title: 66 Y Male run2626_lane12_read1 Cell_13

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN706-S505=Jun7_x_x_077_Cell_13


title: 66 Y Male run2626_lane12_read1 Cell_65

status: Public on May 14 2019

type: SRA

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S517=Jun7_x_x_270_Cell_65

library_source: transcriptomic

data_processing:
FASTQ sequence files were aligned to the human genome version 19 (hg19) using RSEM.
Single-cell were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Fluidigm C1 protocol
Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA)
All aged (65-75 yo) samples were derived from femurs from individuals undergoing hip replacement surgery at the University of Michigan hospital. Donors had no known history of hematological malignancy. Bone marrow mononuclear cells (BM MNC) were isolated using ficoll based density centrifugation and cryopreserved. Additional bone marrow mononuclear cells were purchased from Allcells, Hemacare, Stemcell Technologies, University of Pennsylvania Stem Cell and Xenograft Core, and Cincinnati Children’s Hospital Processing Core for young (18-30 yo) and middle-aged (45-55 yo) donors. For scRNA-seq, bone marrow cells from healthy donors was obtained at Cincinnati Children’s Hospital Medical Center through informed consent under an approved institutional review board research protocol. Mononuclear cells were isolated with Ficoll-Paque (GE Healthcare), then enriched using CD34 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD34+ cells were stained with lineage antibodies conjugated to PerCP-Cy™5.5: CD2 (Becton, Dickinson and Company, clone RPA-2.10), CD3 (Becton, Dickinson and Company, clone UCHT1), CD4 (Becton, Dickinson and Company, clone RPA-T4), CD7 (Becton, Dickinson and Company, clone M-T701), CD8 (Becton, Dickinson and Company, clone RPA-T8), CD10 (Becton, Dickinson and Company, clone HI10a), CD11b (Biolegend, clone ICRF44), CD14 (Becton, Dickinson and Company, clone M5E2), CD19 (eBioscience, clone HIB19), CD20 (eBioscience, clone 2H7), CD24 (Biolegend, clone ML5), CD56 (Becton, Dickinson and Company, clone B159), CD66b (Becton, Dickinson and Company, clone G10F5), Glycophorin A (Biolegend, clone HIR2) and CD90-biotin (eBioscience, clone 5E10). To isolate CD34+CD38- hematopoietic stem and progenitor cells (HSPC), lineage stained cells were stained with: Streptavidin APC-Cy7 (Becton, Dickinson and Company), CD123-PE (eBioscience, clone 6H6), CD34-APC (eBioscience, clone 4H11), CD38-PE-Cy7 (eBioscience, clone HIT2), CD45RA-FITC ( Invitrogen, clone MEM-56). Cell sorting was performed on a BD FACSAria II with a 100um nozzle.
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

tag: cell type


title: 71 Y Female run2620_lane12_read1 Cell_94

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S506=May22_x_x_306_Cell_94


title: 71 Y Female run2620_lane12_read1 Cell_71

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S507=May22_x_x_306_Cell_71


title: 71 Y Female run2620_lane12_read1 Cell_72

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S508=May22_x_x_306_Cell_72


title: 66 Y Male run2626_lane12_read1 Cell_8

description:
66 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2626_lane12_read1_indexN708-S508=Jun7_x_x_077_Cell_8


title: 71 Y Female run2620_lane12_read1 Cell_45

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S505=May22_x_x_302_Cell_45


title: 71 Y Female run2620_lane12_read1 Cell_48

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S508=May22_x_x_306_Cell_48


title: 71 Y Female run2620_lane12_read1 Cell_46

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S506=May22_x_x_302_Cell_46


title: 71 Y Female run2620_lane12_read1 Cell_32

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S508=May22_x_x_302_Cell_32


title: 71 Y Female run2620_lane12_read1 Cell_41

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S517=May22_x_x_302_Cell_41


title: 71 Y Female run2620_lane12_read1 Cell_29

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S505=May22_x_x_302_Cell_29


title: 71 Y Female run2620_lane12_read1 Cell_26

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S502=May22_x_x_302_Cell_26


title: 71 Y Female run2620_lane12_read1 Cell_88

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S508=May22_x_x_306_Cell_88


title: 71 Y Female run2620_lane12_read1 Cell_40

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S508=May22_x_x_302_Cell_40


title: 71 Y Female run2620_lane12_read1 Cell_27

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S503=May22_x_x_302_Cell_27


title: 71 Y Female run2620_lane12_read1 Cell_77

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S505=May22_x_x_306_Cell_77


title: 71 Y Female run2620_lane12_read1 Cell_42

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S502=May22_x_x_302_Cell_42


title: 71 Y Female run2620_lane12_read1 Cell_16

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S508=May22_x_x_302_Cell_16


title: 71 Y Female run2620_lane12_read1 Cell_74

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S502=May22_x_x_306_Cell_74


title: 71 Y Female run2620_lane12_read1 Cell_61

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S505=May22_x_x_306_Cell_61


title: 71 Y Female run2620_lane12_read1 Cell_75

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S503=May22_x_x_306_Cell_75


title: 71 Y Female run2620_lane12_read1 Cell_79

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S507=May22_x_x_306_Cell_79


title: 71 Y Female run2620_lane12_read1 Cell_37

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S505=May22_x_x_302_Cell_37


title: 71 Y Female run2620_lane12_read1 Cell_89

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S517=May22_x_x_306_Cell_89


title: 71 Y Female run2620_lane12_read1 Cell_80

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S508=May22_x_x_306_Cell_80


title: 71 Y Female run2620_lane12_read1 Cell_12

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S504=May22_x_x_302_Cell_12


title: 71 Y Female run2620_lane12_read1 Cell_55

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S507=May22_x_x_306_Cell_55


title: 71 Y Female run2620_lane12_read1 Cell_25

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S517=May22_x_x_302_Cell_25


title: 71 Y Female run2620_lane12_read1 Cell_47

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S507=May22_x_x_302_Cell_47


title: 71 Y Female run2620_lane12_read1 Cell_15

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S507=May22_x_x_302_Cell_15


title: 71 Y Female run2620_lane12_read1 Cell_44

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S504=May22_x_x_302_Cell_44


title: 71 Y Female run2620_lane12_read1 Cell_10

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S502=May22_x_x_302_Cell_10


title: 71 Y Female run2620_lane12_read1 Cell_6

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S506=May22_x_x_302_Cell_6


title: 71 Y Female run2620_lane12_read1 Cell_8

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S508=May22_x_x_302_Cell_8


title: 71 Y Female run2620_lane12_read1 Cell_73

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S517=May22_x_x_306_Cell_73


title: 71 Y Female run2620_lane12_read1 Cell_3

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S503=May22_x_x_302_Cell_3


title: 71 Y Female run2620_lane12_read1 Cell_56

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S508=May22_x_x_306_Cell_56


title: 71 Y Female run2620_lane12_read1 Cell_50

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S502=May22_x_x_306_Cell_50


title: 71 Y Female run2620_lane12_read1 Cell_70

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S506=May22_x_x_306_Cell_70


title: 71 Y Female run2620_lane12_read1 Cell_64

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S508=May22_x_x_306_Cell_64


title: 71 Y Female run2620_lane12_read1 Cell_66

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S502=May22_x_x_306_Cell_66


title: 71 Y Female run2620_lane12_read1 Cell_1

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S517=May22_x_x_302_Cell_1


title: 71 Y Female run2620_lane12_read1 Cell_7

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S507=May22_x_x_302_Cell_7


title: 71 Y Female run2620_lane12_read1 Cell_67

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S503=May22_x_x_306_Cell_67


title: 71 Y Female run2620_lane12_read1 Cell_36

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S504=May22_x_x_302_Cell_36


title: 71 Y Female run2620_lane12_read1 Cell_38

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S506=May22_x_x_302_Cell_38


title: 71 Y Female run2620_lane12_read1 Cell_65

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S517=May22_x_x_306_Cell_65


title: 71 Y Female run2620_lane12_read1 Cell_33

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S517=May22_x_x_302_Cell_33


title: 71 Y Female run2620_lane12_read1 Cell_83

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S503=May22_x_x_306_Cell_83


title: 71 Y Female run2620_lane12_read1 Cell_57

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S517=May22_x_x_306_Cell_57


title: 71 Y Female run2620_lane12_read1 Cell_95

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S507=May22_x_x_306_Cell_95


title: 71 Y Female run2620_lane12_read1 Cell_82

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S502=May22_x_x_306_Cell_82


title: 71 Y Female run2620_lane12_read1 Cell_24

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S508=May22_x_x_302_Cell_24


title: 71 Y Female run2620_lane12_read1 Cell_18

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S502=May22_x_x_302_Cell_18


title: 71 Y Female run2620_lane12_read1 Cell_22

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S506=May22_x_x_302_Cell_22


title: 71 Y Female run2620_lane12_read1 Cell_60

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S504=May22_x_x_306_Cell_60


title: 71 Y Female run2620_lane12_read1 Cell_5

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S505=May22_x_x_302_Cell_5


title: 71 Y Female run2620_lane12_read1 Cell_13

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S505=May22_x_x_302_Cell_13


title: 71 Y Female run2620_lane12_read1 Cell_43

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S503=May22_x_x_302_Cell_43


title: 71 Y Female run2620_lane12_read1 Cell_86

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S506=May22_x_x_306_Cell_86


title: 71 Y Female run2620_lane12_read1 Cell_30

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S506=May22_x_x_302_Cell_30


title: 71 Y Female run2620_lane12_read1 Cell_69

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S505=May22_x_x_306_Cell_69


title: 71 Y Female run2620_lane12_read1 Cell_87

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S507=May22_x_x_306_Cell_87


title: 71 Y Female run2620_lane12_read1 Cell_4

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S504=May22_x_x_302_Cell_4


title: 71 Y Female run2620_lane12_read1 Cell_11

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN704-S503=May22_x_x_302_Cell_11


title: 71 Y Female run2620_lane12_read1 Cell_23

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S507=May22_x_x_302_Cell_23


title: 71 Y Female run2620_lane12_read1 Cell_93

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S505=May22_x_x_306_Cell_93


title: 71 Y Female run2620_lane12_read1 Cell_49

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S517=May22_x_x_306_Cell_49


title: 71 Y Female run2620_lane12_read1 Cell_54

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S506=May22_x_x_306_Cell_54


title: 71 Y Female run2620_lane12_read1 Cell_51

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN708-S503=May22_x_x_306_Cell_51


title: 71 Y Female run2620_lane12_read1 Cell_21

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S505=May22_x_x_302_Cell_21


title: 71 Y Female run2620_lane12_read1 Cell_31

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S507=May22_x_x_302_Cell_31


title: 71 Y Female run2620_lane12_read1 Cell_81

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN710-S517=May22_x_x_306_Cell_81


title: 71 Y Female run2620_lane12_read1 Cell_76

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S504=May22_x_x_306_Cell_76


title: 71 Y Female run2620_lane12_read1 Cell_52

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN709-S504=May22_x_x_306_Cell_52


title: 71 Y Female run2620_lane12_read1 Cell_39

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S507=May22_x_x_302_Cell_39


title: 71 Y Female run2620_lane12_read1 Cell_78

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S506=May22_x_x_306_Cell_78


title: 71 Y Female run2620_lane12_read1 Cell_92

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S504=May22_x_x_306_Cell_92


title: 71 Y Female run2620_lane12_read1 Cell_20

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S504=May22_x_x_302_Cell_20


title: 71 Y Female run2620_lane12_read1 Cell_17

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN703-S517=May22_x_x_302_Cell_17


title: 71 Y Female run2620_lane12_read1 Cell_2

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S502=May22_x_x_302_Cell_2


title: 71 Y Female run2620_lane12_read1 Cell_9

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S517=May22_x_x_302_Cell_9


title: 71 Y Female run2620_lane12_read1 Cell_84

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S504=May22_x_x_306_Cell_84


title: 71 Y Female run2620_lane12_read1 Cell_28

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S504=May22_x_x_302_Cell_28


title: 71 Y Female run2620_lane12_read1 Cell_68

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN711-S504=May22_x_x_306_Cell_68


title: 71 Y Female run2620_lane12_read1 Cell_85

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN702-S505=May22_x_x_306_Cell_85


title: 71 Y Female run2620_lane12_read1 Cell_96

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN706-S508=May22_x_x_306_Cell_96


title: 71 Y Female run2620_lane12_read1 Cell_14

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S506=May22_x_x_302_Cell_14


title: 24 Y Male run2518_lane12_read1 Cell_8

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S508=Feb12_x_x_277_Cell_8


title: 71 Y Female run2620_lane12_read1 Cell_62

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S506=May22_x_x_306_Cell_62


title: 71 Y Female run2620_lane12_read1 Cell_91

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S503=May22_x_x_306_Cell_91


title: 71 Y Female run2620_lane12_read1 Cell_90

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN712-S502=May22_x_x_306_Cell_90


title: 71 Y Female run2620_lane12_read1 Cell_19

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN705-S503=May22_x_x_302_Cell_19


title: 24 Y Male run2518_lane12_read1 Cell_19

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S503=Feb12_x_x_277_Cell_19


title: 24 Y Male run2518_lane12_read1 Cell_12

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S504=Feb12_x_x_277_Cell_12


title: 24 Y Male run2518_lane12_read1 Cell_16

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S508=Feb12_x_x_277_Cell_16


title: 24 Y Male run2518_lane12_read1 Cell_13

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S505=Feb12_x_x_277_Cell_13


title: 24 Y Male run2518_lane12_read1 Cell_9

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN702-S517=Feb12_x_x_277_Cell_9


title: 24 Y Male run2518_lane12_read1 Cell_15

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S507=Feb12_x_x_277_Cell_15


title: 24 Y Male run2518_lane12_read1 Cell_6

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S506=Feb12_x_x_277_Cell_6


title: 24 Y Male run2518_lane12_read1 Cell_2

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN702-S502=Feb12_x_x_277_Cell_2


title: 24 Y Male run2518_lane12_read1 Cell_4

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S504=Feb12_x_x_277_Cell_4


title: 24 Y Male run2518_lane12_read1 Cell_3

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S503=Feb12_x_x_277_Cell_3


title: 24 Y Male run2518_lane12_read1 Cell_7

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S507=Feb12_x_x_277_Cell_7


title: 24 Y Male run2518_lane12_read1 Cell_1

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S517=Feb12_x_x_277_Cell_1


title: 71 Y Female run2620_lane12_read1 Cell_63

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN701-S507=May22_x_x_306_Cell_63


title: 64 Y Female run2518_lane12_read1 Cell_60

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S504=Mar28_x_x_305_Cell_60


title: 24 Y Male run2518_lane12_read1 Cell_18

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S502=Feb12_x_x_277_Cell_18


title: 64 Y Female run2518_lane12_read1 Cell_62

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S506=Mar28_x_x_305_Cell_62


title: 64 Y Female run2518_lane12_read1 Cell_96

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S508=Mar28_x_x_305_Cell_96


title: 24 Y Male run2518_lane12_read1 Cell_17

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S517=Feb12_x_x_277_Cell_17


title: 64 Y Female run2518_lane12_read1 Cell_82

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S502=Mar28_x_x_305_Cell_82


title: 24 Y Male run2518_lane12_read1 Cell_10

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S502=Feb12_x_x_277_Cell_10


title: 64 Y Female run2518_lane12_read1 Cell_49

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S517=Mar28_x_x_305_Cell_49


title: 64 Y Female run2518_lane12_read1 Cell_81

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S517=Mar28_x_x_305_Cell_81


title: 24 Y Male run2518_lane12_read1 Cell_11

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S503=Feb12_x_x_277_Cell_11


title: 64 Y Female run2518_lane12_read1 Cell_91

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S503=Mar28_x_x_305_Cell_91


title: 64 Y Female run2518_lane12_read1 Cell_88

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S508=Mar28_x_x_305_Cell_88


title: 64 Y Female run2518_lane12_read1 Cell_55

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S507=Mar28_x_x_305_Cell_55


title: 64 Y Female run2518_lane12_read1 Cell_85

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN702-S505=Mar28_x_x_305_Cell_85


title: 64 Y Female run2518_lane12_read1 Cell_46

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S506=Mar28_x_x_305_Cell_46


title: 64 Y Female run2518_lane12_read1 Cell_53

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S505=Mar28_x_x_305_Cell_53


title: 64 Y Female run2518_lane12_read1 Cell_72

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S508=Mar28_x_x_305_Cell_72


title: 64 Y Female run2518_lane12_read1 Cell_95

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S507=Mar28_x_x_305_Cell_95


title: 64 Y Female run2518_lane12_read1 Cell_87

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S507=Mar28_x_x_305_Cell_87


title: 64 Y Female run2518_lane12_read1 Cell_75

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S503=Mar28_x_x_305_Cell_75


title: 64 Y Female run2518_lane12_read1 Cell_56

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S508=Mar28_x_x_305_Cell_56


title: 64 Y Female run2518_lane12_read1 Cell_79

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S507=Mar28_x_x_305_Cell_79


title: 64 Y Female run2518_lane12_read1 Cell_61

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S505=Mar28_x_x_305_Cell_61


title: 64 Y Female run2518_lane12_read1 Cell_44

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S504=Mar28_x_x_305_Cell_44


title: 64 Y Female run2518_lane12_read1 Cell_43

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN702-S503=Mar28_x_x_305_Cell_43


title: 64 Y Female run2518_lane12_read1 Cell_78

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN702-S506=Mar28_x_x_305_Cell_78


title: 64 Y Female run2518_lane12_read1 Cell_47

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S507=Mar28_x_x_305_Cell_47


title: 64 Y Female run2518_lane12_read1 Cell_52

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S504=Mar28_x_x_305_Cell_52


title: 64 Y Female run2518_lane12_read1 Cell_77

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S505=Mar28_x_x_305_Cell_77


title: 64 Y Female run2518_lane12_read1 Cell_65

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S517=Mar28_x_x_305_Cell_65


title: 64 Y Female run2518_lane12_read1 Cell_58

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S502=Mar28_x_x_305_Cell_58


title: 64 Y Female run2518_lane12_read1 Cell_42

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S502=Mar28_x_x_305_Cell_42


title: 64 Y Female run2518_lane12_read1 Cell_68

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S504=Mar28_x_x_305_Cell_68


title: 64 Y Female run2518_lane12_read1 Cell_54

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S506=Mar28_x_x_305_Cell_54


title: 64 Y Female run2518_lane12_read1 Cell_41

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S517=Mar28_x_x_305_Cell_41


title: 64 Y Female run2518_lane12_read1 Cell_40

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S508=Mar28_x_x_305_Cell_40


title: 64 Y Female run2518_lane12_read1 Cell_84

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S504=Mar28_x_x_305_Cell_84


title: 64 Y Female run2518_lane12_read1 Cell_90

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S502=Mar28_x_x_305_Cell_90


title: 64 Y Female run2518_lane12_read1 Cell_48

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S508=Mar28_x_x_305_Cell_48


title: 64 Y Female run2518_lane12_read1 Cell_67

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S503=Mar28_x_x_305_Cell_67


title: 64 Y Female run2518_lane12_read1 Cell_71

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN702-S507=Mar28_x_x_305_Cell_71


title: 64 Y Female run2518_lane12_read1 Cell_51

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S503=Mar28_x_x_305_Cell_51


title: 64 Y Female run2518_lane12_read1 Cell_93

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S505=Mar28_x_x_305_Cell_93


title: 64 Y Female run2518_lane12_read1 Cell_80

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S508=Mar28_x_x_305_Cell_80


title: 64 Y Female run2518_lane12_read1 Cell_70

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN701-S506=Mar28_x_x_305_Cell_70


title: 64 Y Female run2518_lane12_read1 Cell_45

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S505=Mar28_x_x_305_Cell_45


title: 64 Y Female run2518_lane12_read1 Cell_89

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S517=Mar28_x_x_305_Cell_89


title: 64 Y Female run2518_lane12_read1 Cell_50

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S502=Mar28_x_x_305_Cell_50


title: 64 Y Female run2518_lane12_read1 Cell_94

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S506=Mar28_x_x_305_Cell_94


title: 64 Y Female run2518_lane12_read1 Cell_74

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S502=Mar28_x_x_305_Cell_74


title: 64 Y Female run2518_lane12_read1 Cell_57

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S517=Mar28_x_x_305_Cell_57


title: 64 Y Female run2518_lane12_read1 Cell_86

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN703-S506=Mar28_x_x_305_Cell_86


title: 64 Y Female run2518_lane12_read1 Cell_66

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S502=Mar28_x_x_305_Cell_66


title: 64 Y Female run2518_lane12_read1 Cell_73

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S517=Mar28_x_x_305_Cell_73


title: 24 Y Female run2518_lane12_read1 Cell_21

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S505=Feb12_x_x_279_Cell_21


title: 24 Y Female run2518_lane12_read1 Cell_26

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S502=Feb12_x_x_279_Cell_26


title: 24 Y Female run2518_lane12_read1 Cell_29

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S505=Feb12_x_x_279_Cell_29


title: 64 Y Female run2518_lane12_read1 Cell_83

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S503=Mar28_x_x_305_Cell_83


title: 24 Y Female run2518_lane12_read1 Cell_23

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S507=Feb12_x_x_279_Cell_23


title: 24 Y Female run2518_lane12_read1 Cell_35

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S503=Feb12_x_x_279_Cell_35


title: 24 Y Female run2518_lane12_read1 Cell_24

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S508=Feb12_x_x_279_Cell_24


title: 24 Y Female run2518_lane12_read1 Cell_28

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN707-S504=Feb12_x_x_279_Cell_28


title: 24 Y Female run2518_lane12_read1 Cell_38

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S506=Feb12_x_x_279_Cell_38


title: 64 Y Female run2518_lane12_read1 Cell_39

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S507=Mar28_x_x_305_Cell_39


title: 24 Y Female run2518_lane12_read1 Cell_36

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S504=Feb12_x_x_279_Cell_36


title: 71 Y Female run2620_lane12_read1 Cell_35

description:
71 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2620_lane12_read1_indexN707-S503=May22_x_x_302_Cell_35


title: 24 Y Female run2518_lane12_read1 Cell_33

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN705-S517=Feb12_x_x_279_Cell_33


title: 24 Y Female run2518_lane12_read1 Cell_27

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S503=Feb12_x_x_279_Cell_27


title: 24 Y Female run2518_lane12_read1 Cell_34

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S502=Feb12_x_x_279_Cell_34


title: 64 Y Female run2518_lane12_read1 Cell_59

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S503=Mar28_x_x_305_Cell_59


title: 24 Y Female run2518_lane12_read1 Cell_20

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN706-S504=Feb12_x_x_279_Cell_20


title: 24 Y Female run2518_lane12_read1 Cell_30

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S506=Feb12_x_x_279_Cell_30


title: 24 Y Female run2518_lane12_read1 Cell_37

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN709-S505=Feb12_x_x_279_Cell_37


title: 24 Y Female run2518_lane12_read1 Cell_32

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN711-S508=Feb12_x_x_279_Cell_32


title: 24 Y Female run2518_lane12_read1 Cell_25

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN704-S517=Feb12_x_x_279_Cell_25


title: 24 Y Female run2518_lane12_read1 Cell_31

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN710-S507=Feb12_x_x_279_Cell_31


title: 24 Y Female run2518_lane12_read1 Cell_22

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN708-S506=Feb12_x_x_279_Cell_22


title: 24 Y Male run2506_lane12_read1 Cell_41

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S517=Feb12_x_x_277_Cell_41


title: 24 Y Male run2506_lane12_read1 Cell_40

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S508=Feb12_x_x_277_Cell_40


title: 24 Y Male run2506_lane12_read1 Cell_39

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S507=Feb12_x_x_277_Cell_39


title: 24 Y Male run2506_lane12_read1 Cell_24

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S508=Feb12_x_x_277_Cell_24


title: 24 Y Male run2506_lane12_read1 Cell_38

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S506=Feb12_x_x_277_Cell_38


title: 24 Y Male run2506_lane12_read1 Cell_16

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S508=Feb12_x_x_277_Cell_16


title: 24 Y Male run2506_lane12_read1 Cell_37

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S505=Feb12_x_x_277_Cell_37


title: 24 Y Male run2506_lane12_read1 Cell_30

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S506=Feb12_x_x_277_Cell_30


title: 24 Y Male run2506_lane12_read1 Cell_23

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S507=Feb12_x_x_277_Cell_23


title: 24 Y Male run2506_lane12_read1 Cell_31

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S507=Feb12_x_x_277_Cell_31


title: 24 Y Male run2506_lane12_read1 Cell_8

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S508=Feb12_x_x_277_Cell_8


title: 64 Y Female run2518_lane12_read1 Cell_69

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S505=Mar28_x_x_305_Cell_69


title: 24 Y Male run2506_lane12_read1 Cell_15

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S507=Feb12_x_x_277_Cell_15


title: 24 Y Male run2506_lane12_read1 Cell_29

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S505=Feb12_x_x_277_Cell_29


title: 24 Y Male run2506_lane12_read1 Cell_36

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S504=Feb12_x_x_277_Cell_36


title: 24 Y Male run2506_lane12_read1 Cell_22

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S506=Feb12_x_x_277_Cell_22


title: 24 Y Male run2506_lane12_read1 Cell_7

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S507=Feb12_x_x_277_Cell_7


title: 24 Y Male run2506_lane12_read1 Cell_14

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S506=Feb12_x_x_277_Cell_14


title: 24 Y Male run2506_lane12_read1 Cell_28

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S504=Feb12_x_x_277_Cell_28


title: 24 Y Male run2506_lane12_read1 Cell_35

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S503=Feb12_x_x_277_Cell_35


title: 24 Y Male run2506_lane12_read1 Cell_21

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S505=Feb12_x_x_277_Cell_21


title: 24 Y Male run2506_lane12_read1 Cell_32

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S508=Feb12_x_x_277_Cell_32


title: 24 Y Male run2506_lane12_read1 Cell_13

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S505=Feb12_x_x_277_Cell_13


title: 24 Y Male run2506_lane12_read1 Cell_6

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S506=Feb12_x_x_277_Cell_6


title: 24 Y Male run2506_lane12_read1 Cell_20

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S504=Feb12_x_x_277_Cell_20


title: 24 Y Male run2506_lane12_read1 Cell_34

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S502=Feb12_x_x_277_Cell_34


title: Biological Replicate 4_treated (C60_4)

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Trimming the sequencing reads using trim-galore (0.4.4); Quality threshold = 10; Length threshold = 30
Alignment of the reads using STAR (2.5.3a); outFilterMultimapNmax 2; Reference: GRChm38
FeatureCounts for assigning reads to genes (1.5.3); Annotation: GRChm38/mm10
Differentially expressed genes were determined using ‘edgeR’ (v3.20.9)
Genome_build: GRChm38/mm10
Supplementary_files_format_and_content: text tab separated tables of gene counts

organism: Mus musculus

source_name: treated primordial follicles

growth_protocol: Total RNA samples were extracted from primordial follicles (snaped frozen and stored at -80)

extract_protocol:
Total RNA samples were extracted using PicoPure® RNA Isolation Kit (Arcturus, Carlsbad, CA, USA) according to manufactuer's instructions
Sequencing libraries were prepared using the Trio RNA-Seq kit (NuGEN Technologies, Inc., San Carlos, CA, USA)
RNA sequenced on the Illumina HiSeq 3000 instrument

treatment_protocol: Offsprings resulted from mitochondrial supplementation vs control

tag: strain background

value: C57Bl/6  x CBA

tag: developmental stage

value: Postnatal day 3

tag: tissue

value: ovarian

value: primordial follicles


title: 24 Y Male run2506_lane12_read1 Cell_5

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S505=Feb12_x_x_277_Cell_5


title: 24 Y Male run2506_lane12_read1 Cell_33

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S517=Feb12_x_x_277_Cell_33


title: 24 Y Male run2506_lane12_read1 Cell_46

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S506=Feb12_x_x_277_Cell_46


title: Biological Replicate 3_treated (C56_4)


title: Biological Replicate 2_treated (C56_3)


title: Biological Replicate 1_treated (C56_1)


title: 24 Y Male run2506_lane12_read1 Cell_26

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S502=Feb12_x_x_277_Cell_26


title: 24 Y Male run2506_lane12_read1 Cell_19

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S503=Feb12_x_x_277_Cell_19


title: Biological Replicate 4_control (301_5)

source_name: control primordial follicles


title: 24 Y Male run2506_lane12_read1 Cell_12

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S504=Feb12_x_x_277_Cell_12


title: Biological Replicate 3_control (301_4)


title: Biological Replicate 2_control (280_6)


title: 24 Y Male run2506_lane12_read1 Cell_25

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S517=Feb12_x_x_277_Cell_25


title: 24 Y Male run2506_lane12_read1 Cell_48

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S508=Feb12_x_x_277_Cell_48


title: 24 Y Male run2506_lane12_read1 Cell_45

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S505=Feb12_x_x_277_Cell_45


title: 24 Y Male run2506_lane12_read1 Cell_47

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S507=Feb12_x_x_277_Cell_47


title: 24 Y Male run2506_lane12_read1 Cell_27

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S503=Feb12_x_x_277_Cell_27


title: Biological Replicate 1_control (280_4)


title: 24 Y Male run2506_lane12_read1 Cell_11

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S503=Feb12_x_x_277_Cell_11


title: 24 Y Male run2506_lane12_read1 Cell_18

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S502=Feb12_x_x_277_Cell_18


title: 24 Y Male run2506_lane12_read1 Cell_17

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S517=Feb12_x_x_277_Cell_17


title: 24 Y Male run2506_lane12_read1 Cell_3

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S503=Feb12_x_x_277_Cell_3


title: 64 Y Female run2518_lane12_read1 Cell_76

description:
64 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2518_lane12_read1_indexN712-S504=Mar28_x_x_305_Cell_76


title: 24 Y Male run2506_lane12_read1 Cell_10

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S502=Feb12_x_x_277_Cell_10


title: 24 Y Male run2506_lane12_read1 Cell_43

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S503=Feb12_x_x_277_Cell_43


title: 24 Y Male run2506_lane12_read1 Cell_9

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S517=Feb12_x_x_277_Cell_9


title: 24 Y Male run2506_lane12_read1 Cell_42

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S502=Feb12_x_x_277_Cell_42


title: 24 Y Male run2506_lane12_read1 Cell_4

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S504=Feb12_x_x_277_Cell_4


title: 24 Y Female run2506_lane12_read1 Cell_55

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S507=Feb12_x_x_279_Cell_55


title: 24 Y Female run2506_lane12_read1 Cell_62

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S506=Feb12_x_x_279_Cell_62


title: 24 Y Female run2506_lane12_read1 Cell_83

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S503=Feb12_x_x_279_Cell_83


title: 24 Y Female run2506_lane12_read1 Cell_69

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S505=Feb12_x_x_279_Cell_69


title: 24 Y Male run2506_lane12_read1 Cell_44

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S504=Feb12_x_x_277_Cell_44


title: 24 Y Female run2506_lane12_read1 Cell_76

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S504=Feb12_x_x_279_Cell_76


title: 24 Y Female run2506_lane12_read1 Cell_90

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN712-S502=Feb12_x_x_279_Cell_90


title: HAI39_Day 6

type: RNA

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling of peripheral blood from influenza infected participant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Influenza infection Day 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from blood collected in paxgene tubes according to manufacturer's instructions.  RNA quality assessed using Agilent Bioanalyzer.

treatment_protocol: Health volunteers were intranasally challenged with 2009 H1N1 influenza virus. Whole blood was collected pre-exposure and days 1, 2, 4, and 6 days following exposure for microarray analysis.

value: Blood

tag: virus strain

value: Influenza virus infection

tag: time p.i.

value: Day 6


title: 24 Y Female run2506_lane12_read1 Cell_89

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S517=Feb12_x_x_279_Cell_89


title: 24 Y Male run2506_lane12_read1 Cell_2

description:
24 Y Male
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S502=Feb12_x_x_277_Cell_2


title: HAI51_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_61

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S505=Feb12_x_x_279_Cell_61


title: HAI3_Day 6


title: HAI1_Day 6


title: HAI23_Day 6


title: HAI33_Day 6


title: HAI53_Day 6


title: HAI50_Day 6


title: HAI61_Day 6


title: HAI42_Day 6


title: HAI41_Day 6


title: HAI5_Day 6


title: HAI11_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_82

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S502=Feb12_x_x_279_Cell_82


title: HAI62_Day 6


title: HAI7_Day 6


title: HAI22_Day 6


title: HAI63_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_54

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S506=Feb12_x_x_279_Cell_54


title: HAI14_Day 6


title: HAI18_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_81

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S517=Feb12_x_x_279_Cell_81


title: 24 Y Female run2506_lane12_read1 Cell_68

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S504=Feb12_x_x_279_Cell_68


title: 24 Y Female run2506_lane12_read1 Cell_60

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S504=Feb12_x_x_279_Cell_60


title: 24 Y Female run2506_lane12_read1 Cell_75

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN711-S503=Feb12_x_x_279_Cell_75


title: HAI10_Day 6


title: HAI71_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_53

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S505=Feb12_x_x_279_Cell_53


title: 24 Y Female run2506_lane12_read1 Cell_74

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S502=Feb12_x_x_279_Cell_74


title: 24 Y Female run2506_lane12_read1 Cell_67

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN710-S503=Feb12_x_x_279_Cell_67


title: HAI32_Day 6


title: HAI26_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_73

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S517=Feb12_x_x_279_Cell_73


title: 24 Y Female run2506_lane12_read1 Cell_52

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S504=Feb12_x_x_279_Cell_52


title: 24 Y Female run2506_lane12_read1 Cell_59

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S503=Feb12_x_x_279_Cell_59


title: 24 Y Female run2506_lane12_read1 Cell_65

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S517=Feb12_x_x_279_Cell_65


title: HAI9_Day 6

description: Gene expression profiling of peripheral blood from influenza infected participant


title: 24 Y Female run2506_lane12_read1 Cell_51

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S503=Feb12_x_x_279_Cell_51


title: 24 Y Female run2506_lane12_read1 Cell_66

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN709-S502=Feb12_x_x_279_Cell_66


title: HAI56_Day 6


title: PD40_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_57

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S517=Feb12_x_x_279_Cell_57


title: 24 Y Female run2506_lane12_read1 Cell_58

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN708-S502=Feb12_x_x_279_Cell_58


title: 24 Y Female run2506_lane12_read1 Cell_50

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN707-S502=Feb12_x_x_279_Cell_50


title: PD48_Day 6


title: HAI54_Day 6


title: HAI8_Day 6


title: HAI73_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_49

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S517=Feb12_x_x_279_Cell_49


title: HAI12_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_88

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S508=Feb12_x_x_279_Cell_88


title: 24 Y Female run2506_lane12_read1 Cell_96

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN706-S508=Feb12_x_x_279_Cell_96


title: HAI58_Day 6


title: HAI31_Day 6 [2]


title: HAI34_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_95

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN705-S507=Feb12_x_x_279_Cell_95


title: 24 Y Female run2506_lane12_read1 Cell_80

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S508=Feb12_x_x_279_Cell_80


title: HAI43_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_72

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S508=Feb12_x_x_279_Cell_72


title: 24 Y Female run2506_lane12_read1 Cell_79

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S507=Feb12_x_x_279_Cell_79


title: 24 Y Female run2506_lane12_read1 Cell_94

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S506=Feb12_x_x_279_Cell_94


title: 24 Y Female run2506_lane12_read1 Cell_87

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN704-S507=Feb12_x_x_279_Cell_87


title: 24 Y Female run2506_lane12_read1 Cell_93

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S505=Feb12_x_x_279_Cell_93


title: 24 Y Female run2506_lane12_read1 Cell_86

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN703-S506=Feb12_x_x_279_Cell_86


title: 24 Y Female run2506_lane12_read1 Cell_71

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S507=Feb12_x_x_279_Cell_71


title: 24 Y Female run2506_lane12_read1 Cell_64

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S508=Feb12_x_x_279_Cell_64


title: 24 Y Female run2506_lane12_read1 Cell_85

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S505=Feb12_x_x_279_Cell_85


title: 24 Y Female run2506_lane12_read1 Cell_78

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S506=Feb12_x_x_279_Cell_78


title: HAI52_Day 6

description: Gene expression profiling of peripheral blood from influenza infected participant


title: 24 Y Female run2506_lane12_read1 Cell_63

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S507=Feb12_x_x_279_Cell_63


title: HAI31_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_70

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S506=Feb12_x_x_279_Cell_70


title: 24 Y Female run2506_lane12_read1 Cell_92

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN702-S504=Feb12_x_x_279_Cell_92


title: 24 Y Female run2506_lane12_read1 Cell_56

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S508=Feb12_x_x_279_Cell_56


title: HAI67_Day 6


title: PD39_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_77

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S505=Feb12_x_x_279_Cell_77


title: HAI19_Day 6


title: HAI4_Day 6


title: HAI29_Day 6


title: 24 Y Female run2506_lane12_read1 Cell_84

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S504=Feb12_x_x_279_Cell_84


title: 24 Y Female run2506_lane12_read1 Cell_91

description:
24 Y Female
Lin - CD34+ CD38- Hematopoietic Stem and Progenitor cells
run2506_lane12_read1_indexN701-S503=Feb12_x_x_279_Cell_91


title: HAI35_Day 6


title: HAI30_Day 6


title: HAI59_Day 6


title: HAI46_Day 6


title: HAI70_Day 6


title: HAI68_Day 6


title: HAI37_Day 6


title: HAI74_Day 6


title: HAI44_Day 6 [2]


title: HAI44_Day 6


title: HAI65_Day 6


title: BD-8045: RNA-seq subject 36

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Quality assessment was done with FastQC
Alignment to GenCode hg38 was done using  STAR
Genes counts are assigned using the FeatureCounts  tool (subread package)
The final counts were filtered for genes that had less than 3 counts across samples log transformed and quantile normalized. As RNA samples were processed in two separate batched both final datasets were corrected for batch difference with linear regression.
Genome_build: GenCode hg38
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample

molecule: polyA RNA

source_name: whole blood

extract_protocol:
RNA was extracted using the MagMAX\textsuperscript{TM} for Stabilized Blood Tubes RNA Isolation Kit (Fisher) following the manufacturer's protocol.
Libraries were constructed using the TruSeq Stranded mRNA kit (Illumina) at the Epigenetic core at the Weil Cornell medical college. The samples were sequenced SE100 to an average depth of 48.8 million reads.

value: whole blood


title: HAI48_Day 6


title: BD-8044: RNA-seq subject 35


title: BD-8042: RNA-seq subject 33


title: BD-8043: RNA-seq subject 34


title: HAI72_Day 6


title: BD-8041: RNA-seq subject 32


title: BD-8034: RNA-seq subject 30


title: BD-8038: RNA-seq subject 31


title: BD-8033: RNA-seq subject 29


title: BD-8031: RNA-seq subject 27


title: BD-8030: RNA-seq subject 26


title: BD-8032: RNA-seq subject 28


title: HAI36_Day 6


title: BD-8029: RNA-seq subject 25


title: HAI2_Day 6


title: BD-8027: RNA-seq subject 23


title: BD-8028: RNA-seq subject 24


title: BD-8026: RNA-seq subject 22


title: BD-8025: RNA-seq subject 21


title: BD-8021: RNA-seq subject 19


title: HAI47_Day 6


title: HAI49_Day 6


title: BD-8024: RNA-seq subject 20


title: HAI64_Day 6


title: HAI57_Day 6


title: HAI60_Day 6


title: HAI55_Day 6


title: B08020: RNA-seq subject 18


title: HAI45_Day 6


title: B08019: RNA-seq subject 17


title: HAI40_Day 6


title: HAI6_Day 6


title: B08018: RNA-seq subject 16


title: B08017: RNA-seq subject 15


title: PD46_Day 6


title: PD47_Day 6


title: PD41_Day 6


title: B08015: RNA-seq subject 14


title: PD34_Day 6


title: PD45_Day 6


title: PD37_Day 6


title: PD44_Day 6


title: PD38_Day 6


title: PD43_Day 6


title: B08011: RNA-seq subject 11


title: HAI17_Day 6


title: PD42_Day 6


title: B08010: RNA-seq subject 10


title: HAI20_Day 6


title: HAI24_Day 6


title: B08009: RNA-seq subject 9


title: B08008: RNA-seq subject 8


title: B08007: RNA-seq subject 7


title: B08005: RNA-seq subject 5


title: B08006: RNA-seq subject 6


title: HAI21_Day 6


title: HAI15_Day 6


title: B08013: RNA-seq subject 13


title: HAI16_Day 6


title: HAI27_Day 6


title: B08012: RNA-seq subject 12


title: HAI69_Day 6


title: B08002: RNA-seq subject 2


title: B08004: RNA-seq subject 4


title: HAI39_Day 4

source_name: Influenza infection Day 4

value: Day 4


title: B08003: RNA-seq subject 3


title: HAI34_Day 4


title: HAI41_Day 4


title: HAI51_Day 4


title: HAI42_Day 4


title: HAI28_Day 6


title: Sample 21_Neural induction +dox D6 rep1 RNAseq

city: Durham

first: Lee

middle: F

last: Langer

state: NC

address: 111 TW Alexander Dr

department: ESCBL

institute: NIEHS

data_processing:
Samples 1–12:
Quality trimmed with sickle (default parameters)
Adaptor removal with cutadapt (1.8.1 with Python 2.7.9)
Algined with STAR_2.5.1b with the following parameters: --runThreadN 5 --outReadsUnmapped Fastx   --outMultimapperOrder Random  --outSAMtype BAM   SortedByCoordinate   Unsorted --outWigType bedGraph      --outWigStrand Stranded      --outWigNorm None      --outFilterType Normal   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1
bam file converted to positive and negative bw files
Samples 13–18:
Quality trimmed with sickle (default parameters)
Adaptor removal with cutadapt (1.12 with Python 2.7.13)
Aligned with bowtie2 VN:2.3.0 with the following parameters:  --wrapper basic-0 -x hg19 -X 2000 -N 1 -p 8 --no-mixed --dovetail --no-discordant --passthrough -1
Removal of mitochondrial reads and non-uniquely aligned reads by filtering out .bam file entries with XS tag
Deduplication with PICARD VN:1.110(1752):  MarkDuplicates.jar MAX_RECORDS_IN_RAM=5000000 VERBOSITY=DEBUG REMOVE_DUPLICATES=true ASSUME_SORTED=true
Collection of nucleosome-free reads by collecting all fragments less than or equal to 135 bp in length
Peak-calling with macs2; macs2 callpeak --nomodel -t {} -n {.} --nolambda --keep-dup all --slocal 10000 -q 0.005
Removal of regions that are prone to false positives by reverse filtering with seq.cov1.ONHG19_sort.bed; http://eqtl.uchicago.edu/Masking/
Samples 19-22:
Quality trimmed with sickle (default parameters, except for "-q 26")
Adaptor removal with cutadapt (cutadapt 1.8.1 with Python 2.7.9)
Algined with STAR_2.5.1b with the following parameters: --outReadsUnmapped Fastx   --outMultimapperOrder Random   --outSAMtype BAM   SortedByCoordinate   Unsorted      --outWigType bedGraph      --outWigStrand Stranded      --outWigNorm None      --outFilterType Normal   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1
bam file converted to positive and negative bw files
Samples 23–30:
Quality trimmed with sickle (default parameters)
Adaptor removal with cutadapt 1.14 with Python 2.7.9
Aligned with bowtie2 VN:2.3.2 with the following parameters: --wrapper basic-0 -x hg19 -X 2000 -N 1 -p 20 --no-mixed --dovetail --no-discordant --passthrough -1
Removal of mitochondrial reads and non-uniquely aligned reads by filtering out .bam file entries with XS tag
Deduplication with Picard VN:1.122: MarkDuplicates.jar MAX_RECORDS_IN_RAM=5000000 VERBOSITY=DEBUG REMOVE_DUPLICATES=true ASSUME_SORTED=true
Collection of nucleosome-free reads by collecting all fragments less than or equal to 135 bp in length
Peak calling with macs2: macs2 callpeak --nomodel -t {} -n {.} --nolambda --keep-dup all --slocal 10000 -q 0.005
Removal of regions that are prone to false positives by reverse filtering with seq.cov1.ONHG19_sort.bed; http://eqtl.uchicago.edu/Masking/
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (sample 1-12, 19-22), bed file with called peaks (sample 13-18, 23-30)

source_name: Neural induction +dox D6

growth_protocol: Neural induction was performed as per the STEMCELL Technology instructions for neural induction using STEMDiffTM Neural Induction Media (#05835)

extract_protocol:
Cells were collected in Accutase (10 min, 27˚), rinsed 1x in PBS, and frozen at -80˚ until use. RNA was isolated with a Norogen total RNA Purification Plus Kit
Total RNA with ribo-Zero for RNAseq

treatment_protocol: 1 µg/ml doxycycline in sterile PBS/day

tag: cell line

value: H1 hESCs

value: human embryonic stem cells

tag: treatment

value: Neural induction +dox D


title: Sample 20_Neural induction -dox D6 rep2 RNAseq

source_name: Neural induction -dox D6

treatment_protocol: No treatment

value: Neural induction -dox D


title: Sample 22_Neural induction +dox D6 rep2 RNAseq


title: Sample 19_Neural induction -dox D6 rep1 RNAseq


title: Sample 9_BAF47-targeting shRNA D0 rep3 RNAseq

source_name: BAF47-targeting shRNA D0

growth_protocol: H1 hESCs were cultured in TeSR™-E8™ growth medium (STEMCELL Technologies, #05990) at 37˚ C in a 5% CO2 atmosphere. Cells were grown feeder-free on a substrate of hESC-qualified MatrigelTM Matrix (Corning™ #354277).

extract_protocol:
Cells were rinsed 3x in cold PBS, collected by scraping, spun at 500g for 3 min, and stored at -80 until use. RNA was isolated with a Norogen total RNA Purification Plus Kit
Total RNA with ribo-Zero for RNAseq

value: H1 hESCs (WA01)

tag: genotype/variation

value: BAF47-targeting shRNA


title: Sample 12_BAF47-targeting shRNA D3 rep3 RNAseq

source_name: BAF47-targeting shRNA D3

value: 1 µg/ml doxycycline in sterile PBS/day


title: Sample 10_BAF47-targeting shRNA D3 rep1 RNAseq


title: Sample 11_BAF47-targeting shRNA D3 rep2 RNAseq


title: B08001: RNA-seq subject 1


title: HAI5_Day 4


title: HAI61_Day 4


title: HAI3_Day 4


title: Sample 8_BAF47-targeting shRNA D0 rep2 RNAseq


title: HAI53_Day 4


title: HAI50_Day 4


title: Sample 6_Non-targeting control shRNA D3 rep3 RNAseq

source_name: Non-targeting control shRNA D3

value: Non-targeting control shRNA


title: HAI63_Day 4


title: Sample 5_Non-targeting control shRNA D3 rep2 RNAseq


title: Sample 7_BAF47-targeting shRNA D0 rep1 RNAseq


title: Sample 4_Non-targeting control shRNA D3 rep1 RNAseq


title: HAI33_Day 4


title: HAI22_Day 4


title: HAI1_Day 4


title: HAI23_Day 4


title: Input-PP1-KO1

first: Hyein

middle: Sophia

last: Cho

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Align to hg19 reference genome using bowtie2 2.2.5
Peak calling to generate signal tracks on on individual replicates using macs2 2.1.1.20160309 with options -B -p 1e-2 using corresponding input
Genome_build: hg19
Supplementary_files_format_and_content: Coverage track in bigWig format

molecule: genomic DNA

source_name: ES-derived progenitors

growth_protocol: ES cells were maintained using complete Essential 8 media, and ES-derived progenitors were generated by differentiation meida described below. When ES cells reach 80 - 90% confluence, directed differentiation was initiated (d0). ES cells were differentiated to day 3 definitive endoderm (DE) stage with 100 ng/ml of Activin A and GSK-3 inhibitor, CHIR-99021. Foregut (FG) stage was induced by 0.25mM L-Ascorbic acid and 50ug/ml of FGF7 and harvested on day 5. Afterward, 1mM of hedgehog inhibitor, SANT-1, 10mM of retinoic acid, and 400uM of BMP inhibitor, LDN were used to generate PDX1+ early pancreatic progenitor 1 (PP1) cells on day 7 and the PDX1+NKX6.1+ pancreatic progenitor (PP2) on day 10.

extract_protocol:
Cells were crosslinked by formaldehyde and lysated by SDS lysis buffer. Sonicated nuclei were incubated with antibody overnight and then pulled down by dynabeads. After washing, decrosslinking was performed to isolate DNA.
Libraries were prepared using the NEBNext® ChIP-seq Library Prep Master Mix Set for Illumina ® (NEB, E6240L)

value: ES-derived progenitors

tag: differentiation stages

value: Pancreatic Progenitors 1

tag: genotype

value: FOXA2 -/-


title: Sample 1_Non-targeting control shRNA D0 rep1 RNAseq

source_name: Non-targeting control shRNA D0


title: HAI18_Day 4


title: HAI7_Day 4


title: HAI71_Day 4


title: PD48_Day 4


title: HAI62_Day 4


title: HAI56_Day 4


title: Input-FG-KO1

value: Foregut


title: HAI32_Day 4

value: Blood


title: Input-DE-KO1

value: Definitive Endoderm


title: Sample 3_Non-targeting control shRNA D0 rep3 RNAseq


title: Input-PP1-WT1

value: wild type


title: Input-PP1-WT2


title: Input-PP1-WT3


title: Sample 2_Non-targeting control shRNA D0 rep2 RNAseq


title: Input-FG-WT1


title: Input-DE-WT2


title: Input-FG-WT2


title: HAI43_Day 4 [2]

value: Influenza virus infection


title: PD40_Day 4

value: Day 4


title: HAI31_Day 4


title: HAI58_Day 4


title: HAI43_Day 4


title: HAI72_Day 4


title: HAI54_Day 4


title: PDX1-PP1-WT1


title: PDX1-PP1-WT2


title: PD39_Day 4


title: HAI73_Day 4


title: HAI29_Day 4


title: HAI46_Day 4


title: HAI52_Day 4


title: HAI19_Day 4


title: HAI26_Day 4


title: HAI59_Day 4 [2]


title: HNF1B-FG-WT1


title: FOXA2-PP1-WT2


title: FOXA2-FG-WT1


title: FOXA2-FG-WT2


title: FOXA2-PP1-WT1


title: Input-DE-WT1


title: HNF1B-FG-WT2


title: HAI2_Day 4


title: FOXA2-DE-WT2


title: FOXA2-DE-WT1


title: HAI67_Day 4


title: HAI69_Day 4


title: GATA4-PP1-WT2


title: HAI68_Day 4


title: GATA4-PP1-WT1


title: HAI30_Day 4


title: GATA4-FG-WT1


title: GATA4-DE-WT2


title: HAI70_Day 4


title: GATA6-PP1-KO2


title: GATA4-FG-WT2


title: GATA6-FG-KO2


title: GATA6-PP1-KO1


title: GATA6-FG-KO1


title: HAI35_Day 4


title: HAI44_Day 4


title: GATA6-DE-KO1


title: HAI37_Day 4


title: HAI4_Day 4


title: HAI59_Day 4


title: HAI45_Day 4


title: HAI40_Day 4


title: HAI36_Day 4


title: GATA4-DE-WT1


title: HAI47_Day 4


title: HAI48_Day 4


title: HAI6_Day 4


title: HAI49_Day 4


title: GATA6-PP1-WT2


title: HAI74_Day 4


title: GATA6-FG-WT2


title: GATA6-FG-WT1


title: GATA6-PP1-WT1


title: GATA6-DE-WT1


title: H3K27ac-PP1-KO2


title: GATA6-DE-KO2


title: GATA6-DE-WT2


title: H3K27ac-PP1-KO1


title: H3K27ac-FG-KO2


title: HAI57_Day 4


title: HAI55_Day 4


title: PD41_Day 4


title: H3K27ac-PP1-WT2


title: PD46_Day 4


title: HAI65_Day 4


title: PD47_Day 4


title: HAI64_Day 4


title: H3K27ac-FG-WT1


title: H3K27ac-FG-WT2


title: PD38_Day 4


title: PD37_Day 4


title: H3K27ac-DE-KO1


title: H3K27ac-DE-WT2


title: PD44_Day 4


title: PD34_Day 4


title: H3K27ac-DE-WT1


title: H3K27ac-FG-KO1


title: PD43_Day 4


title: H3K4me1-PP1-KO2


title: PD42_Day 4


title: H3K27ac-DE-KO2


title: HAI24_Day 4


title: HAI27_Day 4


title: H3K27ac-PP1-WT1


title: HAI28_Day 4


title: HAI16_Day 4


title: PD45_Day 4


title: H3K4me1-PP1-KO1


title: H3K4me1-FG-KO2


title: HAI15_Day 4


title: H3K4me1-FG-KO1


title: H3K4me1-DE-KO2


title: HAI17_Day 4


title: H3K4me1-DE-KO1


title: H3K4me1-PP1-WT1


title: H3K4me1-FG-WT1


title: H3K4me1-PP1-WT2


title: H3K4me1-FG-WT2


title: ATAC-seq_PP1-FOXA2 KO2

data_processing:
Align to hg19 reference genome using bowtie2 2.2.5
Peak calling to generate signal tracks on on individual replicates using macs2 2.1.1.20160309 with options -B -p 1e-2 --shift -100 --extsize 200
Genome_build: hg19
Supplementary_files_format_and_content: Coverage track in bigWig format

growth_protocol: ES cells were maintained using complete Essential 8 media, and ES-derived progenitors were generated by differentiation media described below. When ES cells reach 80 - 90% confluence, directed differentiation was initiated (d0). ES cells were differentiated to day 3 definitive endoderm (DE) stage with 100 ng/ml of Activin A and GSK-3 inhibitor, CHIR-99021. Foregut (FG) stage was induced by 0.25mM L-Ascorbic acid and 50ug/ml of FGF7 and harvested on day 5. Afterward, 1mM of hedgehog inhibitor, SANT-1, 10mM of retinoic acid, and 400uM of BMP inhibitor, LDN were used to generate PDX1+ early pancreatic progenitor 1 (PP1) cells on day 7.

extract_protocol:
50,000 cells were lysed in ATAC lysis buffer and tagmented (Illumina Nextera DNA Library Preparation Kit). After adding SDS, the samples were purified with 2X Agencourt AMPure XP beads (Beckman Coulter A63881)
Samples were amplified using NEBNext Q5 Hot Start HiFi PCR Master Mix. The concentration of samples was checked using PicoGreen and median fragment size was checked using the Agilent D1000 screentape on the Agilent Technologies 2200 TapeStation. Samples were sequenced PE50 on a HiSeq 2500.

tag: differentiation stage


title: ATAC-seq_PP1-FOXA2 KO1


title: HAI21_Day 4


title: ATAC-seq_PP1-WT1


title: HAI34_Day 2

source_name: Influenza infection Day 2

value: Day 2


title: HAI7_Day 2


title: HAI41_Day 2


title: HAI11_Day 2


title: HAI10_Day 2


title: HAI39_Day 2


title: HAI1_Day 2


title: HAI20_Day 4


title: HAI50_Day 2


title: ATAC-seq_PP1-WT2


title: HAI42_Day 2


title: ATAC-seq_FG-FOXA2 KO2


title: HAI5_Day 2


title: HAI3_Day 2


title: H3K4me1-DE-WT2


title: H3K4me1-DE-WT1


title: HAI53_Day 2


title: ATAC-seq_FG-WT2


title: ATAC-seq_DE-FOXA2 KO2


title: ATAC-seq_DE-FOXA2 KO1


title: ATAC-seq_FG-WT1


title: ATAC-seq_FG-FOXA2 KO1


title: HAI61_Day 2


title: ATAC-seq_DE-WT1


title: HAI23_Day 2


title: HAI63_Day 2


title: HAI51_Day 2


title: HAI33_Day 2


title: ATAC-seq_DE-WT2


title: ATAC-seq_ES-WT2

source_name: Embryonic Stem cells

value: Embryonic Stem cells


title: HAI14_Day 2


title: ATAC-seq_ES-WT1


title: HAI62_Day 2


title: HAI18_Day 2


title: HAI9_Day 2


title: RNA-seq_PP2-FOXA2 KO3

data_processing:
Align to hg19 and GENCODE v19 using STAR 2.5.3a
Gene quantification by --quantMode GeneCounts option in STAR
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification count in txt format

growth_protocol: ES cells were maintained using complete Essential 8 media, and ES-derived progenitors were generated by differentiation media described below. When ES cells reach 80 - 90% confluence, directed differentiation was initiated (d0). ES cells were differentiated to day 3 definitive endoderm (DE) stage with 100 ng/ml of Activin A and GSK-3 inhibitor, CHIR-99021. Foregut (FG) stage was induced by 0.25mM L-Ascorbic acid and 50ug/ml of FGF7 and harvested on day 5. Afterward, 1mM of hedgehog inhibitor, SANT-1, 10mM of retinoic acid, and 400uM of BMP inhibitor, LDN were used to generate PDX1+ early pancreatic progenitor 1 (PP1) cells on day 7 and the PDX1+NKX6.1+ pancreatic progenitor (PP2) on day 10.

extract_protocol:
Cells were lysed in TRIzol (Thermo Fisher Scientific, 15596018) and total RNA was isolated using the miRNeasy Mini Kit (QIAGEN, 217004).
RNA libraries were prepared for sequencing using standard Illumina protocols; 3' RNA-Seq

value: Pancreatic Progenitors 2


title: RNA-seq_PP2-FOXA2 KO1


title: RNA-seq_PP2-WT3


title: RNA-seq_PP2-FOXA2 KO2


title: RNA-seq_PP2-WT2


title: HAI71_Day 2


title: RNA-seq_PP1-FOXA2 KO3


title: JW14-4B-193A

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using Bowtie v2
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated values files including FPKM values for each sample.

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted from the bone marrows of mice transplanted with IM-induced leukemias using TRIzol. Phenol-chloroform-isoamyl extraction and ethanol precipitation were performed. Total RNA (1 μg) was treated with DNase I at room temperature for 15 min. The integrity of the DNase I-treated RNA was analyzed on an Agilent 2100 Bioanalyzer before selection of poly(A) mRNA. Selection for poly(A) mRNA and subsequent cDNA synthesis and library preparation were carried out using the Illumina TruSeq RNA sample preparation kit according to the manufacturer's protocol. cDNA was fragmented (200-bp peak) with a Covaris E210 ultrasonicator prior to library preparation.
cDNA libraries were prepared for sequecing using standard Illumina protocols

treatment_protocol: Not applicable

value: Leukemia

tag: strain

value: C57Bl/6 x 129Sv/Jae F1

tag: mutagen


title: JW81-59B-202A


title: JW81-59B-200A


title: RNA-seq_PP1-FOXA2 KO1


title: RNA-seq_PP2-WT1


title: JW14-4B-192A


title: PD40_Day 2


title: HAI12_Day 2


title: HAI54_Day 2


title: RNA-seq_PP1-WT3


title: 8633-18B-270A


title: HAI73_Day 2


title: HAI72_Day 2


title: HAI56_Day 2


title: RNA-seq_PP1-FOXA2 KO2


title: HAI32_Day 2


title: RNA-seq_PP1-WT2


title: HAI43_Day 2


title: 8633-18B-269A


title: HAI8_Day 2


title: HAI31_Day 2


title: HAI29_Day 2


title: HAI58_Day 2


title: RNA-seq_PP1-WT1


title: PD48_Day 2


title: PD39_Day 2


title: HAI52_Day 2


title: HAI46_Day 2


title: 4638-73B-220B


title: 4638-73B-216A


title: RNA-seq_FG-FOXA2 KO3


title: HAI59_Day 2 [2]


title: RNA-seq_FG-FOXA2 KO1


title: RNA-seq_FG-WT3


title: 5C-29B-180A


title: 20M-116B-225A


title: 5C-29B-117A


title: 20M-116B-226A


title: RNA-seq_FG-FOXA2 KO2


title: RNA-seq_FG-WT2


title: RNA-seq_FG-WT1


title: 2M-127B-262AA


title: HAI70_Day 2


title: HAI30_Day 2


title: HAI19_Day 2


title: HAI44_Day 2


title: RNA-seq_DE-FOXA2 KO3


title: HAI26_Day 2


title: HAI59_Day 2


title: 2M-127B-259A


title: HAI35_Day 2


title: HAI2_Day 2


title: HAI67_Day 2


title: HAI74_Day 2


title: RNA-seq_DE-FOXA2 KO2


title: HAI37_Day 2


title: HAI68_Day 2


title: HAI69_Day 2


title: 78A-143B-190A


title: HAI40_Day 2


title: HAI36_Day 2


title: RNA-seq_DE-WT3


title: 73M-19A-249A


title: RNA-seq_DE-FOXA2 KO1


title: 78A-143B-191A


title: HAI48_Day 2


title: RNA-seq_DE-WT2


title: HAI49_Day 2


title: 73M-19A-243A


title: RNA-seq_DE-WT1


title: 73A-46B-183B


title: HAI60_Day 2


title: RNA-seq_ES-FOXA2 KO2


title: HAI47_Day 2


title: HAI45_Day 2


title: HAI65_Day 2


title: 73A-46B-183A


title: HAI4_Day 2


title: RNA-seq_ES-WT3


title: HAI55_Day 2


title: HAI57_Day 2


title: HAI6_Day 2


title: RNA-seq_ES-FOXA2 KO3


title: H2C KD tumor sh4 expt 3 mouse 3

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
The total RNA sequence data for the cell lines were aligned to mm10/GRCm38 with GENCODE vM13 primary assembly using STAR 2.7. The parameter sjdbOverhang for the length of the genomic sequence around the annotated junction is 100.
The RNA sequence data for the tumors  were aligned to the mouse genome NCBI37/mm9 using TopHat 2.1.0.
Sequencing reads were mapped using BWA and/or Bowtie using the mouse mm10 reference genome. Variant calling was performed using mpileup and/or GATK HaplotypeCaller. Germline variants in the Mouse Genome Project (mgp.v5) were filtered out; low quality variants (quality score ≤ 30) were also removed. Remaining variants were annotated using Annovar to identify nonsynonymous single nucleotide variants and indels.
Genome_build: NCBI37/mm9 for RNAseq and mm10 for exome-seq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and vcf files for each Sample

source_name: H2C KD tumor sh4

growth_protocol: Mvt1 mouse mammary carcinoma cell lines containing shRNA-mediated knockdown of Rnaseh2c or a scramble control shRNA were cultured in DMEM containing 10% FBS, 1% Penacillin and Streptomycin, 1% glutamine, and 10ug/mL puromycin for shRNA selection. Cells were cultured at 37 degrees C with 5% CO2 and passaged at approximatly 1:10 dilution every 2-3 days.

extract_protocol:
RNA was extracted from small sections of primary tumor tissue using TriPure, followed by organic extraction with chloroform and precipitation by isopropanol. RNA was then purified using the RNeasy® Mini Kit (Qiagen) with on-column DNase digestion. RNA quality was tested using the Agilent 2200 TapeStation electrophoresis system, and samples with an RNA integrity number (RIN) score >7 were sent for sequencing .
For mRNA samples: mRNA sequencing was performed using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry. Sample reads were trimmed to remove adapters and low-quality bases using Trimmomatic software and aligned with the reference mouse mm9 genome and Ensemble v70 transcripts using Tophat software. RNA mapping statistics were calculated using Picard software. Library complexity was measured by unique fragments in the mapped reads using Picard’s MarkDuplicate utility.

treatment_protocol: Mvt1 mouse mammary carcinoma cell lines were transduced with either scramble control or Rnaseh2c-targetting shRNA (sh4).

value: FVB

tag: in vivo timepoint

value: 30 days post tumor implantation

value: primary mammary tumors

value: Rnaseh2c knockdown


title: H2C KD tumor sh4 expt 1 mouse 10


title: HAI64_Day 2


title: PD47_Day 2


title: RNA-seq_ES-FOXA2 KO1


title: RNA-seq_ES-WT2


title: H2C KD tumor scr expt 3 mouse 8

source_name: H2C KD tumor scr


title: RNA-seq_ES-WT1


title: H2C KD tumor sh4 expt 2 mouse 4


title: H2C KD tumor scr expt 2 mouse 4


title: PD46_Day 2


title: 99x3s3

city: Buffalo

first: Erik

last: Knudsen

address: 665 Elm St.

department: Molecular & Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
RNA-sequencing was performed on total RNA using Illumina HiSeq.
RNA reads were aligned using Tophat2.
Counts were generated from aligned BAM files using HTSeq.
Counts from human aligned genes were log-normalized using the edgeR R package.
Genome_build: Hg19 with mm10 concatenated
Supplementary_files_format_and_content: tab-delimited text file (gene sample expression matrix) includes gene TMM normalized values for each sample

source_name: Patient derived xenograft - pancreatic cancer

growth_protocol: Mice were implanted subcutaneously with the established PDX models. When tumors reached a volume of 200 mm3 they were randomized to treatment cohorts.

extract_protocol:
RNA was isolated from snap frozen tumor tissue using RNeasy Plus Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated by gastric gavage with vehicle control, single agent Palbociclib (PD-0332991, 100 mg/kg) diluted in 50 mM lactate buffer at pH 4.0, or the combination with TAK-228 (MLN0128, 0.5 mg/kg) diluted in 30% PEG400, 0.5% Tween 80, and 5% propylene glycol.  Mice were treated daily for 5 days then tissue was collected for sequencing.

value: Patient derived xenograft

value: palbociclib

tag: disease state

value: pancreatic cancer

tag: tumor source


title: H2C KD tumor scr expt 1 mouse 7


title: PD38_Day 2 [2]

value: Blood


title: PD34_Day 2


title: H2C KD cell line sh4 plate 3

source_name: H2C KD cell line sh4


title: 99x3p4

value: vehicle control


title: PD44_Day 2


title: 99x3p3

value: palbociclib + TAK228


title: 99x3p2


title: H2C KD cell line sh4 plate 1


title: H2C KD cell line sh4 plate 2


title: HAI17_Day 2

value: Influenza virus infection


title: PD38_Day 2


title: H2C KD cell line scr plate 3

source_name: H2C KD cell line scr

value: wild type


title: PD45_Day 2

value: Day 2


title: 99x3q5


title: 99x3m1


title: HAI28_Day 2


title: 99x3k2


title: PD43_Day 2


title: PD41_Day 2


title: H2C KD cell line scr plate 1


title: 99x3j3


title: HAI16_Day 2


title: H2C KD lung met sh4 mouse 8 met 2

data_processing:
library strategy: exome-seq
The total RNA sequence data for the cell lines were aligned to mm10/GRCm38 with GENCODE vM13 primary assembly using STAR 2.7. The parameter sjdbOverhang for the length of the genomic sequence around the annotated junction is 100.
The RNA sequence data for the tumors  were aligned to the mouse genome NCBI37/mm9 using TopHat 2.1.0.
Sequencing reads were mapped using BWA and/or Bowtie using the mouse mm10 reference genome. Variant calling was performed using mpileup and/or GATK HaplotypeCaller. Germline variants in the Mouse Genome Project (mgp.v5) were filtered out; low quality variants (quality score ≤ 30) were also removed. Remaining variants were annotated using Annovar to identify nonsynonymous single nucleotide variants and indels.
Genome_build: NCBI37/mm9 for RNAseq and mm10 for exome-seq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and vcf files for each Sample

source_name: H2C KD lung met sh4 mouse

extract_protocol:
Metastases were dissociated using a sterile disposable pestle in a microcentrifuge tube in tail lysis buffer (100 mM Tris pH8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl). 160 ug of Proteinase K (Invitrogen) was added to the tube and contents were incubated at 55 ℃ overnight then for an additional 1hr with shaking at 1400 rpm. Genomic DNA was then isolated from the dissociated metastases using the DNA miniprep kit (Zymo Research) according to the manufacturer’s instructions. DNA quality was tested using the Agilent 2200 TapeStation electrophoresis system, and samples were sent for sequencing
For mRNA samples: mRNA sequencing was performed using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry. Sample reads were trimmed to remove adapters and low-quality bases using Trimmomatic software and aligned with the reference mouse mm9 genome and Ensemble v70 transcripts using Tophat software. RNA mapping statistics were calculated using Picard software. Library complexity was measured by unique fragments in the mapped reads using Picard’s MarkDuplicate utility.

value: pulmonary metastasis


title: H2C KD cell line scr plate 2


title: HAI20_Day 2


title: PD42_Day 2


title: HAI15_Day 2


title: HAI21_Day 2


title: PD37_Day 2


title: HAI27_Day 2


title: HAI24_Day 2


title: HAI42_Day 1

source_name: Influenza infection Day 1

value: Day 1


title: 99x3j1


title: HAI39_Day 1


title: H2C KD lung met sh4 mouse 8 met 1


title: HAI9_Day 1


title: HAI51_Day 1


title: HAI50_Day 1


title: HAI11_Day 1


title: HAI41_Day 1


title: HAI3_Day 1


title: H2C KD lung met sh4 mouse 2 met 1


title: 97x4i5


title: HAI1_Day 1


title: 97x4j1-2


title: H2C KD lung met sh4 mouse 10 met 1


title: 97x4i3


title: HAI7_Day 1


title: H2C KD lung met scr mouse 9 met 1

source_name: H2C KD lung met scr mouse


title: HAI5_Day 1


title: H2C KD lung met scr mouse 8 met 1


title: 97x4i2


title: HAI61_Day 1


title: HAI53_Day 1


title: HAI63_Day 1


title: H2C KD lung met scr mouse 7 met 2


title: 97x4i1


title: 97x4h1


title: 97x4j1


title: RNA_LRH-1_cKO_+OvS

city: Sherbrooke

first: Nicolas

last: Gévry

state: Québec

address: 2500 boulevard de l'université

country: Canada

institute: Université de Sherbrooke

description: 3 replicats

data_processing:
For RNA-seq, reads were filtered using Trimmomatic and aligned to the mouse reference genome mm9 using TopHat (2.0.12). Quantification of transcript abundances was performed using Kallisto. Generated data were normalized using Remove Unwanted Variation using control genes (RUVg) from RUVseq. The DESeq2 R package was then used to generate differential gene expression analysis.
Genome_build: mm9

source_name: ovarian granulosa cells

extract_protocol:
Total RNA from granulosa cells of CTL or LRH-1 cKO mice following 0 and 4h post hCG was extracted with RNeasy Mini Kits (Qiagen) as per the manufacturer’s instructions.
Librairies were performed as previously described (Baby et al., ACS Synth Biol, 2018) starting with 300 ng of RNA

treatment_protocol: Granulosa-specific depletion of LRH-1 (Nr5a2) from primary follicle forward was generated by crossing Nr5a2 floxed (Nr5a2 f/f) mice with mice expressing Cre-recombinase driven by the anti-Müllerian type II receptor (Amhr2 Cre/+) to produce conditional knockout (cKO) mice (genotype Nr5a2 f/f Amhr2 Cre/+). Control mice (CTL) correspond to non-mutant, Nr5a2 f/f Amhr2 Cre/- females. Super stimulation was achieved in 22- to 25-day-old mice by intraperitoneal injection of 5 IU equine chorionic gonadotropin (eCG) to stimulate follicular development, followed by the injection of 5 IU of human chorionic gonadodotropin (hCG) 44 hours post eCG, to induce ovulation. After euthanasia, ovaries were collected and granulosa cells were isolated by ovarian puncture at 0 hours (-OvS) and 4 hours post hCG (+OvS).

value: ovarian granulosa cells


title: HAI33_Day 1


title: RNA_LRH-1_cKO_-OvS

description: 3 replicats


title: HAI34_Day 1


title: HAI18_Day 1


title: HAI62_Day 1


title: HAI10_Day 1


title: 97x4g4


title: 97x4g1


title: HAI32_Day 1


title: 828x5j5


title: H2C KD lung met scr mouse 7 met 1


title: RNA_LRH-1_CTL_+OvS

description: 3 replicats


title: RNA_LRH-1_CTL_-OvS

description: 3 replicats


title: HAI23_Day 1


title: HAI71_Day 1


title: HAI14_Day 1


title: HAI22_Day 1


title: 828x5j1


title: embryo7-2,1,P target site amplicon

first: Michelle

middle: M

last: Chan

institute: UCSF

description:
CRISPR-based lineage traced embryo
processed data file: embryo7_BestTree17507.nwt.txt

data_processing:
10x cellranger v2.0.1
Normalization in Seurat ("LogNormalize")
Genome_build: mm10
Supplementary_files_format_and_content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); allele table containing filtered lineage tracer calls.
Supplementary_files_format_and_content: *nwt.txt: Newick files represent the best reconstructed tree. embryo2_BestTreeGreedy.nwt.txt represents the final tree for the embryo2a and embryo2b samples merged.

source_name: E8.5 embryo

growth_protocol: Mouse embryos were cultured in vitro in KSOM at 37 ºC in 5% CO2 from the zygote to the blastocyst stage and subsequently transferred into the uterine horns of pseudopregnant females until isolation 6 or 7 days later.

extract_protocol:
Embryos were dissociated to single cell suspensions by adding 100 uL of TrypLE (Invitrogen, #12605010) and pipetting the embryo or embryo pieces every 5 minutes for ~30 minutes until complete dissociation was visually confirmed.  Trypsin was deactivated by adding 100 uL  PBS+BSA is added to the droplet and moving cells into a 1.5 mL eppendorf tube, followed by several rounds of additional collection with 100 to 200 uL of PBS+BSA to a final volume of 1 mL. Single cells were lysed in droplets using the 10x Chromium instrument.
10X Genomics Chromium Prep v2; PCR enrichment of target site amplicon from 10x cDNA pool. Refer to Methods in manuscript for primers sequences and PCR conditions.

treatment_protocol: To enable in vivo lineage tracing, B6D2F1 strain female mice (age 6 to 8 weeks, Jackson Labs) were superovulated by sequential intraperitoneal injection of Pregnant Mare Serum Gonadotropin (5IU per mouse, Prospec Protein Specialists) and Human Chorionic Gonadotropin (5IU, Millipore) 46 hours apart.  Twelve hours after delivery of the second hormone, MII stage oocytes were isolated and injected with in vitro transcribed piggyBAC transposase mRNA (100 ng/ul) prepared in an injection buffer (5 mM Tris buffer, 0.1 mM EDTA, pH = 7.4).  Decapitated sperm isolated from an 8 week old Gt(ROSA)26Sortm1.1(CAG=cas9*,EGFP)Fezh/J strain mouse (Jackson labs, PMID 25263330) was resuspended with the purified piggyBAC library in the same injection buffer at concentrations ranging from 0.5 to 1.4 ug/uL.  Transposase-injected oocytes were then fertilized by piezo-actuated intracytoplasmic sperm injection (ICSI) as previously described (PMID 17406589).  Injected embryos were cultured in 25 uL EmbryoMax® KSOM drops (Millipore) covered in mineral oil (Irvine Scientific) in batches of 25-50 embryos.  After 84 or 96 hours, successfully cavitated blastocysts were screened for uniform fluorescence of the target sequence cassette and transferred into one uterine horn of 6-10 week old pseudopregnant CD-1 strain female mice (Charles River).  Uterine transfer results in an ~24 hour lag, so the day of transfer was scored as E2.5 and embryos were dissected from euthanized animals 6 or 7 days later at ~E8.5 or E9.5, depending on the experiment.

value: whole embryo


title: 828x5h2


title: PD40_Day 1


title: embryo6-2,1,2 target site amplicon

description:
CRISPR-based lineage traced embryo
processed data file: embryo6_BestTreeGreedy.nwt.txt


title: HAI58_Day 1


title: HAI29_Day 1


title: HAI12_Day 1


title: HAI30_Day 1


title: HAI8_Day 1


title: HAI56_Day 1


title: HAI73_Day 1 [2]


title: 828x5e5


title: embryo5-2,1,2 target site amplicon

description:
CRISPR-based lineage traced embryo
processed data file: embryo5_BestTree2366.nwt.txt


title: 828x5d4


title: HAI43_Day 1 [2]


title: HAI43_Day 1


title: embryo3-1,1,1 target site amplicon

description:
CRISPR-based lineage traced embryo
processed data file: embryo3_BestTreeGreedy.nwt.txt


title: HAI73_Day 1


title: embryo4-2,1,2 target site amplicon

description: CRISPR-based lineage traced embryo


title: HAI54_Day 1


title: 828x5b2


title: embryo2b-1,1,1 target site amplicon

description:
CRISPR-based lineage traced embryo
processed data file: embryo2_BestTreeGreedy.nwt.txt


title: 828x5c2


title: 828x5b1


title: embryo2a-1,1,1 target site amplicon


title: 828x5a5


title: embryo1-P,1,P target site amplicon

description:
CRISPR-based lineage traced embryo
processed data file: embryo1_BestTree8420.nwt.txt


title: 827x4i4


title: PD48_Day 1


title: 827x4i3