title: PN_24h_KnotGAL4_GH146_K17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 632


title: PN_24h_KnotGAL4_GH146_K15

status: Public on Nov 11 2020

type: SRA

city: Stanford

first: Qijing

last: Xie

state: California

address: Bass Biology Building, Room 334

department: Department of Biology

country: USA

institute: Howard Hughes Medical Institute

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 630

library_source: transcriptomic

data_processing:
de-mutiplexd (bcl2fastq 2.19.0.316)
alignment (STAR 2.5.4)
gene count (HTseq 0.11.2, default settings except ‘‘-m  536 intersection-strict’)
normalization (gene counts were rescaled to counts per million reads (CPM), and log transformed to Log2(CPM+1) for processed data)
filtering (cells with fewer than 100,000 uniquely mapped reads were excluded, and cells with high expression of neuronal markers are retained for processed data)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: annotated .h5ad files of high-quality neurons

molecule: total RNA

organism: Drosophila melanogaster

extract_protocol: Modified SMART-seq2 (Li et al. 2017)

tag: cell type

value: neuron

tag: genotype

tag: Stage

value: 24h APF

tag: number of cells


title: PN_24h_KnotGAL4_GH146_L11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 650


title: PN_24h_KnotGAL4_GH146_K13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 628


title: PN_24h_KnotGAL4_GH146_K11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 626


title: PN_24h_KnotGAL4_GH146_K12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 627


title: PN_24h_KnotGAL4_GH146_J9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 624


title: PN_24h_KnotGAL4_GH146_K10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 625


title: PN_24h_KnotGAL4_GH146_J7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 622


title: PN_24h_KnotGAL4_GH146_J6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 621


title: PN_24h_KnotGAL4_GH146_J8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 623


title: PN_24h_SplitGAL4_ID28_E5

description:
single cell
24h_PN_all.h5ad
Sample 881


title: PN_24h_KnotGAL4_GH146_J3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 618


title: PN_24h_KnotGAL4_GH146_J5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 620


title: PN_24h_KnotGAL4_GH146_K21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 637


title: PN_24h_KnotGAL4_GH146_J24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 616


title: PN_24h_KnotGAL4_GH146_J20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 612


title: PN_24h_KnotGAL4_GH146_J22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 614


title: PN_24h_KnotGAL4_GH146_J1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 611


title: PN_24h_KnotGAL4_GH146_J23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 615


title: PN_24h_KnotGAL4_GH146_K16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 631


title: PN_24h_KnotGAL4_GH146_J19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 610


title: PN_24h_KnotGAL4_GH146_J18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 609


title: PN_24h_KnotGAL4_GH146_J16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 607


title: PN_24h_KnotGAL4_GH146_J15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 606


title: PN_24h_KnotGAL4_GH146_K14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 629


title: PN_24h_KnotGAL4_GH146_J17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 608


title: PN_24h_KnotGAL4_GH146_J14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 605


title: PN_24h_KnotGAL4_GH146_J13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 604


title: PN_24h_KnotGAL4_GH146_J12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 603


title: PN_24h_KnotGAL4_GH146_I9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 600


title: PN_24h_KnotGAL4_GH146_I8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 599


title: PN_24h_KnotGAL4_GH146_I7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 598


title: PN_24h_KnotGAL4_GH146_J2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 617


title: PN_24h_KnotGAL4_GH146_J11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 602


title: PN_24h_KnotGAL4_GH146_J4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 619


title: PN_24h_KnotGAL4_GH146_I6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 597


title: PN_24h_KnotGAL4_GH146_I4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 595


title: PN_24h_KnotGAL4_GH146_I3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 594


title: PN_24h_KnotGAL4_GH146_I5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 596


title: PN_24h_KnotGAL4_GH146_I22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 590


title: PN_24h_KnotGAL4_GH146_I24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 592


title: PN_24h_KnotGAL4_GH146_I23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 591


title: PN_24h_KnotGAL4_GH146_I2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 593


title: PN_24h_KnotGAL4_GH146_I20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 588


title: PN_24h_KnotGAL4_GH146_I1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 587


title: PN_24h_KnotGAL4_GH146_I21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 589


title: PN_24h_KnotGAL4_GH146_I15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 582


title: PN_24h_KnotGAL4_GH146_I18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 585


title: PN_24h_KnotGAL4_GH146_J10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 601


title: PN_24h_KnotGAL4_GH146_I14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 581


title: PN_24h_KnotGAL4_GH146_I11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 578


title: PN_24h_KnotGAL4_GH146_I12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 579


title: PN_24h_KnotGAL4_GH146_H9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 576


title: PN_24h_KnotGAL4_GH146_I10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 577


title: PN_24h_KnotGAL4_GH146_I13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 580


title: PN_24h_KnotGAL4_GH146_H7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 574


title: PN_24h_KnotGAL4_GH146_H8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 575


title: PN_24h_KnotGAL4_GH146_H6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 573


title: PN_24h_KnotGAL4_GH146_H4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 571


title: PN_24h_KnotGAL4_GH146_H5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 572


title: PN_24h_KnotGAL4_GH146_H3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 570


title: PN_24h_KnotGAL4_GH146_H24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 568


title: PN_24h_KnotGAL4_GH146_H23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 567


title: PN_24h_KnotGAL4_GH146_H21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 565


title: PN_24h_KnotGAL4_GH146_H1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 563


title: PN_24h_KnotGAL4_GH146_H2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 569


title: PN_24h_KnotGAL4_GH146_H20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 564


title: PN_24h_KnotGAL4_GH146_H19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 562


title: PN_24h_KnotGAL4_GH146_I19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 586


title: PN_24h_KnotGAL4_GH146_I16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 583


title: PN_24h_KnotGAL4_GH146_H18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 561


title: PN_24h_KnotGAL4_GH146_H17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 560


title: PN_24h_KnotGAL4_GH146_I17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 584


title: PN_24h_KnotGAL4_GH146_H16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 559


title: PN_24h_KnotGAL4_GH146_H15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 558


title: PN_24h_KnotGAL4_GH146_H12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 555


title: PN_24h_KnotGAL4_GH146_H13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 556


title: PN_24h_KnotGAL4_GH146_H14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 557


title: PN_24h_KnotGAL4_GH146_H11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 554


title: PN_24h_KnotGAL4_GH146_G6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 549


title: PN_24h_KnotGAL4_GH146_G9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 552


title: PN_24h_KnotGAL4_GH146_H10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 553


title: PN_24h_KnotGAL4_GH146_G8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 551


title: PN_24h_KnotGAL4_GH146_G4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 547


title: PN_24h_KnotGAL4_GH146_G7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 550


title: PN_24h_KnotGAL4_GH146_H22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 566


title: PN_24h_KnotGAL4_GH146_G3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 546


title: PN_24h_KnotGAL4_GH146_G24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 544


title: PN_24h_KnotGAL4_GH146_G23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 543


title: PN_24h_KnotGAL4_GH146_G2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 545


title: PN_24h_KnotGAL4_GH146_G22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 542


title: PN_24h_KnotGAL4_GH146_G20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 540


title: PN_24h_KnotGAL4_GH146_G19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 538


title: PN_24h_KnotGAL4_GH146_G17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 536


title: PN_24h_KnotGAL4_GH146_G18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 537


title: PN_24h_KnotGAL4_GH146_G21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 541


title: PN_24h_KnotGAL4_GH146_G15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 534


title: PN_24h_KnotGAL4_GH146_G14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 533


title: PN_24h_KnotGAL4_GH146_G13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 532


title: PN_24h_KnotGAL4_GH146_G16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 535


title: PN_24h_KnotGAL4_GH146_G11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 530


title: PN_24h_KnotGAL4_GH146_G12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 531


title: PN_24h_KnotGAL4_GH146_F9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 528


title: PN_24h_KnotGAL4_GH146_G10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 529


title: PN_24h_KnotGAL4_GH146_F8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 527


title: PN_24h_KnotGAL4_GH146_G5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 548


title: PN_24h_KnotGAL4_GH146_F7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 526


title: PN_24h_KnotGAL4_GH146_F6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 525


title: PN_24h_KnotGAL4_GH146_F4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 523


title: PN_24h_KnotGAL4_GH146_F5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 524


title: PN_24h_KnotGAL4_GH146_F24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 520


title: PN_24h_KnotGAL4_GH146_F2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 521


title: PN_24h_KnotGAL4_GH146_F3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 522


title: PN_24h_KnotGAL4_GH146_F23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 519


title: PN_24h_KnotGAL4_GH146_G1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 539


title: PN_24h_KnotGAL4_GH146_F22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 518


title: PN_24h_KnotGAL4_GH146_F21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 517


title: PN_24h_KnotGAL4_GH146_F19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 514


title: PN_24h_KnotGAL4_GH146_F17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 512


title: PN_24h_KnotGAL4_GH146_F18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 513


title: PN_24h_KnotGAL4_GH146_F1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 515


title: PN_24h_KnotGAL4_GH146_F20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 516


title: PN_24h_KnotGAL4_GH146_F16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 511


title: PN_24h_KnotGAL4_GH146_F14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 509


title: PN_24h_KnotGAL4_GH146_F13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 508


title: PN_24h_KnotGAL4_GH146_E9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 504


title: PN_24h_KnotGAL4_GH146_F10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 505


title: PN_24h_KnotGAL4_GH146_F12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 507


title: PN_24h_KnotGAL4_GH146_F11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 506


title: PN_24h_KnotGAL4_GH146_E8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 503


title: PN_24h_KnotGAL4_GH146_E7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 502


title: PN_24h_KnotGAL4_GH146_E6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 501


title: PN_24h_KnotGAL4_GH146_E3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 498


title: PN_24h_KnotGAL4_GH146_E5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 500


title: PN_24h_KnotGAL4_GH146_E21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 493


title: PN_24h_KnotGAL4_GH146_E23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 495


title: PN_24h_KnotGAL4_GH146_E2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 497


title: PN_24h_KnotGAL4_GH146_E19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 490


title: PN_24h_KnotGAL4_GH146_E22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 494


title: PN_24h_KnotGAL4_GH146_E24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 496


title: PN_24h_KnotGAL4_GH146_E20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 492


title: PN_24h_KnotGAL4_GH146_F15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 510


title: PN_24h_KnotGAL4_GH146_E18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 489


title: PN_24h_KnotGAL4_GH146_E1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 491


title: PN_24h_KnotGAL4_GH146_E13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 484


title: PN_24h_KnotGAL4_GH146_E12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 483


title: PN_24h_KnotGAL4_GH146_E14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 485


title: PN_24h_KnotGAL4_GH146_E16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 487


title: PN_24h_KnotGAL4_GH146_E11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 482


title: PN_24h_KnotGAL4_GH146_E10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 481


title: PN_24h_KnotGAL4_GH146_D5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 476


title: PN_24h_KnotGAL4_GH146_D4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 475


title: PN_24h_KnotGAL4_GH146_D3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 474


title: PN_24h_KnotGAL4_GH146_D24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 472


title: PN_24h_KnotGAL4_GH146_D7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 478


title: PN_24h_KnotGAL4_GH146_D2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 473


title: PN_24h_KnotGAL4_GH146_D23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 471


title: PN_24h_KnotGAL4_GH146_D21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 469


title: PN_24h_KnotGAL4_GH146_D22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 470


title: PN_24h_KnotGAL4_GH146_D20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 468


title: PN_24h_KnotGAL4_GH146_E15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 486


title: PN_24h_KnotGAL4_GH146_D1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 467


title: PN_24h_KnotGAL4_GH146_D18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 465


title: PN_24h_KnotGAL4_GH146_D16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 463


title: PN_24h_KnotGAL4_GH146_D17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 464


title: PN_24h_KnotGAL4_GH146_D19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 466


title: PN_24h_KnotGAL4_GH146_D12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 459


title: PN_24h_KnotGAL4_GH146_D9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 480


title: PN_24h_KnotGAL4_GH146_D14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 461


title: PN_24h_KnotGAL4_GH146_D15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 462


title: PN_24h_KnotGAL4_GH146_D8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 479


title: PN_24h_KnotGAL4_GH146_D11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 458


title: PN_24h_KnotGAL4_GH146_D6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 477


title: PN_24h_KnotGAL4_GH146_D13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 460


title: PN_24h_KnotGAL4_GH146_C9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 456


title: PN_24h_KnotGAL4_GH146_D10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 457


title: PN_24h_KnotGAL4_GH146_C6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 453


title: PN_24h_KnotGAL4_GH146_C8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 455


title: PN_24h_KnotGAL4_GH146_C5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 452


title: PN_24h_KnotGAL4_GH146_C7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 454


title: PN_24h_KnotGAL4_GH146_C3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 450


title: PN_24h_KnotGAL4_GH146_C4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 451


title: PN_24h_KnotGAL4_GH146_C23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 447


title: PN_24h_KnotGAL4_GH146_C24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 448


title: PN_24h_KnotGAL4_GH146_C2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 449


title: PN_24h_KnotGAL4_GH146_C22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 446


title: PN_24h_KnotGAL4_GH146_C21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 445


title: PN_24h_KnotGAL4_GH146_E4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 499


title: PN_24h_KnotGAL4_GH146_C20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 444


title: PN_24h_KnotGAL4_GH146_C1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 443


title: PN_24h_KnotGAL4_GH146_C18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 441


title: PN_24h_KnotGAL4_GH146_C19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 442


title: PN_24h_KnotGAL4_GH146_C14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 437


title: PN_24h_KnotGAL4_GH146_C16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 439


title: PN_24h_KnotGAL4_GH146_C11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 434


title: PN_24h_KnotGAL4_GH146_B8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 431


title: PN_24h_KnotGAL4_GH146_C10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 433


title: PN_24h_KnotGAL4_GH146_B9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 432


title: PN_24h_KnotGAL4_GH146_C13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 436


title: PN_24h_KnotGAL4_GH146_B7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 430


title: PN_24h_KnotGAL4_GH146_B6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 429


title: PN_24h_KnotGAL4_GH146_B5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 428


title: PN_24h_KnotGAL4_GH146_B2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 425


title: PN_24h_KnotGAL4_GH146_B23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 423


title: PN_24h_KnotGAL4_GH146_B3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 426


title: PN_24h_KnotGAL4_GH146_B22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 422


title: PN_24h_KnotGAL4_GH146_B21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 421


title: PN_24h_KnotGAL4_GH146_J21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 613


title: PN_24h_KnotGAL4_GH146_B24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 424


title: PN_24h_KnotGAL4_GH146_B20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 420


title: PN_24h_KnotGAL4_GH146_B19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 418


title: PN_24h_KnotGAL4_GH146_B18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 417


title: PN_24h_KnotGAL4_GH146_C15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 438


title: PN_24h_KnotGAL4_GH146_B16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 415


title: PN_24h_KnotGAL4_GH146_C17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 440


title: PN_24h_KnotGAL4_GH146_B17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 416


title: PN_24h_KnotGAL4_GH146_C12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 435


title: PN_24h_KnotGAL4_GH146_B14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 413


title: PN_24h_KnotGAL4_GH146_B15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 414


title: PN_24h_KnotGAL4_GH146_B13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 412


title: PN_24h_KnotGAL4_GH146_B12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 411


title: PN_24h_KnotGAL4_GH146_B11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 410


title: PN_24h_KnotGAL4_GH146_B4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 427


title: PN_24h_KnotGAL4_GH146_A7

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 406


title: PN_24h_KnotGAL4_GH146_B10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 409


title: PN_24h_KnotGAL4_GH146_A9

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 408


title: PN_24h_KnotGAL4_GH146_A6

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 405


title: PN_24h_KnotGAL4_GH146_A8

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 407


title: PN_24h_KnotGAL4_GH146_A5

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 404


title: PN_24h_KnotGAL4_GH146_A4

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 403


title: PN_24h_KnotGAL4_GH146_A3

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 402


title: PN_24h_KnotGAL4_GH146_B1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 419


title: PN_24h_KnotGAL4_GH146_A24

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 400


title: PN_24h_KnotGAL4_GH146_A20

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 396


title: PN_24h_KnotGAL4_GH146_A21

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 397


title: PN_24h_KnotGAL4_GH146_A23

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 399


title: PN_24h_KnotGAL4_GH146_A1

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 395


title: PN_24h_KnotGAL4_GH146_A22

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 398


title: PN_24h_KnotGAL4_GH146_A17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 392


title: PN_24h_KnotGAL4_GH146_A19

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 394


title: PN_24h_KnotGAL4_GH146_A16

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 391


title: PN_24h_KnotGAL4_GH146_A13

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 388


title: PN_24h_KnotGAL4_GH146_A18

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 393


title: PN_24h_KnotGAL4_GH146_A15

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 390


title: PN_24h_KnotGAL4_GH146_A14

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 389


title: PN_24h_KnotGAL4_GH146_A12

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 387


title: PN_24h_KnotGAL4_GH146_A11

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 386


title: PN_24h_SplitGAL4_ID7_P9

description:
single cell
24h_PN_all.h5ad
Sample 384


title: PN_24h_KnotGAL4_GH146_A10

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 385


title: PN_24h_SplitGAL4_ID7_P8

description:
single cell
24h_PN_all.h5ad
Sample 383


title: PN_24h_SplitGAL4_ID7_P4

description:
single cell
24h_PN_all.h5ad
Sample 379


title: PN_24h_SplitGAL4_ID7_P2

description:
single cell
24h_PN_all.h5ad
Sample 377


title: PN_24h_SplitGAL4_ID7_P7

description:
single cell
24h_PN_all.h5ad
Sample 382


title: PN_24h_KnotGAL4_GH146_A2

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 401


title: PN_24h_SplitGAL4_ID7_P6

description:
single cell
24h_PN_all.h5ad
Sample 381


title: PN_24h_SplitGAL4_ID7_P3

description:
single cell
24h_PN_all.h5ad
Sample 378


title: PN_24h_SplitGAL4_ID7_P5

description:
single cell
24h_PN_all.h5ad
Sample 380


title: PN_24h_SplitGAL4_ID7_P23

description:
single cell
24h_PN_all.h5ad
Sample 375


title: PN_24h_SplitGAL4_ID7_P22

description:
single cell
24h_PN_all.h5ad
Sample 374


title: PN_24h_SplitGAL4_ID7_P24

description:
single cell
24h_PN_all.h5ad
Sample 376


title: PN_24h_SplitGAL4_ID7_P1

description:
single cell
24h_PN_all.h5ad
Sample 371


title: PN_24h_SplitGAL4_ID7_P18

description:
single cell
24h_PN_all.h5ad
Sample 369


title: PN_24h_SplitGAL4_ID7_P16

description:
single cell
24h_PN_all.h5ad
Sample 367


title: PN_24h_SplitGAL4_ID7_P20

description:
single cell
24h_PN_all.h5ad
Sample 372


title: PN_24h_SplitGAL4_ID7_P12

description:
single cell
24h_PN_all.h5ad
Sample 363


title: PN_24h_SplitGAL4_ID7_P15

description:
single cell
24h_PN_all.h5ad
Sample 366


title: PN_24h_SplitGAL4_ID7_P11

description:
single cell
24h_PN_all.h5ad
Sample 362


title: PN_24h_SplitGAL4_ID7_P10

description:
single cell
24h_PN_all.h5ad
Sample 361


title: PN_24h_SplitGAL4_ID7_P19

description:
single cell
24h_PN_all.h5ad
Sample 370


title: PN_24h_SplitGAL4_ID7_P21

description:
single cell
24h_PN_all.h5ad
Sample 373


title: PN_24h_SplitGAL4_ID7_O9

description:
single cell
24h_PN_all.h5ad
Sample 360


title: PN_24h_SplitGAL4_ID7_O7

description:
single cell
24h_PN_all.h5ad
Sample 358


title: PN_24h_SplitGAL4_ID7_O6

description:
single cell
24h_PN_all.h5ad
Sample 357


title: PN_24h_SplitGAL4_ID7_P13

description:
single cell
24h_PN_all.h5ad
Sample 364


title: PN_24h_SplitGAL4_ID7_O5

description:
single cell
24h_PN_all.h5ad
Sample 356


title: PN_24h_SplitGAL4_ID7_O3

description:
single cell
24h_PN_all.h5ad
Sample 354


title: PN_24h_SplitGAL4_ID7_O4

description:
single cell
24h_PN_all.h5ad
Sample 355


title: ACh Donor 2, 21-days TGF-B1 exposure, analyzed on Day 21_rep2

city: Bethesda

first: Kathryn

last: Futrega

state: MD

address: 30 Convent Ave

department: NIDCR

institute: NIH

data_processing:
The primary sequence data was generated using the Illumina bcl2fastq  2.20.0.422 pipeline.
The cleaned sequence reads were then aligned against the Homo sapiens genome (Build version HG38).
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences.
The transcripts were assembled with the Stringtie tool v1.3.3 utilising the reads alignment with hg38 and reference annotation based assembly option (RABT).
edgeR (version 3.22.5) was used to perform differential expression analysis.
Genome_build: HG38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalised log counts per million (CPM) values for each sample

organism: Homo sapiens

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 42

growth_protocol: BMSC and ACh were first expanded in low glucose DMEM with GlutaMAX and sodium pyruvate, 10% fetal bovine serum (FBS), 100 U/ml penicillin/streptomycin (PenStrep), all from Thermo Fisher, 10 ng/mL fibroblast growth factor-1 (FGF-1; Peprotech), and 5 µg/mL porcine heparin sodium salt (Sigma) in a 2% O2, 5% CO2, 37 °C incubator, and passaged using 0.25% trypsin/EDTA (Thermo Fisher) when ~80% confluent. Fresh flasks were re-seeded at ~1,500 cells per cm2.

extract_protocol:
Samples were crushed in RLT buffer (Qiagen) containing β-mercaptoethanol (Sigma) and RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase I (Qiagen) digestion, as per manufacturer's instructions.
Illumina's TruSeq stranded RNA sample preparation protocol was used for processing samples. This protocol includes the following steps:  cDNA Synthesis: Purification of mRNA (via oligo(dT) beads), Fragmentation of mRNA with divalent cations and heat 1st strand cDNA synthesis (randomly primed), 2nd strand cDNA synthesis; and   cDNA library preparation: DNA fragment end repair (blunt ending of DNA fragments), 3' Adenylation of DNA fragments, Sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments), Amplification of library via PCR.

treatment_protocol: For chondrogenic differentiation culture, chondrogenic induction media consisted of high glucose DMEM supplemented with GlutaMAX and sodium pyruvate, 1x insulin-transferrin-selenium-ethanolamine (ITS-X), PenStrep (all from Thermo Fisher), 200 μM ascorbic acid 2-phosphate (Sigma), 40 μg/mL l-proline (Sigma), and 10 ng/mL TGF-β1 (Peprotech) where specified.  The cells labelled “day 0”  were never supplemented with TGF-β1.  Cells were force-aggregated in the well plates by centrifugation at 500 x g for 3 minutes.  Full medium exchanges were performed every 2 days or on specified day of TGF-β1 removal.  For TGF-β1 removal, the cell pellets were rinsed once with 4 mL PBS, then fresh induction medium without TGF-β1 was added.  In micro-pellet cultures, cells were seeded at 1.25 million per well of a 6-well plate. At this seeding density, ~250 micro-pellets are formed in each well, with each micro-pellet containing ~5,000 BMSC.  Each well contained 4 mL of total culture medium.

tag: tissue

value: Articular cartilage from knee

value: Articular chondrocytes (ACh), (Lonza, Lot#:BF3307)

tag: treatment


title: ACh Donor 2, 21-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 43


title: PN_24h_SplitGAL4_ID7_O2

description:
single cell
24h_PN_all.h5ad
Sample 353


title: ACh Donor 2, 7-days TGF-B1 exposure, analyzed on Day 7_rep3

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 40


title: ACh Donor 2, 21-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 41


title: ACh Donor 2, 7-days TGF-B1 exposure, analyzed on Day 7_rep2

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 39


title: PN_24h_SplitGAL4_ID7_O23

description:
single cell
24h_PN_all.h5ad
Sample 351


title: ACh Donor 2, 7-days TGF-B1 exposure, analyzed on Day 7_rep1

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 38


title: PN_24h_SplitGAL4_ID7_P14

description:
single cell
24h_PN_all.h5ad
Sample 365


title: PN_24h_SplitGAL4_ID7_P17

description:
single cell
24h_PN_all.h5ad
Sample 368


title: ACh Donor 2, 3-days TGF-B1 exposure, analyzed on Day 3_rep3

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 37


title: PN_24h_SplitGAL4_ID7_O21

description:
single cell
24h_PN_all.h5ad
Sample 349


title: ACh Donor 2, 3-days TGF-B1 exposure, analyzed on Day 3_rep2

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 36


title: PN_24h_SplitGAL4_ID7_O8

description:
single cell
24h_PN_all.h5ad
Sample 359


title: PN_24h_SplitGAL4_ID7_O1

description:
single cell
24h_PN_all.h5ad
Sample 347


title: ACh Donor 2, 1-day TGF-B1 exposure, analyzed on Day 1_rep3

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 34


title: ACh Donor 2, 3-days TGF-B1 exposure, analyzed on Day 3_rep1

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 35


title: PN_24h_SplitGAL4_ID7_O20

description:
single cell
24h_PN_all.h5ad
Sample 348


title: ACh Donor 2, 1-day TGF-B1 exposure, analyzed on Day 1_rep2

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 33


title: ACh Donor 2, 1-day TGF-B1 exposure, analyzed on Day 1_rep1

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 32


title: ACh Donor 2 Day 0_rep 3

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 31

value: ACh Donor 2 Day 0_rep 3


title: PN_24h_SplitGAL4_ID7_O19

description:
single cell
24h_PN_all.h5ad
Sample 346


title: PN_24h_SplitGAL4_ID7_O18

description:
single cell
24h_PN_all.h5ad
Sample 345


title: ACh Donor 2 Day 0_rep 2

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 30

value: ACh Donor 2 Day 0_rep 2


title: PN_24h_SplitGAL4_ID7_O17

description:
single cell
24h_PN_all.h5ad
Sample 344


title: PN_24h_KnotGAL4_GH146_E17

description:
single cell
24h_PN_all.h5ad, knot_24h_48h_adult.h5ad
Sample 488


title: PN_24h_SplitGAL4_ID7_O24

description:
single cell
24h_PN_all.h5ad
Sample 352


title: PN_24h_SplitGAL4_ID7_O16

description:
single cell
24h_PN_all.h5ad
Sample 343


title: BMSC Donor 3, 21-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 21-year-old female, expanded BMSC, Passage 50

value: Bone marrow aspirate from illiac crest

value: Bone marrow stromal cell


title: BMSC Donor 3, 21-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 21-year-old female, expanded BMSC, Passage 49


title: ACh Donor 2 Day 0_rep 1

source_name: 50-year-old male, expanded Articular chondrocyte (ACh), Passage 29

value: ACh Donor 2 Day 0_rep 1


title: PN_24h_SplitGAL4_ID7_O13

description:
single cell
24h_PN_all.h5ad
Sample 340


title: PN_24h_SplitGAL4_ID7_O14

description:
single cell
24h_PN_all.h5ad
Sample 341


title: PN_24h_SplitGAL4_ID7_O22

description:
single cell
24h_PN_all.h5ad
Sample 350


title: BMSC Donor 3, 21-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 21-year-old female, expanded BMSC, Passage 48


title: BMSC Donor 3, 7-days TGF-B1 exposure, analyzed on Day 7_rep3

source_name: 21-year-old female, expanded BMSC, Passage 47


title: BMSC Donor 3, 7-days TGF-B1 exposure, analyzed on Day 7_rep2

source_name: 21-year-old female, expanded BMSC, Passage 46


title: PN_24h_SplitGAL4_ID7_O10

description:
single cell
24h_PN_all.h5ad
Sample 337


title: BMSC Donor 3, 7-days TGF-B1 exposure, analyzed on Day 7_rep1

source_name: 21-year-old female, expanded BMSC, Passage 45


title: BMSC Donor 3, 3-days TGF-B1 exposure, analyzed on Day 3_rep3

source_name: 21-year-old female, expanded BMSC, Passage 44


title: BMSC Donor 3, 3-days TGF-B1 exposure, analyzed on Day 3_rep2

source_name: 21-year-old female, expanded BMSC, Passage 43


title: PN_24h_SplitGAL4_ID7_N6

description:
single cell
24h_PN_all.h5ad
Sample 333


title: PN_24h_SplitGAL4_ID7_N8

description:
single cell
24h_PN_all.h5ad
Sample 335


title: PN_24h_SplitGAL4_ID7_N7

description:
single cell
24h_PN_all.h5ad
Sample 334


title: BMSC Donor 3, 3-days TGF-B1 exposure, analyzed on Day 3_rep1

source_name: 21-year-old female, expanded BMSC, Passage 42


title: BMSC Donor 3, 1-day TGF-B1 exposure, analyzed on Day 1_rep2

source_name: 21-year-old female, expanded BMSC, Passage 40


title: BMSC Donor 3, 1-day TGF-B1 exposure, analyzed on Day 1_rep3

source_name: 21-year-old female, expanded BMSC, Passage 41


title: PN_24h_SplitGAL4_ID7_O15

description:
single cell
24h_PN_all.h5ad
Sample 342


title: PN_24h_SplitGAL4_ID7_N4

description:
single cell
24h_PN_all.h5ad
Sample 331


title: PN_24h_SplitGAL4_ID7_N3

description:
single cell
24h_PN_all.h5ad
Sample 330


title: PN_24h_SplitGAL4_ID7_O11

description:
single cell
24h_PN_all.h5ad
Sample 338


title: PN_24h_SplitGAL4_ID7_N2

description:
single cell
24h_PN_all.h5ad
Sample 329


title: BMSC Donor 3, 1-day TGF-B1 exposure, analyzed on Day 1_rep1

source_name: 21-year-old female, expanded BMSC, Passage 39


title: BMSC Donor 3 Day 0_rep 3

source_name: 21-year-old female, expanded BMSC, Passage 38

value: BMSC Donor 3 Day 0_rep 3


title: BMSC Donor 2, 21-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 44-year-old male, expanded BMSC, Passage 36


title: BMSC Donor 3 Day 0_rep 2

source_name: 21-year-old female, expanded BMSC, Passage 37

value: BMSC Donor 3 Day 0_rep 2


title: PN_24h_SplitGAL4_ID7_N24

description:
single cell
24h_PN_all.h5ad
Sample 328


title: PN_24h_SplitGAL4_ID7_N23

description:
single cell
24h_PN_all.h5ad
Sample 327


title: PN_24h_SplitGAL4_ID7_N22

description:
single cell
24h_PN_all.h5ad
Sample 326


title: PN_24h_SplitGAL4_ID7_O12

description:
single cell
24h_PN_all.h5ad
Sample 339


title: BMSC Donor 2, 21-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 44-year-old male, expanded BMSC, Passage 35


title: BMSC Donor 3 Day 0_rep 1

source_name: 21-year-old female, expanded BMSC, Passage 36

value: BMSC Donor 3 Day 0_rep 1


title: BMSC Donor 2, 21-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 44-year-old male, expanded BMSC, Passage 34


title: PN_24h_SplitGAL4_ID7_N9

description:
single cell
24h_PN_all.h5ad
Sample 336


title: BMSC Donor 2, 7-days TGF-B1 exposure, analyzed on Day 7_rep3

source_name: 44-year-old male, expanded BMSC, Passage 33


title: PN_24h_SplitGAL4_ID7_N20

description:
single cell
24h_PN_all.h5ad
Sample 324


title: PN_24h_SplitGAL4_ID7_N5

description:
single cell
24h_PN_all.h5ad
Sample 332


title: BMSC Donor 2, 7-days TGF-B1 exposure, analyzed on Day 7_rep2

source_name: 44-year-old male, expanded BMSC, Passage 32


title: PN_24h_SplitGAL4_ID7_N19

description:
single cell
24h_PN_all.h5ad
Sample 322


title: PN_24h_SplitGAL4_ID7_N18

description:
single cell
24h_PN_all.h5ad
Sample 321


title: PN_24h_SplitGAL4_ID7_N17

description:
single cell
24h_PN_all.h5ad
Sample 320


title: BMSC Donor 2, 7-days TGF-B1 exposure, analyzed on Day 7_rep1

source_name: 44-year-old male, expanded BMSC, Passage 31


title: BMSC Donor 2, 3-days TGF-B1 exposure, analyzed on Day 3_rep2

source_name: 44-year-old male, expanded BMSC, Passage 29


title: BMSC Donor 2, 3-days TGF-B1 exposure, analyzed on Day 3_rep3

source_name: 44-year-old male, expanded BMSC, Passage 30


title: PN_24h_SplitGAL4_ID7_N16

description:
single cell
24h_PN_all.h5ad
Sample 319


title: BMSC Donor 2, 3-days TGF-B1 exposure, analyzed on Day 3_rep1

source_name: 44-year-old male, expanded BMSC, Passage 28


title: PN_24h_SplitGAL4_ID7_N15

description:
single cell
24h_PN_all.h5ad
Sample 318


title: PN_24h_SplitGAL4_ID7_N14

description:
single cell
24h_PN_all.h5ad
Sample 317


title: BMSC Donor 2, 1-day TGF-B1 exposure, analyzed on Day 1_rep2

source_name: 44-year-old male, expanded BMSC, Passage 26


title: BMSC Donor 2, 1-day TGF-B1 exposure, analyzed on Day 1_rep1

source_name: 44-year-old male, expanded BMSC, Passage 25


title: PN_24h_SplitGAL4_ID7_N13

description:
single cell
24h_PN_all.h5ad
Sample 316


title: BMSC Donor 2, 1-day TGF-B1 exposure, analyzed on Day 1_rep3

source_name: 44-year-old male, expanded BMSC, Passage 27


title: PN_24h_SplitGAL4_ID7_N12

description:
single cell
24h_PN_all.h5ad
Sample 315


title: BMSC Donor 2 Day 0_rep 2

source_name: 44-year-old male, expanded BMSC, Passage 23

value: BMSC Donor 2 Day 0_rep 2


title: BMSC Donor 2 Day 0_rep 3

source_name: 44-year-old male, expanded BMSC, Passage 24

value: BMSC Donor 2 Day 0_rep 3


title: BMSC Donor 2 Day 0_rep 1

source_name: 44-year-old male, expanded BMSC, Passage 22

value: BMSC Donor 2 Day 0_rep 1


title: ACh Donor 1, 21-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 29

value: Articular chondrocytes (ACh), (Lonza, Lot#:BF3339)


title: ACh Donor 1, 21-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 28


title: PN_24h_SplitGAL4_ID7_M9

description:
single cell
24h_PN_all.h5ad
Sample 312


title: ACh Donor 1, 21-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 27


title: PN_24h_SplitGAL4_ID7_N1

description:
single cell
24h_PN_all.h5ad
Sample 323


title: PN_24h_SplitGAL4_ID7_M6

description:
single cell
24h_PN_all.h5ad
Sample 309


title: PN_24h_SplitGAL4_ID7_N11

description:
single cell
24h_PN_all.h5ad
Sample 314


title: ACh Donor 1, 7-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 26


title: PN_24h_SplitGAL4_ID7_M5

description:
single cell
24h_PN_all.h5ad
Sample 308


title: PN_24h_SplitGAL4_ID7_N21

description:
single cell
24h_PN_all.h5ad
Sample 325


title: ACh Donor 1, 7-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 25


title: ACh Donor 1, 7-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 24


title: PN_24h_SplitGAL4_ID7_M4

description:
single cell
24h_PN_all.h5ad
Sample 307


title: PN_24h_SplitGAL4_ID7_M3

description:
single cell
24h_PN_all.h5ad
Sample 306


title: PN_24h_SplitGAL4_ID7_M24

description:
single cell
24h_PN_all.h5ad
Sample 304


title: PN_24h_SplitGAL4_ID7_M2

description:
single cell
24h_PN_all.h5ad
Sample 305


title: ACh Donor 1, 3-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 23


title: ACh Donor 1, 3-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 22


title: PN_24h_SplitGAL4_ID7_M22

description:
single cell
24h_PN_all.h5ad
Sample 302


title: PN_24h_SplitGAL4_ID7_N10

description:
single cell
24h_PN_all.h5ad
Sample 313


title: PN_24h_SplitGAL4_ID7_M23

description:
single cell
24h_PN_all.h5ad
Sample 303


title: ACh Donor 1, 7-days TGF-B1 exposure, analyzed on Day 7_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 17


title: ACh Donor 1, 1-day TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 19


title: PN_24h_SplitGAL4_ID7_M8

description:
single cell
24h_PN_all.h5ad
Sample 311


title: ACh Donor 1, 3-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 21


title: ACh Donor 1, 1-day TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 18


title: PN_24h_SplitGAL4_ID7_M21

description:
single cell
24h_PN_all.h5ad
Sample 301


title: ACh Donor 1, 1-day TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 20


title: PN_24h_SplitGAL4_ID7_M20

description:
single cell
24h_PN_all.h5ad
Sample 300


title: ACh Donor 1, 3-days TGF-B1 exposure, analyzed on Day 3_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 14


title: PN_24h_SplitGAL4_ID7_M7

description:
single cell
24h_PN_all.h5ad
Sample 310


title: PN_24h_SplitGAL4_ID7_M19

description:
single cell
24h_PN_all.h5ad
Sample 298


title: PN_24h_SplitGAL4_ID7_M17

description:
single cell
24h_PN_all.h5ad
Sample 296


title: ACh Donor 1, 3-days TGF-B1 exposure, analyzed on Day 3_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 13


title: PN_24h_SplitGAL4_ID7_M16

description:
single cell
24h_PN_all.h5ad
Sample 295


title: ACh Donor 1, 7-days TGF-B1 exposure, analyzed on Day 7_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 16


title: PN_24h_SplitGAL4_ID7_M18

description:
single cell
24h_PN_all.h5ad
Sample 297


title: ACh Donor 1, 7-days TGF-B1 exposure, analyzed on Day 7_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 15


title: PN_24h_SplitGAL4_ID7_M15

description:
single cell
24h_PN_all.h5ad
Sample 294


title: PN_24h_SplitGAL4_ID7_M14

description:
single cell
24h_PN_all.h5ad
Sample 293


title: ACh Donor 1, 3-days TGF-B1 exposure, analyzed on Day 3_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 12


title: PN_24h_SplitGAL4_ID7_M13

description:
single cell
24h_PN_all.h5ad
Sample 292


title: PN_24h_SplitGAL4_ID7_M12

description:
single cell
24h_PN_all.h5ad
Sample 291


title: PN_24h_SplitGAL4_ID7_M1

description:
single cell
24h_PN_all.h5ad
Sample 299


title: ACh Donor 1 Day 0_rep 3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 8

value: ACh Donor 1 Day 0_rep 3


title: ACh Donor 1, 1-days TGF-B1 exposure, analyzed on Day 1_rep2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 10


title: ACh Donor 1, 1-days TGF-B1 exposure, analyzed on Day 1_rep1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 9


title: ACh Donor 1, 1-days TGF-B1 exposure, analyzed on Day 1_rep3

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 11


title: PN_24h_SplitGAL4_ID7_M11

description:
single cell
24h_PN_all.h5ad
Sample 290

value: neuron


title: ACh Donor 1 Day 0_rep 2

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 7

value: ACh Donor 1 Day 0_rep 2


title: PN_24h_SplitGAL4_ID7_M10

description:
single cell
24h_PN_all.h5ad
Sample 289

value: 24h APF


title: PN_24h_SplitGAL4_ID7_L8

description:
single cell
24h_PN_all.h5ad
Sample 287


title: ACh Donor 1 Day 0_rep 1

source_name: 34-year-old male, expanded Articular chondrocyte (ACh), Passage 6

value: Articular cartilage from knee

value: ACh Donor 1 Day 0_rep 1


title: BMSC Donor 1, 21-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 24-year-old male, expanded BMSC, Passage 26


title: BMSC Donor 1, 21-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 24-year-old male, expanded BMSC, Passage 25


title: BMSC Donor 1, 21-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 24-year-old male, expanded BMSC, Passage 24


title: PN_24h_SplitGAL4_ID7_L5

description:
single cell
24h_PN_all.h5ad
Sample 284


title: BMSC Donor 1, 7-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 24-year-old male, expanded BMSC, Passage 23


title: PN_24h_SplitGAL4_ID7_L7

description:
single cell
24h_PN_all.h5ad
Sample 286


title: BMSC Donor 1, 7-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 24-year-old male, expanded BMSC, Passage 22


title: PN_24h_SplitGAL4_ID7_L6

description:
single cell
24h_PN_all.h5ad
Sample 285


title: PN_24h_SplitGAL4_ID7_L4

description:
single cell
24h_PN_all.h5ad
Sample 283


title: PN_24h_SplitGAL4_ID7_L3

description:
single cell
24h_PN_all.h5ad
Sample 282


title: BMSC Donor 1, 7-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 24-year-old male, expanded BMSC, Passage 21


title: BMSC Donor 1, 3-days TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 24-year-old male, expanded BMSC, Passage 20


title: PN_24h_SplitGAL4_ID7_L24

description:
single cell
24h_PN_all.h5ad
Sample 280


title: BMSC Donor 1, 3-days TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 24-year-old male, expanded BMSC, Passage 19


title: PN_24h_SplitGAL4_ID7_L2

description:
single cell
24h_PN_all.h5ad
Sample 281


title: PN_24h_SplitGAL4_ID7_L23

description:
single cell
24h_PN_all.h5ad
Sample 279


title: PN_24h_SplitGAL4_ID7_L22

description:
single cell
24h_PN_all.h5ad
Sample 278


title: PN_24h_SplitGAL4_ID7_L21

description:
single cell
24h_PN_all.h5ad
Sample 277


title: PN_24h_SplitGAL4_ID7_L20

description:
single cell
24h_PN_all.h5ad
Sample 276


title: BMSC Donor 1, 3-days TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 24-year-old male, expanded BMSC, Passage 18


title: BMSC Donor 1, 1-day TGF-B1 exposure, analyzed on Day 21_rep2

source_name: 24-year-old male, expanded BMSC, Passage 16


title: PN_24h_SplitGAL4_ID7_L9

description:
single cell
24h_PN_all.h5ad
Sample 288


title: PN_24h_SplitGAL4_ID7_L1

description:
single cell
24h_PN_all.h5ad
Sample 275


title: BMSC Donor 1, 1-day TGF-B1 exposure, analyzed on Day 21_rep1

source_name: 24-year-old male, expanded BMSC, Passage 15


title: BMSC Donor 1, 7-days TGF-B1 exposure, analyzed on Day 7_rep2

source_name: 24-year-old male, expanded BMSC, Passage 13


title: PN_24h_SplitGAL4_ID7_L19

description:
single cell
24h_PN_all.h5ad
Sample 274


title: PN_24h_SplitGAL4_ID7_L18

description:
single cell
24h_PN_all.h5ad
Sample 273


title: PN_24h_SplitGAL4_ID7_L17

description:
single cell
24h_PN_all.h5ad
Sample 272


title: BMSC Donor 1, 3-days TGF-B1 exposure, analyzed on Day 3_rep3

source_name: 24-year-old male, expanded BMSC, Passage 11


title: BMSC Donor 1, 7-days TGF-B1 exposure, analyzed on Day 7_rep1

source_name: 24-year-old male, expanded BMSC, Passage 12


title: PN_24h_SplitGAL4_ID7_L16

description:
single cell
24h_PN_all.h5ad
Sample 271


title: BMSC Donor 1, 3-days TGF-B1 exposure, analyzed on Day 3_rep2

source_name: 24-year-old male, expanded BMSC, Passage 10


title: PN_24h_SplitGAL4_ID7_L15

description:
single cell
24h_PN_all.h5ad
Sample 270


title: PN_24h_SplitGAL4_ID7_L14

description:
single cell
24h_PN_all.h5ad
Sample 269


title: BMSC Donor 1, 1-day TGF-B1 exposure, analyzed on Day 1_rep2

source_name: 24-year-old male, expanded BMSC, Passage 7


title: BMSC Donor 1, 1-day TGF-B1 exposure, analyzed on Day 1_rep3

source_name: 24-year-old male, expanded BMSC, Passage 8


title: BMSC Donor 1, 3-days TGF-B1 exposure, analyzed on Day 3_rep1

source_name: 24-year-old male, expanded BMSC, Passage 9


title: PN_24h_SplitGAL4_ID7_L12

description:
single cell
24h_PN_all.h5ad
Sample 267


title: BMSC Donor 1, 1-day TGF-B1 exposure, analyzed on Day 21_rep3

source_name: 24-year-old male, expanded BMSC, Passage 17


title: BMSC Donor 1, 1-day TGF-B1 exposure, analyzed on Day 1_rep1

source_name: 24-year-old male, expanded BMSC, Passage 6


title: BMSC Donor 1 Day 0_rep 3

source_name: 24-year-old male, expanded BMSC, Passage 5

value: BMSC Donor 1 Day 0_rep 3


title: PN_24h_SplitGAL4_ID7_L11

description:
single cell
24h_PN_all.h5ad
Sample 266


title: BMSC Donor 1, 7-days TGF-B1 exposure, analyzed on Day 7_rep3

source_name: 24-year-old male, expanded BMSC, Passage 14

value: Bone marrow aspirate from illiac crest


title: BMSC Donor 1 Day 0_rep 2

source_name: 24-year-old male, expanded BMSC, Passage 4

value: Bone marrow stromal cell

value: BMSC Donor 1 Day 0_rep 2


title: BMSC Donor 1 Day 0_rep 1

source_name: 24-year-old male, expanded BMSC, Passage 3

value: BMSC Donor 1 Day 0_rep 1


title: PN_24h_SplitGAL4_ID7_K9

description:
single cell
24h_PN_all.h5ad
Sample 264


title: PN_24h_SplitGAL4_ID7_L10

description:
single cell
24h_PN_all.h5ad
Sample 265


title: PN_24h_SplitGAL4_ID7_K6

description:
single cell
24h_PN_all.h5ad
Sample 261


title: PN_24h_SplitGAL4_ID7_K7

description:
single cell
24h_PN_all.h5ad
Sample 262


title: PN_24h_SplitGAL4_ID7_K5

description:
single cell
24h_PN_all.h5ad
Sample 260


title: PN_24h_SplitGAL4_ID7_K3

description:
single cell
24h_PN_all.h5ad
Sample 258


title: PN_24h_SplitGAL4_ID7_K2

description:
single cell
24h_PN_all.h5ad
Sample 257


title: PN_24h_SplitGAL4_ID7_K24

description:
single cell
24h_PN_all.h5ad
Sample 256


title: PN_24h_SplitGAL4_ID7_K23

description:
single cell
24h_PN_all.h5ad
Sample 255


title: PN_24h_SplitGAL4_ID7_L13

description:
single cell
24h_PN_all.h5ad
Sample 268


title: PN_24h_SplitGAL4_ID7_K20

description:
single cell
24h_PN_all.h5ad
Sample 252


title: PN_24h_SplitGAL4_ID7_K21

description:
single cell
24h_PN_all.h5ad
Sample 253


title: PN_24h_SplitGAL4_ID7_K1

description:
single cell
24h_PN_all.h5ad
Sample 251


title: PN_24h_SplitGAL4_ID7_K18

description:
single cell
24h_PN_all.h5ad
Sample 249


title: PN_24h_SplitGAL4_ID7_K17

description:
single cell
24h_PN_all.h5ad
Sample 248


title: PN_24h_SplitGAL4_ID7_K19

description:
single cell
24h_PN_all.h5ad
Sample 250


title: PN_24h_SplitGAL4_ID7_K14

description:
single cell
24h_PN_all.h5ad
Sample 245


title: PN_24h_SplitGAL4_ID7_K15

description:
single cell
24h_PN_all.h5ad
Sample 246


title: PN_24h_SplitGAL4_ID7_K13

description:
single cell
24h_PN_all.h5ad
Sample 244


title: PN_24h_SplitGAL4_ID7_K12

description:
single cell
24h_PN_all.h5ad
Sample 243


title: PN_24h_SplitGAL4_ID7_J9

description:
single cell
24h_PN_all.h5ad
Sample 240


title: PN_24h_SplitGAL4_ID7_J8

description:
single cell
24h_PN_all.h5ad
Sample 239


title: PN_24h_SplitGAL4_ID7_K11

description:
single cell
24h_PN_all.h5ad
Sample 242


title: PN_24h_SplitGAL4_ID7_J7

description:
single cell
24h_PN_all.h5ad
Sample 238


title: PN_24h_SplitGAL4_ID7_K4

description:
single cell
24h_PN_all.h5ad
Sample 259


title: PN_24h_SplitGAL4_ID7_J5

description:
single cell
24h_PN_all.h5ad
Sample 236


title: PN_24h_SplitGAL4_ID7_J24

description:
single cell
24h_PN_all.h5ad
Sample 232


title: PN_24h_SplitGAL4_ID7_J4

description:
single cell
24h_PN_all.h5ad
Sample 235


title: PN_24h_SplitGAL4_ID7_J3

description:
single cell
24h_PN_all.h5ad
Sample 234


title: PN_24h_SplitGAL4_ID7_J23

description:
single cell
24h_PN_all.h5ad
Sample 231


title: PN_24h_SplitGAL4_ID7_J22

description:
single cell
24h_PN_all.h5ad
Sample 230


title: PN_24h_SplitGAL4_ID7_J21

description:
single cell
24h_PN_all.h5ad
Sample 229


title: PN_24h_SplitGAL4_ID7_K8

description:
single cell
24h_PN_all.h5ad
Sample 263


title: PN_24h_SplitGAL4_ID7_K10

description:
single cell
24h_PN_all.h5ad
Sample 241


title: PN_24h_SplitGAL4_ID7_J2

description:
single cell
24h_PN_all.h5ad
Sample 233


title: PN_24h_SplitGAL4_ID7_J6

description:
single cell
24h_PN_all.h5ad
Sample 237


title: PN_24h_SplitGAL4_ID7_K22

description:
single cell
24h_PN_all.h5ad
Sample 254


title: PN_24h_SplitGAL4_ID7_J20

description:
single cell
24h_PN_all.h5ad
Sample 228


title: PN_24h_SplitGAL4_ID7_J19

description:
single cell
24h_PN_all.h5ad
Sample 226


title: PN_24h_SplitGAL4_ID7_J18

description:
single cell
24h_PN_all.h5ad
Sample 225


title: PN_24h_SplitGAL4_ID7_K16

description:
single cell
24h_PN_all.h5ad
Sample 247


title: PN_24h_SplitGAL4_ID7_J17

description:
single cell
24h_PN_all.h5ad
Sample 224


title: PN_24h_SplitGAL4_ID7_J16

description:
single cell
24h_PN_all.h5ad
Sample 223


title: PN_24h_SplitGAL4_ID7_J12

description:
single cell
24h_PN_all.h5ad
Sample 219


title: PN_24h_SplitGAL4_ID7_J15

description:
single cell
24h_PN_all.h5ad
Sample 222


title: PN_24h_SplitGAL4_ID7_J13

description:
single cell
24h_PN_all.h5ad
Sample 220


title: PN_24h_SplitGAL4_ID7_J11

description:
single cell
24h_PN_all.h5ad
Sample 218


title: PN_24h_SplitGAL4_ID7_I9

description:
single cell
24h_PN_all.h5ad
Sample 216


title: PN_24h_SplitGAL4_ID7_J10

description:
single cell
24h_PN_all.h5ad
Sample 217


title: PN_24h_SplitGAL4_ID7_J1

description:
single cell
24h_PN_all.h5ad
Sample 227


title: PN_24h_SplitGAL4_ID7_I20

description:
single cell
24h_PN_all.h5ad
Sample 204


title: PN_24h_SplitGAL4_ID7_I23

description:
single cell
24h_PN_all.h5ad
Sample 207


title: PN_24h_SplitGAL4_ID7_I3

description:
single cell
24h_PN_all.h5ad
Sample 210


title: PN_24h_SplitGAL4_ID7_I8

description:
single cell
24h_PN_all.h5ad
Sample 215


title: PN_24h_SplitGAL4_ID7_I6

description:
single cell
24h_PN_all.h5ad
Sample 213


title: PN_24h_SplitGAL4_ID7_I22

description:
single cell
24h_PN_all.h5ad
Sample 206


title: PN_24h_SplitGAL4_ID7_I17

description:
single cell
24h_PN_all.h5ad
Sample 200


title: PN_24h_SplitGAL4_ID7_I5

description:
single cell
24h_PN_all.h5ad
Sample 212


title: PN_24h_SplitGAL4_ID7_I7

description:
single cell
24h_PN_all.h5ad
Sample 214


title: PN_24h_SplitGAL4_ID7_I2

description:
single cell
24h_PN_all.h5ad
Sample 209


title: PN_24h_SplitGAL4_ID7_I21

description:
single cell
24h_PN_all.h5ad
Sample 205


title: PN_24h_SplitGAL4_ID7_I14

description:
single cell
24h_PN_all.h5ad
Sample 197


title: PN_24h_SplitGAL4_ID7_I24

description:
single cell
24h_PN_all.h5ad
Sample 208


title: PN_24h_SplitGAL4_ID7_I4

description:
single cell
24h_PN_all.h5ad
Sample 211


title: PN_24h_SplitGAL4_ID7_I16

description:
single cell
24h_PN_all.h5ad
Sample 199


title: PN_24h_SplitGAL4_ID7_I12

description:
single cell
24h_PN_all.h5ad
Sample 195


title: PN_24h_SplitGAL4_ID7_I10

description:
single cell
24h_PN_all.h5ad
Sample 193


title: PN_24h_SplitGAL4_ID7_I15

description:
single cell
24h_PN_all.h5ad
Sample 198


title: PN_24h_SplitGAL4_ID7_H9

description:
single cell
24h_PN_all.h5ad
Sample 192


title: PN_24h_SplitGAL4_ID7_I13

description:
single cell
24h_PN_all.h5ad
Sample 196


title: PN_24h_SplitGAL4_ID7_J14

description:
single cell
24h_PN_all.h5ad
Sample 221


title: PN_24h_SplitGAL4_ID7_H7

description:
single cell
24h_PN_all.h5ad
Sample 190


title: PN_24h_SplitGAL4_ID7_H6

description:
single cell
24h_PN_all.h5ad
Sample 189


title: PN_24h_SplitGAL4_ID7_H4

description:
single cell
24h_PN_all.h5ad
Sample 187


title: PN_24h_SplitGAL4_ID7_H8

description:
single cell
24h_PN_all.h5ad
Sample 191


title: PN_24h_SplitGAL4_ID7_H5

description:
single cell
24h_PN_all.h5ad
Sample 188


title: PN_24h_SplitGAL4_ID7_I19

description:
single cell
24h_PN_all.h5ad
Sample 202


title: PN_24h_SplitGAL4_ID7_I18

description:
single cell
24h_PN_all.h5ad
Sample 201


title: PN_24h_SplitGAL4_ID7_I1

description:
single cell
24h_PN_all.h5ad
Sample 203


title: PN_24h_SplitGAL4_ID7_I11

description:
single cell
24h_PN_all.h5ad
Sample 194


title: PN_24h_SplitGAL4_ID7_H3

description:
single cell
24h_PN_all.h5ad
Sample 186


title: PN_24h_SplitGAL4_ID7_H20

description:
single cell
24h_PN_all.h5ad
Sample 180


title: PN_24h_SplitGAL4_ID7_H22

description:
single cell
24h_PN_all.h5ad
Sample 182


title: PN_24h_SplitGAL4_ID7_H19

description:
single cell
24h_PN_all.h5ad
Sample 178


title: PN_24h_SplitGAL4_ID7_H15

description:
single cell
24h_PN_all.h5ad
Sample 174


title: PN_24h_SplitGAL4_ID7_H14

description:
single cell
24h_PN_all.h5ad
Sample 173


title: PN_24h_SplitGAL4_ID7_H18

description:
single cell
24h_PN_all.h5ad
Sample 177


title: PN_24h_SplitGAL4_ID7_H17

description:
single cell
24h_PN_all.h5ad
Sample 176


title: PN_24h_SplitGAL4_ID7_H1

description:
single cell
24h_PN_all.h5ad
Sample 179


title: PN_24h_SplitGAL4_ID7_H10

description:
single cell
24h_PN_all.h5ad
Sample 169


title: PN_24h_SplitGAL4_ID7_H21

description:
single cell
24h_PN_all.h5ad
Sample 181


title: PN_24h_SplitGAL4_ID7_H11

description:
single cell
24h_PN_all.h5ad
Sample 170


title: PN_24h_SplitGAL4_ID7_G6

description:
single cell
24h_PN_all.h5ad
Sample 165


title: PN_24h_SplitGAL4_ID7_G8

description:
single cell
24h_PN_all.h5ad
Sample 167


title: PN_24h_SplitGAL4_ID7_H12

description:
single cell
24h_PN_all.h5ad
Sample 171


title: PN_24h_SplitGAL4_ID7_H13

description:
single cell
24h_PN_all.h5ad
Sample 172


title: PN_24h_SplitGAL4_ID7_H24

description:
single cell
24h_PN_all.h5ad
Sample 184


title: PN_24h_SplitGAL4_ID7_G4

description:
single cell
24h_PN_all.h5ad
Sample 163


title: PN_24h_SplitGAL4_ID7_G3

description:
single cell
24h_PN_all.h5ad
Sample 162


title: PN_24h_SplitGAL4_ID7_H16

description:
single cell
24h_PN_all.h5ad
Sample 175


title: PN_24h_SplitGAL4_ID7_G2

description:
single cell
24h_PN_all.h5ad
Sample 161


title: PN_24h_SplitGAL4_ID7_H23

description:
single cell
24h_PN_all.h5ad
Sample 183


title: PN_24h_SplitGAL4_ID7_G24

description:
single cell
24h_PN_all.h5ad
Sample 160


title: PN_24h_SplitGAL4_ID7_G23

description:
single cell
24h_PN_all.h5ad
Sample 159


title: PN_24h_SplitGAL4_ID7_G22

description:
single cell
24h_PN_all.h5ad
Sample 158


title: PN_24h_SplitGAL4_ID7_G7

description:
single cell
24h_PN_all.h5ad
Sample 166


title: PN_24h_SplitGAL4_ID7_H2

description:
single cell
24h_PN_all.h5ad
Sample 185


title: PN_24h_SplitGAL4_ID7_G5

description:
single cell
24h_PN_all.h5ad
Sample 164


title: PN_24h_SplitGAL4_ID7_G21

description:
single cell
24h_PN_all.h5ad
Sample 157


title: PN_24h_SplitGAL4_ID7_G20

description:
single cell
24h_PN_all.h5ad
Sample 156


title: PN_24h_SplitGAL4_ID7_G9

description:
single cell
24h_PN_all.h5ad
Sample 168


title: PN_24h_SplitGAL4_ID7_G1

description:
single cell
24h_PN_all.h5ad
Sample 155


title: PN_24h_SplitGAL4_ID7_G18

description:
single cell
24h_PN_all.h5ad
Sample 153


title: PN_24h_SplitGAL4_ID7_G17

description:
single cell
24h_PN_all.h5ad
Sample 152


title: PN_24h_SplitGAL4_ID7_G16

description:
single cell
24h_PN_all.h5ad
Sample 151


title: PN_24h_SplitGAL4_ID7_G15

description:
single cell
24h_PN_all.h5ad
Sample 150


title: PN_24h_SplitGAL4_ID7_G14

description:
single cell
24h_PN_all.h5ad
Sample 149


title: PN_24h_SplitGAL4_ID7_G19

description:
single cell
24h_PN_all.h5ad
Sample 154


title: PN_24h_SplitGAL4_ID7_G13

description:
single cell
24h_PN_all.h5ad
Sample 148


title: PN_24h_SplitGAL4_ID7_G12

description:
single cell
24h_PN_all.h5ad
Sample 147


title: PN_24h_SplitGAL4_ID7_F8

description:
single cell
24h_PN_all.h5ad
Sample 143


title: PN_24h_SplitGAL4_ID7_F9

description:
single cell
24h_PN_all.h5ad
Sample 144


title: PN_24h_SplitGAL4_ID7_G10

description:
single cell
24h_PN_all.h5ad
Sample 145


title: PN_24h_SplitGAL4_ID7_F7

description:
single cell
24h_PN_all.h5ad
Sample 142


title: PN_24h_SplitGAL4_ID7_F6

description:
single cell
24h_PN_all.h5ad
Sample 141


title: PN_24h_SplitGAL4_ID7_F5

description:
single cell
24h_PN_all.h5ad
Sample 140


title: PN_24h_SplitGAL4_ID7_G11

description:
single cell
24h_PN_all.h5ad
Sample 146


title: PN_24h_SplitGAL4_ID7_F3

description:
single cell
24h_PN_all.h5ad
Sample 138


title: PN_24h_SplitGAL4_ID7_F24

description:
single cell
24h_PN_all.h5ad
Sample 136


title: PN_24h_SplitGAL4_ID7_F23

description:
single cell
24h_PN_all.h5ad
Sample 135


title: PN_24h_SplitGAL4_ID7_F4

description:
single cell
24h_PN_all.h5ad
Sample 139


title: PN_24h_SplitGAL4_ID7_F20

description:
single cell
24h_PN_all.h5ad
Sample 132


title: PN_24h_SplitGAL4_ID7_F21

description:
single cell
24h_PN_all.h5ad
Sample 133


title: PN_24h_SplitGAL4_ID7_F19

description:
single cell
24h_PN_all.h5ad
Sample 130


title: PN_24h_SplitGAL4_ID7_F2

description:
single cell
24h_PN_all.h5ad
Sample 137


title: PN_24h_SplitGAL4_ID7_F22

description:
single cell
24h_PN_all.h5ad
Sample 134


title: PN_24h_SplitGAL4_ID7_F1

description:
single cell
24h_PN_all.h5ad
Sample 131


title: PN_24h_SplitGAL4_ID7_F17

description:
single cell
24h_PN_all.h5ad
Sample 128


title: PN_24h_SplitGAL4_ID7_F16

description:
single cell
24h_PN_all.h5ad
Sample 127


title: PN_24h_SplitGAL4_ID7_F15

description:
single cell
24h_PN_all.h5ad
Sample 126


title: PN_24h_SplitGAL4_ID7_F14

description:
single cell
24h_PN_all.h5ad
Sample 125


title: PN_24h_SplitGAL4_ID7_F12

description:
single cell
24h_PN_all.h5ad
Sample 123


title: PN_24h_SplitGAL4_ID7_F11

description:
single cell
24h_PN_all.h5ad
Sample 122


title: PN_24h_SplitGAL4_ID7_E7

description:
single cell
24h_PN_all.h5ad
Sample 118


title: PN_24h_SplitGAL4_ID7_E8

description:
single cell
24h_PN_all.h5ad
Sample 119


title: PN_24h_SplitGAL4_ID7_F10

description:
single cell
24h_PN_all.h5ad
Sample 121


title: PN_24h_SplitGAL4_ID7_E4

description:
single cell
24h_PN_all.h5ad
Sample 115


title: PN_24h_SplitGAL4_ID7_E5

description:
single cell
24h_PN_all.h5ad
Sample 116


title: PN_24h_SplitGAL4_ID7_E2

description:
single cell
24h_PN_all.h5ad
Sample 113


title: PN_24h_SplitGAL4_ID7_E24

description:
single cell
24h_PN_all.h5ad
Sample 112


title: PN_24h_SplitGAL4_ID7_E23

description:
single cell
24h_PN_all.h5ad
Sample 111


title: PN_24h_SplitGAL4_ID7_E22

description:
single cell
24h_PN_all.h5ad
Sample 110


title: PN_24h_SplitGAL4_ID7_E20

description:
single cell
24h_PN_all.h5ad
Sample 108


title: PN_24h_SplitGAL4_ID7_E21

description:
single cell
24h_PN_all.h5ad
Sample 109


title: PN_24h_SplitGAL4_ID7_F18

description:
single cell
24h_PN_all.h5ad
Sample 129


title: PN_24h_SplitGAL4_ID7_E17

description:
single cell
24h_PN_all.h5ad
Sample 104


title: PN_24h_SplitGAL4_ID7_E1

description:
single cell
24h_PN_all.h5ad
Sample 107


title: PN_24h_SplitGAL4_ID7_E19

description:
single cell
24h_PN_all.h5ad
Sample 106


title: PN_24h_SplitGAL4_ID7_E18

description:
single cell
24h_PN_all.h5ad
Sample 105


title: PN_24h_SplitGAL4_ID7_E13

description:
single cell
24h_PN_all.h5ad
Sample 100


title: PN_24h_SplitGAL4_ID7_E14

description:
single cell
24h_PN_all.h5ad
Sample 101


title: PN_24h_SplitGAL4_ID7_E12

description:
single cell
24h_PN_all.h5ad
Sample 99


title: PN_24h_SplitGAL4_ID7_E15

description:
single cell
24h_PN_all.h5ad
Sample 102


title: PN_24h_SplitGAL4_ID7_E16

description:
single cell
24h_PN_all.h5ad
Sample 103


title: PN_24h_SplitGAL4_ID7_E11

description:
single cell
24h_PN_all.h5ad
Sample 98


title: PN_24h_SplitGAL4_ID7_E10

description:
single cell
24h_PN_all.h5ad
Sample 97


title: PN_24h_SplitGAL4_ID7_F13

description:
single cell
24h_PN_all.h5ad
Sample 124


title: PN_24h_SplitGAL4_ID7_D9

description:
single cell
24h_PN_all.h5ad
Sample 96


title: PN_24h_SplitGAL4_ID7_E6

description:
single cell
24h_PN_all.h5ad
Sample 117


title: PN_24h_SplitGAL4_ID7_D8

description:
single cell
24h_PN_all.h5ad
Sample 95


title: PN_24h_SplitGAL4_ID7_E9

description:
single cell
24h_PN_all.h5ad
Sample 120


title: PN_24h_SplitGAL4_ID7_E3

description:
single cell
24h_PN_all.h5ad
Sample 114


title: PN_24h_SplitGAL4_ID7_D6

description:
single cell
24h_PN_all.h5ad
Sample 93


title: PN_24h_SplitGAL4_ID7_D4

description:
single cell
24h_PN_all.h5ad
Sample 91


title: PN_24h_SplitGAL4_ID7_D5

description:
single cell
24h_PN_all.h5ad
Sample 92


title: PN_24h_SplitGAL4_ID7_D24

description:
single cell
24h_PN_all.h5ad
Sample 88


title: PN_24h_SplitGAL4_ID7_D2

description:
single cell
24h_PN_all.h5ad
Sample 89


title: PN_24h_SplitGAL4_ID7_D21

description:
single cell
24h_PN_all.h5ad
Sample 85


title: PN_24h_SplitGAL4_ID7_D22

description:
single cell
24h_PN_all.h5ad
Sample 86


title: PN_24h_SplitGAL4_ID7_D20

description:
single cell
24h_PN_all.h5ad
Sample 84


title: PN_24h_SplitGAL4_ID7_D18

description:
single cell
24h_PN_all.h5ad
Sample 81


title: PN_24h_SplitGAL4_ID7_D17

description:
single cell
24h_PN_all.h5ad
Sample 80


title: PN_24h_SplitGAL4_ID7_D15

description:
single cell
24h_PN_all.h5ad
Sample 78


title: PN_24h_SplitGAL4_ID7_D16

description:
single cell
24h_PN_all.h5ad
Sample 79


title: PN_24h_SplitGAL4_ID7_D11

description:
single cell
24h_PN_all.h5ad
Sample 74


title: PN_24h_SplitGAL4_ID7_D19

description:
single cell
24h_PN_all.h5ad
Sample 82


title: PN_24h_SplitGAL4_ID7_C7

description:
single cell
24h_PN_all.h5ad
Sample 70


title: PN_24h_SplitGAL4_ID7_C9

description:
single cell
24h_PN_all.h5ad
Sample 72


title: PN_24h_SplitGAL4_ID7_C24

description:
single cell
24h_PN_all.h5ad
Sample 64


title: PN_24h_SplitGAL4_ID7_C2

description:
single cell
24h_PN_all.h5ad
Sample 65


title: PN_24h_SplitGAL4_ID7_C23

description:
single cell
24h_PN_all.h5ad
Sample 63


title: PN_24h_SplitGAL4_ID7_D7

description:
single cell
24h_PN_all.h5ad
Sample 94


title: PN_24h_SplitGAL4_ID7_D10

description:
single cell
24h_PN_all.h5ad
Sample 73


title: PN_24h_SplitGAL4_ID7_D12

description:
single cell
24h_PN_all.h5ad
Sample 75


title: PN_24h_SplitGAL4_ID7_C3

description:
single cell
24h_PN_all.h5ad
Sample 66


title: PN_24h_SplitGAL4_ID7_D13

description:
single cell
24h_PN_all.h5ad
Sample 76


title: PN_24h_SplitGAL4_ID7_D14

description:
single cell
24h_PN_all.h5ad
Sample 77


title: PN_24h_SplitGAL4_ID7_C5

description:
single cell
24h_PN_all.h5ad
Sample 68


title: PN_24h_SplitGAL4_ID7_C22

description:
single cell
24h_PN_all.h5ad
Sample 62


title: PN_24h_SplitGAL4_ID7_C18

description:
single cell
24h_PN_all.h5ad
Sample 57


title: PN_24h_SplitGAL4_ID7_D3

description:
single cell
24h_PN_all.h5ad
Sample 90


title: PN_24h_SplitGAL4_ID7_C4

description:
single cell
24h_PN_all.h5ad
Sample 67


title: PN_24h_SplitGAL4_ID7_D1

description:
single cell
24h_PN_all.h5ad
Sample 83


title: PN_24h_SplitGAL4_ID7_C21

description:
single cell
24h_PN_all.h5ad
Sample 61


title: PN_24h_SplitGAL4_ID7_D23

description:
single cell
24h_PN_all.h5ad
Sample 87


title: PN_24h_SplitGAL4_ID7_C8

description:
single cell
24h_PN_all.h5ad
Sample 71


title: PN_24h_SplitGAL4_ID7_C6

description:
single cell
24h_PN_all.h5ad
Sample 69


title: PN_24h_SplitGAL4_ID7_C20

description:
single cell
24h_PN_all.h5ad
Sample 60


title: PN_24h_SplitGAL4_ID7_C1

description:
single cell
24h_PN_all.h5ad
Sample 59


title: PN_24h_SplitGAL4_ID7_C16

description:
single cell
24h_PN_all.h5ad
Sample 55


title: PN_24h_SplitGAL4_ID7_C19

description:
single cell
24h_PN_all.h5ad
Sample 58


title: PN_24h_SplitGAL4_ID7_C14

description:
single cell
24h_PN_all.h5ad
Sample 53


title: PN_24h_SplitGAL4_ID7_C12

description:
single cell
24h_PN_all.h5ad
Sample 51


title: PN_24h_SplitGAL4_ID7_C17

description:
single cell
24h_PN_all.h5ad
Sample 56


title: PN_24h_SplitGAL4_ID7_C13

description:
single cell
24h_PN_all.h5ad
Sample 52


title: PN_24h_SplitGAL4_ID7_C15

description:
single cell
24h_PN_all.h5ad
Sample 54


title: PN_24h_SplitGAL4_ID7_C11

description:
single cell
24h_PN_all.h5ad
Sample 50


title: PN_24h_SplitGAL4_ID7_C10

description:
single cell
24h_PN_all.h5ad
Sample 49


title: PN_24h_SplitGAL4_ID7_B8

description:
single cell
24h_PN_all.h5ad
Sample 47


title: PN_24h_SplitGAL4_ID7_B9

description:
single cell
24h_PN_all.h5ad
Sample 48


title: PN_24h_SplitGAL4_ID7_B3

description:
single cell
24h_PN_all.h5ad
Sample 42


title: PN_24h_SplitGAL4_ID7_B21

description:
single cell
24h_PN_all.h5ad
Sample 37


title: PN_24h_SplitGAL4_ID7_B2

description:
single cell
24h_PN_all.h5ad
Sample 41


title: PN_24h_SplitGAL4_ID7_B23

description:
single cell
24h_PN_all.h5ad
Sample 39


title: PN_24h_SplitGAL4_ID7_B24

description:
single cell
24h_PN_all.h5ad
Sample 40


title: PN_24h_SplitGAL4_ID7_B20

description:
single cell
24h_PN_all.h5ad
Sample 36


title: PN_24h_SplitGAL4_ID7_B4

description:
single cell
24h_PN_all.h5ad
Sample 43


title: PN_24h_SplitGAL4_ID7_B6

description:
single cell
24h_PN_all.h5ad
Sample 45


title: PN_24h_SplitGAL4_ID7_B1

description:
single cell
24h_PN_all.h5ad
Sample 35


title: PN_24h_SplitGAL4_ID7_B15

description:
single cell
24h_PN_all.h5ad
Sample 30


title: PN_24h_SplitGAL4_ID7_B17

description:
single cell
24h_PN_all.h5ad
Sample 32


title: PN_24h_SplitGAL4_ID7_B19

description:
single cell
24h_PN_all.h5ad
Sample 34


title: PN_24h_SplitGAL4_ID7_B5

description:
single cell
24h_PN_all.h5ad
Sample 44


title: PN_24h_SplitGAL4_ID7_B16

description:
single cell
24h_PN_all.h5ad
Sample 31


title: PN_24h_SplitGAL4_ID7_B12

description:
single cell
24h_PN_all.h5ad
Sample 27


title: PN_24h_SplitGAL4_ID7_B14

description:
single cell
24h_PN_all.h5ad
Sample 29


title: PN_24h_SplitGAL4_ID7_B11

description:
single cell
24h_PN_all.h5ad
Sample 26


title: PN_24h_SplitGAL4_ID7_B10

description:
single cell
24h_PN_all.h5ad
Sample 25


title: PN_24h_SplitGAL4_ID7_A9

description:
single cell
24h_PN_all.h5ad
Sample 24


title: PN_24h_SplitGAL4_ID7_A8

description:
single cell
24h_PN_all.h5ad
Sample 23


title: PN_24h_SplitGAL4_ID7_A6

description:
single cell
24h_PN_all.h5ad
Sample 21


title: PN_24h_SplitGAL4_ID7_A5

description:
single cell
24h_PN_all.h5ad
Sample 20


title: PN_24h_SplitGAL4_ID7_B7

description:
single cell
24h_PN_all.h5ad
Sample 46


title: PN_24h_SplitGAL4_ID7_A4

description:
single cell
24h_PN_all.h5ad
Sample 19


title: PN_24h_SplitGAL4_ID7_B22

description:
single cell
24h_PN_all.h5ad
Sample 38


title: PN_24h_SplitGAL4_ID7_A3

description:
single cell
24h_PN_all.h5ad
Sample 18


title: PN_24h_SplitGAL4_ID7_B18

description:
single cell
24h_PN_all.h5ad
Sample 33


title: PN_24h_SplitGAL4_ID7_A2

description:
single cell
24h_PN_all.h5ad
Sample 17


title: PN_24h_SplitGAL4_ID7_A24

description:
single cell
24h_PN_all.h5ad
Sample 16


title: PN_24h_SplitGAL4_ID7_A22

description:
single cell
24h_PN_all.h5ad
Sample 14


title: PN_24h_SplitGAL4_ID7_A21

description:
single cell
24h_PN_all.h5ad
Sample 13


title: PN_24h_SplitGAL4_ID7_A23

description:
single cell
24h_PN_all.h5ad
Sample 15


title: PN_24h_SplitGAL4_ID7_B13

description:
single cell
24h_PN_all.h5ad
Sample 28


title: PN_24h_SplitGAL4_ID7_A20

description:
single cell
24h_PN_all.h5ad
Sample 12


title: PN_24h_SplitGAL4_ID7_A17

description:
single cell
24h_PN_all.h5ad
Sample 8


title: PN_24h_SplitGAL4_ID7_A19

description:
single cell
24h_PN_all.h5ad
Sample 10


title: PN_24h_SplitGAL4_ID7_A18

description:
single cell
24h_PN_all.h5ad
Sample 9


title: PN_24h_SplitGAL4_ID7_A16

description:
single cell
24h_PN_all.h5ad
Sample 7


title: PN_24h_SplitGAL4_ID7_A7

description:
single cell
24h_PN_all.h5ad
Sample 22


title: PN_24h_SplitGAL4_ID7_A15

description:
single cell
24h_PN_all.h5ad
Sample 6


title: PN_24h_SplitGAL4_ID7_A13

description:
single cell
24h_PN_all.h5ad
Sample 4


title: PN_24h_SplitGAL4_ID7_A14

description:
single cell
24h_PN_all.h5ad
Sample 5


title: PN_24h_SplitGAL4_ID7_A12

description:
single cell
24h_PN_all.h5ad
Sample 3


title: PN_24h_SplitGAL4_ID7_A10

description:
single cell
24h_PN_all.h5ad
Sample 1


title: PN_24h_SplitGAL4_ID7_A1

description:
single cell
24h_PN_all.h5ad
Sample 11


title: PN_24h_SplitGAL4_ID7_A11

description:
single cell
24h_PN_all.h5ad
Sample 2


title: MCI-NC_114

type: RNA

city: Obu

first: Daichi

last: Shigemizu

state: Aichi

address: 7-430 Morioka-cho

country: Japan

institute: National Center for Geriatrics and Gerontology

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.)

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: diagnosis

value: MCI-NC

tag: age

tag: Sex

value: female

tag: day


title: OA3_LJ

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description: Gene Expression data from osteoarthritis synovial biopsy

hyb_protocol: GeneChip Human Genome U133 Plus 2.0 arrays were hybridized overnight at 45°C with 10 μg fragmented biotinylated cRNA. The slides were then washed and stained using a EukGE‐WS2v5 fluidics protocol on a GeneChip Fluidics Station 450.

scan_protocol: The slides were scanned on a GeneChip Scanner 3000 (Affymetrix).

data_processing: Analyses of the microarray data were performed using GeneSpring GX software (Agilent). Fluorescence intensity data were normalized using robust multiarray analysis.

label: biotin

source_name: OA synovium large joint

label_protocol: Complementary RNA (cRNA) was synthesized from 100 ng total RNA, and biotin-labelled according to a standard Affymetrix procedure (GeneChip 3′ IVT Plus).

extract_protocol: Total RNA was extracted from the synovial biopsies using a NucleoSpin RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips.

treatment_protocol: Ten patients with active RA were included in the study. All patients met the ACR/EULAR 2010 RA classification criteria. For each patient, synovial biopsies were obtained the same day from a swollen small (metacarpo-phalangeal joint or wrist) and a large (knee) joint, using a US-guided biopsy procedure in small joints and needle-arthroscopy in large joints. 6 to 10 synovial biopsy fragments were obtained from each joint. Half of them were stored at -80°C after overnight incubation in RNA-Later solution (Invitrogen). The other half was fixed overnight in 10% formalin buffer at pH 7.0 and embedded in paraffin for histologic and immunohistochemistry analyses. Synovial biopsies from the knee of 4 osteoarthritis (OA) patients were used as control for the transcriptomic studies.

value: synovial tissue

value: osteoarthritis

tag: joint size

value: large joint

tag: gender

value: M

tag: acpa/rf positivity

tag: crp (mg/l)


title: MCI-NC_112


title: OA1_LJ

value: F


title: RA10_SJ

description: Gene Expression data from rheumatoid arthritis synovial biopsy

source_name: RA synovium small joint

value: rheumatoid arthritis (RA)

value: small joint

value: Y


title: OA4_LJ


title: RA9_SJ

value: N


title: MCI-NC_111


title: MCI-NC_110


title: MCI-NC_113

value: male


title: RA7_SJ


title: RA8_SJ


title: RA4_LJ

source_name: RA synovium large joint


title: RA7_LJ


title: RA6_LJ


title: RA8_LJ


title: RA10_LJ


title: RA9_LJ


title: RA5_LJ


title: OA2_LJ


title: RA3_SJ


title: RA5_SJ


title: RA2_LJ


title: RA6_SJ


title: MCI-NC_108


title: MCI-NC_109


title: MCI-NC_107


title: MCI-NC_104


title: MCI-NC_102


title: MCI-NC_105


title: RA3_LJ


title: MCI-NC_103


title: MCI-NC_106


title: MCI-NC_098


title: RA2_SJ


title: MCI-NC_096


title: MCI-NC_101


title: RA4_SJ


title: MCI-NC_100


title: MCI-NC_099


title: Epidermis-young-rep5

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Epidermis from young group

hyb_protocol: The prepared targets were hybridized to Affymetrix Human U133 Plus 2.0 arrays.

scan_protocol: Arrays were scanned with Affymetrix GeneChip Scanner 3000 7G.

data_processing: Affymetrix Expression Console software was used to obtain MAS5 normalized values.

source_name: Epidermis, young

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted from skin samples with RNA iso (Takara Bio, Shiga, Japan).

value: Epidermis

tag: age group

value: Young


title: Epidermis-young-rep1

description: Epidermis from young group


title: MCI-NC_097


title: RA1_SJ


title: Epidermis-young-rep4

description: Epidermis from young group


title: Epidermis-young-rep2

description: Epidermis from young group


title: MCI-NC_093


title: MCI-NC_094


title: Dermis-young-rep5

description: Dermis from young group

source_name: Dermis, young

value: Dermis


title: Dermis-young-rep1

description: Dermis from young group


title: Epidermis-young-rep3

description: Epidermis from young group


title: Dermis-young-rep2

description: Dermis from young group


title: Dermis-young-rep4

description: Dermis from young group


title: MCI-NC_090


title: MCI-NC_089


title: Dermis-young-rep3

description: Dermis from young group


title: MCI-NC_091


title: MCI-NC_092


title: MCI-NC_087


title: MCI-NC_095


title: GEX_BU-TM-16

city: jacksonville

last: Zhao

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
The single cell sequence preprocessing was performed using the standard10X Genomics Cell Ranger Single Cell Software Suite v.3.0.0.
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering and differential expression analyses were performed using Seurat v.3.1.
Genome_build: mm10
Supplementary_files_format_and_content: matrix files

organism: Mus musculus

source_name: cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P) (Cat#130-092-628, Myltenyi Biotec) at 37˚C in the gentleMACS™ Octo Dissociator with Heaters (Myltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat#130-096-733, Myltenyi Biotec) followed by the red blood cell lysis (Cat#130-094-183, Myltenyi Biotec) and dead cell removal (Cat#130-090-101, Myltenyi Biotec) according to the manufacturer’s instructions. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
Single-cell RNA-seq (scRNAseq) was performed on the isolated cortical samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3′ gene expression (3′ GEX) V3 kit, using a targeted input of ~ 6,000 to 9,000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina, San Diego, CA) targeting a depth of 25,000–50,000 reads per cell.

treatment_protocol: Mice were treated with tamoxifen to induce TREM2 expression in microglia. The control mice were given vehicle (corn oil).

tag: background strain

value: TREM2-R47H+/+; Cx3cr1CreER/+

value: Induced


title: GEX_BU-TM-12


title: GEX_BU-TM-8


title: MCI-NC_088

value: MCI-NC


title: Epidermis-old-rep4

description: Epidermis from old group

source_name: Epidermis, old

value: Old


title: MCI-NC_084


title: MCI-NC_086


title: MCI-NC_085


title: Epidermis-old-rep3

description: Epidermis from old group


title: MCI-NC_083

value: female


title: MCI-NC_082


title: MCI-NC_080


title: MCI-NC_081


title: MCI-NC_079


title: GEX_BU-TM-11

value: Control


title: GEX_BU-TM-15


title: GEX_BU-TM-4


title: Epidermis-old-rep1

description: Epidermis from old group


title: Epidermis-old-rep5

description: Epidermis from old group


title: GEX_BU-TM-7


title: Dermis-old-rep5

description: Dermis from old group

source_name: Dermis, old


title: Dermis-old-rep3

description: Dermis from old group


title: Dermis-old-rep2

description: Dermis from old group


title: MCI-NC_078


title: MCI-NC_077


title: Dermis-old-rep4

description: Dermis from old group


title: Dermis-old-rep1

description: Dermis from old group


title: Epidermis-old-rep2

description: Epidermis from old group


title: GEX_BU-TM-14

value: TREM2-WT+/+; Cx3cr1CreER/+


title: GEX_BU-TM-3


title: GEX_BU-TM-10


title: GEX_BU-TM-13


title: GEX_BU-TM-2


title: GEX_BU-TM-5


title: GEX_BU-TM-6


title: BU-FTM-20

treatment_protocol: Mice were treated with tamoxifen at two months of age to induce TREM2 expression in microglia. The control mice were given vehicle (corn oil).

value: 5xFAD+/-;TREM2-R47H+/+; Cx3cr1CreER/+


title: MCI-NC_072


title: BU-FTM-24


title: MCI-NC_070


title: MCI-NC_074


title: MCI-NC_071


title: MCI-NC_075


title: BU-FTM-16


title: MCI-NC_076


title: MCI-NC_073


title: BU-FTM-12


title: MCI-NC_069


title: MCI-NC_068


title: BU-FTM-8


title: MCI-NC_067


title: GEX_BU-TM-9


title: BU-FTM-4


title: GEX_BU-TM-1


title: MCI-NC_063


title: MCI-NC_065


title: MCI-NC_062


title: BU-FTM-23


title: BU-FTM-19


title: BU-FTM-15


title: BU-FTM-11


title: BU-FTM-7


title: MCI-NC_066


title: BU-FTM-22

value: 5xFAD+/-;TREM2-WT+/+; Cx3cr1CreER/+


title: BU-FTM-18


title: MCI-NC_064


title: MCI-NC_056


title: MCI-NC_059


title: MCI-NC_061


title: MCI-NC_055


title: MCI-NC_058


title: BU-FTM-10


title: MCI-NC_060


title: MCI-NC_053


title: MCI-NC_054


title: BU-FTM-6


title: RA1_LJ

value: synovial tissue

value: rheumatoid arthritis (RA)

value: large joint

value: F


title: MCI-NC_052


title: MCI-NC_051

value: male


title: NC

city: Daqing

first: Xuecang

last: Li

address: 39 Xinyang Road

country: China

institute: School of Medical Informatics, Daqing Campus, Harbin Medical University

description: circRNAs and coding genes from control group in the HepG2 cells

hyb_protocol: Assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set hybridization rotator to rotate at 10 rpm. Hybridize at 65°C for 17 hours. Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2505C)

data_processing: The data were analyzed using Agilent Feature Extraction (FE) Software

source_name: NC in HepG2

label_protocol: Elute the cleaned cRNA sample by transferring the RNeasy column to 1.5 mL collection tube. Add appropriate RNase-free water directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm. RNeasy Mini Kit (Qiagen p/n 74104)

growth_protocol: Tissues between 0.5 and 250mg should be immersed in liquid nitrogen within 15 minutes to cool down rapidly. Tissues with small volume transported by liquid nitrogen are preserved with RNA later and transported on dry ice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Incubate samples in a circulating water bath at 40°C for 2 hours

tag: cell line

tag: genotype/variation

value: control


title: siFOXA1

description: circRNAs and coding genes from siFOXA1 in the HepG2 cells

source_name: siFOXA1 in HepG2


title: BU-FTM-2

tag: genotype


title: BU-FTM-21


title: BU-FTM-17


title: BU-FTM-14


title: BU-FTM-13


title: BU-FTM-9


title: BU-FTM-5


title: BU-FTM-3


title: MCI-NC_057


title: BU-FTM-1


title: GEX_BU-EFTM-20

treatment_protocol: Mice were treated with tamoxifen at birth to induce TREM2 expression in microglia. The control mice were given vehicle (corn oil).


title: MCI-NC_050


title: MCI-NC_047


title: MCI-NC_049


title: MCI-NC_048


title: MCI-NC_046


title: GEX_BU-EFTM-24


title: GEX_BU-EFTM-8


title: MCI-NC_045


title: GEX_BU-EFTM-12


title: MCI-NC_043


title: MCI-NC_044


title: N2 OP50

city: Tainan

first: Cheng-Rung

last: Huang

address: University Road

country: Taiwan

institute: National Cheng Kung University

data_processing:
Basecalls performed using Illumina GA Pipeline v1.3
Raw reads produced from sequencing machines contain dirty reads which contain adapters, unknown or low quality bases. These data will negatively affect following bioinformatics analysis. Therefore, dirty raw reads are discarded.
Reads after filtering dirty raw reads, on which all following analysis are based.
The calculation of Unigene expression uses RPKM method (Reads Per kb per Million reads) (Mortazavi, Williams et al. 2008)
Genome_build: ce6
Supplementary_files_format_and_content: xls files include RPKM values for each Sample

organism: Caenorhabditis elegans

source_name: N2 WT C. elegans whole cells

extract_protocol:
All worms were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: wild type

value: fed with OP50 for 6 hr


title: GEX_BU-EFTM-16


title: MCI-NC_040


title: MCI-NC_041


title: MCI-NC_042


title: N2 EDL933

value: fed with EDL933 for 6 hr


title: GEX_BU-EFTM-23


title: GEX_BU-EFTM-4

value: Induced


title: MCI-NC_039

value: MCI-NC


title: GEX_BU-EFTM-19


title: GEX_BU-EFTM-15


title: GEX_BU-EFTM-11


title: 9m-2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

library_source: genomic

data_processing:
Reduced alignment index generated using BSSeeker2 v2.1.8 with the following parameters; --aligner=bowtie2 -r -l 40 -u 500 -c C-CGG
Trimmed fastq files aligned using BSSeeker2 v2.1.8 using the following parameters; --aligner=bowtie2 --bt2--end-to-end --bt2-p 16 -r --low=40 --up=500 -f bam
Methylation values were called for methylat from alignments using BSSeeker2 v2.1.8 using the default parameters;
Genome_build: rn6
Supplementary_files_format_and_content: CGmap methylation call files; tab separated text file;  (1) chromosome (2) nucleotide on Watson (+) strand (3) position (4) context (CG/CHG/CHH) (5) dinucleotide-context (CA/CC/CG/CT) (6) methylation-level = #_of_C / (#_of_C + #_of_T) (7) #_of_C (8) = #_of_C + #_of_T (

molecule: genomic DNA

organism: Rattus norvegicus

source_name: whole blood

extract_protocol:
500ul of whole blood was collected via retro-orbital bleedings into heparinized tubes, spun, and the plasma removed. Buffy coat and red blood cells were frozen at -80 degrees C until DNA extraction. Following proteinase K and RNAse A treatments, DNA was isolated from rat blood cells using QIAmp DNA Mini Kit following manufacturer’s instructions using a QIAcube automated device. DNA was eluted from columns in 200 µL of AE buffer, concentrated in 20 µL 10 mM Tris-HCl, pH 8.5, 0.1 mM EDTA using Genomic DNA Clean & Concentrator-10, and quantified using a Qubit 2.0.
100ng of DNA isolated from whole blood was digested with MspI restriction enzyme (NEB, Ipswich, MA, USA), carried out end-repair/adenylation (NEB) and ligation with TruSeq barcoded adapters (Illumina, San Diego, CA, USA). DNA fragments of size range 200-300bp were selected with SPRI magnetic beads (ABM, Richmond, BC, CA), followed by bisulfite treatment (Millipore, Billerica, MA, USA), and PCR amplification (Bioline, Taunton, MA, USA). Libraries were sequenced by multiplexing 8 libraries per lane on the Illumina HiSeq2500 sequencer, with 100bp single end reads.

tag: age (months)


title: 13m-1


title: 22m-1


title: 24m-3


title: 14m-2


title: 12m-6


title: 16m-1


title: MCI-NC_038


title: MCI-NC_036


title: 4m-2


title: 15m-1


title: MCI-NC_035


title: MCI-NC_034


title: GEX_BU-EFTM-7


title: GEX_BU-EFTM-3


title: 8m-1


title: 14m-5


title: 12m-3


title: 20m-1


title: GEX_BU-EFTM-22


title: MCI-NC_037


title: MCI-NC_033


title: 7m-5


title: 4m-5


title: GEX_BU-EFTM-18


title: 21m-3


title: MCI-NC_031


title: 22m-4


title: 19m-1


title: 23m-1


title: GEX_BU-EFTM-10


title: 26m-3


title: GEX_BU-EFTM-6


title: MCI-NC_030


title: MCI-NC_029


title: GEX_BU-EFTM-2


title: MCI-NC_032


title: MCI-NC_028


title: 21m-2


title: 11m-2


title: 11m-1


title: 1m-6


title: 8m-4


title: 22m-5


title: GEX_BU-EFTM-21


title: GEX_BU-EFTM-17


title: MCI-NC_026


title: 19m-2


title: MCI-NC_025


title: GEX_BU-EFTM-14


title: GEX_BU-EFTM-13


title: 2m-2


title: 20m-2


title: 20m-5


title: GEX_BU-EFTM-9


title: 7m-4


title: 10m-3


title: 15m-3


title: MCI-NC_027


title: GEX_BU-EFTM-5


title: 5m-2


title: 27m-1


title: 12m-5


title: MCI-NC_022


title: GEX_BU-EFTM-1


title: MCI-NC_023


title: TREM-17

data_processing:
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-Seq analytic pipeline: MAP-RSeq Version 3.0 (Kalari et al., 2014).
Reads were mapped to the mouse reference genome mm10 using STAR v.2.5.2b using default settings (Dobin et al., 2013). The gene counts were generated using FeatureCounts v.1.5.1 (Liao et al., 2014) with the gene definitions files from Ensembl v78. Quality checks after alignment was done using RSeqQC v.3.0.0 (Wang et al., 2012).
Conditional Quantile Normalization (CQN) was performed on the raw gene counts to correct for gene length differences, GC bias, global technical variations, and to obtain similar quantile-by-quantile distributions of gene expression levels across samples (Hansen et al., 2012). Based on the bi-modal distribution of the CQN normalized and log2-transformed reads per kb per million (RPKM) gene expression values, genes with average log2 RPKM >= 1 in at least one group were considered expressed. Using this selection threshold, 18,100 genes were included in the downstream analysis.
Sample TREM-17 was revealed as outlier by Principal Component Analysis (PCA), and was subsequently removed from downstream analyses.
Genome_build: mm10
Supplementary_files_format_and_content: .txt file of raw gene counts

extract_protocol:
Total RNA was extracted from the cortex using Trizol reagent and cleaned using RNeasy spin columns with DNase treatment to remove contaminating genomic DNA.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions, employing poly-A mRNA enrichment using oligo-dT magnetic beads


title: 18m-6


title: 9m-4


title: TREM-15


title: MCI-NC_024


title: 19m-3


title: MCI-NC_021


title: MCI-NC_019


title: 6m-3


title: 4m-3


title: 24m-6


title: 20m-6


title: TREM-14


title: MCI-NC_018


title: MCI-NC_020


title: TREM-12


title: MCI-NC_017


title: TREM-2


title: MCI-NC_015


title: 5m-4


title: 26m-2


title: 5m-5


title: 26m-1


title: TREM-23

value: TREM2-R47H+/+; Cx3cr1CreER/+


title: 7m-3


title: TREM-13


title: MCI-NC_014


title: TREM-22


title: TREM-20


title: 24m-4


title: 13m-3


title: TREM-6


title: 17m-3


title: 21m-6


title: 10m-1


title: TREM-19


title: 2m-1


title: MCI-NC_012

value: female


title: 2m-4


title: MCI-NC_016


title: MCI-NC_011


title: 14m-3


title: TREM-9


title: 25m-6


title: TREM-5

value: Control


title: 8m-6


title: MCI-NC_010


title: 26m-5


title: MCI-NC_013


title: MCI-NC_009


title: MCI-NC_008


title: 10m-6


title: 6m-1


title: TREM-3

value: TREM2-WT+/+; Cx3cr1CreER/+