title: DSGC, P7, Spig1-GFP, up, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_21


title: DSGC, P10, Spig1-GFP, up, rep39

status: Public on Aug 19 2022

type: SRA

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

country: USA

institute: Johns Hopkins University School of Medicine

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_38

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 v2.1.0. SAM files were converted to BAM files using SAMtools v1.3.1. Transcript abundance estimation and normalization were performed using the Cuffquant and Cuffnorm tools, respectively, in Cufflinks v2.2.1. Downstream analyses were performed using Monocle2 in R v3.5.1.
Assembly: mm10
Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell
Supplementary files format and content: Cuffnorm matrix containing annotations for each gene
Supplementary files format and content: Cuffnorm matrix containing annotations for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Retinas were dissected in cold Hibernate A medium (BrainBits) lacking Ca2+, Mg2+, and phenol red. Retinas were dissociated in papain (Worthington, LS003126), 1.1 mM EDTA, and 5.5 mM Cysteine-HCl dissolved in Hibernate A (no Ca2+, Mg2+, or phenol red) for 30 min at 37°C. Cells were then incubated with Brilliant Violet 421-conjugated Anti-CD11b antibody (1:300; BioLegend, Catalog No. 101251) for 30 min at 4 C to label CD11b+ microglia, which can be CTB-Alexa 647+. Cells were incubated with propidium iodide to label dead cells. Single GFP+ CTB-Alexa 647+ CD11b– and GFP– CTB-Alexa 647+ CD11b– cells were sorted into individual tubes containing 3500 U/ml RNase inhibitor (New England Biolabs), 140 U/ml DNase (New England Biolabs), and 0.17% v/v Triton X-100 in water using a MoFlo Legacy cell sorter (Beckman Coulter, Miami, FL).
Single-cell DNA libraries were prepared according to the Smart-seq2 protocol (Picelli et al., Nature Protocols, 2014) and sequenced using an Illumina NextSeq 500 sequencer (75 bp paired-end reads, 400 million total reads).

tag: tissue

value: Retina

tag: cell type

value: ON DSGC

tag: genotype

tag: age

tag: preferred direction

value: up


title: DSGC, P8, Spig1-GFP, up, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_23


title: DSGC, P4, Spig1-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_20

value: down


title: DSGC, P7, Spig1-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_14


title: DSGC, P12, Spig1-GFP, up, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_34


title: DSGC, P5, Spig1-GFP, down, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_32


title: DSGC, P10, Spig1-GFP, up, rep40

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_39


title: DSGC, P10, Spig1-GFP, up, rep38

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_37


title: DSGC, P7, Spig1-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_15


title: DSGC, P10, Spig1-GFP, up, rep36

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_35


title: DSGC, P10, Spig1-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_27


title: DSGC, P10, Spig1-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_28


title: DSGC, P10, Spig1-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_26


title: DSGC, P5, Spig1-GFP, up, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_34


title: DSGC, P4, Spig1-GFP, up, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_20


title: DSGC, P4, Spig1-GFP, up, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_19


title: DSGC, P5, HB9-GFP, down, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_31

value: ON-OFF DSGC


title: DSGC, P5, HB9-GFP, down, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_33


title: DSGC, P4, HB9-GFP, down, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_34


title: DSGC, P14, HB9-GFP, down, rep40

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_39


title: DSGC, P12, HB9-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_24


title: DSGC, P14, HB9-GFP, down, rep38

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_37


title: DSGC, P10, Spig1-GFP, up, rep37

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_36


title: DSGC, P4, HB9-GFP, down, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_32


title: DSGC, P12, HB9-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_25


title: DSGC, P10, HB9-GFP, down, rep44

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_43


title: DSGC, P5, HB9-GFP, down, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_30


title: DSGC, P14, HB9-GFP, down, rep37

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_36


title: DSGC, P4, HB9-GFP, down, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_33


title: DSGC, P10, HB9-GFP, down, rep43

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_42


title: DSGC, P14, HB9-GFP, down, rep41

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_40


title: DSGC, P10, HB9-GFP, down, rep41

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_40


title: DSGC, P5, HB9-GFP, down, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_32


title: DSGC, P10, Pcdh9-Cre, unknown, rep73

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_72

value: unknown


title: DSGC, P10, Pcdh9-Cre, unknown, rep72

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_71


title: DSGC, P12, HB9-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_23


title: DSGC, P10, Pcdh9-Cre, unknown, rep67

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_66


title: DSGC, P10, HB9-GFP, down, rep42

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_41


title: DSGC, P10, Pcdh9-Cre, unknown, rep68

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_67


title: DSGC, P10, HB9-GFP, down, rep45

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_44


title: DSGC, P10, Pcdh9-Cre, unknown, rep74

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_73


title: DSGC, P10, Pcdh9-Cre, unknown, rep62

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_61


title: DSGC, P10, Pcdh9-Cre, unknown, rep70

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_69


title: DSGC, P10, Pcdh9-Cre, unknown, rep66

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_65


title: DSGC, P14, HB9-GFP, down, rep39

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_38


title: DSGC, P10, Pcdh9-Cre, unknown, rep71

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_70


title: DSGC, P10, Pcdh9-Cre, unknown, rep60

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_59


title: DSGC, P10, Pcdh9-Cre, unknown, rep69

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_68


title: DSGC, P10, Pcdh9-Cre, unknown, rep65

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_64


title: DSGC, P10, Pcdh9-Cre, unknown, rep58

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_57


title: DSGC, P8, HB9-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_25


title: DSGC, P10, Pcdh9-Cre, unknown, rep56

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_55


title: DSGC, P10, Pcdh9-Cre, unknown, rep64

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_63


title: DSGC, P10, Pcdh9-Cre, unknown, rep54

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_53


title: DSGC, P10, Pcdh9-Cre, unknown, rep63

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_62


title: DSGC, P10, Pcdh9-Cre, unknown, rep59

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_58


title: DSGC, P10, Pcdh9-Cre, unknown, rep57

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_56


title: DSGC, P12, Spig1-GFP, down, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_32


title: DSGC, P8, HB9-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_27


title: DSGC, P10, Pcdh9-Cre, unknown, rep61

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_60


title: DSGC, P10, Pcdh9-Cre, unknown, rep55

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_54


title: DSGC, P8, Spig1-GFP, up, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_22


title: DSGC, P10, Pcdh9-Cre, unknown, rep53

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_52


title: DSGC, P12, Spig1-GFP, down, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_30


title: DSGC, P8, HB9-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_26


title: DSGC, P10, Pcdh9-Cre, unknown, rep52

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_51


title: DSGC, P12, Spig1-GFP, down, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_31


title: DSGC, P12, Spig1-GFP, up, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_32


title: DSGC, P8, Spig1-GFP, up, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_20


title: DSGC, P12, Spig1-GFP, down, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_29


title: DSGC, P8, HB9-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_24


title: DSGC, P8, Spig1-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_21


title: DSGC, P7, Spig1-GFP, up, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_18


title: DSGC, P8, Spig1-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_22


title: DSGC, P5, Spig1-GFP, up, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_30


title: DSGC, P8, Spig1-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_23


title: DSGC, P12, Spig1-GFP, down, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_33


title: DSGC, P8, Spig1-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_24


title: DSGC, P5, Spig1-GFP, down, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_30


title: DSGC, P5, Spig1-GFP, down, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_29


title: DSGC, P8, Spig1-GFP, up, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_21


title: DSGC, P12, Spig1-GFP, up, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_31


title: DSGC, P7, Spig1-GFP, up, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_17


title: DSGC, P12, Spig1-GFP, up, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_33


title: DSGC, P4, Spig1-GFP, up, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_18


title: DSGC, P4, Spig1-GFP, up, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_16


title: DSGC, P4, Spig1-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_17


title: DSGC, P5, Spig1-GFP, up, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_31


title: DSGC, P5, Spig1-GFP, up, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_29


title: DSGC, P5, Spig1-GFP, up, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_28


title: DSGC, P5, Spig1-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_28


title: DSGC, P10, Spig1-GFP, up, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_32


title: DSGC, P7, Spig1-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_12


title: DSGC, P4, Spig1-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_16


title: DSGC, P4, Spig1-GFP, up, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_17


title: DSGC, P5, HB9-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_28


title: DSGC, P7, Spig1-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_13


title: DSGC, P10, Spig1-GFP, up, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_34


title: DSGC, P12, Spig1-GFP, up, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_30


title: DSGC, P4, HB9-GFP, down, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_30


title: DSGC, P10, Spig1-GFP, up, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_33


title: DSGC, P4, HB9-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_28


title: DSGC, P14, HB9-GFP, down, rep36

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_35


title: DSGC, P10, Spig1-GFP, up, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_31


title: DSGC, P10, Spig1-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_25


title: DSGC, P14, HB9-GFP, down, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_34


title: DSGC, P12, HB9-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_22


title: DSGC, P14, HB9-GFP, down, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_32


title: DSGC, P5, Spig1-GFP, down, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_31


title: DSGC, P12, HB9-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_21


title: DSGC, P10, Spig1-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_24


title: DSGC, P5, HB9-GFP, down, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_29


title: DSGC, P4, HB9-GFP, down, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_31


title: DSGC, P10, HB9-GFP, down, rep37

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_36


title: DSGC, P12, HB9-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_20


title: DSGC, P10, HB9-GFP, down, rep36

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_35


title: DSGC, P10, Pcdh9-Cre, unknown, rep51

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_50


title: DSGC, P10, HB9-GFP, down, rep38

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_37


title: DSGC, P5, HB9-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_27


title: DSGC, P4, HB9-GFP, down, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_29


title: DSGC, P14, HB9-GFP, down, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_33


title: DSGC, P10, Pcdh9-Cre, unknown, rep50

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_49


title: DSGC, P10, Pcdh9-Cre, unknown, rep49

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_48


title: DSGC, P10, Pcdh9-Cre, unknown, rep43

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_42


title: DSGC, P10, Pcdh9-Cre, unknown, rep46

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_45


title: DSGC, P10, Pcdh9-Cre, unknown, rep41

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_40


title: DSGC, P10, Pcdh9-Cre, unknown, rep48

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_47


title: DSGC, P10, Pcdh9-Cre, unknown, rep42

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_41


title: DSGC, P10, HB9-GFP, down, rep39

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_38


title: DSGC, P10, Pcdh9-Cre, unknown, rep40

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_39


title: DSGC, P10, Pcdh9-Cre, unknown, rep45

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_44


title: DSGC, P4, HB9-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_24


title: DSGC, P4, HB9-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_25


title: DSGC, P10, Pcdh9-Cre, unknown, rep37

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_36


title: DSGC, P10, Pcdh9-Cre, unknown, rep47

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_46


title: DSGC, P10, Pcdh9-Cre, unknown, rep38

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_37


title: DSGC, P10, Pcdh9-Cre, unknown, rep44

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_43


title: DSGC, P10, HB9-GFP, down, rep40

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_39


title: DSGC, P10, Pcdh9-Cre, unknown, rep39

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_38


title: DSGC, P10, Pcdh9-Cre, unknown, rep36

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_35


title: DSGC, P10, Pcdh9-Cre, unknown, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_34


title: DSGC, P4, HB9-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_26


title: DSGC, P4, HB9-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_27


title: DSGC, P10, Pcdh9-Cre, unknown, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_33


title: DSGC, P8, Spig1-GFP, up, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_19


title: DSGC, P8, Spig1-GFP, up, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_17


title: DSGC, P8, HB9-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_22


title: DSGC, P12, Spig1-GFP, up, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_29


title: DSGC, P8, Spig1-GFP, up, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_18


title: DSGC, P8, HB9-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_21


title: DSGC, P8, HB9-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_23


title: DSGC, P7, Spig1-GFP, up, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_15


title: DSGC, P12, Spig1-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_27


title: DSGC, P12, Spig1-GFP, up, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_26


title: DSGC, P12, Spig1-GFP, up, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_27


title: DSGC, P12, Spig1-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_28


title: DSGC, P12, Spig1-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_25


title: DSGC, P12, Spig1-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_26


title: DSGC, P5, Spig1-GFP, up, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_27


title: DSGC, P5, Spig1-GFP, up, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_26


title: DSGC, P5, Spig1-GFP, up, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_25


title: DSGC, P5, Spig1-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_25


title: DSGC, P7, Spig1-GFP, up, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_16


title: DSGC, P5, Spig1-GFP, up, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_24


title: DSGC, P5, Spig1-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_27


title: DSGC, P5, Spig1-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_26


title: DSGC, P5, Spig1-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_24


title: DSGC, P4, Spig1-GFP, up, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_15


title: DSGC, P8, Spig1-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_18


title: DSGC, P8, Spig1-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_20


title: DSGC, P8, Spig1-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_19


title: DSGC, P4, Spig1-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_15


title: DSGC, P4, Spig1-GFP, up, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_14


title: DSGC, P4, Spig1-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_13


title: DSGC, P10, Spig1-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_23


title: DSGC, P4, Spig1-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_14


title: DSGC, P10, Spig1-GFP, up, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_28


title: DSGC, P7, Spig1-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_11


title: DSGC, P12, Spig1-GFP, up, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_28


title: DSGC, P10, Spig1-GFP, up, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_29


title: DSGC, P10, Spig1-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_21


title: DSGC, P10, Spig1-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_22


title: DSGC, P10, Spig1-GFP, up, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_30


title: DSGC, P5, HB9-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_25


title: DSGC, P5, HB9-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_26


title: DSGC, P14, HB9-GFP, down, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_31


title: DSGC, P14, HB9-GFP, down, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_30


title: DSGC, P12, HB9-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_18


title: DSGC, P12, HB9-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_19


title: DSGC, P14, HB9-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_27


title: DSGC, P14, HB9-GFP, down, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_29


title: DSGC, P12, HB9-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_17


title: DSGC, P10, HB9-GFP, down, rep35

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_34


title: DSGC, P10, Spig1-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_20


title: DSGC, P5, HB9-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_24


title: DSGC, P10, Spig1-GFP, up, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_27


title: DSGC, P10, HB9-GFP, down, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_31


title: DSGC, P10, HB9-GFP, down, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_30


title: DSGC, P10, HB9-GFP, down, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_32


title: DSGC, P10, HB9-GFP, down, rep34

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_33


title: DSGC, P5, HB9-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_23


title: DSGC, P10, Pcdh9-Cre, unknown, rep33

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_32


title: DSGC, P10, Pcdh9-Cre, unknown, rep32

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_31


title: DSGC, P10, Pcdh9-Cre, unknown, rep31

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_30


title: DSGC, P10, Pcdh9-Cre, unknown, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_26


title: DSGC, P14, HB9-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_28


title: DSGC, P10, Pcdh9-Cre, unknown, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_29


title: DSGC, P10, Pcdh9-Cre, unknown, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_25


title: DSGC, P10, Pcdh9-Cre, unknown, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_23


title: DSGC, P10, Pcdh9-Cre, unknown, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_21


title: DSGC, P10, Pcdh9-Cre, unknown, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_22


title: DSGC, P10, Pcdh9-Cre, unknown, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_28


title: DSGC, P10, Pcdh9-Cre, unknown, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_20


title: DSGC, P10, Pcdh9-Cre, unknown, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_27


title: DSGC, P10, Pcdh9-Cre, unknown, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_24


title: DSGC, P4, HB9-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_22


title: DSGC, P10, Pcdh9-Cre, unknown, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_19


title: DSGC, P4, HB9-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_20


title: DSGC, P4, HB9-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_21


title: DSGC, P10, Pcdh9-Cre, unknown, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_14


title: DSGC, P12, Spig1-GFP, up, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_24


title: DSGC, P12, Spig1-GFP, up, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_23


title: DSGC, P12, Spig1-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_24


title: DSGC, P12, Spig1-GFP, up, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_25


title: DSGC, P4, HB9-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_23


title: DSGC, P12, Spig1-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_21


title: DSGC, P10, Pcdh9-Cre, unknown, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_18


title: DSGC, P12, Spig1-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_20


title: DSGC, P10, Pcdh9-Cre, unknown, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_15


title: DSGC, P12, Spig1-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_23


title: DSGC, P8, Spig1-GFP, up, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_15


title: DSGC, P12, Spig1-GFP, up, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_21


title: DSGC, P12, Spig1-GFP, up, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_22


title: DSGC, P10, Pcdh9-Cre, unknown, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_17


title: DSGC, P8, Spig1-GFP, up, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_16


title: DSGC, P8, Spig1-GFP, up, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_14


title: DSGC, P7, Spig1-GFP, up, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_14


title: DSGC, P8, Spig1-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_15


title: DSGC, P8, Spig1-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_17


title: DSGC, P10, Pcdh9-Cre, unknown, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_16


title: DSGC, P7, Spig1-GFP, up, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_13


title: DSGC, P5, Spig1-GFP, up, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_23


title: DSGC, P7, Spig1-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_10


title: DSGC, P12, Spig1-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_22


title: DSGC, P8, Spig1-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_16


title: DSGC, P7, Spig1-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_9


title: DSGC, P5, Spig1-GFP, up, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_22


title: DSGC, P5, Spig1-GFP, up, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_20


title: DSGC, P5, Spig1-GFP, up, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_21


title: DSGC, P5, Spig1-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_23


title: DSGC, P5, Spig1-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_22


title: DSGC, P5, Spig1-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_20


title: DSGC, P10, Spig1-GFP, up, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_25


title: DSGC, P4, Spig1-GFP, up, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_13


title: DSGC, P10, Spig1-GFP, up, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_26


title: DSGC, P4, Spig1-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_12


title: DSGC, P10, Spig1-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_19


title: DSGC, P10, Spig1-GFP, up, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_24


title: DSGC, P10, Spig1-GFP, up, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_23


title: DSGC, P10, Spig1-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_18


title: DSGC, P4, Spig1-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_11


title: DSGC, P10, Spig1-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_17


title: DSGC, P5, Spig1-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_21


title: DSGC, P5, HB9-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_22


title: DSGC, P5, HB9-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_21


title: DSGC, P8, HB9-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_20


title: DSGC, P4, Spig1-GFP, up, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_12


title: DSGC, P8, HB9-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_18


title: DSGC, P10, Spig1-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_16


title: DSGC, P8, HB9-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_19


title: DSGC, P14, HB9-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_26


title: DSGC, P5, HB9-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_19


title: DSGC, P10, HB9-GFP, down, rep30

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_29


title: DSGC, P14, HB9-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_25


title: DSGC, P5, HB9-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_20


title: DSGC, P14, HB9-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_23


title: DSGC, P14, HB9-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_24


title: DSGC, P12, HB9-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_16


title: DSGC, P10, HB9-GFP, down, rep27

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_26


title: DSGC, P10, HB9-GFP, down, rep28

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_27


title: DSGC, P10, HB9-GFP, down, rep29

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_28


title: DSGC, P10, HB9-GFP, down, rep26

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_25


title: DSGC, P12, HB9-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_15


title: DSGC, P10, Pcdh9-Cre, unknown, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_10


title: DSGC, P10, Pcdh9-Cre, unknown, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_4


title: DSGC, P10, Pcdh9-Cre, unknown, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_9


title: DSGC, P10, Pcdh9-Cre, unknown, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_8


title: DSGC, P10, Pcdh9-Cre, unknown, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_13


title: DSGC, P10, Pcdh9-Cre, unknown, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_6


title: DSGC, P10, Pcdh9-Cre, unknown, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_7


title: DSGC, P10, Pcdh9-Cre, unknown, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_3


title: DSGC, P8, Spig1-GFP, up, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_12


title: DSGC, P10, Pcdh9-Cre, unknown, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_5


title: DSGC, P10, Pcdh9-Cre, unknown, rep2

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_1


title: DSGC, P10, Pcdh9-Cre, unknown, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_2


title: DSGC, P8, Spig1-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_14


title: DSGC, P10, Pcdh9-Cre, unknown, rep1

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_0


title: DSGC, P8, Spig1-GFP, up, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_13


title: DSGC, P8, Spig1-GFP, up, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_11


title: DSGC, P10, HB9-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_21


title: DSGC, P10, HB9-GFP, down, rep24

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_23


title: DSGC, P10, HB9-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_19


title: DSGC, P10, HB9-GFP, down, rep25

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_24


title: DSGC, P10, Pcdh9-Cre, unknown, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_11


title: DSGC, P10, HB9-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_20


title: DSGC, P8, Spig1-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_12


title: DSGC, P8, Spig1-GFP, up, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_9


title: DSGC, P8, Spig1-GFP, up, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_10


title: DSGC, P7, Spig1-GFP, up, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_12


title: DSGC, P5, Spig1-GFP, up, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_19


title: DSGC, P10, Pcdh9-Cre, unknown, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
P10_12


title: DSGC, P5, Spig1-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_19


title: DSGC, P8, Spig1-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_11


title: DSGC, P8, Spig1-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_13


title: DSGC, P4, Spig1-GFP, up, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_11


title: DSGC, P12, Spig1-GFP, up, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_18


title: DSGC, P7, Spig1-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_8


title: DSGC, P10, Spig1-GFP, up, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_21


title: DSGC, P10, HB9-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_22


title: DSGC, P5, Spig1-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_17


title: DSGC, P4, Spig1-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_10


title: DSGC, P12, Spig1-GFP, up, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_20


title: DSGC, P4, HB9-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_19


title: DSGC, P12, Spig1-GFP, up, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_19


title: DSGC, P8, HB9-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_17


title: DSGC, P10, Spig1-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_15


title: DSGC, P5, HB9-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_18


title: DSGC, P12, Spig1-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_18


title: DSGC, P14, HB9-GFP, down, rep22

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_21


title: DSGC, P12, HB9-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_14


title: DSGC, P12, HB9-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_13


title: DSGC, P8, Spig1-GFP, up, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_8


title: DSGC, P5, Spig1-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_18


title: Horse7_pre

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

country: Germany

institute: Ruhr University Bochum

library_source: transcriptomic

data_processing:
Raw reads were quality- trimmed and mapped to the equine reference genome (EquCap3.0) using CLC Workbench 2020.
Supplementary files format and content: .csv
Supplementary files format and content: raw and normalized read counts

molecule: total RNA

organism: Equus caballus

source_name: Liver

extract_protocol:
Snap-frozen liver biopsy specimens were used for RNA isolation and NGS. RNA was isolated from mechanically homogenized liver biopsy specimens using the Machery Nagel RNA extraction kit according to the manufacturer’s instructions
The RNA sequencing library was generated from 500 ng total RNA using Dynabeads mRNA DIRECT Micro Purification kit (Thermo Fisher Scientific, Waltham, MA) for mRNA purification, fol- lowed by NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs, Ipswich, MA), both according to the manufacturer’s protocols. The libraries were treated with Illumina Free Adapter Blocking and sequenced on Illumina NovaSeq 6000 using the NovaSeq 6000 S1 reagent kit (100 cycles, paired-end run 2 x50 bp), with an average of 5 x 10^7 reads per RNA sample.

value: Liver

tag: inoculation [ml]

tag: inoculation [copies]

tag: Sex

value: F

tag: breed

value: Hanoverian Warmblood


title: DSGC, P12, Spig1-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_19


title: Horse6_pre

value: Zangersheide


title: DSGC, P8, Spig1-GFP, up, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_7


title: Horse5_pre

value: Oldenburger Warmblood


title: DSGC, P10, Spig1-GFP, up, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_22


title: DSGC, P8, Spig1-GFP, up, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_6


title: DSGC, P8, Spig1-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_8


title: Horse4_pre


title: Horse7_inoculated_7


title: Horse2_pre

value: Trotter


title: DSGC, P8, Spig1-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_10


title: DSGC, P8, Spig1-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_9


title: DSGC, P8, Spig1-GFP, up, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_5


title: DSGC, P7, Spig1-GFP, up, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_11


title: Horse1_pre

value: M

value: Austrian Warmblood


title: DSGC, P10, HB9-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_18


title: DSGC, P8, Spig1-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_7


title: Horse4_inoculated_4


title: Horse5_inoculated_5


title: DSGC, P7, Spig1-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_7


title: Horse1_inoculated_1


title: DSGC, P7, Spig1-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_6


title: DSGC, P14, HB9-GFP, down, rep23

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_22


title: Stab 6

city: St. Louis

first: Simon

last: Tang

state: MO

address: 425 S. Euclid Ave, Campus Box 8233, Tang Lab, Washington University School of Medicine

department: Orthopaedic Surgery

institute: Washington University in St. Louis

data_processing:
fastq files were coverted to filtered.feature.bc.matrix.h5 files for each sample by the Washington University Genome Technology Access Center
.h5 files were read into Partek Flow software for analysis
For CON and Stab samples, only cells with <10% mitochondrial features, gene counts of 500-3000 and UMI (unique molecular identifier) counts between 500-30,000 were determined to be of sufficient quality to include in the analyses (Partek FlowTM, Partek Inc).
Under these selection criteria, the total number of cells from rat samples was 42,560 and 51,365 for CON and LDP at 2 weeks post-surgery, 27,064 and 28,293 for CON and LDP at 8 weeks post-surgery, respectively.
In order to identify resident cell populations, we first performed Principal Com-ponents Analysis (PCA) on pooled data from n=4 CON samples at 2 weeks, and then again for the 8 weeks samples.
The percentage of cells mapped to each cluster was evaluated for each tissue sample at both 2 and 8 weeks post-surgery as a test of inter-subject variability and appropriate-ness of the clustering scheme.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include count values for each gene sorted by cluster for each sample

organism: Rattus norvegicus

source_name: Lumber spine

extract_protocol:
Intervertebrals discs (IVDs) were harvested and tissue was isolated at room temperature; tissue was then immediately transferred into the digestion medium 0.3% pronase and 0.2% Typle 2 collagenase (< 4h total) to obtain IVD cells  at 37 degrees Celsius. Once the IVDs were digested into a single cell suspension, the cells were immediately put on ice and expedited to the Genome Technology and Access Center at Washington University in St. Louis.
The input samples were submitted to the Washington University Genome Technology Access Center to obtain and sequence the cDNA libraries (10XGenomics, 3’v3.1; Illumina NovaSeq S4) according to established protocols

treatment_protocol: Rats (n=8, male Sprague-Dawley, 8 weeks) underwent surgery for retroperitoneal exposure of the L4-L6 -lumbar spine. The L4-5 and L5-6 IVDs each received a single stab injury via a 27G needle and allowed to recover postoperatively for either 2 (n=4) or 8 weeks (n=4)

value: Intervertebral disc

tag: strain

value: Sprague-Dawley

value: male

value: 8 weeks old

tag: treatment

value: Injured

tag: timepoint

value: 8 weeks


title: Horse6_inoculated_6


title: Stab 8


title: DSGC, P7, Spig1-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_5

value: Retina

value: ON DSGC

value: down


title: Stab 7


title: DSGC, P7, Spig1-GFP, up, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_9

value: up


title: DSGC, P7, Spig1-GFP, up, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_8


title: Stab 5


title: Control 7

value: Uninjured


title: Control 5


title: Control 8


title: Horse2_inoculated_2

value: Liver

value: F


title: DSGC, P5, Spig1-GFP, up, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_16


title: DSGC, P7, Spig1-GFP, up, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_7


title: DSGC, P5, Spig1-GFP, up, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_18


title: DSGC, P7, Spig1-GFP, up, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_10


title: DSGC, P5, Spig1-GFP, up, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_14


title: DSGC, P5, Spig1-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_15


title: DSGC, P5, Spig1-GFP, up, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_15


title: DSGC, P5, Spig1-GFP, up, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_17


title: Control 3

value: 2 weeks


title: DSGC, P5, Spig1-GFP, up, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_13


title: Stab 4


title: Stab 2


title: DSGC, P5, Spig1-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_16


title: Stab 1


title: Control 4


title: DSGC, P5, Spig1-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_14


title: Stab 3


title: DSGC, P5, Spig1-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_13


title: Control 2


title: DSGC, P5, Spig1-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_11


title: DSGC, P5, Spig1-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_12


title: DSGC, P4, Spig1-GFP, up, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_10


title: DSGC, P4, Spig1-GFP, up, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_7


title: DSGC, P4, Spig1-GFP, up, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_9


title: CDA-HFD_Wk16_6775

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the mouse genome assembly GRCm38.
Assembly: GRCm38
Supplementary files format and content: TSV count matrices

source_name: CDA-HFD fed liver week 16

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: liver

tag: diet

value: CDA-HFD

tag: time point

value: Week 16


title: CDA-HFD_Wk16_6777


title: CDA-HFD_Wk16_6778


title: DSGC, P4, Spig1-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_9


title: CDA-HFD_Wk16_6774


title: DSGC, P4, Spig1-GFP, up, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_8


title: CDA-HFD_Wk16_6773


title: DSGC, P4, Spig1-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_8


title: CDA-HFD_Wk16_6772


title: DSGC, P4, Spig1-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_7


title: DSGC, P12, Spig1-GFP, up, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_17


title: CDA-HFD_Wk8_6757

source_name: CDA-HFD fed liver week 8

value: Week 8


title: DSGC, P12, Spig1-GFP, up, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_16


title: CDA-HFD_Wk8_6754


title: DSGC, P12, Spig1-GFP, up, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_13


title: Control 1

value: Intervertebral disc

value: Sprague-Dawley


title: CDA-HFD_Wk16_6776


title: DSGC, P12, Spig1-GFP, up, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_15


title: DSGC, P12, Spig1-GFP, up, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_14


title: DSGC, P12, Spig1-GFP, up, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_12


title: CDA-HFD_Wk8_6751


title: CDA-HFD_Wk8_6755


title: CDA-HFD_Wk8_6756


title: DSGC, P12, Spig1-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_15


title: DSGC, P12, Spig1-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_14


title: CDA-HFD_Wk8_6750


title: Chow_Wk0_6749

source_name: Normal chow fed liver week 0

value: Normal Chow

value: Week 0


title: Chow_Wk0_6747


title: Chow_Wk0_6748


title: CDA-HFD_Wk8_6752


title: CDA-HFD_Wk8_6753


title: CDA-HFD_Wk16_6771


title: Control 6

value: male

value: 8 weeks old

value: 8 weeks


title: Chow_Wk0_6746


title: DSGC, P12, Spig1-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_13

value: Retina

value: ON DSGC

value: down


title: DSGC, P12, Spig1-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_12


title: DSGC, P10, Spig1-GFP, up, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_19

value: up


title: DSGC, P10, Spig1-GFP, up, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_18


title: DSGC, P10, Spig1-GFP, up, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_20


title: DSGC, P12, Spig1-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_17


title: Oil_5382

source_name: Corn oil vehicle treated liver

value: Corn oil vehicle


title: Chow_Wk0_6745


title: Oil_5383


title: DSGC, P12, Spig1-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_16


title: Oil_5380


title: DSGC, P10, Spig1-GFP, up, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_15


title: DSGC, P10, Spig1-GFP, up, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_17


title: DSGC, P10, Spig1-GFP, up, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_16


title: Oil_5381


title: CCl4_5371

source_name: CCl4 treated liver


title: DSGC, P10, Spig1-GFP, up, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_14


title: CCl4_5369


title: Oil_5379


title: DSGC, P10, Spig1-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_12


title: CCl4_5370


title: CCl4_5368


title: DSGC, P10, Spig1-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_13


title: DSGC, P10, Spig1-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_10


title: CCl4_5367


title: DSGC, P8, HB9-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_16

value: ON-OFF DSGC


title: DSGC, P8, HB9-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_15


title: CCl4_5366

value: liver


title: clone_10x

city: Cambridge

last: Bode

email: db704@cam.ac.uk, 1danielbode@gmail.com

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
The UMI counts per cell were calculated using the cellranger package (v3.1.0) and downstream analysis was performed using the scanpy package
Low quality cells were excluded with following criteria per cell: <1500 genes, <5000 UMI counts or >10% of counts mapped to the mitochondrial genes. Putative doublet cells were removed using the scrublet tool (threshold of 0.3).
Genome_build: mm10
Supplementary_files_format_and_content: h5 file containing raw counts for all cells

source_name: Bone marrow

growth_protocol: Expansion cultures (28 days) of long-term HSCs were performed as previously described (Wilkinson et al., 2019). HSCs were isolated and deposited into 96-well plates using fluourescence-activated flow sorting prior to culturing.

extract_protocol:
Haematopoietic Stem Cells (HSCs) were extracted from primary mouse bone marrow, derived from C57BL/6 mice (8-16 weks) for scRNA-seq. All extracted tissues were lineage depleted prior to FACS sorting.
Droplet scRNA-Seq experiment was performed using the 10x Genomics Single Cell 3' v3 kit.

treatment_protocol: Expansion of HSCs was performed as perviously described (Wilkinson et al., 2019).

value: 8-16 weeks

value: wild type

tag: batch


title: hibHSC34 [i715_i517]

description:
i715_i517
counts_single_cell_rnaseq.txt

data_processing:
bulk RNA-seq: reads were trimmed using trim_galore (parameters: --paired --quality 30 --clip_R2 3) and aligned using STAR (default parameters). Gene counts were acquired using HTSeq (parameters: --format=bam --stranded=reverse --type=exon --mode=intersection-nonempty --additional-attr=gene_name)
scRNA-seq: Raw reads were aligned to the Mus musculous genome build (mm10) using STAR and read counts were computed using featureCounts.
scRNA-seq: Cells from which low-quality libraries with insufficient sequencing depths were generated were excluded by setting the threshold of number of mapped reads to >1e5 and <3e7, with mapped reads comprising nuclear genes, mitochondrial genes and ERCCs. A minimum threshold of 20% for reads mapping to known genes was set, in order to exclude empty wells and dead cells. In addition, the threshold for reads mapping to mitochondrial genes was >0.075, to ensure a minimum of 7.5% of reads to map to non-mitochondrial genes. Finally, an ERCC cutoff of 5% and a high gene cutoff of 1800 were selected.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing raw counts for each sample (HT-Seq counts)

growth_protocol: For hibernation cultures, Haematopoietic Stem Cells (HSCs), isolated from primary mouse bone marrow, were cultured in the presence of 20 ng/mL IL-11 but absence of Stem Cell Factor (SCF) and (TPO) to retain HSCs. Expansion cultures (28 days) of single long-term HSCs were performed as previously described (Wilkinson et al., 2019).

extract_protocol:
Haematopoietic Stem Cells (HSCs) were extracted from primary mouse bone marrow, derived from C57BL/6 mice(12-16 weks) for scRNA-seq and Fgd5(ZsGreen•ZsGreen/+) for bulk RNA-seq. To isolate fetal liver HSCs, fetal livers were harvested from E14.5 embryos. All extracted tissues were lineage depleted prior to FACS sorting. HSCs were defined as EPCR-high, CD45+, Sca-1+, CD48-low/neg, CD150+. Expansion cultures were FACS sorted to separate ELSK and nonELSK cell fractions. HSCs in hibernation conditions and freshly isolated fetal liver were FACS sorted to be deposited in 96 well plates (one cell per well), containing lysis buffer and subsequently processed using the previously described Smart-Seq2 protocol (Picelli et al., 2014).
Smart-Seq2 protocol performed as previously described (Picelli et al., 2014). Libraries were prepared using Illumina Nextera libraries, single end reads and 50bp read lengths. The pooled libraries were sequenced on an Illumina HiSeq 4000. Bulk RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-seq Kit v2 – Pico Input mammalian (Takara Bio, CA, USA), paired end and 50bp read length. The libraries were sequenced on an Illumina Novaseq.

treatment_protocol: Hibernating HSCs were cultured in the presence of 20 ng/mL IL-11 but absence of Stem Cell Factor (SCF) and (TPO). Expansion of single HSCs was performed as perviously described (Wilkinson et al., 2019).

value: 12-16 weeks


title: hibHSC36 [i715_i522]

description:
i715_i522
counts_single_cell_rnaseq.txt


title: Oil_5378


title: DSGC, P10, Spig1-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_14


title: hibHSC33 [i715_i516]

description:
i715_i516
counts_single_cell_rnaseq.txt


title: hibHSC35 [i715_i518]

description:
i715_i518
counts_single_cell_rnaseq.txt


title: DSGC, P8, HB9-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_14


title: DSGC, P8, HB9-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_13


title: DSGC, P5, HB9-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_16


title: DSGC, P5, HB9-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_17


title: DSGC, P10, Spig1-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_11


title: DSGC, P8, HB9-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_12


title: M

city: Augusta

first: Kai

last: Jiao

state: GA

address: 1462 Laney Walker Blvd.

department: Center for Biotechnology and Genomic Medicine

institute: Medical College of Georgia at Augusta University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger count software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mitral valve leaflets

extract_protocol:
Mitral leaflets were dissected from E17.5 control and mutant embryos and digested with 0.05% Trypsin to obtain single cells. For each genotype, samples were pooled from 3-4 hearts. To collect viable single cells, 7-amino-actinomycin (7-AAD, ThermoFisher, for labeling nonviable cells) stained cells were sorted using a FACS Aria II sorter (BD BioSciences).
Preparation of the single cell transcriptome libraries was performed using 10xGenomics Single Cell 3ʹ v3 Reagent Kits, following the manufacturer’s instructions.

value: mitral valve leaflets

value: Nfatc1-Cre, Dicer loxp/loxp


title: DSGC, P5, HB9-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_14


title: C

description: 10X Genomics


title: hibHSC32 [i715_i515]

description:
i715_i515
counts_single_cell_rnaseq.txt


title: DSGC, P4, HB9-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_18


title: hibHSC31 [i715_i513]

description:
i715_i513
counts_single_cell_rnaseq.txt


title: DSGC, P5, HB9-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_15


title: DSGC, P5, HB9-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_13


title: FL52 [i715_i506]

description:
i715_i506
counts_single_cell_rnaseq.txt

source_name: Fetal liver


title: FL51 [i715_i505]

description:
i715_i505
counts_single_cell_rnaseq.txt


title: DSGC, P5, HB9-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_12


title: FL50 [i715_i503]

description:
i715_i503
counts_single_cell_rnaseq.txt


title: FL54 [i715_i508]

description:
i715_i508
counts_single_cell_rnaseq.txt


title: DSGC, P4, HB9-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_16


title: DSGC, P4, HB9-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_13


title: DSGC, P4, HB9-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_15


title: FL53 [i715_i507]

description:
i715_i507
counts_single_cell_rnaseq.txt


title: hibHSC29 [i714_i518]

description:
i714_i518
counts_single_cell_rnaseq.txt


title: DSGC, P14, HB9-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_16


title: DSGC, P14, HB9-GFP, down, rep20

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_19


title: FL48 [i714_i507]

description:
i714_i507
counts_single_cell_rnaseq.txt


title: DSGC, P4, HB9-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_14


title: DSGC, P4, HB9-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_17


title: DSGC, P14, HB9-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_17


title: hibHSC30 [i714_i522]

description:
i714_i522
counts_single_cell_rnaseq.txt


title: DSGC, P14, HB9-GFP, down, rep19

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_18


title: FL49 [i714_i508]

description:
i714_i508
counts_single_cell_rnaseq.txt


title: hibHSC27 [i714_i513]

description:
i714_i513
counts_single_cell_rnaseq.txt


title: DSGC, P14, HB9-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_15


title: DSGC, P14, HB9-GFP, down, rep21

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_20


title: hibHSC28 [i714_i515]

description:
i714_i515
counts_single_cell_rnaseq.txt


title: FL46 [i714_i503]

description:
i714_i503
counts_single_cell_rnaseq.txt


title: FL47 [i714_i506]

description:
i714_i506
counts_single_cell_rnaseq.txt


title: DSGC, P12, HB9-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_10


title: DSGC, P14, HB9-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_14


title: hibHSC25 [i712_i521]

description:
i712_i521
counts_single_cell_rnaseq.txt


title: DSGC, P12, HB9-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_12


title: hibHSC24 [i712_i518]

description:
i712_i518
counts_single_cell_rnaseq.txt


title: DSGC, P10, HB9-GFP, down, rep17

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_16


title: DSGC, P10, HB9-GFP, down, rep15

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_14


title: DSGC, P10, HB9-GFP, down, rep16

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_15


title: FL45 [i714_i502]

description:
i714_i502
counts_single_cell_rnaseq.txt


title: DSGC, P10, HB9-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_13


title: DSGC, P8, Spig1-GFP, up, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_4


title: DSGC, P8, Spig1-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_6


title: DSGC, P12, HB9-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_11


title: DSGC, P10, HB9-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_12


title: DSGC, P8, Spig1-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_5


title: DSGC, P8, Spig1-GFP, up, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U8_3


title: hibHSC26 [i712_i522]

description:
i712_i522
counts_single_cell_rnaseq.txt


title: DSGC, P10, HB9-GFP, down, rep18

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H10_17


title: DSGC, P7, Spig1-GFP, up, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_6


title: DSGC, P8, Spig1-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_4


title: hibHSC23 [i712_i517]

description:
i712_i517
counts_single_cell_rnaseq.txt


title: DSGC, P7, Spig1-GFP, up, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_5


title: DSGC, P8, Spig1-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D8_3


title: hibHSC17 [i711_i516]

description:
i711_i516
counts_single_cell_rnaseq.txt


title: FL42 [i712_i506]

description:
i712_i506
counts_single_cell_rnaseq.txt


title: hibHSC22 [i712_i513]

description:
i712_i513
counts_single_cell_rnaseq.txt


title: hibHSC16 [i711_i515]

description:
i711_i515
counts_single_cell_rnaseq.txt


title: hibHSC18 [i711_i517]

description:
i711_i517
counts_single_cell_rnaseq.txt


title: hibHSC19 [i711_i518]

description:
i711_i518
counts_single_cell_rnaseq.txt


title: hibHSC20 [i711_i520]

description:
i711_i520
counts_single_cell_rnaseq.txt


title: FL44 [i712_i508]

description:
i712_i508
counts_single_cell_rnaseq.txt


title: hibHSC21 [i711_i521]

description:
i711_i521
counts_single_cell_rnaseq.txt


title: FL40 [i712_i503]

description:
i712_i503
counts_single_cell_rnaseq.txt


title: DSGC, P7, Spig1-GFP, up, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_3


title: hibHSC15 [i711_i513]

description:
i711_i513
counts_single_cell_rnaseq.txt


title: FL41 [i712_i505]

description:
i712_i505
counts_single_cell_rnaseq.txt


title: FL43 [i712_i507]

description:
i712_i507
counts_single_cell_rnaseq.txt


title: DSGC, P7, Spig1-GFP, up, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_4


title: FL37 [i711_i506]

description:
i711_i506
counts_single_cell_rnaseq.txt


title: FL39 [i711_i508]

description:
i711_i508
counts_single_cell_rnaseq.txt


title: FL38 [i711_i507]

description:
i711_i507
counts_single_cell_rnaseq.txt


title: DSGC, P7, Spig1-GFP, up, rep3

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U7_2


title: DSGC, P7, Spig1-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_4


title: FL36 [i711_i505]

description:
i711_i505
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, up, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_12


title: DSGC, P7, Spig1-GFP, down, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D7_3


title: FL34 [i711_i502]

description:
i711_i502
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, up, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_10


title: hibHSC14 [i710_i522]

description:
i710_i522
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, up, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_11


title: hibHSC13 [i710_i520]

description:
i710_i520
counts_single_cell_rnaseq.txt


title: hibHSC11 [i710_i517]

description:
i710_i517
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_9


title: DSGC, P5, Spig1-GFP, up, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_9


title: DSGC, P5, Spig1-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_8


title: hibHSC12 [i710_i518]

description:
i710_i518
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_10


title: DSGC, P5, Spig1-GFP, up, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_7


title: DSGC, P5, Spig1-GFP, up, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U5_8


title: FL35 [i711_i503]

description:
i711_i503
counts_single_cell_rnaseq.txt


title: DSGC, P4, Spig1-GFP, up, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_6


title: FL33 [i710_i508]

description:
i710_i508
counts_single_cell_rnaseq.txt


title: hibHSC10 [i710_i516]

description:
i710_i516
counts_single_cell_rnaseq.txt


title: hibHSC9 [i710_i515]

description:
i710_i515
counts_single_cell_rnaseq.txt


title: FL32 [i710_i507]

description:
i710_i507
counts_single_cell_rnaseq.txt


title: FL31 [i710_i506]

description:
i710_i506
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_6


title: FL30 [i710_i505]

description:
i710_i505
counts_single_cell_rnaseq.txt


title: hibHSC7 [i707_i522]

description:
i707_i522
counts_single_cell_rnaseq.txt


title: DSGC, P5, Spig1-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D5_7


title: hibHSC8 [i710_i513]

description:
i710_i513
counts_single_cell_rnaseq.txt


title: DSGC, P4, Spig1-GFP, up, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_5


title: hibHSC6 [i707_i521]

description:
i707_i521
counts_single_cell_rnaseq.txt


title: DSGC, P4, Spig1-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_6


title: DSGC, P4, Spig1-GFP, up, rep4

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_3


title: DSGC, P4, Spig1-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_5


title: DSGC, P4, Spig1-GFP, up, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U4_4


title: hibHSC3 [i707_i516]

description:
i707_i516
counts_single_cell_rnaseq.txt


title: hibHSC5 [i707_i520]

description:
i707_i520
counts_single_cell_rnaseq.txt


title: DSGC, P4, Spig1-GFP, down, rep5

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D4_4


title: DSGC, P12, Spig1-GFP, up, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_11


title: FL29 [i707_i507]

description:
i707_i507
counts_single_cell_rnaseq.txt


title: hibHSC1 [i707_i513]

description:
i707_i513
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, up, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_8


title: FL28 [i707_i506]

description:
i707_i506
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, up, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_10


title: FL27 [i707_i505]

description:
i707_i505
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, up, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_6


title: hibHSC4 [i707_i517]

description:
i707_i517
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, up, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_7


title: FL25 [i707_i502]

description:
i707_i502
counts_single_cell_rnaseq.txt


title: FL24 [i706_i508]

description:
i706_i508
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, up, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U12_9


title: hibHSC2 [i707_i515]

description:
i707_i515
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_11


title: DSGC, P12, Spig1-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_10


title: FL26 [i707_i503]

description:
i707_i503
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_6


title: DSGC, P12, Spig1-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_9


title: FL23 [i706_i507]

description:
i706_i507
counts_single_cell_rnaseq.txt


title: DSGC, P12, Spig1-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_8


title: DSGC, P10, Spig1-GFP, up, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_13


title: DSGC, P12, Spig1-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D12_7


title: FL21 [i706_i505]

description:
i706_i505
counts_single_cell_rnaseq.txt


title: FL20 [i706_i503]

description:
i706_i503
counts_single_cell_rnaseq.txt


title: FL22 [i706_i506]

description:
i706_i506
counts_single_cell_rnaseq.txt


title: FL19 [i705_i507]

description:
i705_i507
counts_single_cell_rnaseq.txt


title: FL16 [i705_i503]

description:
i705_i503
counts_single_cell_rnaseq.txt


title: FL17 [i705_i505]

description:
i705_i505
counts_single_cell_rnaseq.txt


title: FL18 [i705_i506]

description:
i705_i506
counts_single_cell_rnaseq.txt


title: DSGC, P10, Spig1-GFP, up, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_12


title: DSGC, P10, Spig1-GFP, up, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_9


title: FL15 [i705_i502]

description:
i705_i502
counts_single_cell_rnaseq.txt


title: DSGC, P10, Spig1-GFP, up, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_11


title: DSGC, P10, Spig1-GFP, up, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_10


title: FL14 [i704_i507]

description:
i704_i507
counts_single_cell_rnaseq.txt


title: DSGC, P10, Spig1-GFP, up, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_8


title: DSGC, P10, Spig1-GFP, up, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
U10_7


title: FL13 [i704_i506]

description:
i704_i506
counts_single_cell_rnaseq.txt


title: DSGC, P10, Spig1-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_7


title: DSGC, P10, Spig1-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_9


title: DSGC, P8, HB9-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_11


title: DSGC, P10, Spig1-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_6


title: DSGC, P10, Spig1-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_8


title: FL8 [i703_i505]

description:
i703_i505
counts_single_cell_rnaseq.txt


title: FL10 [i703_i507]

description:
i703_i507
counts_single_cell_rnaseq.txt


title: FL11 [i704_i502]

description:
i704_i502
counts_single_cell_rnaseq.txt


title: FL6 [i703_i502]

description:
i703_i502
counts_single_cell_rnaseq.txt


title: DSGC, P10, Spig1-GFP, down, rep6

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
D10_5


title: FL12 [i704_i505]

description:
i704_i505
counts_single_cell_rnaseq.txt


title: FL5 [i702_i507]

description:
i702_i507
counts_single_cell_rnaseq.txt


title: DSGC, P8, HB9-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_7


title: DSGC, P8, HB9-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_10


title: FL4 [i702_i505]

description:
i702_i505
counts_single_cell_rnaseq.txt


title: DSGC, P8, HB9-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_6


title: DSGC, P8, HB9-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_9


title: DSGC, P5, HB9-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_10


title: FL9 [i703_i506]

description:
i703_i506
counts_single_cell_rnaseq.txt


title: DSGC, P5, HB9-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_8


title: FL7 [i703_i503]

description:
i703_i503
counts_single_cell_rnaseq.txt


title: DSGC, P5, HB9-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_11


title: FL1 [i701_i506]

description:
i701_i506
counts_single_cell_rnaseq.txt


title: FL2 [i701_i507]

description:
i701_i507
counts_single_cell_rnaseq.txt


title: HUVEC_static_rep1

city: Berlin

first: Petra

last: Knaus

state: Berlin

address: Thielallee 63

department: Department of Chemistry and Biochemistry

institute: Freie Universität Berlin

data_processing:
Single-end, 75-bp reads from Illumina sequencing were mapped to the reference genome (hg19) using the STAR mapper (splice junctions based on RefSeq; options: ‐‐alignIntronMin20 ‐‐alignIntronMax500000 ‐‐outFilterMismatchNmax 10). Differential gene expression was ascertained using the DESeq2 package.
Assembly: hg19
Supplementary files format and content: Excel sheet containing RPKM values for each sample.

organism: Homo sapiens

source_name: Umbilical vein

growth_protocol: Cells were seeded on gelatin-coated µ-Slide I 0.4 Luer (ibidi GmbH) at 2.5 *106 cells/ ml and cultured for 48 h to reach confluency in full medium before the experiment with daily medium exchange.

extract_protocol:
Cellular RNA was isolated using the NucleoSpin RNA XS isolation kit (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions.
After initial quality control using Agilent's Bioanalyzer, sequencing libraries were prepared from 500 ng of total RNA per sample following Roche's stranded “KAPA RNA HyperPrep” library preparation protocol for single indexed Illumina libraries: First, the polyA-RNA fraction was enriched using oligo-dT-probed paramagnetic beads. Enriched RNA was heat-fragmented and subjected to first strand synthesis using random priming. The second strand was synthesized incorporating dUTP instead of dTTP to preserve strand information. Afterwards, A-tailing Illumina sequencing compatible adapters were ligated. Following bead-based clean-up steps, the libraries were amplified using 10 cycles of PCR. Library quality and size was checked with qBit, Agilent Bioanalyzer, and qPCR. Sequencing was carried out in biological triplicates on an Illumina HiSeq 4000 system in SR75bp mode (single read, 75 bp read length) yielding between 46 and 69 million fragments per sample.

treatment_protocol: Shear stress was applied using the ibidi pump system (ibidi GmbH) with the associated software (V. 1.5.4). Two pump systems were used to allow simultaneous application of LSS (1 dyn/cm2) and HSS (30 dyn/cm2). Cells were allowed to adapt to increasing levels of shear stress in an adaption phase (2.5 h: 2.5 dyn/cm2 for 60 min, 5 dyn/cm2 for 30 min, 10 dyn/cm2 for 30 min, 20 dyn/cm2 for 30 min, 30 dyn/cm2 for 24 h). Static controls were seeded in silicone forms with the same area as µ-Slides and cultured in 10 cm dishes. For LSS and HSS we used WHITE and YELLOW-and-GREEN perfusion sets (ibidi GmbH), respectively.

value: Umbilical vein

tag: cell line

value: HUVEC

value: Endothelial

value: WT

value: Static (0 dyn/cm^2)


title: HUVEC_HSS_rep2

value: HSS (30 dyn/cm^2)


title: FL3 [i702_i503]

description:
i702_i503
counts_single_cell_rnaseq.txt


title: HUVEC_LSS_rep3

value: LSS (1 dyn/cm^2)


title: HUVEC_static_rep3


title: DSGC, P4, HB9-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_12

value: Retina

value: down


title: DSGC, P5, HB9-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_7


title: DSGC, P4, HB9-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_11


title: HUVEC_HSS_rep1


title: HUVEC_HSS_rep3


title: DSGC, P8, HB9-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H8_8


title: DSGC, P4, HB9-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_7


title: HUVEC_static_rep2


title: DSGC, P5, HB9-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_6


title: HUVEC_LSS_rep1


title: SKM-28TM-BBz CAR-T cells, Day13 [sample6]

city: Yokohama

first: Taku

last: Kouro

state: Kanagawa

address: 2-3-2 Nakao, Asahi-ku

department: Division of Cancer Immunotherapy

country: Japan

institute: Kanagawa Cancer Center Research Institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke v1.5.2 (parameter- -l 15 -q 0.2 -n 0.05)
Trimmed sequence reads were mapped to hg19 using HISAT2 v2.0.4 (Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8)
Sequence reads were mapped to genes using Bowtie2
Supplementary files format and content: hg19
Supplementary files format and content: tab-delimited text files include TPM values as matrix file

source_name: PBMC

growth_protocol: PBMC was prepared using lymphoprep and stimulated with plate-coated anti-CD3 mAb and 100U/ml IL-2 in AIM-V medium supplemented with 10% AB serum.

extract_protocol:
On day 9 and 13, CAR positive cells were labelled with biotin-anti-mouse IgG (Jackson Laboratory) and streptavidin-PE and sorted on FACSAriaII cell sorter.
RNA was harvested using Rneasy mini kit (Qiagen). 0.4 ~ 2.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following manufacturer's protocols.

treatment_protocol: Retrovirus supernatants for each CAR was obtained using Phoenix-Ampho packaging cell line and infected to activated PBMC using retronectin (Takara) following manufacturer's instruction.

value: PBMC

value: SKM-28TM-BBz CAR-T cells

value: male

value: Retrovirus-mediated CAR induction

tag: time

value: Day 13


title: CD19-28TM-BBz CAR-T cells, Day13 [sample8]

tag: tissue

value: CD19-28TM-BBz CAR-T cells


title: DSGC, P14, HB9-GFP, down, rep12

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_11

tag: cell type

value: ON-OFF DSGC


title: DSGC, P5, HB9-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H5_9

tag: genotype


title: DSGC, P4, HB9-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_9

tag: age


title: SKM-28z CAR-T cells, Day13 [sample5]

value: SKM-28z CAR-T cells


title: DSGC, P4, HB9-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_8

tag: preferred direction


title: CD19-28z CAR-T cells, day13 [sample7]

value: CD19-28z CAR-T cells


title: HUVEC_LSS_rep2

value: Umbilical vein

value: HUVEC


title: DSGC, P14, HB9-GFP, down, rep14

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_13


title: DSGC, P14, HB9-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_7


title: DSGC, P4, HB9-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H4_10


title: DSGC, P12, HB9-GFP, down, rep10

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_9


title: DSGC, P14, HB9-GFP, down, rep11

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_10


title: CD19-28TM-BBz CAR-T cells, Day9 [sample4]

value: Day 9


title: DSGC, P14, HB9-GFP, down, rep13

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_12


title: DSGC, P12, HB9-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_8


title: DSGC, P14, HB9-GFP, down, rep9

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H14_8


title: SKM-28TM-BBz CAR-T cells, Day9 [sample2]


title: DSGC, P12, HB9-GFP, down, rep8

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_7


title: CD19-28z CAR-T cells, day9 [sample3]


title: Melanoma, 1.2 MG/KG, Collected 20 days relative to first dose (RNA_80024179_EQ9103039)

city: Houston

first: David

middle: S

last: Hong

state: TX

address: 1515 Holcombe Boulevard Unit 455

institute: University of Texas M.D. Anderson Cancer Center

description:
SUBJID: 80024179
Supp Table S2 deid_subjects (This file represents patients with response data.  Only a subset of these patients had RNA-seq data.)
Supp Table S6 deid_geneexpression

data_processing:
Transcript levels were quantified by the Personalis ACE Cancer Transcriptome Analysis pipeline (Menlo Park, CA)
STAR version 2.4.2a-p1 was used to align reads to the US National Center for Biotechnology Information hs37d5 annotation 105 reference genome
Assembly: hs37d5 annotation 105 reference genome
Supplementary files format and content: comma-separated value files include TPM values for genes expressed in >5% of samples and had standard deviation >1 for expression in log2 TPM

source_name: tumor biopsy

extract_protocol:
AllPrep DNA/RNA FFPE Tissue Kit (QIAGEN)
SureSelect Target Enrichment Kit (Agilent) and TruSeq Rapid SBS (Illumina)

tag: disease state

value: Melanoma

value: utomilumab

tag: dose

value: 1.2 MG/KG

tag: Stage

value: STAGE IV

tag: response to_prior_therapy

value: REFRACTORY

tag: best objective_response

value: Objective progression

value: tumor biopsy

tag: subjid


title: DSGC, P12, HB9-GFP, down, rep7

description:
SmartSeq2
genes.attr_table
genes.count_table
genes.fpkm_table
samples.table
H12_6

value: Retina

value: down