamine (0.25 mM; Stemgent), all-trans RA (2 mM; Sigma), hNOGGIN (50 ng/ml), and hFGF10 (50 ng/ml) for 2 days, with the medium changed every day. At d8, the medium was changed to DMEM with 1% vol/vol B27 supplement (Life Technologies), ascorbic acid (50 mg/ml; Sigma), hNOGGIN (50 ng/ml), hEGF (50 ng/ml), nicotinamide (10 mM; Sigma) and hActivin A (3 ng/ml). All cytokines were purchased from R&D Systems unless otherwise stated. Cultures were maintained in a 5% CO2, 5% O2, 90% N2 environment.

extract_protocol:
Bulk-cell RNA-seq (Sample 001-016)
For E10.5, E14.5 and E17.5 dorsal and ventral pancreases, a total of 5-7 x 10e4 sorted cells were used to isolate total RNA using the Rneasy Micro Kit (Qiagen, 74004). Poly(A) RNA was further purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).
Libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) according to the manufacturer's instructions.
Single-cell RNA-seq (Sample 023-541, 568-586, 607-631, 671-674)
Libraries were prepared according the Smart-seq2 method as previously reported (Picelli et al., 2014).
2 ng cDNA were subjected to prepare the libraries using the TruePrep DNA Library Prep Kit (TD502, Vazyme).

tag: embryonic day

tag: sorting


title: E9.5_VPR_Pdx1-pos_1_22

description:
Sample 628
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_23

description:
Sample 629
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_24

description:
Sample 630
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_21

description:
Sample 627
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_20

description:
Sample 626
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_18

description:
Sample 624
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_19

description:
Sample 625
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_14

description:
Sample 620
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_13

description:
Sample 619
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_12

description:
Sample 618
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_17

description:
Sample 623
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_16

description:
Sample 622
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_15

description:
Sample 621
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_11

description:
Sample 617
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_06

description:
Sample 612
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_08

description:
Sample 614
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_05

description:
Sample 611
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_07

description:
Sample 613
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_04

description:
Sample 610
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_03

description:
Sample 609
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_01

description:
Sample 607
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_10

description:
Sample 616
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: SmadKO_2

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
Read alignment and mapping done with TopHat, version 2.1.1
Gene and transcript level computation done with CuffQuant, Version 2.2.1
Normalized abundance measurements generated by CuffNorm, Version 2.2.1, using quartile normalization
CuffDiff, Version 2.2.1, quartile normalization, per-condition dispersion
Genome_build: mm9
Supplementary_files_format_and_content: genes.fpkm_table containing normalized gene expression levels outputted by CuffNorm

source_name: jejunal crypts

growth_protocol: RNAs were extracted from crypt jejunal epithelia of the indicated genotypes (Smad4f/f;Villin-CreER(T2)  and Smad4f/f; Ex3f/+;Villin-CreER(T2)) in triplicates, one day following 4 consecutive days of tamoxifen injection. Uninjected mice served as control. After flushing the freshly harvested jejunum with cold PBS, the epithelia was dissociated from underlying mesenchyme by incubating with 3 mM EDTA/PBS at 4°C as described previously (Perekatt, 2014), and filtered through 70 micron filter to isolate the crypts. The crypts were washed with PBS, and pelleted to remove excess PBS prior to addition of TRIzol for RNA extraction according to manufacturer’s protocols.

extract_protocol:
same as above
Illumina TruSeq RNA Library Prep kit v2

tag: tissue

value: jejunal crypts

value: tamoxifen


title: Control_1

description: Smad4KO_only_genes.fpkm_table ; SmadBcat_only_genes.fpkm_table

value: control mouse

value: vehicle


title: SmadKOBcatEx3_0

value: Smad4f/f; Ex3f/+;Villin-CreER(T2)


title: SmadKO_1


title: E9.5_VPR_Pdx1-pos_1_09

description:
Sample 615
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: SmadKOBcatEx3_1


title: SmadKO_0


title: Control_0


title: SmadKOBcatEx3_2


title: Control_2


title: E9.5_VPR_Pdx1-pos_1_02

description:
Sample 608
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_14

description:
Sample 584
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz

tag: culture time


title: E9.5_VPR_Pdx1-pos_2_07

description:
Sample 577
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_15

description:
Sample 585
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_02

description:
Sample 572
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_03

description:
Sample 573
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_12

description:
Sample 582
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_11

description:
Sample 581
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_16

description:
Sample 586
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_10

description:
Sample 580
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_13

description:
Sample 583
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_06

description:
Sample 576
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_04

description:
Sample 574
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_08

description:
Sample 578
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_01

description:
Sample 571
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_27

description:
Sample 569
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_26

description:
Sample 568
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_1_28

description:
Sample 570
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_09

description:
Sample 579
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_22

description:
Sample 539
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz

source_name: Dorsal Pdx1-expression region


title: E9.5_DPR_Pdx1-pos_2_23

description:
Sample 540
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_20

description:
Sample 537
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_19

description:
Sample 536
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_24

description:
Sample 541
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_21

description:
Sample 538
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_15

description:
Sample 532
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_14

description:
Sample 531
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_17

description:
Sample 534
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_18

description:
Sample 535
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_VPR_Pdx1-pos_2_05

description:
Sample 575
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_16

description:
Sample 533
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_13

description:
Sample 530
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_12

description:
Sample 529
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_09

description:
Sample 526
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_11

description:
Sample 528
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_10

description:
Sample 527
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_06

description:
Sample 523
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_04

description:
Sample 521
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_05

description:
Sample 522
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_01

description:
Sample 518
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_07

description:
Sample 517
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_05

description:
Sample 515
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_03

description:
Sample 513
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_06

description:
Sample 516
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_3_03

description:
Sample 509
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_01

description:
Sample 511
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_02

description:
Sample 512
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_3_04

description:
Sample 510
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_08

description:
Sample 525
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_11

description:
Sample 505
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_3_02

description:
Sample 508
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_02

description:
Sample 519
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_07

description:
Sample 524
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_08

description:
Sample 502
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_10

description:
Sample 504
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_12

description:
Sample 506
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_09

description:
Sample 503
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_07

description:
Sample 501
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_2_03

description:
Sample 520
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_06

description:
Sample 500
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_02

description:
Sample 496
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_01

description:
Sample 495
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_04

description:
Sample 498
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_5_05

description:
Sample 494
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_5_02

description:
Sample 491
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_5_04

description:
Sample 493
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_5_01

description:
Sample 490
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_5_03

description:
Sample 492
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_4_01

description:
Sample 489
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E9.5_DPR_Pdx1-pos_1_04

description:
Sample 514
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_10

description:
Sample 488
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_06

description:
Sample 484
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_08

description:
Sample 486
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_07

description:
Sample 485
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_02

description:
Sample 480
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_04

description:
Sample 482
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_03

description:
Sample 497
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_09

description:
Sample 487
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_03

description:
Sample 481
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_01

description:
Sample 479
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_5_03

description:
Sample 476
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_6_05

description:
Sample 483
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_10

description:
Sample 472
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_5_02

description:
Sample 475
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_5_04

description:
Sample 477
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-low_6_05

description:
Sample 499
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_5_05

description:
Sample 478
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_11

description:
Sample 473
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_08

description:
Sample 470
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_06

description:
Sample 468
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_07

description:
Sample 469
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_05

description:
Sample 467
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_09

description:
Sample 471
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_04

description:
Sample 466
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_03

description:
Sample 465
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_02

description:
Sample 464
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-high_4_01

description:
Sample 463
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_10

description:
Sample 461
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz

source_name: Liver Bud


title: E10.5_VPR_Pdx1-high_5_01

description:
Sample 474
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_08

description:
Sample 459
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_05

description:
Sample 456
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_09

description:
Sample 460
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_03

description:
Sample 454
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_06

description:
Sample 457
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_04

description:
Sample 455
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_3_06

description:
Sample 451
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_09

description:
Sample 444
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_01

description:
Sample 452
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_02

description:
Sample 453
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_10

description:
Sample 445
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_3_05

description:
Sample 450
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_08

description:
Sample 443
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_3_01

description:
Sample 446
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_3_02

description:
Sample 447
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_07

description:
Sample 442
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_06

description:
Sample 441
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_3_04

description:
Sample 449
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_05

description:
Sample 440
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_03

description:
Sample 438
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_04

description:
Sample 439
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_02

description:
Sample 437
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_18

description:
Sample 435
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_11

description:
Sample 462
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_Liver_2_07

description:
Sample 458
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_17

description:
Sample 434
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_15

description:
Sample 432
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_14

description:
Sample 431
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_3_03

description:
Sample 448
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_16

description:
Sample 433
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_13

description:
Sample 430
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_3_01

description:
Sample 507
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_07

description:
Sample 424
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_10

description:
Sample 427
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_09

description:
Sample 426
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_05

description:
Sample 422
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_08

description:
Sample 425
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_03

description:
Sample 420
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-pos_2_01

description:
Sample 436
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_01

description:
Sample 418
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_02

description:
Sample 419
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_04

description:
Sample 421
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_5_02

description:
Sample 414
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_5_01

description:
Sample 413
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_5_03

description:
Sample 415
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_4_04

description:
Sample 412
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_4_02

description:
Sample 410
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_4_01

description:
Sample 409
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_5_04

description:
Sample 416
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_4_03

description:
Sample 411
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_6_03

description:
Sample 408
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_11

description:
Sample 428
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_6_02

description:
Sample 407
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_12

description:
Sample 429
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_6_06

description:
Sample 423
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_5_03

description:
Sample 403
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_5_05

description:
Sample 405
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_5_04

description:
Sample 404
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_6_01

description:
Sample 406
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_5_02

description:
Sample 402
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_4_04

description:
Sample 400
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_4_01

description:
Sample 397
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_4_03

description:
Sample 399
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-high_4_02

description:
Sample 398
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_20

description:
Sample 288
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_22

description:
Sample 290
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_19

description:
Sample 287
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_18

description:
Sample 286
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_21

description:
Sample 289
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_17

description:
Sample 285
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_15

description:
Sample 283
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_13

description:
Sample 281
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_DPR_Pdx1-low_5_05

description:
Sample 417
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_12

description:
Sample 280
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz


title: E10.5_VPR_Pdx1-pos_2_11

description:
Sample 279
processed data file:
Single-cell_RNA-seq_Read_Count.txt.gz
Single-cell_RNA-seq_RPKM.txt.gz