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  • Cell clustering and visualization

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    Bang Tran
    16 views15 pages
    This document contains t-SNE plots of cell types from three different single cell RNA sequencing datasets: biase_cell_type1, deng_cell_type1, and deng_cell_type2. Each plot shows cell clusters of different cell types, developmental stages, or experimental conditions.

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    Original Title

    tSNE_PINS_SC3_SINCERA_SEURAT.pdf

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    This document contains t-SNE plots of cell types from three different single cell RNA sequencing datasets: biase_cell_type1, deng_cell_type1, and deng_cell_type2. Each plot shows cell clusters of different cell types, developmental stages, or experimental conditions.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    16 views15 pages

    Cell clustering and visualization

    Uploaded by

    Bang Tran
    This document contains t-SNE plots of cell types from three different single cell RNA sequencing datasets: biase_cell_type1, deng_cell_type1, and deng_cell_type2. Each plot shows cell clusters of different cell types, developmental stages, or experimental conditions.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    of 15

    biase_cell_type1

    20 20
    20

    0 0

    tSNE2

    tSNE2
    0
    tSNE2

    −20 −20 −20

    −10 −5 0 5 10 15 −10 −5 0 5 10 15 −10 −5 0 5 10 15


    tSNE1 tSNE1 tSNE1

    original 2cell 4cell zygote pins1 1 2 3 pins2 1 2 3

    20 20 20

    0
    tSNE2

    0 0
    tSNE2

    tSNE2
    −20
    −20 −20

    −10 −5 0 5 10 15
    −10 −5 0 5 10 15 tSNE1 −10 −5 0 5 10 15
    tSNE1 tSNE1
    1 3 5 7
    sincera
    sc3 1 2 3 2 4 6 seurat 0 1
    deng_cell_type1

    25 25
    25

    tSNE2
    0
    tSNE2

    tSNE2
    0 0

    −25 −25
    −25

    −50 −50
    −20 −10 0 10 20 30 −50 −20 −10 0 10 20 30
    tSNE1 −20 −10 0 10 20 30 tSNE1
    tSNE1
    16cell 4cell blast 1−1 2−1 3−1
    original pins2
    2cell 8cell zygote pins1 1 2 3 1−2 2−2 3−2

    25 25 25
    tSNE2

    0
    tSNE2

    tSNE2
    0 0

    −25
    −25 −25

    −50
    −20 −10 0 10 20 30 −50 −50
    tSNE1 −20 −10 0 10 20 30 −20 −10 0 10 20 30
    tSNE1 tSNE1
    1 3 5
    sc3
    2 4 6 sincera 1 2 3 4 seurat 0 1 2 3
    deng_cell_type2

    25 25
    25

    tSNE2
    0
    tSNE2

    tSNE2
    0 0

    −25 −25
    −25

    −50 −50
    −20 −10 0 10 20 30 −50 −20 −10 0 10 20 30
    tSNE1 −20 −10 0 10 20 30 tSNE1
    tSNE1
    16cell 8cell earlyblast lateblast midblast 1−1 2−1 3−1
    original pins2
    4cell early2cell late2cell mid2cell zy pins1 1 2 3 1−2 2−2 3−2

    25 25 25
    tSNE2

    0
    tSNE2

    tSNE2
    0 0

    −25
    −25 −25

    −50
    −20 −10 0 10 20 30 −50 −50
    tSNE1 −20 −10 0 10 20 30 −20 −10 0 10 20 30
    tSNE1 tSNE1
    1 3 5
    sc3
    2 4 6 sincera 1 2 3 4 seurat 0 1 2 3
    goolam_cell_type1

    20 20
    20

    10 10
    10

    tSNE2

    tSNE2
    tSNE2

    0 0
    0

    −10 −10
    −10

    −20 −20 −20

    −10 0 10 −10 0 10 −10 0 10


    tSNE1 tSNE1 tSNE1

    original 16cell 2cell 4cell 8cell blast pins1 1 2 pins2 1 2−1 2−2

    20
    20 20

    10
    10 10
    tSNE2

    0
    tSNE2

    tSNE2
    0 0
    −10

    −10 −10
    −20

    −20 −20
    −10 0 10
    tSNE1
    −10 0 10 −10 0 10
    tSNE1 1 12 2 5 8 tSNE1
    sincera 10 13 3 6 9
    sc3 1 2 11 14 4 7 seurat 0 1 2 3
    klein_cell_type1 60 60
    60

    30 30
    30

    tSNE2
    tSNE2
    tSNE2

    0
    0
    0

    −30
    −30 −30

    −25 0 25 50
    −25 0 25 50 −25 0 25 50 tSNE1
    tSNE1 tSNE1
    1−1 1−3 2−2 2−4
    pins2
    original d0 d2 d4 d7 pins1 1 2 1−2 2−1 2−3

    60 60 60

    30
    tSNE2
    30 0
    30

    −30
    tSNE2

    tSNE2
    0
    −25 0 25 50 0
    tSNE1

    −30 1 18 26 34 42
    10 19 27 35 43 −30
    11 2 28 36 44
    12 20 29 37 5
    −25 0 25 50
    tSNE1 sincera 13 21 3 38 6
    −25 0 25 50
    14 22 30 39 7 tSNE1
    1 12 3 6 9 15 23 31 4 8
    sc3 10 13 4 7 16 24 32 40 9 0 2 4 6 8
    seurat
    11 2 5 8 17 25 33 41 1 3 5 7 9
    kolodziejczyk_cell_type1
    40 40
    40

    20 20
    20

    tSNE2

    tSNE2
    tSNE2

    0 0
    0

    −20 −20 −20

    −40 −20 0 20 −40 −20 0 20 −40 −20 0 20


    tSNE1 tSNE1 tSNE1

    original 2i a2i lif pins1 1 2 pins2 1−1 1−2 2−1 2−2

    40 40 40

    20
    20
    20
    tSNE2

    tSNE2
    tSNE2

    0
    0
    0

    −20
    −20
    −20
    −40 −20 0 20
    tSNE1 −40 −20 0 20
    −40 −20 0 20 tSNE1
    tSNE1 1 12 15 4 7
    sincera 10 13 2 5 8 0 2 4 6
    seurat
    sc3 1 2 3 4 5 11 14 3 6 9 1 3 5
    patel_cell_type1

    20
    20
    20

    tSNE2
    0

    tSNE2
    tSNE2

    0
    0

    −20

    −20 −20

    −20 0 20
    tSNE1
    −20 0 20 −20 0 20
    tSNE1 tSNE1 1−1 2−2 3−2 3−5 5−1
    pins2 1−2 2−3 3−3 4−1 5−2
    original MGH26 MGH28 MGH29 MGH30 MGH31 pins1 1 2 3 4 5 2−1 3−1 3−4 4−2

    20 20 20
    tSNE2

    tSNE2

    tSNE2
    0
    0

    −20
    −20
    −20

    −20 0 20
    tSNE1 −20 0 20
    tSNE1 −20 0 20
    1 13 17 4 8 tSNE1
    10 14 18 5 9 1 2 5 8
    sc3
    11 15 2 6 sincera 10 3 6 9 0 2 4
    seurat
    12 16 3 7 11 4 7 1 3 5
    pollen_cell_type1

    20 20
    20
    tSNE2

    tSNE2
    tSNE2
    0 0
    0

    −20
    −20
    −20

    −20 0 20 40
    tSNE1 −20 0 20 40
    −20 0 20 40 tSNE1
    2338 GW16 hiPSC Kera tSNE1
    original 2339 GW21 HL60 NPC 1−1 1−3 1−5 2−2
    pins2
    BJ GW21+3 K562 pins1 1 2 1−2 1−4 2−1

    20 20 20
    tSNE2
    tSNE2

    tSNE2
    0
    0 0

    −20
    −20 −20

    −20 0 20 40
    −20 0 20 40 tSNE1 −20 0 20 40
    tSNE1 tSNE1
    1 2 5 8
    1 2 4 6 8 sincera 10 3 6 9 0 2 4
    sc3 seurat
    10 3 5 7 9 11 4 7 1 3 5
    pollen_cell_type2

    20 20
    20

    tSNE2
    tSNE2
    tSNE2

    0
    0
    0

    −20
    −20 −20

    −20 0 20 40
    −20 0 20 40 −20 0 20 40 tSNE1
    tSNE1 tSNE1
    1−1 1−3 1−5 2−2
    pins2
    original blood dermal neural pluripotent pins1 1 2 1−2 1−4 2−1

    20 20 20
    tSNE2
    tSNE2

    tSNE2
    0
    0 0

    −20
    −20 −20

    −20 0 20 40
    −20 0 20 40 tSNE1 −20 0 20 40
    tSNE1 tSNE1
    1 2 5 8
    1 2 4 6 8 sincera 10 3 6 9 0 2 4
    sc3 seurat
    10 3 5 7 9 11 4 7 1 3 5
    treutlein_cell_type1

    2.5 2.5
    2.5

    tSNE2

    tSNE2
    0.0 0.0
    tSNE2

    0.0

    −2.5 −2.5 −2.5

    −5.0 −5.0 −5.0

    −6 −3 0 3 −6 −3 0 3 −6 −3 0 3
    tSNE1 tSNE1 tSNE1

    original AT1 AT2 BP ciliated Clara pins1 1 2 3 pins2 1−1 1−2 2−1 2−2 3

    2.5
    tSNE2 2.5 2.5

    0.0
    tSNE2

    tSNE2
    0.0 0.0

    −2.5
    −2.5 −2.5

    −5.0
    −5.0 −6 −3 0 3 −5.0

    −6 −3 0 3 tSNE1 −6 −3 0 3
    tSNE1 tSNE1
    1 3 5 7
    sincera
    sc3 1 2 3 2 4 6 8 seurat 0 1
    usoskin_cell_type1

    20 20
    20

    tSNE2

    tSNE2
    0 0
    tSNE2

    −20 −20 −20

    −25 0 25 −25 0 25 −25 0 25


    tSNE1 tSNE1 tSNE1

    original NF NP PEP TH pins1 1 2 pins2 1−1 1−2 1−3 2−1 2−2

    20
    20 20
    tSNE2

    0
    tSNE2

    tSNE2
    0 0

    −20

    −20 −20
    −25 0 25
    tSNE1

    1 14 19 23 7
    −25 0 25 −25 0 25
    tSNE1 10 15 2 3 8 tSNE1
    sincera 11 16 20 4 9
    1 3 5 7 9 12 17 21 5 0 2 4 6
    sc3 seurat
    2 4 6 8 13 18 22 6 1 3 5
    usoskin_cell_type2

    20 20
    20
    tSNE2

    tSNE2

    tSNE2
    0 0 0

    −20
    −20 −20

    −25 0 25
    tSNE1 −25 0 25 −25 0 25
    tSNE1 tSNE1
    NF1 NF4/5 NP2 PEP2
    original
    NF2/3 NP1 PEP1 TH pins1 1 2 pins2 1−1 1−2 1−3 2−1 2−2

    20
    20 20
    tSNE2

    0
    tSNE2

    tSNE2
    0 0

    −20

    −20 −20
    −25 0 25
    tSNE1

    1 14 19 23 7
    −25 0 25 −25 0 25
    tSNE1 10 15 2 3 8 tSNE1
    sincera 11 16 20 4 9
    1 3 5 7 9 12 17 21 5 0 2 4 6
    sc3 seurat
    2 4 6 8 13 18 22 6 1 3 5
    yan_cell_type1 15 15
    15

    10 10
    10

    5 5 5
    tSNE2

    tSNE2

    tSNE2
    0 0 0

    −5
    −5 −5

    −10
    −10 −10

    −20 −10 0 10 20 30
    tSNE1 −20 −10 0 10 20 30 −20 −10 0 10 20 30
    tSNE1 tSNE1
    16cell 4cell blast
    original
    2cell 8cell zygote pins1 1 2 pins2 1 2−1 2−2

    15 15 15

    10 10 10

    5
    5 5
    tSNE2
    tSNE2

    tSNE2
    0
    0 0

    −5
    −5 −5

    −10
    −10 −10

    −20 −10 0 10 20 30
    −20 −10 0 10 20 30 tSNE1 −20 −10 0 10 20 30
    tSNE1 tSNE1
    1 3 5 7
    sincera
    sc3 1 2 3 2 4 6 seurat 0 1 2 3
    yan_cell_type2 15 15
    15

    10 10
    10

    5 5 5
    tSNE2

    tSNE2

    tSNE2
    0 0 0

    −5
    −5 −5

    −10
    −10 −10

    −20 −10 0 10 20 30
    tSNE1 −20 −10 0 10 20 30 −20 −10 0 10 20 30
    tSNE1 tSNE1
    2cell 8cell morula zygote
    original
    4cell lateblast oocyte pins1 1 2 pins2 1 2−1 2−2

    15 15 15

    10 10 10

    5
    5 5
    tSNE2
    tSNE2

    tSNE2
    0
    0 0

    −5
    −5 −5

    −10
    −10 −10

    −20 −10 0 10 20 30
    −20 −10 0 10 20 30 tSNE1 −20 −10 0 10 20 30
    tSNE1 tSNE1
    1 3 5 7
    sincera
    sc3 1 2 3 2 4 6 seurat 0 1 2 3
    zeisel_cell_type1

    30 30
    30
    tSNE2

    tSNE2

    tSNE2
    0 0 0

    −30
    −30 −30

    −50 −25 0 25 50
    tSNE1 −50 −25 0 25 50 −50 −25 0 25 50
    tSNE1 tSNE1
    astrocytes endothelial interneurons mural s1pyramidal
    al
    ca1pyramidal ependymal microglia oligodendrocytes pins1 1 2 3 4 5 pins2 1−1 1−2 2−1 2−2

    30
    30
    30
    tSNE2

    tSNE2
    0
    tSNE2

    −30
    0

    −30
    −50 −25 0 25 50
    tSNE1 −30

    1 16 22 29 35
    −50 −25 0 25 50
    10 17 23 3 4 tSNE1
    11 18 24 30 5
    −50 −25 0 25 50
    sc3 12 19 25 31 6 tSNE1 0 12 2 6
    13 2 26 32 7 1 13 3 7
    seurat
    14 20 27 33 8 1 3 5 7 10 14 4 8
    sincera
    15 21 28 34 9 2 4 6 8 11 15 5 9

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