title: 36Y Female HSCe 61

description: run1907_lane12_read1_indexN708-S505=Oct26_Cell_29


title: 36Y Female HSCe 60

status: Public on May 11 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: run1907_lane12_read1_indexN708-S504=Oct26_Cell_36

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 an 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:
Single cell CD34+CD38- HSCe were prepared using the C1™ Single-Cell Auto Prep System (Fluidigm, San Fransisco, CA), according to the manufacturer’s instructions. Flow-sorted cells were counted and resuspended at a concentration of 350 cells per mL PBS then loaded onto a primed C1 Single-Cell Auto Prep Integrated Fluidic Chip for mRNA-Seq (5-10 mm).
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

treatment_protocol: Miltenyi Automacs Pro separator (Miltenyi, San Diego, CA) was used to enrich bone marrow MNC for CD34+ cells. The CD34+ fraction was then stained with lineage antibodies conjugated to PerCP-Cy™5.5: CD2, CD3, CD4, CD7, CD10, CD11b, CD14, CD19, CD20, CD24, CD56, CD66b, Glycophorin A, and CD90-biotin, followed by Streptavidin APC-Cy7, CD123-PE, CD34-APC, CD38-PE-Cy7, and CD45RA-FITC. Cell sorting was performed on a BD FACSAria II with a 100 um nozzle.

tag: cell type

value: Lin - CD34+ CD38- Hematopoietic Stem Cell Enriched

tag: donor sex

value: F

tag: donor age


title: 36Y Female HSCe 57

description: run1907_lane12_read1_indexN707-S517=Oct26_Cell_49


title: 36Y Female HSCe 58

description: run1907_lane12_read1_indexN708-S502=Oct26_Cell_50


title: 36Y Female HSCe 59

description: run1907_lane12_read1_indexN708-S503=Oct26_Cell_43


title: 36Y Female HSCe 62

description: run1907_lane12_read1_indexN708-S506=Oct26_Cell_22


title: 36Y Female HSCe 54

description: run1907_lane12_read1_indexN707-S505=Oct26_Cell_21


title: 36Y Female HSCe 53

description: run1907_lane12_read1_indexN707-S504=Oct26_Cell_28


title: 36Y Female HSCe 55

description: run1907_lane12_read1_indexN707-S506=Oct26_Cell_14


title: 36Y Female HSCe 52

description: run1907_lane12_read1_indexN707-S503=Oct26_Cell_35


title: 36Y Female HSCe 56

description: run1907_lane12_read1_indexN707-S507=Oct26_Cell_7


title: 36Y Female HSCe 51

description: run1907_lane12_read1_indexN707-S502=Oct26_Cell_42


title: 36Y Female HSCe 72

description: run1907_lane12_read1_indexN709-S508=Oct26_Cell_16


title: 36Y Female HSCe 65

description: run1907_lane12_read1_indexN708-S517=Oct26_Cell_57


title: 36Y Female HSCe 47

description: run1907_lane12_read1_indexN706-S504=Oct26_Cell_20


title: 36Y Female HSCe 45

description: run1907_lane12_read1_indexN706-S502=Oct26_Cell_34


title: 36Y Female HSCe 46

description: run1907_lane12_read1_indexN706-S503=Oct26_Cell_27


title: 36Y Female HSCe 44

description: run1907_lane12_read1_indexN705-S517=Oct26_Cell_33


title: 36Y Female HSCe 43

description: run1907_lane12_read1_indexN705-S505=Oct26_Cell_5


title: 36Y Female HSCe 50

description: run1907_lane12_read1_indexN706-S517=Oct26_Cell_41


title: 36Y Female HSCe 31

description: run1907_lane12_read1_indexN702-S517=Oct26_Cell_9


title: 36Y Female HSCe 37

description: run1907_lane12_read1_indexN704-S503=Oct26_Cell_11


title: 36Y Female HSCe 35

description: run1907_lane12_read1_indexN703-S517=Oct26_Cell_17


title: 36Y Female HSCe 30

description: run1907_lane12_read1_indexN702-S508=Oct26_Cell_56


title: 36Y Female HSCe 38

description: run1907_lane12_read1_indexN704-S504=Oct26_Cell_4


title: 36Y Female HSCe 39

description: run1907_lane12_read1_indexN704-S517=Oct26_Cell_25


title: 36Y Female HSCe 32

description: run1907_lane12_read1_indexN703-S502=Oct26_Cell_10


title: 36Y Female HSCe 40

description: run1907_lane12_read1_indexN705-S502=Oct26_Cell_26


title: 36Y Female HSCe 34

description: run1907_lane12_read1_indexN703-S508=Oct26_Cell_64


title: 36Y Female HSCe 28

description: run1907_lane12_read1_indexN701-S517=Oct26_Cell_1


title: 36Y Female HSCe 29

description: run1907_lane12_read1_indexN702-S507=Oct26_Cell_63


title: 36Y Female HSCe 36

description: run1907_lane12_read1_indexN704-S502=Oct26_Cell_18


title: 36Y Female HSCe 49

description: run1907_lane12_read1_indexN706-S506=Oct26_Cell_6


title: 36Y Female HSCe 41

description: run1907_lane12_read1_indexN705-S503=Oct26_Cell_19


title: 36Y Female HSCe 33

description: run1907_lane12_read1_indexN703-S503=Oct26_Cell_3


title: 36Y Female HSCe 26

description: run1907_lane12_read1_indexN701-S507=Oct26_Cell_55


title: 36Y Female HSCe 25

description: run1907_lane12_read1_indexN701-S506=Oct26_Cell_62


title: 36Y Female HSCe 22

description: run1906_lane12_read1_indexN712-S502=Oct26_Cell_82


title: 36Y Female HSCe 48

description: run1907_lane12_read1_indexN706-S505=Oct26_Cell_13


title: 36Y Female HSCe 27

description: run1907_lane12_read1_indexN701-S508=Oct26_Cell_48


title: 36Y Female HSCe 24

description: run1906_lane12_read1_indexN712-S517=Oct26_Cell_89


title: 36Y Female HSCe 21

description: run1906_lane12_read1_indexN711-S517=Oct26_Cell_81


title: 36Y Female HSCe 23

description: run1906_lane12_read1_indexN712-S503=Oct26_Cell_75


title: 36Y Female HSCe 42

description: run1907_lane12_read1_indexN705-S504=Oct26_Cell_12


title: 36Y Female HSCe 19

description: run1906_lane12_read1_indexN710-S517=Oct26_Cell_73


title: 36Y Female HSCe 20

description: run1906_lane12_read1_indexN711-S502=Oct26_Cell_74


title: 36Y Female HSCe 18

description: run1906_lane12_read1_indexN707-S508=Oct26_Cell_96


title: 36Y Female HSCe 17

description: run1906_lane12_read1_indexN706-S508=Oct26_Cell_88


title: 36Y Female HSCe 16

description: run1906_lane12_read1_indexN706-S507=Oct26_Cell_95


title: 36Y Female HSCe 7

description: run1906_lane12_read1_indexN703-S504=Oct26_Cell_92


title: 36Y Female HSCe 14

description: run1906_lane12_read1_indexN705-S507=Oct26_Cell_87


title: 36Y Female HSCe 4

description: run1906_lane12_read1_indexN702-S503=Oct26_Cell_91


title: 36Y Female HSCe 13

description: run1906_lane12_read1_indexN705-S506=Oct26_Cell_94


title: 36Y Female HSCe 11

description: run1906_lane12_read1_indexN704-S506=Oct26_Cell_86


title: 36Y Female HSCe 9

description: run1906_lane12_read1_indexN703-S506=Oct26_Cell_78


title: 36Y Female HSCe 5

description: run1906_lane12_read1_indexN702-S504=Oct26_Cell_84


title: 36Y Female HSCe 15

description: run1906_lane12_read1_indexN705-S508=Oct26_Cell_80


title: 71Y Male HSCe 66

description: run1906_lane12_read1_indexN712-S504=Oct19_Chip172_Cell_68

value: M


title: 36Y Female HSCe 6

description: run1906_lane12_read1_indexN702-S505=Oct26_Cell_77


title: 36Y Female HSCe 12

description: run1906_lane12_read1_indexN704-S507=Oct26_Cell_79


title: 36Y Female HSCe 3

description: run1906_lane12_read1_indexN701-S504=Oct26_Cell_76


title: 36Y Female HSCe 1

description: run1906_lane12_read1_indexN701-S502=Oct26_Cell_90


title: 71Y Male HSCe 69

description: run1906_lane12_read1_indexN712-S507=Oct19_Chip172_Cell_47


title: 36Y Female HSCe 10

description: run1906_lane12_read1_indexN704-S505=Oct26_Cell_93


title: 71Y Male HSCe 67

description: run1906_lane12_read1_indexN712-S505=Oct19_Chip172_Cell_61


title: 71Y Male HSCe 65

description: run1906_lane12_read1_indexN711-S508=Oct19_Chip029_Cell_32


title: 36Y Female HSCe 8

description: run1906_lane12_read1_indexN703-S505=Oct26_Cell_85


title: 71Y Male HSCe 64

description: run1906_lane12_read1_indexN711-S507=Oct19_Chip029_Cell_39


title: 71Y Male HSCe 62

description: run1906_lane12_read1_indexN711-S505=Oct19_Chip172_Cell_53


title: 71Y Male HSCe 61

description: run1906_lane12_read1_indexN711-S504=Oct19_Chip172_Cell_60


title: 71Y Male HSCe 60

description: run1906_lane12_read1_indexN711-S503=Oct19_Chip172_Cell_67


title: 71Y Male HSCe 68

description: run1906_lane12_read1_indexN712-S506=Oct19_Chip172_Cell_54


title: 71Y Male HSCe 63

description: run1906_lane12_read1_indexN711-S506=Oct19_Chip172_Cell_46


title: 71Y Male HSCe 59

description: run1906_lane12_read1_indexN710-S508=Oct19_Chip029_Cell_24


title: 71Y Male HSCe 58

description: run1906_lane12_read1_indexN710-S507=Oct19_Chip029_Cell_31


title: 36Y Female HSCe 2

description: run1906_lane12_read1_indexN701-S503=Oct26_Cell_83


title: 71Y Male HSCe 70

description: run1906_lane12_read1_indexN712-S508=Oct19_Chip029_Cell_40


title: 71Y Male HSCe 57

description: run1906_lane12_read1_indexN710-S506=Oct19_Chip029_Cell_38


title: 71Y Male HSCe 54

description: run1906_lane12_read1_indexN710-S503=Oct19_Chip172_Cell_59


title: 71Y Male HSCe 51

description: run1906_lane12_read1_indexN709-S508=Oct19_Chip029_Cell_16


title: 71Y Male HSCe 49

description: run1906_lane12_read1_indexN709-S505=Oct19_Chip029_Cell_37


title: 71Y Male HSCe 56

description: run1906_lane12_read1_indexN710-S505=Oct19_Chip172_Cell_45


title: 71Y Male HSCe 50

description: run1906_lane12_read1_indexN709-S506=Oct19_Chip029_Cell_30


title: 71Y Male HSCe 48

description: run1906_lane12_read1_indexN709-S504=Oct19_Chip029_Cell_44


title: 71Y Male HSCe 44

description: run1906_lane12_read1_indexN708-S508=Oct19_Chip029_Cell_8


title: 71Y Male HSCe 45

description: run1906_lane12_read1_indexN708-S517=Oct19_Chip172_Cell_57


title: 71Y Male HSCe 43

description: run1906_lane12_read1_indexN708-S507=Oct19_Chip029_Cell_15


title: 71Y Male HSCe 47

description: run1906_lane12_read1_indexN709-S503=Oct19_Chip172_Cell_51


title: 71Y Male HSCe 42

description: run1906_lane12_read1_indexN708-S506=Oct19_Chip029_Cell_22


title: 71Y Male HSCe 41

description: run1906_lane12_read1_indexN708-S505=Oct19_Chip029_Cell_29


title: 71Y Male HSCe 40

description: run1906_lane12_read1_indexN708-S504=Oct19_Chip029_Cell_36


title: 71Y Male HSCe 39

description: run1906_lane12_read1_indexN708-S503=Oct19_Chip029_Cell_43


title: 71Y Male HSCe 37

description: run1906_lane12_read1_indexN707-S517=Oct19_Chip172_Cell_49


title: 71Y Male HSCe 36

description: run1906_lane12_read1_indexN707-S507=Oct19_Chip029_Cell_7


title: 71Y Male HSCe 35

description: run1906_lane12_read1_indexN707-S506=Oct19_Chip029_Cell_14


title: 71Y Male HSCe 33

description: run1906_lane12_read1_indexN707-S503=Oct19_Chip029_Cell_35


title: 71Y Male HSCe 32

description: run1906_lane12_read1_indexN707-S502=Oct19_Chip029_Cell_42


title: 71Y Male HSCe 34

description: run1906_lane12_read1_indexN707-S505=Oct19_Chip029_Cell_21


title: 71Y Male HSCe 31

description: run1906_lane12_read1_indexN706-S517=Oct19_Chip029_Cell_41


title: 71Y Male HSCe 30

description: run1906_lane12_read1_indexN706-S506=Oct19_Chip029_Cell_6


title: 71Y Male HSCe 55

description: run1906_lane12_read1_indexN710-S504=Oct19_Chip172_Cell_52


title: 71Y Male HSCe 53

description: run1906_lane12_read1_indexN710-S502=Oct19_Chip172_Cell_66


title: 71Y Male HSCe 29

description: run1906_lane12_read1_indexN706-S505=Oct19_Chip029_Cell_13


title: 71Y Male HSCe 52

description: run1906_lane12_read1_indexN709-S517=Oct19_Chip172_Cell_65


title: 71Y Male HSCe 28

description: run1906_lane12_read1_indexN706-S504=Oct19_Chip029_Cell_20


title: 71Y Male HSCe 27

description: run1906_lane12_read1_indexN706-S503=Oct19_Chip029_Cell_27


title: 71Y Male HSCe 46

description: run1906_lane12_read1_indexN709-S502=Oct19_Chip172_Cell_58


title: 71Y Male HSCe 26

description: run1906_lane12_read1_indexN706-S502=Oct19_Chip029_Cell_34


title: 71Y Male HSCe 24

description: run1906_lane12_read1_indexN705-S505=Oct19_Chip029_Cell_5


title: 71Y Male HSCe 21

description: run1906_lane12_read1_indexN705-S502=Oct19_Chip029_Cell_26


title: 71Y Male HSCe 22

description: run1906_lane12_read1_indexN705-S503=Oct19_Chip029_Cell_19


title: 71Y Male HSCe 38

description: run1906_lane12_read1_indexN708-S502=Oct19_Chip172_Cell_50


title: 71Y Male HSCe 25

description: run1906_lane12_read1_indexN705-S517=Oct19_Chip029_Cell_33


title: 71Y Male HSCe 23

description: run1906_lane12_read1_indexN705-S504=Oct19_Chip029_Cell_12


title: 71Y Male HSCe 17

description: run1906_lane12_read1_indexN704-S503=Oct19_Chip029_Cell_11


title: 71Y Male HSCe 18

description: run1906_lane12_read1_indexN704-S504=Oct19_Chip029_Cell_4


title: 71Y Male HSCe 19

description: run1906_lane12_read1_indexN704-S508=Oct19_Chip172_Cell_72


title: 71Y Male HSCe 16

description: run1906_lane12_read1_indexN704-S502=Oct19_Chip029_Cell_18


title: 71Y Male HSCe 14

description: run1906_lane12_read1_indexN703-S508=Oct19_Chip172_Cell_64


title: 71Y Male HSCe 15

description: run1906_lane12_read1_indexN703-S517=Oct19_Chip029_Cell_17


title: 71Y Male HSCe 20

description: run1906_lane12_read1_indexN704-S517=Oct19_Chip029_Cell_25


title: 71Y Male HSCe 11

description: run1906_lane12_read1_indexN703-S502=Oct19_Chip029_Cell_10


title: 71Y Male HSCe 12

description: run1906_lane12_read1_indexN703-S503=Oct19_Chip029_Cell_3


title: 71Y Male HSCe 13

description: run1906_lane12_read1_indexN703-S507=Oct19_Chip172_Cell_71


title: 71Y Male HSCe 6

description: run1906_lane12_read1_indexN702-S502=Oct19_Chip029_Cell_2


title: 71Y Male HSCe 10

description: run1906_lane12_read1_indexN702-S517=Oct19_Chip029_Cell_9


title: 71Y Male HSCe 9

description: run1906_lane12_read1_indexN702-S508=Oct19_Chip172_Cell_56


title: 71Y Male HSCe 8

description: run1906_lane12_read1_indexN702-S507=Oct19_Chip172_Cell_63


title: 71Y Male HSCe 7

description: run1906_lane12_read1_indexN702-S506=Oct19_Chip172_Cell_70


title: 71Y Male HSCe 4

description: run1906_lane12_read1_indexN701-S508=Oct19_Chip172_Cell_48


title: 71Y Male HSCe 3

description: run1906_lane12_read1_indexN701-S507=Oct19_Chip172_Cell_55


title: 71Y Male HSCe 5

description: run1906_lane12_read1_indexN701-S517=Oct19_Chip029_Cell_1


title: 71Y Male HSCe 1

description: run1906_lane12_read1_indexN701-S505=Oct19_Chip172_Cell_69


title: 71Y Male HSCe 2

description: run1906_lane12_read1_indexN701-S506=Oct19_Chip172_Cell_62


title: 28Y Female HSCe 77

description: run1998_lane12_read1_indexN712-S507=Nov14_Cell_47


title: 28Y Female HSCe 76

description: run1998_lane12_read1_indexN712-S506=Nov14_Cell_54


title: 28Y Female HSCe 75

description: run1998_lane12_read1_indexN712-S505=Nov14_Cell_61


title: 28Y Female HSCe 73

description: run1998_lane12_read1_indexN712-S503=Nov14_Cell_75


title: 28Y Female HSCe 69

description: run1998_lane12_read1_indexN711-S505=Nov14_Cell_53


title: 28Y Female HSCe 70

description: run1998_lane12_read1_indexN711-S506=Nov14_Cell_46


title: 28Y Female HSCe 66

description: run1998_lane12_read1_indexN711-S502=Nov14_Cell_74


title: 28Y Female HSCe 64

description: run1998_lane12_read1_indexN710-S508=Nov14_Cell_24


title: 28Y Female HSCe 60

description: run1998_lane12_read1_indexN710-S502=Nov14_Cell_66


title: 28Y Female HSCe 72

description: run1998_lane12_read1_indexN712-S502=Nov14_Cell_82


title: 28Y Female HSCe 71

description: run1998_lane12_read1_indexN711-S517=Nov14_Cell_81


title: 28Y Female HSCe 55

description: run1998_lane12_read1_indexN709-S502=Nov14_Cell_58


title: 28Y Female HSCe 68

description: run1998_lane12_read1_indexN711-S504=Nov14_Cell_60


title: 28Y Female HSCe 67

description: run1998_lane12_read1_indexN711-S503=Nov14_Cell_67


title: 28Y Female HSCe 74

description: run1998_lane12_read1_indexN712-S504=Nov14_Cell_68


title: 28Y Female HSCe 49

description: run1998_lane12_read1_indexN707-S502=Nov14_Cell_42


title: 28Y Female HSCe 63

description: run1998_lane12_read1_indexN710-S505=Nov14_Cell_45


title: 28Y Female HSCe 65

description: run1998_lane12_read1_indexN710-S517=Nov14_Cell_73


title: 28Y Female HSCe 62

description: run1998_lane12_read1_indexN710-S504=Nov14_Cell_52


title: 28Y Female HSCe 45

description: run1998_lane12_read1_indexN705-S505=Nov14_Cell_5


title: 28Y Female HSCe 58

description: run1998_lane12_read1_indexN709-S507=Nov14_Cell_23


title: 28Y Female HSCe 59

description: run1998_lane12_read1_indexN709-S517=Nov14_Cell_65


title: 28Y Female HSCe 39

description: run1998_lane12_read1_indexN703-S506=Nov14_Cell_78


title: 28Y Female HSCe 57

description: run1998_lane12_read1_indexN709-S504=Nov14_Cell_44


title: 28Y Female HSCe 38

description: run1998_lane12_read1_indexN703-S505=Nov14_Cell_85


title: 28Y Female HSCe 56

description: run1998_lane12_read1_indexN709-S503=Nov14_Cell_51


title: 28Y Female HSCe 54

description: run1998_lane12_read1_indexN708-S517=Nov14_Cell_57


title: 28Y Female HSCe 35

description: run1998_lane12_read1_indexN702-S506=Nov14_Cell_70


title: 28Y Female HSCe 48

description: run1998_lane12_read1_indexN706-S508=Nov14_Cell_88


title: 28Y Female HSCe 41

description: run1998_lane12_read1_indexN703-S508=Nov14_Cell_64


title: 28Y Female HSCe 51

description: run1998_lane12_read1_indexN708-S502=Nov14_Cell_50


title: 28Y Female HSCe 52

description: run1998_lane12_read1_indexN708-S503=Nov14_Cell_43


title: 28Y Female HSCe 34

description: run1998_lane12_read1_indexN702-S505=Nov14_Cell_77


title: 28Y Female HSCe 53

description: run1998_lane12_read1_indexN708-S506=Nov14_Cell_22


title: 28Y Female HSCe 50

description: run1998_lane12_read1_indexN707-S517=Nov14_Cell_49


title: 28Y Female HSCe 47

description: run1998_lane12_read1_indexN705-S508=Nov14_Cell_80


title: 28Y Female HSCe 33

description: run1998_lane12_read1_indexN702-S504=Nov14_Cell_84


title: 28Y Female HSCe 31

description: run1998_lane12_read1_indexN701-S507=Nov14_Cell_55


title: 28Y Female HSCe 44

description: run1998_lane12_read1_indexN704-S508=Nov14_Cell_72


title: 28Y Female HSCe 46

description: run1998_lane12_read1_indexN705-S507=Nov14_Cell_87


title: 28Y Female HSCe 30

description: run1998_lane12_read1_indexN701-S506=Nov14_Cell_62


title: 28Y Female HSCe 43

description: run1998_lane12_read1_indexN704-S507=Nov14_Cell_79


title: 28Y Female HSCe 42

description: run1998_lane12_read1_indexN704-S506=Nov14_Cell_86


title: 28Y Female HSCe 24

description: run1928_lane12_read1_indexN712-S503=Grim_Nov14_Cell_75


title: 28Y Female HSCe 28

description: run1998_lane12_read1_indexN701-S504=Nov14_Cell_76


title: 28Y Female HSCe 61

description: run1998_lane12_read1_indexN710-S503=Nov14_Cell_59


title: 28Y Female HSCe 26

description: run1928_lane12_read1_indexN712-S505=Grim_Nov14_Cell_61


title: 28Y Female HSCe 37

description: run1998_lane12_read1_indexN702-S508=Nov14_Cell_56


title: 28Y Female HSCe 40

description: run1998_lane12_read1_indexN703-S507=Nov14_Cell_71


title: 28Y Female HSCe 36

description: run1998_lane12_read1_indexN702-S507=Nov14_Cell_63


title: 28Y Female HSCe 23

description: run1928_lane12_read1_indexN712-S502=Grim_Nov14_Cell_82


title: 28Y Female HSCe 25

description: run1928_lane12_read1_indexN712-S504=Grim_Nov14_Cell_68


title: 28Y Female HSCe 17

description: run1928_lane12_read1_indexN710-S503=Grim_Nov14_Cell_59


title: 28Y Female HSCe 27

description: run1998_lane12_read1_indexN701-S503=Nov14_Cell_83


title: 28Y Female HSCe 32

description: run1998_lane12_read1_indexN701-S508=Nov14_Cell_48


title: 28Y Female HSCe 21

description: run1928_lane12_read1_indexN711-S504=Grim_Nov14_Cell_60


title: 28Y Female HSCe 15

description: run1928_lane12_read1_indexN709-S517=Grim_Nov14_Cell_65


title: 28Y Female HSCe 16

description: run1928_lane12_read1_indexN710-S502=Grim_Nov14_Cell_66


title: 28Y Female HSCe 13

description: run1928_lane12_read1_indexN708-S517=Grim_Nov14_Cell_57


title: 28Y Female HSCe 20

description: run1928_lane12_read1_indexN711-S503=Grim_Nov14_Cell_67


title: 28Y Female HSCe 18

description: run1928_lane12_read1_indexN710-S517=Grim_Nov14_Cell_73


title: 28Y Female HSCe 29

description: run1998_lane12_read1_indexN701-S505=Nov14_Cell_69


title: Zy24-3

status: Public on May 12 2019

city: Wuhan

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

country: China

institute: Wuhan University

description: Amplified with SMART-Seq Ultra Low Input RNA Kit

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genome TAIR10 using Tophat2.
Expression level are quantified by a software package: RSEM (RNASeq by Expectation Maximization v1.3.0).
Genome_build: Arabidopsis thaliana genome TAIR10

organism: Arabidopsis thaliana

source_name: Zygote at 24 HAP

growth_protocol: In greenhouse under long-day conditions (16 h light/8 h dark) at 22 °C

extract_protocol:
mRNA was extracted with Dynabeads® mRNA DIRECT™ Micro Kit. And SMART-Seq v4 Ultra Low Input RNA Kit was used to generate cDNA library for sequencing
Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: ecotype background

value: Col

tag: developmental stage

value: 24 HAP

value: Zygote


title: 28Y Female HSCe 14

description: run1928_lane12_read1_indexN709-S502=Grim_Nov14_Cell_58


title: 28Y Female HSCe 8

description: run1928_lane12_read1_indexN703-S507=Grim_Nov14_Cell_71


title: 28Y Female HSCe 12

description: run1928_lane12_read1_indexN705-S508=Grim_Nov14_Cell_80


title: 28Y Female HSCe 11

description: run1928_lane12_read1_indexN704-S508=Grim_Nov14_Cell_72


title: 28Y Female HSCe 10

description: run1928_lane12_read1_indexN704-S507=Grim_Nov14_Cell_79


title: 28Y Female HSCe 7

description: run1928_lane12_read1_indexN703-S506=Grim_Nov14_Cell_78


title: 28Y Female HSCe 6

description: run1928_lane12_read1_indexN702-S507=Grim_Nov14_Cell_63


title: 28Y Female HSCe 22

description: run1928_lane12_read1_indexN711-S517=Grim_Nov14_Cell_81


title: 28Y Female HSCe 4

description: run1928_lane12_read1_indexN702-S505=Grim_Nov14_Cell_77


title: 28Y Female HSCe 5

description: run1928_lane12_read1_indexN702-S506=Grim_Nov14_Cell_70


title: 28Y Female HSCe 19

description: run1928_lane12_read1_indexN711-S502=Grim_Nov14_Cell_74


title: 28Y Female HSCe 3

description: run1928_lane12_read1_indexN701-S506=Grim_Nov14_Cell_62


title: 28Y Female HSCe 1

description: run1928_lane12_read1_indexN701-S504=Grim_Nov14_Cell_76


title: 28Y Female HSCe 2

description: run1928_lane12_read1_indexN701-S505=Grim_Nov14_Cell_69


title: JW13_89

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
Single cell
ilc_R_sce_object.rds
ilc_single_cell_expression_matrix.tsv

data_processing:
Reads aligned to a modified mouse genome (addition of 92 ERCC spike-ins and the reporters found in the mouse) using the Salmon pseudoaligner (v0.8.2)
Pseudocounts analysis with the scater library (v1.6.3) (McCarthy et al., 2017), scran library (v1.6.9) (Lun et al., 2016), and sva library (sva: Surrogate Variable Analysis. R package v3.26.0).
Cells with pseudocounts below 3 median-absolute-deviations away from the median were removed. Genes with an average count across all remaining cells of less than 1 were removed.
Size factors were calculated with the scran library (based on the gene counts) and the data normalised by them.
Batch effects were removed using the ComBat empirical Bayes framework from the sva library
Genome_build: GRCm38.68
Supplementary_files_format_and_content: RDS of R SCE object containing metadata and gene expression generated using R,scater,scran and sva; tab-separated normalised gene expression from the SCE object

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
Individual cells were flow cytometrically purified on a 96 well format into 0.2% Triton X-100 containing RNase inhibitor, dNTPs and oligo-dT primers and stored at -80oC.
On thawing, lysates were heated to 72 oC for 3 minutes and subject to reverse transcription, PCR preamplification (26 cycles) and PCR purification.  cDNA library quality was assessed for all samples by qualitative PCR using primers for 18s RNA with an additional check by Bioanalyzer using an Agilent high sensitivity DNA chip on a small subset of libraries. A subset of libraries was quantified using the Qubit dsDNA HS assay kit and an average value used to calculate library dilution to 100-150 pg/ml. cDNA library tagmentation and amplification was performed using the Illumina Nextera XT DNA Library Preparation Kit according to manufacturer’s instructions except that all volumes were reduced 4-fold and tagmentation performed at 55oC for 20 minutes. Nextera index and Illumina adapter sequences were incorporated at the amplification stage (N7xx and S5xx). Amplified and indexed libraries were pooled and purified using Agencourt AMPure XP beads at a ratio of 1:0.9 library to beads and washed with 70% ethanol. Two rounds of purification were performed before a final elution in 1.25x total library volume of Nextera Resuspension buffer

tag: cell phenotype from facs

value: Lin- Id2+ IL7ra+ Kat+

tag: mouse id

tag: tissue

value: Bone marrow


title: JW13_90


title: JW13_9


title: JW13_88


title: JW13_83

value: Negative Control


title: JW13_87


title: JW13_91


title: JW13_85


title: JW13_82


title: JW13_8


title: JW13_86


title: JW13_80


title: JW13_77


title: JW13_81


title: JW13_84


title: JW13_79


title: 28Y Female HSCe 9

description: run1928_lane12_read1_indexN703-S508=Grim_Nov14_Cell_64


title: JW13_76


title: JW13_78


title: JW13_74


title: JW13_73


title: JW13_75


title: JW13_72


title: JW13_70


title: JW13_71


title: JW13_92


title: JW13_7


title: JW13_69


title: JW13_68


title: JW13_67


title: JW13_65


title: JW13_64


title: JW13_63


title: JW13_62


title: JW13_6


title: JW13_60


title: JW13_66


title: JW13_58


title: JW13_56


title: JW13_55


title: JW13_54


title: JW13_53


title: JW13_57


title: JW13_59


title: JW13_52


title: JW13_51


title: JW13_50


title: JW13_49


title: JW13_5


title: JW13_46

value: Lin- Id2+ IL7ra+ Bcl11b+ Gata3lo Kat-


title: JW13_45


title: JW13_44


title: JW13_43


title: JW13_40


title: JW13_41


title: JW13_42


title: JW13_61


title: JW13_39


title: JW13_38


title: JW13_37

value: Lin- Id2+ IL7Ra+ Bcl11b+ CD25+ Gata3hi


title: JW13_34


title: JW13_35


title: JW13_32


title: JW13_33


title: JW13_31


title: JW13_30


title: JW13_27


title: JW13_36


title: JW13_29


title: JW13_47


title: JW13_3


title: JW13_48


title: JW13_26


title: JW13_25


title: JW13_20


title: JW13_4


title: JW13_24


title: JW13_2


title: JW13_22


title: JW13_21


title: JW13_18


title: JW13_17


title: JW13_15


title: JW13_16


title: JW13_19


title: JW13_13


title: JW13_12


title: JW13_28


title: JW13_11


title: JW13_10


title: JW13_23


title: JW12_95


title: JW13_1


title: JW12_96


title: JW12_94


title: JW12_92


title: JW12_93


title: JW12_90


title: JW12_9

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25- a4b7lo/-


title: JW12_89


title: JW12_91


title: JW12_86


title: JW12_85


title: JW12_88


title: JW12_87


title: JW12_81


title: JW12_82


title: JW12_83


title: JW12_84


title: JW12_8


title: JW12_79


title: JW12_78


title: JW12_77


title: JW13_14


title: JW12_75


title: JW12_74


title: JW12_72


title: JW12_7


title: JW12_69


title: JW12_70


title: JW12_71


title: JW12_68


title: JW12_67


title: JW12_80


title: JW12_66


title: JW12_65


title: JW12_62


title: JW12_64


title: JW12_61


title: JW12_56


title: JW12_59


title: JW12_60


title: JW12_54


title: JW12_52


title: JW12_58


title: JW12_53


title: JW12_63


title: JW12_51


title: JW12_76


title: JW12_73


title: JW12_50


title: JW12_49


title: JW12_48


title: JW12_46


title: JW12_42


title: JW12_45


title: JW12_43


title: JW12_44


title: JW12_6

value: Lin- Id2+ IL7Ra+ Bcl11b- CD25- a4b7hi


title: JW12_57


title: JW12_39


title: JW12_38


title: JW12_41


title: JW12_40


title: JW12_47


title: JW12_55


title: JW12_35


title: JW12_37


title: JW12_4


title: JW12_5


title: JW12_33


title: JW12_30


title: JW12_3


title: JW12_32


title: JW12_34


title: JW12_31


title: JW12_29


title: JW12_25


title: JW12_26


title: JW12_27


title: JW12_28


title: JW12_24


title: JW12_22


title: JW12_21


title: JW12_2


title: JW12_19


title: JW12_36


title: JW12_18


title: JW12_17


title: JW12_14


title: JW12_15


title: JW12_13


title: JW12_16


title: JW12_11


title: JW11_95


title: JW11_93


title: JW12_12


title: JW11_94


title: JW12_1


title: JW11_96


title: JW11_91


title: JW11_9


title: JW11_92


title: JW11_89


title: JW12_23


title: JW11_90


title: JW11_88


title: JW11_87


title: JW11_86


title: JW12_20


title: JW11_83


title: JW11_82


title: JW11_81


title: JW12_10


title: JW11_80


title: JW11_8


title: JW11_76


title: JW11_78


title: JW11_77


title: JW11_79


title: JW11_74


title: JW11_72


title: JW11_73


title: JW11_7


title: JW11_70


title: JW11_71


title: JW11_69


title: JW11_67


title: JW11_68


title: JW11_66


title: JW11_63


title: JW11_84


title: JW11_65


title: JW11_62


title: JW11_61


title: JW11_64


title: JW11_85


title: JW11_59


title: JW11_58


title: JW11_6


title: JW11_75


title: JW11_60


title: JW11_57


title: JW11_55


title: JW11_56


title: JW11_54


title: JW11_53


title: JW11_51


title: JW11_52


title: JW11_5


title: JW11_49


title: JW11_48


title: JW11_44


title: JW11_46


title: JW11_47


title: JW11_42


title: JW11_43


title: JW11_45


title: JW11_40


title: JW11_4


title: JW11_39


title: JW11_41


title: JW11_37


title: JW11_36


title: JW11_34


title: JW11_38


title: JW11_33


title: JW11_35


title: JW11_31


title: JW11_32


title: JW11_30


title: JW11_27


title: JW11_50


title: JW11_29


title: JW11_3


title: JW11_26


title: JW11_28


title: JW11_23


title: JW11_25


title: JW11_20


title: JW11_19


title: JW11_2


title: JW11_18


title: JW11_16


title: JW11_17


title: JW11_14


title: JW11_15


title: JW11_13


title: JW11_11


title: JW11_10


title: JW11_12


title: JW7_8

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25- Rorc+


title: JW7_7


title: JW7_6


title: JW7_5

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25-


title: JW7_9


title: JW7_3


title: JW11_24


title: JW7_2


title: JW7_4


title: JW7_18


title: JW7_17


title: JW7_15


title: JW7_14


title: JW7_13


title: JW11_21


title: JW7_12


title: JW7_1


title: JW7_11


title: JW7_10


title: JW6_95


title: JW6_94


title: JW6_92


title: JW6_96


title: JW11_1


title: JW6_91


title: JW6_87


title: JW6_88


title: JW7_16


title: JW6_90


title: JW6_85


title: JW6_83


title: JW6_82


title: JW6_89


title: JW6_86


title: JW6_8


title: JW6_80


title: JW6_84


title: JW6_79


title: JW6_81


title: JW6_77


title: JW6_76


title: JW6_93


title: JW6_74


title: JW6_72


title: JW6_75


title: JW6_73


title: JW6_70


title: JW6_69


title: JW6_9


title: JW6_7


title: JW6_67


title: JW6_68


title: JW11_22


title: JW6_65


title: JW6_66


title: JW6_63


title: JW6_62


title: JW6_6


title: JW6_64


title: JW6_58


title: JW6_78


title: JW6_61


title: JW6_60


title: JW6_55


title: JW6_52


title: JW6_53


title: JW6_51


title: JW6_57


title: JW6_56


title: JW6_54


title: JW6_49


title: JW6_48


title: JW6_59


title: JW6_50


title: JW6_71


title: JW6_47


title: JW6_45


title: JW6_46


title: JW6_44


title: JW6_41


title: JW6_34


title: JW6_39


title: JW6_38


title: JW6_4


title: JW6_42


title: JW6_36


title: JW6_32


title: JW6_40


title: JW6_35


title: JW6_5


title: JW6_33


title: JW6_29


title: JW6_31


title: JW6_28


title: JW6_30


title: JW6_37


title: JW6_26


title: JW6_3


title: JW6_27


title: JW6_25


title: JW6_23


title: JW6_19


title: JW6_20


title: JW6_21


title: JW6_2


title: JW6_17


title: JW6_16


title: JW6_15


title: JW6_24


title: JW6_22


title: JW6_43


title: JW6_1


title: JW6_10


title: JW5_94


title: JW5_96


title: JW5_91


title: JW5_95


title: JW6_13


title: JW5_90


title: JW5_92


title: JW6_11


title: JW5_93


title: JW6_14


title: JW5_89


title: JW6_12


title: JW5_88


title: JW5_84


title: JW5_87


title: JW6_18


title: JW5_83


title: JW5_85


title: JW5_86


title: JW5_82


title: JW5_81


title: JW5_80

value: Lin-


title: JW5_8


title: JW5_9


title: JW5_79


title: JW5_76


title: JW5_75


title: JW5_78


title: JW5_72


title: JW5_77


title: JW5_71


title: JW5_70


title: JW5_73


title: JW5_7


title: JW5_67


title: JW5_69


title: JW5_64


title: JW5_68


title: JW5_66


title: JW5_74


title: JW5_60


title: JW5_6


title: JW5_63


title: JW5_59


title: JW5_61


title: JW5_56


title: JW5_57


title: JW5_58


title: JW5_53


title: JW5_55


title: JW5_52


title: JW5_51


title: JW5_5


title: JW5_65


title: JW5_50


title: JW5_49


title: JW5_47


title: JW5_62


title: JW5_46


title: JW5_44


title: JW5_42


title: JW5_41


title: JW5_4


title: JW5_39


title: JW5_45


title: JW5_38


title: JW5_36


title: JW5_54


title: JW5_35


title: JW5_32


title: JW5_30


title: JW5_34


title: JW5_3


title: JW5_43


title: JW5_29


title: JW5_27


title: JW5_48


title: JW5_28


title: JW5_25


title: JW5_26


title: JW5_23


title: JW5_37


title: JW5_40


title: JW5_22


title: JW5_21


title: JW5_19


title: JW5_18


title: JW5_33


title: JW5_17


title: JW5_16


title: JW5_2


title: JW5_31


title: JW5_12


title: JW5_15


title: JW5_11


title: JW5_13


title: JW5_14


title: JW5_10


title: JW4_95


title: JW5_1


title: JW4_96


title: JW5_24


title: JW4_94


title: JW4_93

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25- a4b7+ Gata3lo Roralo


title: JW5_20


title: JW4_91


title: JW4_9


title: JW4_90


title: JW4_89


title: JW4_86


title: JW4_87


title: JW4_88


title: JW4_83


title: JW4_85


title: JW4_82

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25- a4b7+ Gata3+ Rora+


title: JW4_81


title: JW4_79


title: JW4_84


title: JW4_76


title: JW4_77


title: JW4_8


title: JW4_71


title: JW4_78


title: JW4_73


title: JW4_75


title: JW4_69


title: JW4_74


title: JW4_72


title: JW4_92


title: JW4_68


title: JW4_67


title: JW4_65


title: JW4_66


title: JW4_64


title: JW4_63


title: JW4_80


title: JW4_60


title: JW4_6


title: JW4_61


title: JW4_59


title: JW4_58


title: JW4_57


title: JW4_56


title: JW4_7


title: JW4_55


title: JW4_70


title: JW4_54


title: JW4_53


title: JW4_48


title: JW4_46


title: JW4_49


title: JW4_52


title: JW4_51


title: JW4_44


title: JW4_47


title: JW4_50


title: JW4_5


title: JW4_40


title: JW4_4


title: JW4_41


title: JW4_39


title: JW4_35


title: JW4_42


title: JW4_38


title: JW4_37


title: JW4_34


title: JW4_32


title: JW4_31


title: JW4_33


title: JW4_36


title: JW4_43


title: JW4_30


title: JW4_62


title: JW4_28


title: JW4_25


title: JW4_3


title: JW4_26


title: JW4_27


title: JW4_29


title: JW4_23


title: JW4_22


title: JW4_19


title: JW4_2


title: JW4_17


title: JW4_16


title: JW4_18


title: JW4_21


title: JW4_14


title: JW4_11


title: JW4_10


title: JW4_15


title: JW4_12


title: JW3_95


title: JW3_93


title: JW3_94


title: JW4_20


title: JW4_24


title: JW3_92


title: JW3_91


title: JW3_96


title: JW3_90


title: JW3_9

value: Lin- Id2+ IL7ra+ Bcl11b- CD25- Gata3- Rora-


title: JW3_87


title: JW3_88


title: JW3_85


title: JW3_84


title: JW3_86


title: JW3_83


title: JW3_82


title: JW3_80


title: JW3_81


title: JW4_1


title: JW3_77


title: JW3_75


title: JW3_74


title: JW3_8

value: Lin- Id2+ IL7ra+ Bcl11b- CD25- Gata3hi Rora+


title: JW3_78


title: JW3_70


title: JW3_71


title: JW3_68


title: JW3_69


title: JW3_79


title: JW3_89


title: JW3_7


title: JW3_73


title: JW3_67


title: JW3_64


title: JW3_72


title: JW3_66


title: JW3_65


title: JW3_62


title: JW3_60


title: JW3_6


title: JW3_76


title: JW3_55


title: JW3_58


title: JW3_57


title: JW3_54


title: JW3_51


title: JW3_53


title: JW3_50


title: JW3_52


title: JW3_5


title: JW3_45


title: JW3_46


title: JW3_49


title: JW3_61


title: JW3_48


title: JW3_59


title: JW3_44


title: JW3_63


title: JW3_40


title: JW3_41


title: JW3_43


title: JW3_56


title: JW3_42


title: JW3_4


title: JW4_45


title: JW3_38


title: JW3_37


title: JW3_36


title: JW3_39


title: JW3_34


title: JW3_35


title: JW3_31


title: JW3_33


title: JW3_32


title: JW3_30


title: JW3_3


title: JW3_28


title: JW3_27


title: JW3_29


title: JW3_26


title: JW3_23


title: JW3_25


title: JW3_24


title: JW3_21

value: Lin- Id2+ IL7ra+ Bcl11b- CD25- Gata3int Rora+ Rorc+


title: JW3_22


title: JW3_20


title: JW3_19


title: JW3_11

value: Lin- Id2+ IL7ra+ Bcl11b- CD25- Gata3int Rora+ Rorc-


title: JW3_15


title: JW3_2


title: JW3_12


title: JW3_14


title: JW3_13


title: JW2_96


title: JW2_94


title: JW3_1


title: JW2_92


title: JW2_91


title: JW2_9


title: JW2_89


title: JW3_16


title: JW2_87

value: Lin- Id2+ IL7ra+ Bcl11b- CD25- Gata3lo Roralo/-


title: JW2_88


title: JW2_85


title: JW3_47


title: JW2_83


title: JW2_86


title: JW2_82

value: Lin- Id2hi IL7Ra+ Bcl11b- CD25+


title: JW2_81

value: Bone marrow


title: JW2_80


title: JW2_79


title: JW2_78


title: JW2_77


title: JW2_76


title: JW2_75


title: JW2_90


title: JW2_74


title: JW2_72


title: JW2_70


title: JW2_7


title: JW2_71


title: JW2_69

value: Lin- Id2+ IL7ra+ Bcl11b+ CD25- Gata3lo/-


title: JW2_84


title: JW2_67


title: JW2_66


title: JW2_68


title: JW2_8


title: JW2_65


title: JW2_62


title: JW2_63


title: JW2_61


title: JW2_64


title: JW2_60

value: Lin- Id2+ IL7ra+ Bcl11b+ CD25- Gata3hi


title: JW2_6


title: JW2_59


title: JW2_58


title: JW2_57


title: JW2_56


title: JW2_55


title: JW2_51


title: JW2_52


title: JW2_5


title: JW2_50

value: Lin- Id2+ IL7Ra+ Bcl11b+ CD25+ Gata3hi


title: JW2_49


title: JW2_48


title: JW2_47


title: JW2_46


title: JW2_45


title: JW2_44


title: JW2_43


title: JW2_41


title: JW2_40


title: JW2_38


title: JW2_4

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25- a4b7lo/-


title: JW2_54


title: JW2_36


title: JW2_34


title: JW2_32


title: JW2_33


title: JW2_29


title: JW2_3


title: JW2_30


title: JW2_27


title: JW2_28


title: JW2_31

value: Negative Control


title: JW2_39


title: JW2_24


title: JW2_42


title: JW2_25


title: JW2_23


title: JW2_22


title: JW2_37


title: JW2_26


title: JW2_35


title: JW2_2


title: JW2_20


title: JW2_18


title: JW2_17


title: JW2_14


title: JW2_15


title: JW2_1


title: JW2_12


title: JW2_10


title: JW2_21


title: JW4_13


title: JW2_11


title: JW1_96


title: JW1_95


title: JW1_92


title: JW1_93


title: JW1_91


title: JW1_90


title: JW1_89


title: JW1_88


title: JW1_9


title: JW3_18


title: JW1_87


title: JW2_16


title: JW1_86


title: JW2_13


title: JW1_84


title: JW1_85


title: JW3_10


title: JW1_83


title: JW1_80


title: JW1_81


title: JW1_8


title: JW1_79


title: JW1_78


title: JW1_75


title: JW1_76


title: JW1_77


title: JW2_19


title: JW1_74


title: JW1_70


title: JW1_73


title: JW1_71


title: JW1_72


title: JW1_7


title: JW1_69


title: JW1_68


title: JW2_95


title: JW1_66


title: JW1_67


title: JW1_65


title: JW1_64


title: JW1_82


title: JW1_63


title: JW1_62


title: JW1_61


title: JW1_60


title: JW1_59


title: JW1_58


title: JW2_93


title: JW1_56


title: JW1_54


title: JW1_55


title: JW1_53


title: JW1_52


title: JW1_51


title: JW1_50


title: JW1_5


title: JW1_49


title: JW1_48


title: JW1_47


title: P10ko2

city: Münster

first: Rodrigo

last: Diéguez-Hurtado

address: Röntgenstraße 20

department: Department of Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine/University of Münster

description: ribosomal-associated RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
TopHat2 (version 2.1.1) was used for alignment to the mouse genome assembly (GRCm38.p6 Ensembl release 92)
HTSeq-count (version 0.6.1) was used to generate gene expression count data with the option "-m intersection-nonempty"
DeSeq2 package was used for differential gene expression analysis across samples for protein-coding genes
Genome_build: GRCm38.p6 Ensembl release 92
Supplementary_files_format_and_content: tab-delimited text files include FPKM values (abundance measurement) for each sample.

source_name: Brain cortex

extract_protocol:
Brain cortices were removed, snap frozen in liquid nitrogen, homogenized and subjected to immunoprecipitation with anti-HA beads. Polyribosome-bound RNA was extracted using RNEasy Micro Plus Kit (Qiagen) and assessed for quality in BioAnalyzer 2000 (Agilent).
100 ng of RNA were used for sequencing library preparation with the TruSeq Stranded Total RNA Library Prep Kit (Illumina). Libraries were validated in the 2100 BioAnalyzer and quantified by qPCR and fluorometric analysis (Qubit 2.0, Invitrogen).

value: Brain cortex

tag: age

tag: genotype

value: PdgfrbCreERT2 +/T; Rpl22-HA p/p; Rbpj-lox p/p


title: P10ko3

description: ribosomal-associated RNA


title: JW1_46


title: P10control3

description: ribosomal-associated RNA

value: PdgfrbCreERT2 +/T; Rpl22-HA p/p; Rbpj-lox +/+


title: P10control2

description: ribosomal-associated RNA


title: JW1_6


title: JW1_45


title: JW2_73


title: JW1_57


title: P10control1

description: ribosomal-associated RNA


title: JW3_17


title: JW1_44


title: JW1_43


title: JW1_42


title: P7ko3

description: ribosomal-associated RNA


title: JW1_41


title: P7control3

description: ribosomal-associated RNA


title: JW1_39


title: P7control2

description: ribosomal-associated RNA


title: P7control1

description: ribosomal-associated RNA


title: JW1_4


title: P10ko1

description: ribosomal-associated RNA


title: JW1_38


title: JW1_37


title: JW1_35


title: JW1_36


title: JW1_34


title: JW1_32


title: JW1_28


title: JW1_26

value: Lin- Id2+ IL7Ra+ Bcl11b- CD25+


title: JW1_27


title: P7ko2

description: ribosomal-associated RNA


title: JW1_29


title: JW1_3

value: Lin-


title: P7ko1

description: ribosomal-associated RNA


title: JW1_22


title: JW1_21


title: JW1_25


title: JW1_40


title: JW1_24


title: JW1_23


title: JW1_30


title: JW1_20


title: JW1_19


title: JW1_33


title: JW1_18


title: JW1_31


title: JW1_16


title: RPE and RN_intravitreal injection of VEGF, laser therapy in a continuous mode 2

type: RNA

city: Moscow

first: Aleksandra

middle: Vital'evna

last: Zinov'eva

address: Delegatskaya, 20

country: Russia

institute: MSMSU

hyb_protocol: Amplified RNA was hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina) according to the protocol provided by Illumina

scan_protocol: The analysis of the obtained data was performed with software package GenomeStudio (Illumina, USA), a module of genes expression.

data_processing: The data were normalised using rank invariant using GenomeStudio software (Illumina, CA). GSGX Version: 1.9.0

label: biotin

source_name: retina

label_protocol: 400 ng of each sample of total RNA was amplified with Illumina® TotalPrep™ RNA Amplification Kit (Ambion, USA).

growth_protocol: The study was performed on 4-5-week-old male mice of the line C57BL/6J.

extract_protocol: Total RNA from the isolated tissue samples were extracted with the reagent TRIzol (Invitrogen Life Technologies, USA) according to the guidelines from the manufacturer. Amount of the obtained total RNA was assessed with a spectrophotometer NanoDrop (NanoDrop Technologies, USA) according to the protocol of the manufacturer. Amount of RNA was checked by microarray Agilent Total RNA Nano 6000 (Agilent Technologies, USA).

treatment_protocol: In the first group, intravitreal injection of phosphate-buffered saline (PBS) was performed; in the second, third and fourth groups, intravitreal injection of VEGF was performed; in the third and fourth groups, a day after the intravitreal injection of VEGF, laser radiation was applied. Tissue samples in the animals from group 1 and 2 were taken 2 days after the injection of PBS and VEGF

tag: strain

value: 4-5 week

tag: group

value: Group 4b

value: retinal pigment epithelium, retinal neuroepithelium


title: RPE and RN_1 day after intravitreal injection of VEGF 2

value: Group 2b


title: RPE and RN_intravitreal injection of VEGF, laser therapy in a continuous mode 1

value: Group 4a


title: RPE and RN_1 day after intravitreal injection of VEGF, laser therapy in a micropulse mode 2

value: Group 3b


title: RPE and RN_1 day after intravitreal injection of VEGF 1

value: Group 2a


title: JW1_15

value: Bone marrow


title: RPE and RN_1 day after intravitreal injection of PBS 2

value: Group 1b


title: JW1_2


title: 231_i27w_3

city: St. Louis

first: Dennis

last: Zhu

state: MO

address: 4905 Children’s Place

department: Molecular Microbiology

institute: Washington University

description: rRNA-depleted mRNA

data_processing:
RNA is sequenced using Illumina HiSeq 2500; then basecalls are made using Illumina Casava 1.8 software
Single-end reads were pseudoaligned to the Mtb H37Rv genome and quantified using kallisto with the following parameters --single -l 50 -s 5 -b 100
Genome_build: GenBank assembly GCA_000195955.2
Supplementary_files_format_and_content: tab-delimited processed files show count and tpm (transcripts per million) normalized data for each Mtb transcript

organism: Mycobacterium tuberculosis

source_name: 30mL bacteria culture

growth_protocol: All M. tuberculosis strains were grown at 37° C in Sauton's Broth media (0.5 g L-1 KH2PO4, 0.5 g L-1 MgSO4, 4g L-1 L-asparagine, 60 mL glycerol, 0.05 g L-1 ferric ammonium citrate, 2.0 g L-1 citric acid, 0.1 ml L-1 1% ZnSO4, 0.05% Tween 80, pH 7.0)

extract_protocol:
RNA was prepared from 30mL of log-phase M. tuberculosis using Trizol reagent after bead beating to lyse cells.
RNA was DnaseI treated using the TURBO DNA-free kit from Thermo-Fisher. Ribo-zero was used to deplete ribosomal RNA. Then the RNA library was prepared using standard Illumina protocols.

value: Erdman

value: CardD i27w


title: 230_i27f_2

description: rRNA-depleted mRNA

value: CardD i27f


title: JW1_17

value: Lin- Id2+ IL7ra+ Bcl11b+ CD25- Gata3hi


title: JW1_14


title: JW1_13


title: RPE and RN_1 day after intravitreal injection of PBS 1

value: Group 1a


title: 230_i27f_1

description: rRNA-depleted mRNA


title: JW1_12


title: JW1_11


title: 230_i27f_3

description: rRNA-depleted mRNA


title: RPE and RN_1 day after intravitreal injection of VEGF, laser therapy in a micropulse mode 1

value: Group 3a


title: 196_k125a_3

description: rRNA-depleted mRNA

value: CardD k125a


title: JW1_10

value: Lin- Id2+ IL7ra+ Bcl11b+ CD25- Gata3lo/-


title: 196_k125a_2

description: rRNA-depleted mRNA


title: 196_k125a_1

description: rRNA-depleted mRNA


title: M1-WT_1

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
Gene expression in wild-type peritoneal macrophages 12 hours after treatment with LPS and IFN-γ [rep1]
Normalized_counts_doyoungh.txt

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.4.2, and then aligned to Mus musculus reference genome (GRCm38) using TopHat v2.0.10 with parameters -r 100 --library-type fr-firststrand --mate-std-dev 100 --solexa-quals -p 24 --bowtie-n.
After removing duplicate reads, the number of reads mapped to gene features (GTF file of GRCm38) were counted using HTSeq v0.6.1.
The number of reads counted by HTseq were normalized using the TMM normalization method provided in the edgeR package. The normalized counts were converted to log2-read-counts after adding one to the normalized counts. The log2-read-counts for the samples were then normalized using the quantile normalization method (MATLAB R2011a).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

molecule: polyA RNA

source_name: peritoneal macrophages, wild-type, 12 hr after treatment with LPS and IFN-γ, replicate 1

growth_protocol: 8- to 10-week-old WT and DKO mice were i.p. injected with 3% thioglycollate broth and then sacrificed 4 days later. Peritoneal lavage was undertaken twice using 4 ml of 1×PBS, and harvested cells were then cultured in RPMI1640 (Gibco; 11875-093) plus antibiotics. After 1 hr of culture, suspended cells were discarded and adherent cells were used for experiments.

extract_protocol:
Total RNAs were prepared from WT PMs untreated (Cont-WT) or treated with LPS (100 ng/ml) and IFN-γ (10ng/ml) for 12 hr (M1-WT), and DKO PMs treated with LPS and IFN-γ for 12 hr (M1-DKO). Poly(A) mRNA isolation from total RNAs and fragmentation were performed using the Illumina Truseq Stranded mRNA Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s protocol.
Libraries were prepared for multiplex sequencing using Illumina Truseq Stranded mRNA Sample Prep Kit, according to the manufacturer’s protocol.

treatment_protocol: PMs were isolated from WT and DKO mice then LPS (100 ng/ml) with IFN-γ (10 ng/ml) were treated into cells for 12 hr.

value: peritoneal macrophages

value: wild-type

tag: treatment

value: LPS and IFN-γ for 12 hr


title: Cont-WT_2

description:
Gene expression in wild-type peritoneal macrophages [rep2]
Normalized_counts_doyoungh.txt

source_name: peritoneal macrophages, wild-type, replicate 2

value: no treatment


title: 195_r47e_3

description: rRNA-depleted mRNA

value: CardD r47e


title: 195_r47e_2

description: rRNA-depleted mRNA


title: M1-DKO_2

description:
Gene expression in PDK2/4 double knock-out peritoneal macrophages 12 hours after treatment with LPS and IFN-γ [rep2]
Normalized_counts_doyoungh.txt

source_name: peritoneal macrophages, PDK2/4 double-knockout, 12 hr after treatment with LPS and IFN-γ, replicate 2

value: PDK2/4 double knock-out mutant


title: JW1_1

value: Lin-


title: 195_r47e_1

description: rRNA-depleted mRNA


title: Cont-WT_1

description:
Gene expression in wild-type peritoneal macrophages [rep1]
Normalized_counts_doyoungh.txt

source_name: peritoneal macrophages, wild-type, replicate 1


title: M1-DKO_1

description:
Gene expression in PDK2/4 double knock-out peritoneal macrophages 12 hours after treatment with LPS and IFN-γ [rep1]
Normalized_counts_doyoungh.txt

source_name: peritoneal macrophages, PDK2/4 double-knockout, 12 hr after treatment with LPS and IFN-γ, replicate 1


title: 231_i27w_1

description: rRNA-depleted mRNA


title: VEH.3

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

data_processing:
Fastqc files containing raw RNA sequencing data were trimmed using Trimmomatic (version 0.36). Next, the reads were mapped to the Homo sapiens reference genome from Ensembl database and aligned using the STAR alignment tool (Version 2.5.3). After this, the read counts were generated from SUBREAD (Version 1.5.2) and featured counts were outputted for statistical analysis in R. Quality control and normalization was conducted in R using edgeR (Version 3.20.9).
Statistical Analysis and DEGs: Statistical analysis was conducted in R using limma (Version 3.34.9). Empirical Bayesian statistics were conducted on the fitted model of the contrast matrix. Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene, for each treatment relative to the vehicle control. We considered genes with fold-change >1.5 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: GRCh37

source_name: mammary cells

extract_protocol:
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand.
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000

tag: cell line

tag: gender

value: female

value: breast cancer


title: M1-WT_2

description:
Gene expression in wild-type peritoneal macrophages 12 hours after treatment with LPS and IFN-γ [rep2]
Normalized_counts_doyoungh.txt

source_name: peritoneal macrophages, wild-type, 12 hr after treatment with LPS and IFN-γ, replicate 2


title: 3080_wt_3

description: rRNA-depleted mRNA

value: Erdman

value: CardD wt


title: 3080_wt_2

description: rRNA-depleted mRNA


title: VEH.1


title: VEH.2


title: PA.9


title: 3080_wt_1

description: rRNA-depleted mRNA


title: Nkx2.5+ WT control (hdac1)

first: Joshua

last: Waxman

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology Division

institute: Cincinnati Children's Hospital Medical Center

description: Nkx2.5+_28 hpf experiment_quanification

data_processing:
Strand NGS 3.2 software was used for alignments.
Sequences for alignments were processed and trimmed using the standard RNA-seq pipeline.
DESeq was performed to the median of all samples and a threshold of 1.
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: tab-delimited files of DESeq Normalized expression values

organism: Danio rerio

source_name: Nkx2.5+ cells

extract_protocol:
For whole embryos, they were collected at 48 hours post-fertlilization, RNA was harvested using TRIZOL and a PureLink RNA Micro Kit (Invitrogen). For nkx2.5:ZsYellow+ cells, they were FACS sorted at 28 hours post-fertlization and RNA was harvested using a Single Cell Purification Kit (Norgen Biotek).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB/TU

value: sorted nkx2.5:ZsYellow+ cells

value: 28 hours post-fertilization


title: Nkx2.5+ cyp26 deficient

description: Nkx2.5+_28 hpf experiment_quanification


title: Nkx2.5+ WT control (cyp26)

description: Nkx2.5+_28 hpf experiment_quanification


title: Nkx2.5+ hdac1 depleted

description: Nkx2.5+_28 hpf experiment_quanification


title: 53B_ILC2

city: Durban

first: Alasdair

last: Leslie

address: 719 Umbilo Road

country: South Africa

institute: African Health Research Institute

data_processing:
Demultiplexing was performed using bcl2fastq2-2.17.1.14 (Illumina).
TopHat (2.0.10) and RSEM (1.2.8) were used to perform genome and transcriptome alignment, respectively, against the hg38 reference (Gencode v21).
Picard Tools were used to determine sample quality metrics. Samples with fewer than 10^6 reads or fewer than 10,000 aligned genes were removed from this study.
Gene expression matrices were generated using RSEM.
Differential Expression analysis was performed using DESeq2 (1.14.1).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt file containing counts for each sample.

source_name: ILC2 sorted from lung

extract_protocol:
Total RNA was extracted from cell lysate (RLT +1% BME) using RNAClean XP SPRI beads. Messenger RNA was primed for reverse transcription and PCR using an oligodT RT primer.
Libraries were constructed using a modified version of the Smart-Seq2 protocol described in Trombetta et al., Curr Protoc Mol Biol, (2014). Libraries were sequenced twice on a NextSeq 500 using the 75-cycle High Throughput kit.

tag: disease

value: Tuberculosis

value: Lung

tag: cell population


title: PA.8

tag: cell type


title: 53C_ILC2


title: 53C_ILC3

source_name: ILC3 sorted from lung


title: Cyp26 deficient embryo

description: Whole embryo_48 hpf experiment_quantification

source_name: whole embryo

value: whole embryo

value: 48 hours post-fertilization


title: 53A_ILC3


title: Crg mutant embryo


title: WT control (cyp26) embryo


title: 53A_ILC2


title: PA.7


title: WT control (crg) embryo


title: Eed cKO2

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

data_processing:
RNA-seq reads were aligned to the GRCm38 genome assembly using HISAT 2 (v. 2.1.0) using default parameters.
Expression calculations and differential gene expression analysis were excuted by htseqcount (v. 0.9.1) and DESeq2 (v. 1.2.0) respectively.
Genome_build: GRCm38

source_name: Hippocampus dentate gyrus

extract_protocol:
Hippocampus dentate gyrus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.RNA-seq libraries from WT and EED cKO dentate dyrus at 14-day-old were prepared using Illumina RNA-Seq Preparation Kit.  Total RNA sample QC was measured by Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) .
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

value: Hippocampus dentate gyrus

value: post natal day14


title: OA.6


title: 50C_ILC3


title: WT1


title: WT2


title: OA.5


title: Eed cKO1


title: 50B_ILC3


title: OA.4


title: 50B_ILC2


title: SA.15


title: SA.14


title: SA.13


title: 50A_ILC3


title: 50A_ILC2


title: LA.12


title: 46C_ILC2


title: 50C_ILC2


title: LA.11


title: 46C_ILC3


title: LA.10


title: colon 1 sample 27

city: Hannover

first: Ruth

last: Olmer

address: Carl-Neuberg-Str. 1

department: HTTG

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2000 to 3000ng of labeled cRNA were used for hybridization. Effects on fluorescence incorporation efficiency have been partially compensated by increasing cRNA amounts used for hybridization (3000ng for colon, liver, small intestine instead of 2000ng for all other samples).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction and processing of raw fluorescence intensity values was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were finally normalized by quantile normalization approach.
Normalized processed signal intensity values (non-log). Values of control probes were removed.

source_name: adult tissue (Takara)

label_protocol: 150 to 400ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations. Within this Microarray project cRNA samples derived from liver, colon and small intestine consistently suffered from reduced cRNA yield, cRNA fragment length, and cRNA fluorescence incorporation efficiency as a result of reduced total RNA input integrity. Respective effects on fragment length were partially compensated by increasing total RNA input amounts (250ng, 300ng, 400ng for liver, colon, small intestine, respectively, instead of 150ng for all other samples).

growth_protocol: Undifferentiated cells were grown as monolayer cultures in Essential 8 growth medium on geltrex coated tissue culture flasks.

extract_protocol: Total RNA was isolated from TRIzol®-lysed cells via NucleoSpin® RNA II Kit (Macherey-Nagel).

treatment_protocol: In a stepwise differentiation protocol iPSCs from monolayers in essential 8 (E8) medium (Beers et al., 2012) were first differentiated to DE via STEMdiff™ Definitive Endoderm Kit (TeSR™-E8™ Optimized) from STEMCELL Technologies. DE cells on day 4 of differentiation were cultured for 2 days in the presence of dorsomorphin and ROCK inhibitor. Thereafter, cells were treated for one day with IWP-2. From day 7 until day 15 cells were cultured in the presence of CHIR99021, BMP4 and FGF10.

value: colon

value: adult

value: CFTR WT


title: liver 3 sample 32

value: liver


title: small intestine 3 sample 26

value: small intestine


title: liver 2 sample 31


title: 46A_ILC3


title: colon 3 sample 29


title: colon 2 sample 28


title: liver 1 sample 30


title: donor 1_d15 differentiated intestine_3

tag: donor line

value: donor 1

value: pluripotent stem cell

value: iPS CFTR WT

value: day 15 of differentiation


title: JW1_94

source_name: Bone marrow

value: Lin- Id2+ IL7Ra+ Bcl11b/CD25- a4b7+ Gata3lo Roralo

value: Bone marrow


title: donor 1_d15 differentiated intestine_1


title: small intestine 1  sample 24


title: donor 1_untreated/undifferentiated_3

value: untreated/undifferentiated


title: small intestine 2 sample 25


title: Jurkat shARIEL RNA-seq #2

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets of two control samples and two knockdown samples for ARIEL were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
htseq-count v0.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4, with the intersection-strict mode, was used to analyze differential gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include DEseq2 analysis and rlogNormalized expression for each sample

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium (BioWest) supplemented with 10% FBS (BioWest) in a CO2 incubator.

extract_protocol:
RNA was extracted using an miRNeasy kit (Qiagen) with some modifications.  The cell numbers for each sample were counted before cell pellet was collected. ERCC RNA Spike-in mix (1:10 dilution) wasthen  added to each sample according to the cell numbers (Example: 1ul was added for 1 million cells)  after the addition of Qiazol.  After the addition of chloroform, the samples were transferred to a Maxtract high-density column (Qiagen) to be spun down.  The aqueous layer was then retained for downstream RNA extraction following the manufacturer’s instructions.  The extracted RNA was subjected to DNase treatment (Turbo DNA-freeTM kit, Ambion) according to the manufacturer’s instructions to eliminate any genomic DNA present in the samples and then cleaned up using an RNeasy kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the Illumina Hiseq4000 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: Jurkat cells were infected with lentivirus encoding shRNAs targeting either GFP or ARIEL in the presence of polybrene by centrifugation. The infected cells were then selected with 0.7ug/ml puromycin in RPMI-1640 medium for at least 36 hours after infection. Cell pellets were then collected 72 hours after infection.

value: Jurkat

tag: knockdown

value: ARIEL knockdown


title: 46A_ILC2

value: Tuberculosis

value: Lung


title: Jurkat shARIEL RNA-seq #1


title: Jurkat control (shGFP control for shARIEL) RNA-seq #2

value: control


title: 24B_ILC3


title: donor 6_d15 differentiated intestine_3

value: donor 6


title: donor 1_d15 differentiated intestine_2


title: 24B_ILC2


title: 23C_ILC2


title: donor 1_untreated/undifferentiated_1


title: Jurkat control (shGFP control for shARIEL) RNA-seq #1


title: donor 1_untreated/undifferentiated_2


title: donor 6_untreated/undifferentiated_2


title: donor 6_d15 differentiated intestine_1


title: hypothalamus_Heat exposure_30 d_ replicate 3

city: TianJin

first: Fan

middle: Li

last: Jun

state: TianJin

address: No. 1 Dali Road, Heping District, Tianjin

department: Academy of Military Medical Sciences, Academy of Military Medical Sciences

institute: Institute of Environmental and Operational Medicine

hyb_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). 1. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. 2. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). 3. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). 4. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 5. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer,6. then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 7. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. 8. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. 9. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

organism: Rattus norvegicus

source_name: hypothalamus,Heat exposure 30 d

label_protocol: The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Rat circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

extract_protocol: Total RNA was isolated from the hypothalamus of rats from each group (TRI Reagent® BD, MRC)following the manufacturer's recommendations. The total RNA concentration of each sample was determined, the OD260/OD280 ratio was determined by NanoDrop ND-1000, and the purity of RNA was determined.

treatment_protocol: All rat experiments were performed in accordance with the National Institutes of Health guide for the care and use of Laboratory animals (NIH Publications No. 8023, revised 1978).And they have also been approved by the Ethics Committee for Animal Experimentation of the Tianjin Institute of Health and Environmental Medicine. Sprague Dawley (SD) a total of 28 male rats weighing 180–200 g were maintained under a free-feeding schedule and a 12h –12h (light from 6:00 to 18:00 h)light–dark cycle. Rats were randomly assigned to the HA or C group. The HA group was maintained at a chamber temperature of 35°C ± 1°C and a relative humidity of 55% ± 5% 2 h daily for 30 days.Meanwhile, rats in the C group were maintained at a chamber temperature of 24°C ± 1°C and fed freely for 30 days. On day 31, rats were sacrificed under pentobarbital sodium anesthesia (100 mg/kg) , the whole brain was removed, and the hypothalamus, including the preoptic area, was rapidly removed by vertically incising at the optic chiasm and just anterior to the mammillary bodies with the depth of 2 mm. Then the hypothalamus was placed in liquid nitrogen. Each rat was handled individually to make sure of precise sampling. Frozen samples were stored at 80°C for subsequent analysis.

value: hypothalamus

value: male

value: Heat exposure 30 d


title: donor 2 gene corrected_untreated/undifferentiated_3

value: donor 2 gene corrected

value: CFiPS (p.Phe508del) gene corrected


title: donor 2 gene corrected_d15 differentiated intestine_2

value: pluripotent stem cell


title: donor 2 gene corrected_d15 differentiated intestine_1


title: donor 2 gene corrected_d15 differentiated intestine_3


title: donor 6_untreated/undifferentiated_1

value: iPS CFTR WT


title: donor 6_d15 differentiated intestine_2

value: day 15 of differentiation


title: donor 2 gene corrected_untreated/undifferentiated_2


title: 213C_ILC3

value: Control


title: 213C_ILC2


title: hypothalamus_Heat exposure_30 d_ replicate 2

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.


title: CTLC_ILC3


title: 23B_ILC3


title: C57_T1

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

description: NC

data_processing:
Basecalls performed using Illumina RTA 1.17.21.3
Samples demultiplexed using Casava 1.8.2.
Sequenced fragments were trimmed in for sequencing adapters using Casava and candidates longer than 17bp where mapped to the reference genome mm10 using Tophat version 2.0.10.
Known miRNA extracted from miRBase mm10 version 21 were then quantified by counting the number of reads that fall into each of their location on the genome using HTSeq count version 0.5.4, keeping the contribution of ambiguously matched reads.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include columns: A. miRNA identifier, B. readcount and C. readcount per million reads sequenced (RPM).

source_name: hindlimb muscle

growth_protocol: 1 day post ischemia

extract_protocol:
trizol+miRvana mini kit for small RNA
TruSeq Small RNA Sample Preparation (Illumina)

treatment_protocol: ischemia induced surgically by feroral artery removal

tag: phenotype

value: control normocholesterolemic (NC)

value: ischemic (day 1 post surgery)

value: hindlimb muscle


title: ApoE_T1

description: HC

value: ApoE-/-

value: hypercholesterolemic (HC)


title: CTLC_ILC2

value: Lung


title: hypothalamus_Heat exposure_30 d_ replicate 1


title: donor 2_d15 differentiated intestine_2

value: donor 2

value: CFiPS (p.Phe508del)


title: donor 2 gene corrected_untreated/undifferentiated_1

value: untreated/undifferentiated


title: hypothalamus_Heat exposure_0 d_ replicate 3

source_name: hypothalamus,Heat exposure 0 d

value: hypothalamus

value: male

value: Heat exposure 0 d


title: donor 2_d15 differentiated intestine_3


title: donor 2_d15 differentiated intestine_1


title: SS_HUVECs2_smallRNA

status: Public on May 10 2019

city: Montreal

first: Marie-Pierre

last: Hardy

state: Quebec

address: 2950 Chemin de Polytechnique

department: IRIC

institute: University of Montreal

description:
Small RNA
processed data file: miRNAs_expressed_all_samples.txt

data_processing:
Basecalls performed using Illumina RTA 1.18.64.
Samples demultiplexed using bcl2fastq 2.17.
Sequenced reads for total RNA samples were trimmed for sequencing adapters and low quality extremities using Trimmomatic and mapped to the reference genome using STAR version 2.5.1b. Gene expression were derived from the STAR alignment as readcount and also estimated using RSEM version 1.2.28.
Transcript level abundance were also estimated using kallisto version 0.43.1 using both reference annotations as well as a larger transcript database which include all genomic repeats.
Sequenced reads for small RNA samples were trimmed and mapped using mirdeep2 version 0.0.8 and the miRBase human database.
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited text file where columns are Ensembl 88 gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned.
Supplementary_files_format_and_content: RSEM: Tab-delimited text file where columns correspond to a standard RSEM output for Ensembl 88 gene identifiers (first line identifies the column).
Supplementary_files_format_and_content: Kallisto abundance: Tab-delimited text file where columns are Ensembl 90/91 transcript identifier, transcript length, effective length, estimated counts and TPM abundance values.
Supplementary_files_format_and_content: miRNAs_expressed_all_samples.txt: Tab-delimited text file contains miRNA raw counts and normalized counts for all samples.

source_name: (Serum-starved HUVECs) HUVECs cultured for 4h with serum-free medium

extract_protocol:
TriZol + miRNeasy micro Kit (Qiagen, #217084) with DNase digestion (Qiagen, #79254).
CleanTag kit for small RNAs (TriLink).

value: apoptotic HUVECs

tag: passage


title: donor 2_untreated/undifferentiated_3

value: pluripotent stem cell


title: SS_ApoBodies1_smallRNA

source_name: Apoptotic Bodies (SS-HUVECs-released apoptotic bodies (50 000G pellet))

value: apoptotic bodies


title: SS_HUVECs1_smallRNA


title: SS_ApoExos2_smallRNA

source_name: Apoptotic Exo-like vesicles (SS-HUVECs-released vesicles (200 000G pellet))

value: apoptotic Exo-like vesicles


title: SS_ApoBodies2_smallRNA


title: N_HUVECs2_smallRNA

source_name: Normal HUVECs (HUVECs cultured for 4h with vesicles-free medium)

value: normal HUVECs


title: hypothalamus_Heat exposure_0 d_ replicate 2


title: hypothalamus_Heat exposure_0 d_ replicate 1


title: donor 2_untreated/undifferentiated_2


title: CTCL-2

city: Pittsburgh

first: Patrizia

last: Fuschiotti

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Chromium scRNA-seq data produced by the 10X Chromium Platform were processed to generate sample-specific fastq files.
Processed reads were then examined by quality metrics, mapped to a reference human genome using RNA-seq aligner STAR and assigned to individual cells of origin according to the cell specific barcodes, using the Cell Ranger pipeline (10X Genomics).
To ensure that PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level 10. In this way, cell x gene UMI counting matrices were generated for downstream analyses.
Seurat, an R package developed for single-cell analysis,11 was used to identify distinct cell populations and visualize cell clusters in graphs as in. 8 Specifically, the UMI matrix was filtered such that only cells expressing at least 200 genes were utilized in downstream analysis.
Unwanted sources of variation were regressed out of the data by constructing linear models to predict gene expression based on the number of UMIs per cell as well as the percentage of mitochondrial gene content.
Genome_build: GrCh38 genome
Supplementary_files_format_and_content: Raw dataframe csv files

source_name: Skin tumor

extract_protocol:
Skin biopsies were minced and digested enzymatically (Whole Dissociation Skin Kit, Miltenyi Biotec) for 2 hours at 37°C and further dispersed using the Miltenyi gentleMACS Octo Dissociator. Experimental procedures followed established techniques7 using the Chromium Single Cell 3’ Library V2  kit (10x Genomics). Cell suspensions were separated by the Chromium System (10X Genomics)7,8 into  mini-reaction "partitions" or GEMs formed by oil micro-droplets, each containing a gel bead and a cell. A  1000-fold excess of partitions compared to cells assured that most partitions/GEMs had only one cell per  GEM. Gel beads contained an oligonucleotide scaffold composed of an oligo-dT section for priming  reverse transcription, and barcodes for each cell (10X Genomics) and each transcript (unique molecular   identifier, UMI), as described.9 7,000 cells were loaded into the instrument to obtain data on ~4,000 cells  with a rate of ~3.1% of partitions showing more than one cell/partition. The following steps were all  performed using reagents and protocols developed by 10X Genomics.
The emulsions were transferred from the Chromium chip to a PCR cycler for cDNA synthesis. The emulsion was then broken using a recovery agent, and following Dynabead and SPRI clean up, cDNAs were amplified by PCR (C1000, Bio-Rad). cDNAs were sheared enzymatically into lengths of ~200bp. DNA fragment ends were repaired, A-tailed, and adaptors ligated.

tag: tumor stage

value: IVA T4NxB2M0

tag: disease state

value: CTCL tumor


title: CTCL-5

value: IIB T3N0B0M0


title: N_HUVECs1_smallRNA


title: SS_ApoExos1_totalRNA

extract_protocol:
TriZol + miRNeasy micro Kit (Qiagen, #217084) with DNase digestion (Qiagen, #79254).
KAPA Stranded RNA-Seq Total RNA (KAPA Biosystems).


title: SS_ApoBodies2_totalRNA


title: SS_ApoBodies1_totalRNA


title: SS_HUVECs2_totalRNA


title: SS_HUVECs1_totalRNA


title: donor 2_untreated/undifferentiated_1


title: SS_ApoExos1_smallRNA


title: N_HUVECs1_totalRNA


title: SS_ApoExos2_totalRNA


title: S5 timecourse, differentiation 2, day 7

first: Adrian

last: Veres

state: Massachusetts

address: 7 Divinity Ave

institute: Harvard University

description:
Stage_5.all.processed_counts.tsv.gz
Stage_5.all.cell_metadata.tsv
Stage_5.raw_indrops_counts.tsv.gz
Veres2019_analysis_data.tar
Stage_5.endocrine_pseudotime.cell_metadata.tsv
Stage_5.day0_prog_pseudotime.cell_metadata.tsv
Stage_5.day1_prog_pseudotime.cell_metadata.tsv

data_processing:
All processing steps from raw fastq files to count matrices were performed using the custom pipeline for inDrops data analysis (www.github.com/indrops/indrops) using the the following parameters specified in the YAML file: [trimmomatic arguments]: LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "30". [output_arguments]: filter_alignments_to_softmasked_regions: True. All other parameters were used as in the default_parameters file in the repository github.com/indrops/indrops, commit hash 8a9167.
Genome_build: GRCh38.88
Supplementary_files_format_and_content: '*.raw_indrops_counts.*' files are the raw, unfiltered output from the Indrops processing pipeline. The first column indicates the barcode label using the Indrops pipeline nomenclature, all folllowing columns are UMIFM counts as defined in Klein et al. (2015). The gene corresponding to each column is listed in the header line.
Supplementary_files_format_and_content: '*.processed_counts.*' are filtered counts files, removing undetected genes and filtering cells using the thresholds described in the methods section of Veres et al. 2019. The first column indicates the cell label, all following columns are UMIFM counts for the gene indicated in the header row.
Supplementary_files_format_and_content: '*.cell_metadata.*' files contain metadata associated for all filtered cells in the each dataset. The first row is a header detailing the type of data in each column. These include TSNE coordinates, cluster label annotations and pseudotime values (as appropriate).
Supplementary_files_format_and_content: code_analysis_files.tar is a tarball of all files (primarily loom-formatted) used in generating the analysis, with the accompanying code at https://github.com/meltonlab/scbeta_indrops

source_name: in vitro differentiated pluripotent stem cell

growth_protocol: Human embryonic and pluripotent stem cells were maintained and differentiated as described in the methods of (Veres et al. 2018). Differentiation was carried out using step-wise protocols aimed at gradually producing beta cells in vitro.

extract_protocol:
Differentiated clusters were prepared for single cell RNA sequencing as follows: 1-2 mL suspension culture was sampled from the spinner flask, dissociated with TrypLE Express (5-15 minutes at 37 °C), quenched with cold PBS + 1% BSA and gently dispersed with a P1000 pipette. Cells were then centrifuged (300 rpm, 3 min), resuspended in cold PBS+1% BSA and filtered through a 70 µm mesh filter. Centrifugation, resuspension and filtering was repeated a total of 3 times. Cells were then counted and resuspended to the working dilution for inDrops (100,000 cells/mL) in 1X PBS with 13% Optiprep (Sigma; D1556).
Single cell RNA sequencing was carried out using the inDrops platform, as previously described (Klein 2015, Zilionis 2016). Most samples were run using ‘inDrops v2’ barcoded hydrogel beads (1 Cell Bio, Harvard Single Cell Core), and one experiment used ‘inDrops v3’ beads (Harvard Single Cell Core). Following the inDrops protocol, each biological sample was split into several aliquots of 1000-3000 cells after encapsulation. At least two library aliquots were prepared separately from each sample, indexing using recommended index sequences, pooled and sequencing on a NextSeq 500 (Illumina).

tag: experiment

value: Stage 5 timecourse

value: SC-beta protocol v8

tag: Stage

value: Stage 5


title: S5 timecourse, differentiation 2, day 4

value: in vitro differentiated pluripotent stem cell


title: S5 timecourse, differentiation 2, day 6


title: S5 timecourse, differentiation 1, day 7


title: S5 timecourse, differentiation 2, day 1


title: S5 timecourse, differentiation 2, day 2


title: S5 timecourse, differentiation 2, day 3


title: S5 timecourse, differentiation 2, day 0


title: JW2_53

extract_protocol:
Individual cells were flow cytometrically purified on a 96 well format into 0.2% Triton X-100 containing RNase inhibitor, dNTPs and oligo-dT primers and stored at -80oC.
On thawing, lysates were heated to 72 oC for 3 minutes and subject to reverse transcription, PCR preamplification (26 cycles) and PCR purification.  cDNA library quality was assessed for all samples by qualitative PCR using primers for 18s RNA with an additional check by Bioanalyzer using an Agilent high sensitivity DNA chip on a small subset of libraries. A subset of libraries was quantified using the Qubit dsDNA HS assay kit and an average value used to calculate library dilution to 100-150 pg/ml. cDNA library tagmentation and amplification was performed using the Illumina Nextera XT DNA Library Preparation Kit according to manufacturer’s instructions except that all volumes were reduced 4-fold and tagmentation performed at 55oC for 20 minutes. Nextera index and Illumina adapter sequences were incorporated at the amplification stage (N7xx and S5xx). Amplified and indexed libraries were pooled and purified using Agencourt AMPure XP beads at a ratio of 1:0.9 library to beads and washed with 70% ethanol. Two rounds of purification were performed before a final elution in 1.25x total library volume of Nextera Resuspension buffer

tag: cell phenotype from facs

value: Lin- Id2+ IL7ra+ Bcl11b+ CD25- Gata3hi

tag: mouse id

tag: tissue

value: Bone marrow


title: S5 timecourse, differentiation 1, day 4


title: S5 timecourse, differentiation 1, day 3


title: S5 timecourse, differentiation 2, day 5


title: S5 timecourse, differentiation 1, day 6


title: S5 timecourse, differentiation 1, day 5


title: S5 timecourse, differentiation 1, day 1


title: S5 timecourse, differentiation 1, day 2


title: S5 timecourse, differentiation 1, day 0


title: S6 timecourse, differentiation 3, week 5

description:
Stage_6.all.processed_counts.tsv.gz
Stage_6.all.cell_metadata.tsv
Stage_6.raw_indrops_counts.tsv.gz
Veres2019_analysis_data.tar
Stage_6.scbeta_pseudotime.cell_metadata.tsv
Stage_6.exo.cell_metadata.tsv

value: Stage 6 timecourse

value: Stage 6


title: N_HUVECs2_totalRNA


title: S6 timecourse, differentiation 3, week 4


title: S6 timecourse, differentiation 2, week 5


title: S6 timecourse, differentiation 2, week 4


title: S6 timecourse, differentiation 3, week 1


title: S6 timecourse, differentiation 3, week 0


title: S6 timecourse, differentiation 2, week 3


title: S6 timecourse, differentiation 2, week 2


title: S6 timecourse, differentiation 2, week 1


title: S6 timecourse, differentiation 1, week 5


title: S6 timecourse, differentiation 3, week 2


title: S6 timecourse, differentiation 1, week 4


title: S6 timecourse, differentiation 3, week 3


title: S6 timecourse, differentiation 1, week 1


title: S6 timecourse, differentiation 1, week 0


title: Stages 3 to 6, Protocol x2, Stage 6 complete

value: Stages 3 to 6 timecourse

value: SC-beta protocol x2


title: sstotRNATruseq_100ng D1

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using tophat2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts values for all samples

extract_protocol: RNA libraries were prepared for sequencing according to the kit manufacturer instructions

tag: sample type

value: Mixture 25% A + 75% B (D)

tag: tissue source

value: Tissue mixture

tag: protocol

value: Kit total RNA TruSeq


title: S6 timecourse, differentiation 1, week 3


title: Stages 3 to 6, Protocol x2, Stage 5 complete


title: Stages 3 to 6, Protocol x2, Stage 4 complete

value: Stage 4


title: Mubritinib 200nM

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

institute: The Hospital for Sick Children

description: sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from replicate control screens were summed.
Genome_build: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core gene-targting sgRNA set of of the library.
Supplementary_files_format_and_content: tab seperated sgRNA read counts for each sample

extract_protocol:
Samples were PBS-washed and cell pellets frozen. Genomic DNA was extracted using the QIAamp DNA blood maxi kit (Qiagen).
sgRNA sequences were recovered and fitted with Illumina adaptors by PCR as previously described (Bertomeu et al., 2017).

tag: cell line

value: pre-B lymphoid cell line

tag: genotype/variation

value: pooled sgRNA library

tag: treatment

value: Mubritinib 200nM


title: sstotRNATruseq_100ng D2


title: 0.1% DMSO control

description: sgRNAs PCR-amplified from genomic DNA

tag: cell type

value: 0.1% DMSO control


title: Day 0 control

description: sgRNAs PCR-amplified from genomic DNA

value: Day 0 control


title: Stages 3 to 6, Protocol x1, Stage 5 complete

value: SC-beta protocol x1

value: Stage 5


title: RiboZ_sstotSmarter_10ng B2

value: Human Brain Reference RNA (B)

value: Normal brain tissue mixture

value: Kit RiboZero + SMARTer


title: sstotRNATruseq_100ng C1

value: Mixture 75% A + 25% B (C)


title: sstotRNATruseq_100ng B1


title: sstotRNATruseq_1ug B1


title: RiboG_sstotSmarter_100ng C2

value: Kit RiboGone + SMARTer


title: sstotRNATruseq_1ug C2


title: sstotRNATruseq_100ng B2


title: sstotRNATruseq_100ng A2

value: Universal Human Reference RNA (A)


title: S6 timecourse, differentiation 2, week 0

value: in vitro differentiated pluripotent stem cell

value: Stage 6 timecourse

value: SC-beta protocol v8

value: Stage 6


title: S6 timecourse, differentiation 1, week 2


title: sstotRNATruseq_100ng A1

value: Tissue mixture

value: Kit total RNA TruSeq


title: RiboZ_sstotSmarter_10ng A2


title: sstotRNATruseq_100ng C2


title: SmarterUL_NexteraXT_1ng_130pg D1

value: Mixture 25% A + 75% B (D)

value: Kit SMARTer Ultra-Low + Nextera XT


title: SmarterUL_NexteraXT_1ng_130pg D2


title: mRNATruseq_1ug D2

value: Kit mRNA TruSeq


title: SmarterUL_NexteraXT_1ng_750pg D2


title: SmarterUL_NexteraXT_1ng_750pg D1


title: 53B_ILC3

tag: disease

value: Tuberculosis

value: Lung

tag: cell population


title: SmarterUL_NexteraXT_1ng_130pg C2


title: SmarterUL_NexteraXT_1ng_130pg C1


title: SmarterUL_NexteraXT_1ng_130pg B2

value: Human Brain Reference RNA (B)


title: SmarterUL_NexteraXT_1ng_750pg C1


title: SmarterUL_NexteraXT_1ng_750pg C2


title: SmarterUL_NexteraXT_1ng_130pg B1

value: Normal brain tissue mixture


title: SmarterUL_NexteraXT_1ng_750pg B1


title: SmarterUL_NexteraXT_1ng_750pg B2


title: mRNATruseq_1ug A2


title: SmarterUL_NexteraXT_1ng_130pg A1


title: SmarterUL_NexteraXT_1ng_750pg A1


title: SmarterUL_NexteraXT_1ng_750pg A2


title: SmarterUL_NexteraXT_1ng_130pg A2


title: E14.96H_LTHT10_9_38

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
The 5bp UMI sequence (initially sequenced in read1), are appended at the end of the headers of the reads (here the reads we provide are resulting from this operation)
reads are mapped with tophat v2.0.13 on the mouse genome GRCm38 considering Ensembl78 genes annotations
bam files are processed with umi_tools to deduplicate reads with identical UMI sequence
gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_count.tsv.gz contains the result of gene expression quantification by summarizeOverlaps() for each cell. The integers values represent the number of exonic reads mapping into each gene after UMI correction. The first columns contains the gene name that is quantified.

source_name: cortical cells

extract_protocol:
The putative primary somatosensory cortex S1 was microdissected and incubated in 0.05% trypsin at 37°C for 5 minutes. Following tissue digestion, fetal bovine serum was added to the mix and cells were manually dissociated via up-and-down pipetting. Cells were centrifuged 5min at 300g and the pellet was suspended in 1ml of HBSS then passed on a 70µm cell stainer. FT+ cells, gated on the top 5% brightest cells, were finally FAC-sorted on a MoFloAstrios (Beckman). FAC-sorted FT+ cells (18µl) were mixed with the C1 Suspension Reagent (2µl; Fluidigm) yielding a total of 20µl of cell suspension mix with ~500 cells/μl. The cell suspension mix was loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10- to 17-µm cells (HT-800, Fluidigm #100-57-80). cDNA synthesis and preamplification was processed following the manufacturer’s instructions (C1 system, Fluidigm). Single cell RNA-sequencing libraries of the cDNA were prepared using Nextera XT DNA library prep kit (Illumina). Libraries were multi-plexed and sequenced according to the manufacturer’s recommendations with paired-end reads using HiSeq2500 platform (Illumina) with an expected depth of 1M reads per single cell, and a final mapping read length of 70bp.
SMARTseq v4 kit (Clontech, # 634888)

tag: cluster


title: mRNATruseq_1ug A1


title: E14.96H_LTHT10_5_38


title: E14.96H_LTHT10_6_38


title: E14.96H_LTHT10_4_38


title: E14.96H_LTHT10_1_38

value: Astro


title: E14.96H_LTHT10_3_38


title: E14.96H_LTHT10_2_38


title: E14.96H_LTHT10_9_37


title: E14.96H_LTHT10_8_37


title: E14.96H_LTHT10_7_37


title: E14.96H_LTHT10_3_37


title: E14.96H_LTHT10_6_37


title: E14.96H_LTHT10_2_37


title: E14.96H_LTHT10_10_37


title: E14.96H_LTHT10_7_36


title: E14.96H_LTHT10_9_36


title: E14.96H_LTHT10_6_36


title: E14.96H_LTHT10_10_36


title: E14.96H_LTHT10_2_36


title: E14.96H_LTHT10_9_35


title: E14.96H_LTHT10_1_36


title: E14.96H_LTHT10_6_35


title: E14.96H_LTHT10_7_35


title: E14.96H_LTHT10_5_35


title: E14.96H_LTHT10_2_35


title: E14.96H_LTHT10_9_34


title: E14.96H_LTHT10_8_34


title: E14.96H_LTHT10_4_35


title: E14.96H_LTHT10_5_34


title: E14.96H_LTHT10_6_34


title: E14.96H_LTHT10_7_34


title: E14.96H_LTHT10_1_34


title: E14.96H_LTHT10_1_37


title: E14.96H_LTHT10_2_34


title: E14.96H_LTHT10_9_33


title: E14.96H_LTHT10_5_36


title: E14.96H_LTHT10_3_36


title: E14.96H_LTHT10_8_33


title: E14.96H_LTHT10_6_33


title: E14.96H_LTHT10_10_33


title: E14.96H_LTHT10_5_33


title: E14.96H_LTHT10_9_32


title: E14.96H_LTHT10_7_33


title: E14.96H_LTHT10_2_32


title: E14.96H_LTHT10_10_35


title: E14.96H_LTHT10_7_32


title: E14.96H_LTHT10_1_33


title: E14.96H_LTHT10_10_32


title: E14.96H_LTHT10_1_32


title: E14.96H_LTHT10_5_31


title: E14.96H_LTHT10_2_31


title: E14.96H_LTHT10_7_31


title: E14.96H_LTHT10_4_31


title: E14.96H_LTHT10_9_31


title: E14.96H_LTHT10_4_32


title: E14.96H_LTHT10_6_32


title: E14.96H_LTHT10_6_30


title: E14.96H_LTHT10_9_29


title: E14.96H_LTHT10_5_30


title: E14.96H_LTHT10_7_29


title: E14.96H_LTHT10_8_30


title: E14.96H_LTHT10_6_29


title: E14.96H_LTHT10_1_30


title: E14.96H_LTHT10_9_30


title: E14.96H_LTHT10_10_29


title: E14.96H_LTHT10_3_29


title: E14.96H_LTHT10_9_28


title: E14.96H_LTHT10_1_29


title: E14.96H_LTHT10_8_28


title: E14.96H_LTHT10_5_28


title: E14.96H_LTHT10_5_29


title: E14.96H_LTHT10_10_28


title: E14.96H_LTHT10_4_28


title: E14.96H_LTHT10_1_28


title: E14.96H_LTHT10_1_31


title: E14.96H_LTHT10_3_28


title: E14.96H_LTHT10_8_27


title: E14.96H_LTHT10_5_27


title: E14.96H_LTHT10_7_27


title: E14.96H_LTHT10_1_27


title: E14.96H_LTHT10_6_26


title: E14.96H_LTHT10_4_26


title: E14.96H_LTHT10_9_25


title: E14.96H_LTHT10_2_26


title: E14.96H_LTHT10_7_25


title: E14.96H_LTHT10_6_28


title: E14.96H_LTHT10_6_25


title: E14.96H_LTHT10_3_25


title: E14.96H_LTHT10_8_24


title: E14.96H_LTHT10_1_25


title: E14.96H_LTHT10_2_25


title: E14.96H_LTHT10_6_24


title: E14.96H_LTHT10_9_27


title: E14.96H_LTHT10_3_24


title: E14.96H_LTHT10_9_24


title: E14.96H_LTHT10_5_24


title: E14.96H_LTHT10_2_24


title: E14.96H_LTHT10_6_23


title: E14.96H_LTHT10_5_23


title: E14.96H_LTHT10_7_26


title: E14.96H_LTHT10_3_23


title: E14.96H_LTHT10_2_23


title: E14.96H_LTHT10_3_27


title: E14.96H_LTHT10_5_26


title: E14.96H_LTHT10_10_26


title: E14.96H_LTHT10_5_22


title: E14.96H_LTHT10_9_22


title: E14.96H_LTHT10_4_22


title: E14.96H_LTHT10_3_22


title: E14.96H_LTHT10_10_22


title: E14.96H_LTHT10_2_22


title: E14.96H_LTHT10_1_22


title: E14.96H_LTHT10_8_23


title: E14.96H_LTHT10_7_23


title: E14.96H_LTHT10_7_21


title: E14.96H_LTHT10_5_21


title: E14.96H_LTHT10_8_21


title: E14.96H_LTHT10_3_21


title: E14.96H_LTHT10_7_20


title: E14.96H_LTHT10_6_20


title: E14.96H_LTHT10_4_23


title: E14.96H_LTHT10_9_23


title: E14.96H_LTHT10_2_21


title: E14.96H_LTHT10_10_21


title: E14.96H_LTHT10_10_23


title: E14.96H_LTHT10_4_20


title: E14.96H_LTHT10_5_20


title: E14.96H_LTHT10_10_20


title: E14.96H_LTHT10_1_23


title: E14.96H_LTHT10_6_19


title: E14.96H_LTHT10_8_19


title: E14.96H_LTHT10_7_19


title: E14.96H_LTHT10_5_19


title: E14.96H_LTHT10_10_19


title: E14.96H_LTHT10_4_19


title: E14.96H_LTHT10_9_18


title: E14.96H_LTHT10_3_19


title: E14.96H_LTHT10_4_18


title: E14.96H_LTHT10_8_18


title: E14.96H_LTHT10_3_18


title: E14.96H_LTHT10_10_18


title: E14.96H_LTHT10_4_21


title: E14.96H_LTHT10_1_18


title: E14.96H_LTHT10_2_18


title: E14.96H_LTHT10_1_19


title: E14.96H_LTHT10_8_17


title: E14.96H_LTHT10_4_17


title: E14.96H_LTHT10_3_17


title: E14.96H_LTHT10_7_17


title: E14.96H_LTHT10_5_17


title: E14.96H_LTHT10_7_16


title: E14.96H_LTHT10_1_17


title: E14.96H_LTHT10_3_16


title: E14.96H_LTHT10_8_16


title: E14.96H_LTHT10_9_16


title: E14.96H_LTHT10_1_16


title: E14.96H_LTHT10_4_15


title: E14.96H_LTHT10_5_15


title: E14.96H_LTHT10_8_14


title: E14.96H_LTHT10_1_20


title: E14.96H_LTHT10_3_15


title: E14.96H_LTHT10_5_18


title: E14.96H_LTHT10_5_16


title: E14.96H_LTHT10_5_14


title: E14.96H_LTHT10_4_13


title: E14.96H_LTHT10_7_13


title: E14.96H_LTHT10_1_14


title: E14.96H_LTHT10_2_14


title: E14.96H_LTHT10_3_13


title: E14.96H_LTHT10_2_13


title: E14.96H_LTHT10_7_12


title: E14.96H_LTHT10_1_13


title: E14.96H_LTHT10_6_12


title: E14.96H_LTHT10_8_12


title: E14.96H_LTHT10_10_13


title: E14.96H_LTHT10_8_15


title: E14.96H_LTHT10_5_12


title: E14.96H_LTHT10_9_11


title: E14.96H_LTHT10_4_11


title: E14.96H_LTHT10_3_11


title: E14.96H_LTHT10_10_12


title: E14.96H_LTHT10_5_11


title: E14.96H_LTHT10_9_10


title: E14.96H_LTHT10_6_14


title: E14.96H_LTHT10_6_17


title: E14.96H_LTHT10_7_10


title: E14.96H_LTHT10_2_10


title: E14.96H_LTHT10_3_10


title: E14.96H_LTHT10_1_10


title: E14.96H_LTHT10_9_9


title: E14.96H_LTHT10_8_9


title: E14.96H_LTHT10_5_13


title: E14.96H_LTHT10_7_9


title: E14.96H_LTHT10_3_9


title: E14.96H_LTHT10_4_9


title: E14.96H_LTHT10_5_8


title: E14.96H_LTHT10_3_8


title: E14.96H_LTHT10_9_8


title: E14.96H_LTHT10_2_8


title: E14.96H_LTHT10_3_7


title: E14.96H_LTHT10_5_7


title: E14.96H_LTHT10_7_7


title: E14.96H_LTHT10_9_7


title: E14.96H_LTHT10_1_8


title: E14.96H_LTHT10_10_8


title: E14.96H_LTHT10_1_6


title: E14.96H_LTHT10_2_7


title: E14.96H_LTHT10_7_6


title: E14.96H_LTHT10_9_5


title: E14.96H_LTHT10_5_6


title: E14.96H_LTHT10_3_6


title: E14.96H_LTHT10_8_5


title: E14.96H_LTHT10_5_9


title: E14.96H_LTHT10_7_5


title: E14.96H_LTHT10_6_5


title: E14.96H_LTHT10_9_4


title: E14.96H_LTHT10_2_5


title: E14.96H_LTHT10_6_4


title: E14.96H_LTHT10_3_5


title: E14.96H_LTHT10_5_5


title: E14.96H_LTHT10_7_4


title: E14.96H_LTHT10_9_3


title: E14.96H_LTHT10_3_4


title: E14.96H_LTHT10_10_4


title: E14.96H_LTHT10_8_3


title: E14.96H_LTHT10_5_4


title: E14.96H_LTHT10_7_3


title: E14.96H_LTHT10_5_3


title: E14.96H_LTHT10_5_2


title: E14.96H_LTHT10_6_2


title: E14.96H_LTHT10_9_2


title: E14.96H_LTHT10_3_3


title: E14.96H_LTHT10_7_1


title: E14.96H_LTHT10_4_5


title: E14.96H_LTHT10_1_3


title: E15.96H_LTHT10_18_40


title: E14.96H_LTHT10_9_1


title: E15.96H_LTHT10_15_40


title: E14.96H_LTHT10_3_1


title: E14.96H_LTHT10_6_1


title: E14.96H_LTHT10_4_1


title: E15.96H_LTHT10_14_40


title: E15.96H_LTHT10_11_40


title: E15.96H_LTHT10_12_40


title: E15.96H_LTHT10_18_39


title: E15.96H_LTHT10_20_39


title: E15.96H_LTHT10_15_39


title: E15.96H_LTHT10_17_39


title: E15.96H_LTHT10_11_39


title: E15.96H_LTHT10_19_39


title: E15.96H_LTHT10_16_38


title: E15.96H_LTHT10_17_38


title: E14.96H_LTHT10_6_3


title: E15.96H_LTHT10_12_38


title: E15.96H_LTHT10_20_38


title: E15.96H_LTHT10_18_37


title: E15.96H_LTHT10_11_38


title: E15.96H_LTHT10_20_37