title: 1001700609_F11

value: CGGAGCCT-TAGAGTCTAG


title: 1001700609_C9

status: Public on Feb 27 2018

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
bcl2fastq demux
STAR mapping
Htseq-count 0.7+ gene counting
Stampy virus mapping
Custom script for filtering virus reads
Genome_build: grch38
Supplementary_files_format_and_content: One TSV for each sample containing the counts of gene expression.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human hepatoma (Huh7) cells were obtained from Apath LLC (Brooklyn, NY). Cells were grown in DMEM (Mediatech, Manassas, VA) supplemented with 10% FBS (Omega Scientific, INC, Tarzana, CA), nonessential amino acid, 1% l-glutamine, and 1% penicillin-streptomycin (ThermoFisher Scientific, Waltham, MA) and maintained in a humidified incubator with 5% CO2 at 37°C. C6/36 cells were obtained from ATCC (ATCC CRL-1660, Manassas, VA) and grown in Leibovitz’s L-15 media (Mediatech, Manassas, VA) supplemented with 10% FBS (Omega Scientific, INC, Tarzana, CA, USA) and 1% HEPES (ThermoFisher Scientific, Waltham, MA) in a humidified chamber at 28°C and 0% CO2. Cell lines identity was confirmed via phenotypic studies (low grade infection with hepatitis C virus (Huh7); syncytia formation upon DENV infection (C6/36) (Corner and Ng 1987)). Cells were tested negative for mycoplasma by the MycoAlert mycoplasma detection kit (Lonza, Morristown, NJ).

extract_protocol:
No extraction, single cells are sorted into 0.4ul lysis buffer
Cells are lysed in lysis buffer containing Triton X-100, then RT using template switching oligo and preamplification for 21 cycles as in SmartSeq2 is performed. Cells with different levels of intracellular virus are cherry picked and sequencing libraries are made using illumina’s Nextera XT kit.

treatment_protocol: Infection with dengue or Zika virus.

tag: cell line

tag: barcode

tag: experiment

tag: virus

value: dengue

tag: time[h]

tag: moi

tag: index

value: GGAGCTAC-TCTCCGCTAG

tag: virus-qpcr


title: 1001700609_C20

value: GCGTAGTA-GACTAGCTAG


title: 1001700609_E12

value: GCGTAGTA-TCTCCGCTAG


title: 1001700609_C4

value: GGAGCTAC-TCTAATCTAG


title: 1001700609_E19

value: CGGAGCCT-GACTAGCTAG


title: 1001700609_E7

value: GCGTAGTA-GGCTATCTAG


title: 1001700609_E17

value: CGGAGCCT-CTCTATCTAG


title: 1001700609_D21

value: GCGTAGTA-ATTAAGCTAG


title: 1001700609_D20

value: GCGTAGTA-GGAGTACTAG


title: 1001700609_D18

value: GCGTAGTA-GTAAGACTAG


title: 1001700609_E9

value: GCGTAGTA-TCTAATCTAG


title: 1001700609_C21

value: GCGTAGTA-TCCTCTCTAG


title: 1001700609_C13

value: GGAGCTAC-ATGCGACTAG


title: 1001700609_D2

value: GCGTAGTA-AAGGAGCTAG


title: 1001700609_B22

value: GGAGCTAC-AAGCCTCTAG


title: 1001700609_D14

value: GCGTAGTA-TGCATACTAG


title: 1001700609_D8

value: dengue

value: GCGTAGTA-TAGAGTCTAG


title: 1001700609_C22

value: GCGTAGTA-CTAGCTCTAG


title: 1001700609_C16

value: GCGTAGTA-CTCTATCTAG


title: 1001700609_C7

value: GGAGCTAC-GCCTTACTAG


title: 1001700609_B15

value: GGAGCTAC-ATTAAGCTAG


title: 1001700609_B6

value: GGAGCTAC-GTAAGACTAG


title: 1001700609_A17

value: GGAGCTAC-AAGGAGCTAG


title: 1001700609_C3

value: GGAGCTAC-GGCTATCTAG


title: 1001700609_A11

value: GGAGCTAC-GACTAGCTAG


title: 1001700609_A16

value: GGAGCTAC-CTAGCTCTAG


title: 1001700609_A21

value: GGAGCTAC-TAGAGTCTAG


title: 1001700609_A22

value: GGAGCTAC-TGCATACTAG


title: 1001700609_B12

value: GGAGCTAC-GGAGTACTAG


title: 1001700609_A14

value: GGAGCTAC-TCCTCTCTAG


title: 1001700609_A6

value: ACTCGCTA-TCTCCGCTAG


title: 1001700609_A3

value: ACTCGCTA-TCTAATCTAG


title: 1001700608_P15

value: dengue

value: ACTCGCTA-TGCATACTAG


title: 1001700609_A1

value: ACTCGCTA-AAGCCTCTAG


title: 1001700609_A7

value: ACTCGCTA-ATGCGACTAG


title: 1001700608_P21

value: ACTCGCTA-ATTAAGCTAG


title: 1001700609_A9

value: GGAGCTAC-CTCTATCTAG


title: 1001700608_P19

value: ACTCGCTA-GGAGTACTAG


title: 1001700608_P4

value: ATCTCAGG-ATGCGACTAG


title: 1001700608_P11

value: ACTCGCTA-AAGGAGCTAG


title: 1001700608_P6

value: ACTCGCTA-GACTAGCTAG


title: 1001700608_P5

value: ACTCGCTA-CTCTATCTAG


title: 1001700608_P8

value: ACTCGCTA-CTAGCTCTAG


title: 1001700608_O10

value: ATCTCAGG-GGAGTACTAG


title: 1001700608_P14

value: ACTCGCTA-TAGAGTCTAG


title: 1001700609_A2

value: ACTCGCTA-GGCTATCTAG


title: 1001700608_P7

value: ACTCGCTA-TCCTCTCTAG


title: 1001700608_O22

value: ATCTCAGG-TCTCCGCTAG


title: 1001700608_O8

value: dengue

value: ATCTCAGG-GTAAGACTAG


title: 1001700608_O15

value: ATCTCAGG-AAGCCTCTAG


title: 1001700608_P17

value: ACTCGCTA-GTAAGACTAG


title: 1001700608_O2

value: ATCTCAGG-TAGAGTCTAG


title: 1001700608_O17

value: ATCTCAGG-GGCTATCTAG


title: 1001700608_N18

value: ATCTCAGG-CTAGCTCTAG


title: 1001700608_N13

value: ATCTCAGG-CTCTATCTAG


title: 1001700608_O19

value: ATCTCAGG-TCTAATCTAG


title: 1001700608_N9

value: GCTCATGA-GCCTTACTAG


title: 1001700608_O20

value: ATCTCAGG-GCCTTACTAG


title: 1001700608_M15

value: GCTCATGA-ATTAAGCTAG


title: 1001700608_M13

value: GCTCATGA-GGAGTACTAG


title: 1001700608_N14

value: ATCTCAGG-GACTAGCTAG


title: 1001700608_M9

value: GCTCATGA-TAGAGTCTAG


title: 1001700608_M2

value: GCTCATGA-TCCTCTCTAG


title: 1001700608_O4

value: ATCTCAGG-TGCATACTAG


title: 1001700608_N6

value: dengue

value: GCTCATGA-TCTAATCTAG


title: 1001700608_O12

value: ATCTCAGG-ATTAAGCTAG


title: 1001700609_A4

value: ACTCGCTA-GCCTTACTAG


title: 1001700608_N11

value: GCTCATGA-TCTCCGCTAG


title: 1001700608_M18

value: GCTCATGA-AAGCCTCTAG


title: 1001700608_L1

value: GTAGAGGA-GGCTATCTAG


title: 1001700608_L8

value: GTAGAGGA-TCTAATCTAG


title: 1001700608_K20

value: GTAGAGGA-AAGCCTCTAG


title: 1001700608_K17

value: GTAGAGGA-GGAGTACTAG


title: 1001700608_K18

value: GTAGAGGA-ATTAAGCTAG


title: 1001700608_N12

value: GCTCATGA-ATGCGACTAG


title: 1001700608_M4

value: GCTCATGA-CTAGCTCTAG


title: 1001700608_N19

value: ATCTCAGG-AAGGAGCTAG


title: 1001700608_N16

value: ATCTCAGG-TCCTCTCTAG


title: 1001700608_L17

value: GCTCATGA-CTCTATCTAG


title: 1001700608_M20

value: GCTCATGA-GGCTATCTAG


title: 1001700608_L10

value: dengue

value: GTAGAGGA-GCCTTACTAG


title: 1001700608_J18

value: AAGAGGCA-TCTCCGCTAG


title: 1001700608_L14

value: GTAGAGGA-TCTCCGCTAG


title: 1001700608_J19

value: AAGAGGCA-ATGCGACTAG


title: 1001700608_J10

value: AAGAGGCA-GGCTATCTAG


title: 1001700608_L16

value: GTAGAGGA-ATGCGACTAG


title: 1001700608_K15

value: GTAGAGGA-GTAAGACTAG


title: 1001700608_K12

value: GTAGAGGA-TAGAGTCTAG


title: 1001700608_J11

value: AAGAGGCA-TCTAATCTAG


title: 1001700608_I12

value: AAGAGGCA-GTAAGACTAG


title: 1001700608_L19

value: GCTCATGA-GACTAGCTAG


title: 1001700608_M10

value: GCTCATGA-TGCATACTAG


title: 1001700608_M12

value: GCTCATGA-GTAAGACTAG


title: 1001700608_M7

value: GCTCATGA-AAGGAGCTAG


title: 1001700608_J21

value: GTAGAGGA-CTCTATCTAG


title: 1001700608_K2

value: GTAGAGGA-GACTAGCTAG


title: 1001700608_K9

value: dengue

value: GTAGAGGA-CTAGCTCTAG


title: 1001700608_J14

value: AAGAGGCA-GCCTTACTAG


title: 1001700608_K10

value: GTAGAGGA-AAGGAGCTAG


title: 1001700608_H17

value: AAGAGGCA-GACTAGCTAG


title: 1001700608_H3

value: CGAGGCTG-GCCTTACTAG


title: 1001700608_K4

value: GTAGAGGA-TCCTCTCTAG


title: 1001700608_K14

value: GTAGAGGA-TGCATACTAG


title: 1001700608_G21

value: CGAGGCTG-TCTAATCTAG


title: 1001700608_I1

value: AAGAGGCA-CTAGCTCTAG


title: 1001700608_I4

value: AAGAGGCA-TAGAGTCTAG


title: 1001700608_I2

value: AAGAGGCA-AAGGAGCTAG


title: 1001700608_G19

value: CGAGGCTG-GGCTATCTAG


title: 1001700608_G2

value: CGAGGCTG-TAGAGTCTAG


title: 1001700608_G10

value: CGAGGCTG-GTAAGACTAG


title: 1001700608_I20

value: AAGAGGCA-ATTAAGCTAG


title: 1001700608_H15

value: CGAGGCTG-ATGCGACTAG


title: 1001700608_F9

value: dengue

value: CGAGGCTG-GACTAGCTAG


title: 1001700608_G1

value: CGAGGCTG-AAGGAGCTAG


title: 1001700608_F16

value: CGAGGCTG-CTAGCTCTAG


title: 1001700608_H16

value: AAGAGGCA-CTCTATCTAG


title: 1001700608_I16

value: AAGAGGCA-GGAGTACTAG


title: 1001700608_H19

value: AAGAGGCA-TCCTCTCTAG


title: 1001700608_G14

value: CGAGGCTG-AAGCCTCTAG


title: 1001700608_I11

value: AAGAGGCA-TGCATACTAG


title: 1001700608_G13

value: CGAGGCTG-ATTAAGCTAG


title: 1001700608_F12

value: CGAGGCTG-TCCTCTCTAG


title: 1001700608_E17

value: CTCTCTAC-GGCTATCTAG


title: 1001700608_E11

value: CTCTCTAC-ATTAAGCTAG


title: 1001700608_F2

value: CTCTCTAC-TCTCCGCTAG


title: 1001700608_F6

value: CTCTCTAC-ATGCGACTAG


title: 1001700608_E19

value: CTCTCTAC-TCTAATCTAG


title: 1001700608_E3

value: CTCTCTAC-TGCATACTAG


title: 1001700608_J3

value: dengue

value: AAGAGGCA-AAGCCTCTAG


title: 1001700608_F8

value: CGAGGCTG-CTCTATCTAG


title: 1001700608_G5

value: CGAGGCTG-TGCATACTAG


title: 1001700608_D16

value: CTCTCTAC-TCCTCTCTAG


title: 1001700608_D13

value: CTCTCTAC-GACTAGCTAG


title: 1001700608_D8

value: TAGGCATG-ATGCGACTAG


title: 1001700608_E8

value: CTCTCTAC-GGAGTACTAG


title: 1001700608_C15

value: TAGGCATG-AAGCCTCTAG


title: 1001700608_E20

value: CTCTCTAC-GCCTTACTAG


title: 1001700608_G11

value: CGAGGCTG-GGAGTACTAG


title: 1001700608_E2

value: CTCTCTAC-TAGAGTCTAG


title: 1001700608_D17

value: CTCTCTAC-CTAGCTCTAG


title: 1001700608_C6

value: TAGGCATG-GGAGTACTAG


title: 1001700608_E14

value: CTCTCTAC-AAGCCTCTAG


title: 1001700608_D12

value: CTCTCTAC-CTCTATCTAG


title: 1001700608_B13

value: TAGGCATG-AAGGAGCTAG


title: 1001700608_H13

value: dengue

value: CGAGGCTG-TCTCCGCTAG


title: 1001700608_B11

value: TAGGCATG-TCCTCTCTAG


title: 1001700608_E1

value: CTCTCTAC-AAGGAGCTAG


title: 1001700608_D7

value: TAGGCATG-TCTCCGCTAG


title: 1001700608_C18

value: TAGGCATG-GGCTATCTAG


title: 1001700608_B8

value: TAGGCATG-GACTAGCTAG


title: 1001700608_B5

value: TAGGCATG-CTCTATCTAG


title: 1001700608_E4

value: CTCTCTAC-GTAAGACTAG


title: 1001700608_C4

value: TAGGCATG-GTAAGACTAG


title: 1001700607_P22

value: GGACTCCT-ATGCGACTAG


title: 1001700607_P14

value: GGACTCCT-TCTCCGCTAG


title: 1001700608_D6

value: TAGGCATG-GCCTTACTAG


title: 1001700608_C3

value: TAGGCATG-TGCATACTAG


title: 1001700607_P6

value: GGACTCCT-AAGCCTCTAG


title: 1001700608_B17

value: TAGGCATG-TAGAGTCTAG


title: 1001700607_P8

value: GGACTCCT-GGCTATCTAG


title: 1001700607_P12

value: dengue

value: GGACTCCT-GCCTTACTAG


title: 1001700608_C20

value: TAGGCATG-TCTAATCTAG


title: 1001700607_O21

value: GGACTCCT-ATTAAGCTAG


title: 1001700608_B12

value: TAGGCATG-CTAGCTCTAG


title: 1001700607_N14

value: GGACTCCT-TAGAGTCTAG


title: 1001700607_N12

value: GGACTCCT-AAGGAGCTAG


title: 1001700608_C10

value: TAGGCATG-ATTAAGCTAG


title: 1001700607_P10

value: GGACTCCT-TCTAATCTAG


title: 1001700607_N3

value: GGACTCCT-TCCTCTCTAG


title: 1001700607_M17

value: GGACTCCT-CTCTATCTAG


title: 1001700607_M20

value: GGACTCCT-GACTAGCTAG


title: 1001700607_M16

value: TCCTGAGC-ATGCGACTAG


title: 1001700607_N10

value: GGACTCCT-CTAGCTCTAG


title: 1001700607_L14

value: TCCTGAGC-AAGCCTCTAG


title: 1001700607_O10

value: GGACTCCT-GTAAGACTAG


title: 1001700607_L11

value: TCCTGAGC-GGAGTACTAG


title: 1001700607_L7

value: dengue

value: TCCTGAGC-TGCATACTAG


title: 1001700607_L16

value: TCCTGAGC-GGCTATCTAG


title: 1001700607_L13

value: TCCTGAGC-ATTAAGCTAG


title: 1001700607_O17

value: GGACTCCT-GGAGTACTAG


title: 1001700607_M9

value: TCCTGAGC-TCTCCGCTAG


title: 1001700607_L8

value: TCCTGAGC-GTAAGACTAG


title: 1001700607_M3

value: TCCTGAGC-GCCTTACTAG


title: 1001700607_K20

value: TCCTGAGC-TAGAGTCTAG


title: 1001700607_O7

value: GGACTCCT-TGCATACTAG


title: 1001700607_K15

value: TCCTGAGC-CTAGCTCTAG


title: 1001700607_K5

value: TCCTGAGC-CTCTATCTAG


title: 1001700607_J22

value: AGGCAGAA-TCTCCGCTAG


title: 1001700607_J7

value: AGGCAGAA-AAGCCTCTAG


title: 1001700607_J1

value: AGGCAGAA-ATTAAGCTAG


title: 1001700607_J13

value: AGGCAGAA-TCTAATCTAG


title: 1001700607_I21

value: AGGCAGAA-GGAGTACTAG


title: 1001700607_K9

value: dengue

value: TCCTGAGC-GACTAGCTAG


title: 1001700607_K3

value: AGGCAGAA-ATGCGACTAG


title: 1001700607_L19

value: TCCTGAGC-TCTAATCTAG


title: 1001700607_I16

value: AGGCAGAA-TGCATACTAG


title: 1001700607_I11

value: AGGCAGAA-AAGGAGCTAG


title: 1001700607_I14

value: AGGCAGAA-TAGAGTCTAG


title: 1001700607_J17

value: AGGCAGAA-GCCTTACTAG


title: 1001700607_J11

value: AGGCAGAA-GGCTATCTAG


title: 1001700607_H7

value: CGTACTAG-TCTCCGCTAG


title: 1001700607_I19

value: AGGCAGAA-GTAAGACTAG


title: 1001700607_G6

value: CGTACTAG-AAGCCTCTAG


title: 1001700607_G21

value: CGTACTAG-TCTAATCTAG


title: 1001700607_I9

value: AGGCAGAA-CTAGCTCTAG


title: 1001700607_H12

value: CGTACTAG-ATGCGACTAG


title: 1001700607_F22

value: CGTACTAG-GTAAGACTAG


title: 1001700607_G1

value: CGTACTAG-GGAGTACTAG


title: 1001700607_K18

value: dengue

value: TCCTGAGC-AAGGAGCTAG


title: 1001700607_F9

value: CGTACTAG-TGCATACTAG


title: 1001700607_K12

value: TCCTGAGC-TCCTCTCTAG


title: 1001700607_H5

value: CGTACTAG-GCCTTACTAG


title: 1001700607_D4

value: TAAGGCGA-TCTCCGCTAG


title: 1001700607_D8

value: TAAGGCGA-ATGCGACTAG


title: 1001700607_I3

value: AGGCAGAA-TCCTCTCTAG


title: 1001700607_G3

value: CGTACTAG-ATTAAGCTAG


title: 1001700607_H17

value: AGGCAGAA-CTCTATCTAG


title: 1001700607_C14

value: TAAGGCGA-GGCTATCTAG


title: 1001700607_E16

value: CGTACTAG-TCCTCTCTAG


title: 1001700607_G15

value: CGTACTAG-GGCTATCTAG


title: 1001700607_B18

value: TAAGGCGA-GGAGTACTAG


title: 1001700607_H20

value: AGGCAGAA-GACTAGCTAG


title: 1001700607_B9

value: TAAGGCGA-TGCATACTAG


title: 1001700607_C20

value: TAAGGCGA-TCTAATCTAG


title: 1001700607_B3

value: dengue

value: TAAGGCGA-AAGGAGCTAG


title: 1001700607_F2

value: CGTACTAG-AAGGAGCTAG


title: 1001700607_E10

value: CGTACTAG-GACTAGCTAG


title: 1001700607_A11

value: TAAGGCGA-GACTAGCTAG


title: 1001700607_F6

value: CGTACTAG-TAGAGTCTAG


title: 1001700607_C8

value: TAAGGCGA-ATTAAGCTAG


title: 1001700606_P19

value: CCTAAGAC-AAGCCTTGCA


title: 1001700607_D1

value: TAAGGCGA-GCCTTACTAG


title: 1001700607_B12

value: TAAGGCGA-GTAAGACTAG


title: 1001700607_E20

value: CGTACTAG-CTAGCTCTAG


title: 1001700607_D18

value: CGTACTAG-CTCTATCTAG


title: 1001700607_A14

value: TAAGGCGA-TCCTCTCTAG


title: 1001700606_P4

value: CCTAAGAC-AAGGAGTGCA


title: 1001700607_B6

value: TAAGGCGA-TAGAGTCTAG


title: 1001700607_A20

value: TAAGGCGA-CTAGCTCTAG


title: 1001700606_O20

value: CCTAAGAC-CTAGCTTGCA


title: 1001700606_P12

value: dengue

value: CCTAAGAC-GGAGTATGCA


title: 1001700607_A5

value: TAAGGCGA-CTCTATCTAG


title: 1001700607_C13

value: TAAGGCGA-AAGCCTCTAG


title: 1001700606_O5

value: ACTGAGCG-TCTCCGTGCA


title: 1001700606_O8

value: ACTGAGCG-ATGCGATGCA


title: 1001700606_P9

value: CCTAAGAC-TGCATATGCA


title: 1001700606_P5

value: CCTAAGAC-TAGAGTTGCA


title: 1001700606_O11

value: CCTAAGAC-CTCTATTGCA


title: 1001700606_O17

value: CCTAAGAC-TCCTCTTGCA


title: 1001700606_P10

value: CCTAAGAC-GTAAGATGCA


title: 1001700606_N11

value: ACTGAGCG-GGAGTATGCA


title: 1001700606_P18

value: CCTAAGAC-ATTAAGTGCA


title: 1001700606_O12

value: CCTAAGAC-GACTAGTGCA


title: 1001700606_N16

value: ACTGAGCG-AAGCCTTGCA


title: 1001700606_O3

value: ACTGAGCG-GCCTTATGCA


title: 1001700606_N21

value: ACTGAGCG-TCTAATTGCA


title: 1001700606_N13

value: dengue

value: ACTGAGCG-ATTAAGTGCA


title: 1001700606_N19

value: ACTGAGCG-GGCTATTGCA


title: 1001700606_N1

value: ACTGAGCG-TAGAGTTGCA


title: 1001700606_M20

value: ACTGAGCG-AAGGAGTGCA


title: 1001700606_M17

value: ACTGAGCG-CTAGCTTGCA


title: 1001700606_N7

value: ACTGAGCG-TGCATATGCA


title: 1001700606_M9

value: ACTGAGCG-GACTAGTGCA


title: 1001700606_M12

value: ACTGAGCG-TCCTCTTGCA


title: 1001700606_M2

value: TAGCGCTC-TCTCCGTGCA


title: 1001700606_L21

value: TAGCGCTC-GCCTTATGCA


title: 1001700606_L16

value: TAGCGCTC-GGCTATTGCA


title: 1001700606_L18

value: TAGCGCTC-TCTAATTGCA


title: 1001700606_L11

value: TAGCGCTC-AAGCCTTGCA


title: 1001700606_N10

value: ACTGAGCG-GTAAGATGCA


title: 1001700606_L1

value: TAGCGCTC-GTAAGATGCA


title: 1001700606_L4

value: TAGCGCTC-GGAGTATGCA


title: 1001700606_K19

value: dengue

value: TAGCGCTC-TAGAGTTGCA


title: 1001700606_K16

value: TAGCGCTC-AAGGAGTGCA


title: 1001700606_K6

value: TAGCGCTC-CTCTATTGCA


title: 1001700606_K3

value: ATGCGCAG-TCTCCGTGCA


title: 1001700606_K14

value: TAGCGCTC-CTAGCTTGCA


title: 1001700606_L7

value: TAGCGCTC-ATTAAGTGCA


title: 1001700606_J16

value: ATGCGCAG-TCTAATTGCA


title: 1001700606_K8

value: TAGCGCTC-GACTAGTGCA


title: 1001700606_K22

value: TAGCGCTC-TGCATATGCA


title: 1001700606_J5

value: ATGCGCAG-GGAGTATGCA


title: 1001700606_K10

value: TAGCGCTC-TCCTCTTGCA


title: 1001700606_M4

value: TAGCGCTC-ATGCGATGCA


title: 1001700606_K5

value: ATGCGCAG-ATGCGATGCA


title: 1001700606_I21

value: ATGCGCAG-TAGAGTTGCA


title: 1001700606_I14

value: ATGCGCAG-CTAGCTTGCA


title: 1001700606_M5

value: ACTGAGCG-CTCTATTGCA


title: 1001700606_I15

value: dengue

value: ATGCGCAG-AAGGAGTGCA


title: 1001700606_K1

value: ATGCGCAG-GCCTTATGCA


title: 1001700606_J6

value: ATGCGCAG-ATTAAGTGCA


title: 1001700606_J8

value: ATGCGCAG-AAGCCTTGCA


title: 1001700606_J11

value: ATGCGCAG-GGCTATTGCA


title: 1001700606_I10

value: ATGCGCAG-GACTAGTGCA


title: 1001700606_I12

value: ATGCGCAG-TCCTCTTGCA


title: 1001700606_J3

value: ATGCGCAG-GTAAGATGCA


title: 1001700606_I22

value: ATGCGCAG-TGCATATGCA


title: 1001700606_I7

value: TACGCTGC-ATGCGATGCA


title: 1001700606_I5

value: TACGCTGC-TCTCCGTGCA


title: 1001700606_I8

value: ATGCGCAG-CTCTATTGCA


title: 1001700606_H15

value: TACGCTGC-AAGCCTTGCA


title: 1001700606_I2

value: TACGCTGC-TCTAATTGCA


title: 1001700606_H17

value: TACGCTGC-GGCTATTGCA


title: 1001700606_G22

value: TACGCTGC-TAGAGTTGCA


title: 1001700606_G16

value: dengue

value: TACGCTGC-CTAGCTTGCA


title: 1001700606_H1

value: TACGCTGC-TGCATATGCA


title: 1001700606_H6

value: TACGCTGC-GGAGTATGCA


title: 1001700606_G12

value: TACGCTGC-CTCTATTGCA


title: 1001700606_G21

value: TACGCTGC-AAGGAGTGCA


title: 1001700606_G13

value: TACGCTGC-GACTAGTGCA


title: 1001700606_F21

value: CGGAGCCT-TCTAATTGCA


title: 1001700606_G5

value: CGGAGCCT-TCTCCGTGCA


title: 1001700606_F16

value: CGGAGCCT-AAGCCTTGCA


title: 1001700606_F13

value: CGGAGCCT-ATTAAGTGCA


title: 1001700606_F18

value: CGGAGCCT-GGCTATTGCA


title: 1001700606_I4

value: TACGCTGC-GCCTTATGCA


title: 1001700606_G14

value: TACGCTGC-TCCTCTTGCA


title: 1001700606_F3

value: CGGAGCCT-AAGGAGTGCA


title: 1001700606_G3

value: CGGAGCCT-GCCTTATGCA


title: 1001700606_H11

value: TACGCTGC-ATTAAGTGCA


title: 1001700606_E22

value: dengue

value: CGGAGCCT-TCCTCTTGCA


title: 1001700606_F11

value: CGGAGCCT-GGAGTATGCA


title: 1001700606_G7

value: CGGAGCCT-ATGCGATGCA


title: 1001700606_F1

value: CGGAGCCT-CTAGCTTGCA


title: 1001700606_F6

value: CGGAGCCT-TGCATATGCA


title: 1001700606_F8

value: CGGAGCCT-GTAAGATGCA


title: 1001700606_F4

value: CGGAGCCT-TAGAGTTGCA


title: 1001700606_E19

value: CGGAGCCT-CTCTATTGCA


title: 1001700606_E18

value: GCGTAGTA-ATGCGATGCA


title: 1001700606_E15

value: GCGTAGTA-GCCTTATGCA


title: 1001700606_H3

value: TACGCTGC-GTAAGATGCA


title: 1001700606_E6

value: GCGTAGTA-AAGCCTTGCA


title: 1001700606_E17

value: GCGTAGTA-TCTCCGTGCA


title: 1001700606_E10

value: GCGTAGTA-GGCTATTGCA


title: 1001700606_E12

value: GCGTAGTA-TCTAATTGCA


title: 1001700606_E2

value: GCGTAGTA-GGAGTATGCA


title: 1001700606_E20

value: dengue

value: CGGAGCCT-GACTAGTGCA


title: 1001700606_D20

value: GCGTAGTA-GTAAGATGCA


title: 1001700606_E5

value: GCGTAGTA-ATTAAGTGCA


title: 1001700606_D17

value: GCGTAGTA-TGCATATGCA


title: 1001700606_D16

value: GCGTAGTA-TAGAGTTGCA


title: 1001700606_D8

value: GCGTAGTA-TCCTCTTGCA


title: 1001700606_D5

value: GCGTAGTA-GACTAGTGCA


title: 1001700606_D12

value: GCGTAGTA-CTAGCTTGCA


title: 1001700606_C22

value: GCGTAGTA-CTCTATTGCA


title: 1001700606_C21

value: GGAGCTAC-ATGCGATGCA


title: 1001700606_C1

value: GGAGCTAC-GGAGTATGCA


title: 1001700606_B22

value: GGAGCTAC-GTAAGATGCA


title: 1001700606_C3

value: GGAGCTAC-ATTAAGTGCA


title: 1001700606_B16

value: GGAGCTAC-AAGGAGTGCA


title: 1001700606_B19

value: GGAGCTAC-TAGAGTTGCA


title: 1001700606_B15

value: GGAGCTAC-CTAGCTTGCA


title: 1001700606_B12

value: dengue

value: GGAGCTAC-CTCTATTGCA


title: 1001700606_B20

value: GGAGCTAC-TGCATATGCA


title: 1001700606_C18

value: GGAGCTAC-TCTCCGTGCA


title: 1001700606_B4

value: ACTCGCTA-TCTCCGTGCA


title: 1001700606_B14

value: GGAGCTAC-TCCTCTTGCA


title: 1001700606_C13

value: GGAGCTAC-TCTAATTGCA


title: 1001700606_C6

value: GGAGCTAC-AAGCCTTGCA


title: 1001700606_B13

value: GGAGCTAC-GACTAGTGCA


title: 1001700606_C10

value: GGAGCTAC-GGCTATTGCA


title: 1001700606_A1

value: ACTCGCTA-GGAGTATGCA


title: 1001700606_A11

value: ACTCGCTA-GGCTATTGCA


title: 1001700606_A8

value: ACTCGCTA-AAGCCTTGCA


title: 1001700606_A21

value: ACTCGCTA-GCCTTATGCA


title: 1001700606_A13

value: ACTCGCTA-TCTAATTGCA


title: 1001700606_A5

value: ACTCGCTA-ATTAAGTGCA


title: 1001700606_B7

value: ACTCGCTA-ATGCGATGCA


title: 1001700605_P21

value: dengue

value: ACTCGCTA-GTAAGATGCA


title: 1001700605_O14

value: ATCTCAGG-TCTCCGTGCA


title: 1001700606_C16

value: GGAGCTAC-GCCTTATGCA


title: 1001700606_D14

value: GCGTAGTA-AAGGAGTGCA


title: 1001700605_O19

value: ACTCGCTA-GACTAGTGCA


title: 1001700605_O22

value: ACTCGCTA-AAGGAGTGCA


title: 1001700605_O15

value: ATCTCAGG-ATGCGATGCA


title: 1001700605_O5

value: ATCTCAGG-GGAGTATGCA


title: 1001700605_O8

value: ATCTCAGG-AAGCCTTGCA


title: 1001700605_O16

value: ACTCGCTA-CTCTATTGCA


title: 1001700605_M21

value: ATCTCAGG-GACTAGTGCA


title: 1001700605_O3

value: ATCTCAGG-GTAAGATGCA


title: 1001700605_P20

value: ACTCGCTA-TGCATATGCA


title: 1001700605_O2

value: ATCTCAGG-TGCATATGCA


title: 1001700605_O20

value: ACTCGCTA-TCCTCTTGCA


title: 1001700605_N14

value: ATCTCAGG-CTAGCTTGCA


title: 1001700605_O11

value: dengue

value: ATCTCAGG-TCTAATTGCA


title: 1001700605_N21

value: ATCTCAGG-AAGGAGTGCA


title: 1001700605_P17

value: ACTCGCTA-TAGAGTTGCA


title: 1001700605_N6

value: ATCTCAGG-TCCTCTTGCA


title: 1001700605_O21

value: ACTCGCTA-CTAGCTTGCA


title: 1001700605_M16

value: ATCTCAGG-CTCTATTGCA


title: 1001700605_O1

value: ATCTCAGG-TAGAGTTGCA


title: 1001700605_O12

value: ATCTCAGG-GCCTTATGCA


title: 1001700605_O6

value: ATCTCAGG-ATTAAGTGCA


title: 1001700605_M15

value: GCTCATGA-ATGCGATGCA


title: 1001700605_M9

value: GCTCATGA-TCTAATTGCA


title: 1001700605_M11

value: GCTCATGA-GCCTTATGCA


title: 1001700605_L22

value: GCTCATGA-GGCTATTGCA


title: 1001700605_L17

value: GCTCATGA-ATTAAGTGCA


title: 1001700605_M12

value: GCTCATGA-TCTCCGTGCA


title: 1001700605_L21

value: GCTCATGA-AAGCCTTGCA


title: 1001700605_L12

value: dengue

value: GCTCATGA-TGCATATGCA


title: 1001700605_L10

value: GCTCATGA-TAGAGTTGCA


title: 1001700605_L8

value: GCTCATGA-AAGGAGTGCA


title: 1001700605_J16

value: GTAGAGGA-TCTAATTGCA


title: 1001700605_J17

value: GTAGAGGA-GCCTTATGCA


title: 1001700605_J15

value: GTAGAGGA-GGCTATTGCA


title: 1001700605_O9

value: ATCTCAGG-GGCTATTGCA


title: 1001700605_K10

value: GCTCATGA-CTCTATTGCA


title: 1001700605_J12

value: GTAGAGGA-ATTAAGTGCA


title: 1001700605_K11

value: GCTCATGA-GACTAGTGCA


title: 1001700605_L15

value: GCTCATGA-GGAGTATGCA


title: 1001700605_K2

value: GTAGAGGA-TCTCCGTGCA


title: 1001700605_J14

value: GTAGAGGA-AAGCCTTGCA


title: 1001700605_J7

value: GTAGAGGA-TAGAGTTGCA


title: 1001700605_J8

value: GTAGAGGA-TGCATATGCA


title: 1001700605_H15

value: AAGAGGCA-TCTCCGTGCA


title: 1001700605_J9

value: dengue

value: GTAGAGGA-GTAAGATGCA


title: 1001700605_H12

value: AAGAGGCA-GCCTTATGCA


title: 1001700605_H21

value: AAGAGGCA-ATGCGATGCA


title: 1001700605_J2

value: GTAGAGGA-AAGGAGTGCA


title: 1001700605_K21

value: GCTCATGA-CTAGCTTGCA


title: 1001700605_L14

value: GCTCATGA-GTAAGATGCA


title: 1001700605_J10

value: GTAGAGGA-GGAGTATGCA


title: 1001700605_K9

value: GTAGAGGA-ATGCGATGCA


title: 1001700605_K17

value: GCTCATGA-TCCTCTTGCA


title: 1001700605_H2

value: AAGAGGCA-GGCTATTGCA


title: 1001700605_I3

value: GTAGAGGA-CTCTATTGCA


title: 1001700605_G19

value: AAGAGGCA-AAGCCTTGCA


title: 1001700605_I10

value: GTAGAGGA-TCCTCTTGCA


title: 1001700605_G6

value: AAGAGGCA-TAGAGTTGCA


title: 1001700605_G9

value: AAGAGGCA-GGAGTATGCA


title: 1001700605_G3

value: AAGAGGCA-AAGGAGTGCA


title: 1001700605_G8

value: dengue

value: AAGAGGCA-GTAAGATGCA


title: 1001700605_F14

value: AAGAGGCA-CTCTATTGCA


title: 1001700605_F19

value: AAGAGGCA-TCCTCTTGCA


title: 1001700605_H9

value: AAGAGGCA-TCTAATTGCA


title: 1001700605_F21

value: AAGAGGCA-CTAGCTTGCA


title: 1001700605_F11

value: CGAGGCTG-ATGCGATGCA


title: 1001700605_F8

value: CGAGGCTG-GCCTTATGCA


title: 1001700605_I21

value: GTAGAGGA-CTAGCTTGCA


title: 1001700605_F6

value: CGAGGCTG-TCTAATTGCA


title: 1001700605_I6

value: GTAGAGGA-GACTAGTGCA


title: 1001700605_E12

value: CGAGGCTG-GGAGTATGCA


title: 1001700605_G12

value: AAGAGGCA-ATTAAGTGCA


title: 1001700605_E15

value: CGAGGCTG-ATTAAGTGCA


title: 1001700605_E22

value: CGAGGCTG-GGCTATTGCA


title: 1001700605_E9

value: CGAGGCTG-GTAAGATGCA


title: 1001700605_E19

value: CGAGGCTG-AAGCCTTGCA


title: 1001700605_E7

value: dengue

value: CGAGGCTG-TGCATATGCA


title: 1001700605_E5

value: CGAGGCTG-TAGAGTTGCA


title: 1001700605_E3

value: CGAGGCTG-AAGGAGTGCA


title: 1001700605_G7

value: AAGAGGCA-TGCATATGCA


title: 1001700605_D17

value: CGAGGCTG-CTAGCTTGCA


title: 1001700605_F18

value: AAGAGGCA-GACTAGTGCA


title: 1001700605_F10

value: CGAGGCTG-TCTCCGTGCA


title: 1001700605_D3

value: CTCTCTAC-GCCTTATGCA


title: 1001700605_D8

value: CTCTCTAC-ATGCGATGCA


title: 1001700605_C18

value: CTCTCTAC-GGCTATTGCA


title: 1001700605_C17

value: CTCTCTAC-AAGCCTTGCA


title: 1001700605_C16

value: CTCTCTAC-ATTAAGTGCA


title: 1001700605_C15

value: CTCTCTAC-GGAGTATGCA


title: 1001700605_C14

value: CTCTCTAC-GTAAGATGCA


title: 1001700605_C11

value: CTCTCTAC-TGCATATGCA


title: 1001700605_D13

value: CGAGGCTG-GACTAGTGCA


title: 1001700605_B18

value: dengue

value: CTCTCTAC-GACTAGTGCA


title: 1001700605_C3

value: CTCTCTAC-TCCTCTTGCA


title: 1001700605_B14

value: TAGGCATG-ATGCGATGCA


title: 1001700605_C4

value: CTCTCTAC-CTAGCTTGCA


title: 1001700605_B13

value: TAGGCATG-TCTCCGTGCA


title: 1001700605_C7

value: CTCTCTAC-AAGGAGTGCA


title: 1001700605_B15

value: CTCTCTAC-CTCTATTGCA


title: 1001700605_B11

value: TAGGCATG-GCCTTATGCA


title: 1001700605_B8

value: TAGGCATG-TCTAATTGCA


title: 1001700605_B4

value: TAGGCATG-GGCTATTGCA


title: 1001700605_B1

value: TAGGCATG-AAGCCTTGCA


title: 1001700605_D9

value: CGAGGCTG-CTCTATTGCA


title: 1001700605_A22

value: TAGGCATG-ATTAAGTGCA


title: 1001700605_D4

value: CTCTCTAC-TCTCCGTGCA


title: 1001700605_D14

value: CGAGGCTG-TCCTCTTGCA


title: 1001700605_A18

value: TAGGCATG-TGCATATGCA


title: 1001700605_D1

value: dengue

value: CTCTCTAC-TCTAATTGCA


title: 1001700605_A21

value: TAGGCATG-GGAGTATGCA


title: 1001700605_A14

value: TAGGCATG-AAGGAGTGCA


title: 1001700605_A1

value: TAGGCATG-CTCTATTGCA


title: 1001700605_C9

value: CTCTCTAC-TAGAGTTGCA


title: 1001700605_A6

value: TAGGCATG-GACTAGTGCA


title: 1001700605_A16

value: TAGGCATG-TAGAGTTGCA


title: 1001700604_P21

value: GGACTCCT-ATGCGATGCA


title: 1001700605_A20

value: TAGGCATG-GTAAGATGCA


title: 1001700605_A11

value: TAGGCATG-CTAGCTTGCA


title: 1001700605_A8

value: TAGGCATG-TCCTCTTGCA


title: 1001700604_P11

value: GGACTCCT-GGCTATTGCA


title: 1001700604_P18

value: GGACTCCT-TCTCCGTGCA


title: 1001700604_P8

value: GGACTCCT-ATTAAGTGCA


title: 1001700604_O16

value: GGACTCCT-AAGGAGTGCA


title: 1001700604_P9

value: GGACTCCT-AAGCCTTGCA


title: 1001700604_P7

value: dengue

value: GGACTCCT-GGAGTATGCA


title: 1001700604_O18

value: GGACTCCT-TAGAGTTGCA


title: 1001700604_P12

value: GGACTCCT-TCTAATTGCA


title: 1001700604_P5

value: GGACTCCT-GTAAGATGCA


title: 1001700604_P14

value: GGACTCCT-GCCTTATGCA


title: 1001700604_N19

value: TCCTGAGC-ATGCGATGCA


title: 1001700604_O20

value: GGACTCCT-TGCATATGCA


title: 1001700604_N10

value: TCCTGAGC-TCTAATTGCA


title: 1001700604_N9

value: TCCTGAGC-GGCTATTGCA


title: 1001700604_O4

value: GGACTCCT-CTCTATTGCA


title: 1001700604_O11

value: GGACTCCT-TCCTCTTGCA


title: 1001700604_N17

value: TCCTGAGC-TCTCCGTGCA


title: 1001700604_O13

value: GGACTCCT-CTAGCTTGCA


title: 1001700604_M18

value: TCCTGAGC-GGAGTATGCA


title: 1001700604_M8

value: TCCTGAGC-TAGAGTTGCA


title: 1001700604_N4

value: TCCTGAGC-AAGCCTTGCA


title: 1001700604_N12

value: dengue

value: TCCTGAGC-GCCTTATGCA


title: 1001700604_M13

value: TCCTGAGC-GTAAGATGCA


title: 1001700604_M6

value: TCCTGAGC-AAGGAGTGCA


title: 1001700604_M10

value: TCCTGAGC-TGCATATGCA


title: 1001700604_L19

value: TCCTGAGC-GACTAGTGCA


title: 1001700604_L16

value: TCCTGAGC-CTCTATTGCA


title: 1001700604_M4

value: TCCTGAGC-CTAGCTTGCA


title: 1001700604_M3

value: TCCTGAGC-TCCTCTTGCA


title: 1001700604_L8

value: AGGCAGAA-GCCTTATGCA


title: 1001700604_L14

value: AGGCAGAA-ATGCGATGCA


title: 1001700604_L12

value: AGGCAGAA-TCTCCGTGCA


title: 1001700604_O9

value: GGACTCCT-GACTAGTGCA


title: 1001700604_K15

value: AGGCAGAA-ATTAAGTGCA


title: 1001700604_L2

value: AGGCAGAA-TCTAATTGCA


title: 1001700604_M20

value: TCCTGAGC-ATTAAGTGCA


title: 1001700604_K21

value: AGGCAGAA-GGCTATTGCA


title: 1001700604_K6

value: dengue

value: AGGCAGAA-TGCATATGCA


title: 1001700604_K14

value: AGGCAGAA-GGAGTATGCA


title: 1001700604_K8

value: AGGCAGAA-GTAAGATGCA


title: 1001700604_K20

value: AGGCAGAA-AAGCCTTGCA


title: 1001700604_J9

value: AGGCAGAA-AAGGAGTGCA


title: 1001700604_I15

value: AGGCAGAA-CTCTATTGCA


title: 1001700604_I20

value: AGGCAGAA-GACTAGTGCA


title: 1001700604_I7

value: CGTACTAG-TCTCCGTGCA


title: 1001700604_J3

value: AGGCAGAA-CTAGCTTGCA


title: 1001700604_J16

value: AGGCAGAA-TAGAGTTGCA


title: 1001700604_I21

value: AGGCAGAA-TCCTCTTGCA


title: 1001700604_I10

value: CGTACTAG-ATGCGATGCA


title: 1001700604_I4

value: CGTACTAG-GGCTATTGCA


title: 1001700604_H21

value: CGTACTAG-AAGCCTTGCA


title: 1001700604_I5

value: CGTACTAG-TCTAATTGCA


title: 1001700604_H18

value: CGTACTAG-ATTAAGTGCA


title: 1001700604_I6

value: dengue

value: CGTACTAG-GCCTTATGCA


title: 1001700604_G11

value: CGTACTAG-CTAGCTTGCA


title: 1001700604_G3

value: CGTACTAG-GACTAGTGCA


title: 1001700604_H8

value: CGTACTAG-TAGAGTTGCA


title: 1001700604_G6

value: CGTACTAG-TCCTCTTGCA


title: 1001700604_G12

value: CGTACTAG-AAGGAGTGCA


title: 1001700604_H13

value: CGTACTAG-GTAAGATGCA


title: 1001700604_H9

value: CGTACTAG-TGCATATGCA


title: 1001700604_F11

value: TAAGGCGA-ATGCGATGCA


title: 1001700604_F8

value: TAAGGCGA-GCCTTATGCA


title: 1001700604_E12

value: TAAGGCGA-AAGCCTTGCA


title: 1001700604_E21

value: TAAGGCGA-GGCTATTGCA


title: 1001700604_E10

value: TAAGGCGA-ATTAAGTGCA


title: 1001700604_D11

value: TAAGGCGA-GTAAGATGCA


title: 1001700604_F20

value: CGTACTAG-CTCTATTGCA


title: 1001700604_F2

value: TAAGGCGA-TCTAATTGCA


title: 1001700604_C10

value: dengue

value: TAAGGCGA-CTAGCTTGCA


title: 1001700604_D8

value: TAAGGCGA-TGCATATGCA


title: 1001700604_E3

value: TAAGGCGA-GGAGTATGCA


title: 1001700604_F9

value: TAAGGCGA-TCTCCGTGCA


title: 1001700604_D6

value: TAAGGCGA-TAGAGTTGCA


title: 1001700604_A13

value: TAAGGCGA-CTCTATTGCA


title: 1001700603_P13

value: CCTAAGAC-GTAAGAACGT


title: 1001700603_P17

value: CCTAAGAC-GGAGTAACGT


title: 1001700604_H14

value: CGTACTAG-GGAGTATGCA


title: 1001700603_P21

value: CCTAAGAC-ATTAAGACGT


title: 1001700603_P1

value: CCTAAGAC-TAGAGTACGT


title: 1001700604_A16

value: TAAGGCGA-GACTAGTGCA


title: 1001700604_A20

value: TAAGGCGA-TCCTCTTGCA


title: 1001700603_P6

value: CCTAAGAC-TGCATAACGT


title: 1001700603_O22

value: CCTAAGAC-AAGGAGACGT


title: 1001700603_O10

value: CCTAAGAC-TCCTCTACGT


title: 1001700603_O4

value: dengue

value: CCTAAGAC-CTCTATACGT


title: 1001700603_O1

value: ACTGAGCG-TCTCCGACGT


title: 1001700603_N21

value: ACTGAGCG-GCCTTAACGT


title: 1001700603_O5

value: CCTAAGAC-GACTAGACGT


title: 1001700603_N16

value: ACTGAGCG-AAGCCTACGT


title: 1001700603_O2

value: ACTGAGCG-ATGCGAACGT


title: 1001700603_N19

value: ACTGAGCG-TCTAATACGT


title: 1001700603_N6

value: ACTGAGCG-GTAAGAACGT


title: 1001700604_C21

value: TAAGGCGA-AAGGAGTGCA


title: 1001700603_N12

value: ACTGAGCG-ATTAAGACGT


title: 1001700603_N10

value: ACTGAGCG-GGAGTAACGT


title: 1001700603_N1

value: ACTGAGCG-TAGAGTACGT


title: 1001700603_M20

value: ACTGAGCG-CTAGCTACGT


title: 1001700603_N3

value: ACTGAGCG-TGCATAACGT


title: 1001700603_M22

value: ACTGAGCG-AAGGAGACGT


title: 1001700603_N17

value: ACTGAGCG-GGCTATACGT


title: 1001700603_M19

value: dengue

value: ACTGAGCG-TCCTCTACGT


title: 1001700603_M5

value: TAGCGCTC-TCTAATACGT


title: 1001700603_M10

value: TAGCGCTC-TCTCCGACGT


title: 1001700603_M4

value: TAGCGCTC-GGCTATACGT


title: 1001700603_M7

value: TAGCGCTC-GCCTTAACGT


title: 1001700603_O17

value: CCTAAGAC-CTAGCTACGT


title: 1001700603_M1

value: TAGCGCTC-AAGCCTACGT


title: 1001700603_L16

value: TAGCGCTC-GGAGTAACGT


title: 1001700603_M13

value: TAGCGCTC-ATGCGAACGT


title: 1001700603_L12

value: TAGCGCTC-GTAAGAACGT


title: 1001700603_L7

value: TAGCGCTC-TAGAGTACGT


title: 1001700603_L5

value: TAGCGCTC-AAGGAGACGT


title: 1001700603_M17

value: ACTGAGCG-GACTAGACGT


title: 1001700603_L18

value: TAGCGCTC-ATTAAGACGT


title: 1001700603_K10

value: TAGCGCTC-TCCTCTACGT


title: 1001700603_K4

value: ATGCGCAG-ATGCGAACGT


title: 1001700603_J8

value: dengue

value: ATGCGCAG-AAGCCTACGT


title: 1001700603_J5

value: ATGCGCAG-GGAGTAACGT


title: 1001700603_J7

value: ATGCGCAG-ATTAAGACGT


title: 1001700603_I10

value: ATGCGCAG-TAGAGTACGT


title: 1001700603_I2

value: ATGCGCAG-GACTAGACGT


title: 1001700603_H11

value: ATGCGCAG-CTCTATACGT


title: 1001700603_I8

value: ATGCGCAG-AAGGAGACGT


title: 1001700603_J11

value: ATGCGCAG-TCTAATACGT


title: 1001700603_L10

value: TAGCGCTC-TGCATAACGT


title: 1001700603_H7

value: TACGCTGC-TCTCCGACGT


title: 1001700603_K2

value: ATGCGCAG-TCTCCGACGT


title: 1001700603_H5

value: TACGCTGC-GCCTTAACGT


title: 1001700603_K13

value: TAGCGCTC-CTAGCTACGT


title: 1001700603_J3

value: ATGCGCAG-GTAAGAACGT


title: 1001700603_M16

value: ACTGAGCG-CTCTATACGT


title: 1001700603_J12

value: ATGCGCAG-GCCTTAACGT


title: 1001700603_G12

value: dengue

value: TACGCTGC-AAGCCTACGT


title: 1001700603_K6

value: TAGCGCTC-CTCTATACGT


title: 1001700603_G10

value: TACGCTGC-ATTAAGACGT


title: 1001700603_G4

value: TACGCTGC-TGCATAACGT


title: 1001700603_G8

value: TACGCTGC-GGAGTAACGT


title: 1001700603_J9

value: ATGCGCAG-GGCTATACGT


title: 1001700603_K8

value: TAGCGCTC-GACTAGACGT


title: 1001700603_I6

value: ATGCGCAG-CTAGCTACGT


title: 1001700603_G3

value: TACGCTGC-TAGAGTACGT


title: 1001700603_G2

value: TACGCTGC-AAGGAGACGT


title: 1001700603_F21

value: TACGCTGC-TCCTCTACGT


title: 1001700603_I4

value: ATGCGCAG-TCCTCTACGT


title: 1001700603_F17

value: TACGCTGC-CTCTATACGT


title: 1001700603_F9

value: CGGAGCCT-TCTAATACGT


title: 1001700603_F7

value: CGGAGCCT-GGCTATACGT


title: 1001700603_H1

value: TACGCTGC-GGCTATACGT


title: 1001700603_J1

value: dengue

value: ATGCGCAG-TGCATAACGT


title: 1001700603_F5

value: CGGAGCCT-AAGCCTACGT


title: 1001700603_H3

value: TACGCTGC-TCTAATACGT


title: 1001700603_E22

value: CGGAGCCT-GTAAGAACGT


title: 1001700603_E20

value: CGGAGCCT-TGCATAACGT


title: 1001700603_H9

value: TACGCTGC-ATGCGAACGT


title: 1001700603_E3

value: GCGTAGTA-TCTCCGACGT


title: 1001700603_F15

value: CGGAGCCT-ATGCGAACGT


title: 1001700603_G1

value: TACGCTGC-CTAGCTACGT


title: 1001700603_E1

value: GCGTAGTA-GCCTTAACGT


title: 1001700603_F10

value: CGGAGCCT-GCCTTAACGT


title: 1001700603_E16

value: CGGAGCCT-AAGGAGACGT


title: 1001700603_F2

value: CGGAGCCT-GGAGTAACGT


title: 1001700603_D20

value: GCGTAGTA-GGCTATACGT


title: 1001700603_F12

value: CGGAGCCT-TCTCCGACGT


title: 1001700603_G6

value: TACGCTGC-GTAAGAACGT


title: 1001700603_E18

value: dengue

value: CGGAGCCT-TAGAGTACGT


title: 1001700603_F18

value: TACGCTGC-GACTAGACGT


title: 1001700603_F3

value: CGGAGCCT-ATTAAGACGT


title: 1001700603_D6

value: GCGTAGTA-TAGAGTACGT


title: 1001700603_D4

value: GCGTAGTA-AAGGAGACGT


title: 1001700603_D3

value: GCGTAGTA-CTAGCTACGT


title: 1001700603_C16

value: GCGTAGTA-GACTAGACGT


title: 1001700603_E5

value: GCGTAGTA-ATGCGAACGT


title: 1001700603_E7

value: CGGAGCCT-CTCTATACGT


title: 1001700603_E15

value: CGGAGCCT-CTAGCTACGT


title: 1001700603_E11

value: CGGAGCCT-TCCTCTACGT


title: 1001700603_C11

value: GGAGCTAC-ATGCGAACGT


title: 1001700603_C9

value: GGAGCTAC-TCTCCGACGT


title: 1001700603_C5

value: GGAGCTAC-TCTAATACGT


title: 1001700603_E9

value: CGGAGCCT-GACTAGACGT


title: 1001700603_C3

value: GGAGCTAC-GGCTATACGT


title: 1001700603_D12

value: dengue

value: GCGTAGTA-ATTAAGACGT


title: 1001700603_D17

value: GCGTAGTA-AAGCCTACGT


title: 1001700603_B10

value: GGAGCTAC-GTAAGAACGT


title: 1001700603_B12

value: GGAGCTAC-GGAGTAACGT


title: 1001700603_B4

value: GGAGCTAC-AAGGAGACGT


title: 1001700603_C13

value: GCGTAGTA-CTCTATACGT


title: 1001700603_B1

value: GGAGCTAC-CTAGCTACGT


title: 1001700603_A17

value: GGAGCTAC-CTCTATACGT


title: 1001700603_A19

value: GGAGCTAC-GACTAGACGT


title: 1001700603_D8

value: GCGTAGTA-TGCATAACGT


title: 1001700603_D10

value: GCGTAGTA-GTAAGAACGT


title: 1001700603_D21

value: GCGTAGTA-TCTAATACGT


title: 1001700603_B20

value: GGAGCTAC-ATTAAGACGT


title: 1001700603_B8

value: GGAGCTAC-TGCATAACGT


title: 1001700603_A7

value: ACTCGCTA-TCTAATACGT


title: 1001700602_P19

value: ACTCGCTA-GTAAGAACGT


title: 1001700603_D11

value: dengue

value: GCGTAGTA-GGAGTAACGT


title: 1001700603_A9

value: ACTCGCTA-GCCTTAACGT


title: 1001700603_D2

value: GCGTAGTA-TCCTCTACGT


title: 1001700603_A1

value: ACTCGCTA-GGAGTAACGT


title: 1001700602_P16

value: ACTCGCTA-AAGGAGACGT


title: 1001700603_A11

value: ACTCGCTA-TCTCCGACGT


title: 1001700603_A4

value: ACTCGCTA-AAGCCTACGT


title: 1001700603_A16

value: ACTCGCTA-ATGCGAACGT


title: 1001700603_A22

value: GGAGCTAC-TCCTCTACGT


title: 1001700603_B21

value: GGAGCTAC-AAGCCTACGT


title: 1001700603_A6

value: ACTCGCTA-GGCTATACGT


title: 1001700602_O16

value: ATCTCAGG-ATGCGAACGT


title: 1001700603_B6

value: GGAGCTAC-TAGAGTACGT


title: 1001700603_A2

value: ACTCGCTA-ATTAAGACGT


title: 1001700602_O12

value: ATCTCAGG-TCTAATACGT


title: 1001700602_P18

value: ACTCGCTA-TGCATAACGT


title: 1001700602_P8

value: dengue

value: ACTCGCTA-TCCTCTACGT


title: 1001700602_P14

value: ACTCGCTA-CTAGCTACGT


title: 1001700602_P17

value: ACTCGCTA-TAGAGTACGT


title: 1001700602_O18

value: ACTCGCTA-GACTAGACGT


title: 1001700602_O13

value: ATCTCAGG-GCCTTAACGT


title: 1001700602_O17

value: ACTCGCTA-CTCTATACGT


title: 1001700602_O8

value: ATCTCAGG-AAGCCTACGT


title: 1001700602_O10

value: ATCTCAGG-GGCTATACGT


title: 1001700602_O6

value: ATCTCAGG-ATTAAGACGT


title: 1001700603_C7

value: GGAGCTAC-GCCTTAACGT


title: 1001700602_N15

value: ATCTCAGG-TCCTCTACGT


title: 1001700602_N16

value: ATCTCAGG-CTAGCTACGT


title: 1001700602_O14

value: ATCTCAGG-TCTCCGACGT


title: 1001700602_N9

value: GCTCATGA-TCTCCGACGT


title: 1001700602_N13

value: ATCTCAGG-CTCTATACGT


title: 1001700602_N21

value: ATCTCAGG-TAGAGTACGT


title: 1001700602_M21

value: dengue

value: GCTCATGA-AAGCCTACGT


title: 1001700602_N22

value: ATCTCAGG-TGCATAACGT


title: 1001700602_N18

value: ATCTCAGG-AAGGAGACGT


title: 1001700602_M17

value: GCTCATGA-GGAGTAACGT


title: 1001700602_O3

value: ATCTCAGG-GTAAGAACGT


title: 1001700602_N4

value: GCTCATGA-GGCTATACGT


title: 1001700602_M15

value: GCTCATGA-GTAAGAACGT


title: 1001700602_M7

value: GCTCATGA-TCCTCTACGT


title: 1001700602_N11

value: GCTCATGA-ATGCGAACGT


title: 1001700602_L19

value: GTAGAGGA-GCCTTAACGT


title: 1001700602_L20

value: GTAGAGGA-TCTCCGACGT


title: 1001700602_M19

value: GCTCATGA-ATTAAGACGT


title: 1001700602_N14

value: ATCTCAGG-GACTAGACGT


title: 1001700602_L15

value: GTAGAGGA-AAGCCTACGT


title: 1001700602_L13

value: GTAGAGGA-ATTAAGACGT


title: 1001700602_K19

value: GTAGAGGA-TAGAGTACGT


title: 1001700602_M12

value: dengue

value: GCTCATGA-TAGAGTACGT


title: 1001700602_L12

value: GTAGAGGA-GGAGTAACGT


title: 1001700602_M14

value: GCTCATGA-TGCATAACGT


title: 1001700602_O4

value: ATCTCAGG-GGAGTAACGT


title: 1001700602_N8

value: GCTCATGA-GCCTTAACGT


title: 1001700602_M11

value: GCTCATGA-AAGGAGACGT


title: 1001700602_K3

value: AAGAGGCA-GCCTTAACGT


title: 1001700602_N6

value: GCTCATGA-TCTAATACGT


title: 1001700602_M3

value: GCTCATGA-CTCTATACGT


title: 1001700602_K4

value: AAGAGGCA-TCTCCGACGT


title: 1001700602_L16

value: GTAGAGGA-GGCTATACGT


title: 1001700602_K15

value: GTAGAGGA-CTAGCTACGT


title: 1001700602_M10

value: GCTCATGA-CTAGCTACGT


title: 1001700602_K18

value: GTAGAGGA-AAGGAGACGT


title: 1001700602_J10

value: AAGAGGCA-GGCTATACGT


title: 1001700602_L18

value: GTAGAGGA-TCTAATACGT


title: 1001700602_M2

value: dengue

value: GTAGAGGA-ATGCGAACGT


title: 1001700602_M5

value: GCTCATGA-GACTAGACGT


title: 1001700602_K14

value: GTAGAGGA-TCCTCTACGT


title: 1001700602_I19

value: AAGAGGCA-GTAAGAACGT


title: 1001700602_I21

value: AAGAGGCA-ATTAAGACGT


title: 1001700602_K9

value: GTAGAGGA-CTCTATACGT


title: 1001700602_K5

value: AAGAGGCA-ATGCGAACGT


title: 1001700602_J11

value: AAGAGGCA-TCTAATACGT


title: 1001700602_I20

value: AAGAGGCA-GGAGTAACGT


title: 1001700602_L6

value: GTAGAGGA-GTAAGAACGT


title: 1001700602_I17

value: AAGAGGCA-TAGAGTACGT


title: 1001700602_I9

value: AAGAGGCA-GACTAGACGT


title: 1001700602_I4

value: AAGAGGCA-CTCTATACGT


title: 1001700602_I10

value: AAGAGGCA-TCCTCTACGT


title: 1001700602_I15

value: AAGAGGCA-AAGGAGACGT


title: 1001700602_G19

value: CGAGGCTG-TCTCCGACGT


title: 1001700602_L3

value: dengue

value: GTAGAGGA-TGCATAACGT


title: 1001700602_J3

value: AAGAGGCA-AAGCCTACGT


title: 1001700602_K11

value: GTAGAGGA-GACTAGACGT


title: 1001700602_G14

value: CGAGGCTG-GCCTTAACGT


title: 1001700602_I18

value: AAGAGGCA-TGCATAACGT


title: 1001700602_F22

value: CGAGGCTG-ATTAAGACGT


title: 1001700602_F13

value: CGAGGCTG-AAGGAGACGT


title: 1001700602_G13

value: CGAGGCTG-TCTAATACGT


title: 1001700602_I11

value: AAGAGGCA-CTAGCTACGT


title: 1001700602_F15

value: CGAGGCTG-TAGAGTACGT


title: 1001700602_F7

value: CGAGGCTG-CTCTATACGT


title: 1001700602_G8

value: CGAGGCTG-GGCTATACGT


title: 1001700602_F4

value: CTCTCTAC-ATGCGAACGT


title: 1001700602_F20

value: CGAGGCTG-GTAAGAACGT


title: 1001700602_E16

value: CTCTCTAC-GCCTTAACGT


title: 1001700602_G22

value: CGAGGCTG-ATGCGAACGT


title: 1001700602_E14

value: dengue

value: CTCTCTAC-TCTAATACGT


title: 1001700602_E8

value: CTCTCTAC-AAGCCTACGT


title: 1001700602_G3

value: CGAGGCTG-AAGCCTACGT


title: 1001700602_D16

value: CTCTCTAC-TAGAGTACGT


title: 1001700602_D11

value: CTCTCTAC-CTAGCTACGT


title: 1001700602_F21

value: CGAGGCTG-GGAGTAACGT


title: 1001700602_D18

value: CTCTCTAC-GTAAGAACGT


title: 1001700602_E7

value: CTCTCTAC-ATTAAGACGT


title: 1001700602_F11

value: CGAGGCTG-TCCTCTACGT


title: 1001700602_E3

value: CTCTCTAC-GGAGTAACGT


title: 1001700602_E13

value: CTCTCTAC-GGCTATACGT


title: 1001700602_D12

value: CTCTCTAC-AAGGAGACGT


title: 1001700602_C21

value: TAGGCATG-ATGCGAACGT


title: 1001700602_D17

value: CTCTCTAC-TGCATAACGT


title: 1001700602_F12

value: CGAGGCTG-CTAGCTACGT


title: 1001700602_D10

value: CTCTCTAC-TCCTCTACGT


title: 1001700602_C10

value: dengue

value: TAGGCATG-GCCTTAACGT


title: 1001700602_B9

value: TAGGCATG-ATTAAGACGT


title: 1001700602_E20

value: CTCTCTAC-TCTCCGACGT


title: 1001700602_B12

value: TAGGCATG-AAGCCTACGT


title: 1001700602_D9

value: CTCTCTAC-GACTAGACGT


title: 1001700602_F10

value: CGAGGCTG-GACTAGACGT


title: 1001700602_C18

value: TAGGCATG-TCTCCGACGT


title: 1001700602_C9

value: TAGGCATG-TCTAATACGT


title: 1001700602_B2

value: TAGGCATG-TAGAGTACGT


title: 1001700602_D7

value: CTCTCTAC-CTCTATACGT


title: 1001700602_C8

value: TAGGCATG-GGCTATACGT


title: 1001700602_B8

value: TAGGCATG-GGAGTAACGT


title: 1001700602_B6

value: TAGGCATG-GTAAGAACGT


title: 1001700602_B1

value: TAGGCATG-AAGGAGACGT


title: 1001700602_B4

value: TAGGCATG-TGCATAACGT


title: 1001700602_A8

value: TAGGCATG-TCCTCTACGT


title: 1001700602_A18

value: dengue

value: TAGGCATG-CTAGCTACGT


title: 1001700602_A1

value: TAGGCATG-CTCTATACGT


title: 1001700601_P22

value: GGACTCCT-ATGCGAACGT


title: 1001700601_P15

value: GGACTCCT-TCTAATACGT


title: 1001700601_P20

value: GGACTCCT-TCTCCGACGT


title: 1001700601_P8

value: GGACTCCT-AAGCCTACGT


title: 1001700601_P6

value: GGACTCCT-ATTAAGACGT


title: 1001700601_P11

value: GGACTCCT-GGCTATACGT


title: 1001700601_P18

value: GGACTCCT-GCCTTAACGT


title: 1001700601_O19

value: GGACTCCT-GTAAGAACGT


title: 1001700601_O21

value: GGACTCCT-GGAGTAACGT


title: 1001700602_F18

value: CGAGGCTG-TGCATAACGT


title: 1001700602_A6

value: TAGGCATG-GACTAGACGT


title: 1001700601_O16

value: GGACTCCT-TAGAGTACGT


title: 1001700601_O14

value: GGACTCCT-AAGGAGACGT


title: 1001700601_O10

value: GGACTCCT-CTAGCTACGT


title: 1001700601_O3

value: dengue

value: GGACTCCT-CTCTATACGT


title: 1001700601_N17

value: TCCTGAGC-GCCTTAACGT


title: 1001700601_O7

value: GGACTCCT-TCCTCTACGT


title: 1001700601_O5

value: GGACTCCT-GACTAGACGT


title: 1001700601_N19

value: TCCTGAGC-TCTCCGACGT


title: 1001700601_M15

value: TCCTGAGC-ATTAAGACGT


title: 1001700601_M13

value: TCCTGAGC-GGAGTAACGT


title: 1001700601_N22

value: TCCTGAGC-ATGCGAACGT


title: 1001700601_N12

value: TCCTGAGC-TCTAATACGT


title: 1001700601_L19

value: TCCTGAGC-TGCATAACGT


title: 1001700601_M9

value: TCCTGAGC-GTAAGAACGT


title: 1001700601_K3

value: AGGCAGAA-TCTCCGACGT


title: 1001700601_K6

value: AGGCAGAA-ATGCGAACGT


title: 1001700601_K9

value: TCCTGAGC-CTCTATACGT


title: 1001700601_L12

value: TCCTGAGC-AAGGAGACGT


title: 1001700601_K18

value: TCCTGAGC-CTAGCTACGT


title: 1001700601_J13

value: dengue

value: AGGCAGAA-GGCTATACGT


title: 1001700601_O17

value: GGACTCCT-TGCATAACGT


title: 1001700601_K14

value: TCCTGAGC-TCCTCTACGT


title: 1001700601_J22

value: AGGCAGAA-GCCTTAACGT


title: 1001700601_K13

value: TCCTGAGC-GACTAGACGT


title: 1001700601_J15

value: AGGCAGAA-TCTAATACGT


title: 1001700601_N8

value: TCCTGAGC-GGCTATACGT


title: 1001700601_J11

value: AGGCAGAA-ATTAAGACGT


title: 1001700601_J9

value: AGGCAGAA-GGAGTAACGT


title: 1001700601_L14

value: TCCTGAGC-TAGAGTACGT


title: 1001700601_M20

value: TCCTGAGC-AAGCCTACGT


title: 1001700601_I7

value: AGGCAGAA-CTAGCTACGT


title: 1001700601_J8

value: AGGCAGAA-GTAAGAACGT


title: 1001700601_I21

value: AGGCAGAA-TAGAGTACGT


title: 1001700601_I3

value: AGGCAGAA-TCCTCTACGT


title: 1001700601_I22

value: AGGCAGAA-TGCATAACGT


title: 1001700601_G12

value: dengue

value: CGTACTAG-GCCTTAACGT


title: 1001700601_I15

value: AGGCAGAA-AAGGAGACGT


title: 1001700601_G7

value: CGTACTAG-TCTAATACGT


title: 1001700601_G20

value: AGGCAGAA-CTCTATACGT


title: 1001700601_H3

value: AGGCAGAA-GACTAGACGT


title: 1001700601_G17

value: CGTACTAG-ATGCGAACGT


title: 1001700601_J12

value: AGGCAGAA-AAGCCTACGT


title: 1001700601_G2

value: CGTACTAG-AAGCCTACGT


title: 1001700601_G4

value: CGTACTAG-GGCTATACGT


title: 1001700601_F21

value: CGTACTAG-ATTAAGACGT


title: 1001700601_F18

value: CGTACTAG-GGAGTAACGT


title: 1001700601_F15

value: CGTACTAG-GTAAGAACGT


title: 1001700601_E15

value: CGTACTAG-TCCTCTACGT


title: 1001700601_F8

value: CGTACTAG-TAGAGTACGT


title: 1001700601_E22

value: CGTACTAG-CTAGCTACGT


title: 1001700601_E8

value: CGTACTAG-CTCTATACGT


title: 1001700601_F3

value: dengue

value: CGTACTAG-AAGGAGACGT


title: 1001700601_D19

value: TAAGGCGA-ATGCGAACGT


title: 1001700601_D12

value: TAAGGCGA-GCCTTAACGT


title: 1001700601_C8

value: TAAGGCGA-ATTAAGACGT


title: 1001700601_B13

value: TAAGGCGA-GGAGTAACGT


title: 1001700601_D6

value: TAAGGCGA-GGCTATACGT


title: 1001700601_D16

value: TAAGGCGA-TCTCCGACGT


title: 1001700601_G14

value: CGTACTAG-TCTCCGACGT


title: 1001700601_E13

value: CGTACTAG-GACTAGACGT


title: 1001700601_B8

value: TAAGGCGA-TGCATAACGT


title: 1001700601_A8

value: TAAGGCGA-CTAGCTACGT


title: 1001700601_D9

value: TAAGGCGA-TCTAATACGT


title: 1001700601_A6

value: TAAGGCGA-TCCTCTACGT


title: 1001700601_D3

value: TAAGGCGA-AAGCCTACGT


title: 1001700601_B10

value: TAAGGCGA-GTAAGAACGT


title: 1001700601_F14

value: CGTACTAG-TGCATAACGT


title: 1001700601_B3

value: dengue

value: TAAGGCGA-AAGGAGACGT


title: 1001700601_B7

value: TAAGGCGA-TAGAGTACGT


title: 1001700601_A4

value: TAAGGCGA-GACTAGACGT


title: F9_Suz12_sh

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mouse reference transcriptome (Ensembl 89) and genome (GRCm38, mm10) by STAR-2.5.2b [46] with parameters recommended by the ENCODE project
Transcripts per million (TPM) were calculated by RSEM with default parameters.
Differentially expressed genes were identified by edgeR-3.16.5 [49] given absolute fold change > 2 and FDR < 10-3
Genome_build: mm10

molecule: polyA RNA

organism: Mus musculus

source_name: F9 with Suz12 knockdown

growth_protocol: F9 cells were grown on 0.1% gelatin treated plates and grown in the high glucose DMEM media. Cells were sub cultured every 48h.

extract_protocol:
Total RNA was extracted by TRI-Solution and treated with DNaseI.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For differentiation, F9 cells were treated with 1uM RA for 3 days.

tag: tissue

value: Testis

tag: disease

value: Embryonal carcinoma

tag: morpology

value: Epithelial


title: F9_Eed_sh

source_name: F9 with Eed knockdown


title: F9_Ctrl_sh

source_name: F9 with control knockdown


title: F9_D0

source_name: Undifferentiated


title: 1001700601_A2

value: TAAGGCGA-CTCTATACGT


title: F9_Ezh2_sh

source_name: F9 with Ezh2 knockdown


title: F9_D3

source_name: Retinoic acid differentiated


title: nc HEY cells transfected with mir-429 at T48, biological rep2

type: RNA

city: New York

first: Loukia

last: Lili

state: NY

address: 770 Lexington Ave, 14-07 14th floor

department: Icahn School of Medicine at Mount Sinai

country: USA

institute: The Institute for Next Generation Healthcare

description: Gene expression data from HEY cells at 48hr mir-429 transfection

hyb_protocol: Human Genome U133 Plus 2.0 Arrays were hybridized, with rotation 60 rpm for 16 hr at 45˚C; then wash and stain with Fluidics protocol FS450_0001 (Affymetrix)

scan_protocol: Chips were scanned on Affymetrix GeneChip scanner 7G

data_processing: The data were analyzed with RMA method using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: HEY cells after 48hr of mir-429 transfection

label_protocol: RNA was converted into ds cDNA then amplified and Biotin labeled with Applause 3'-Amp System (NUGen)

growth_protocol: HEY cells (ATCC CRL-3252) were cultured in RPMI-1640 media with 10% FBS and 1% antibiotic-antimycotic solution. Transfection was carried out in exponentially growing cells

extract_protocol: RNA was extracted with RNeasy KIT from Qiagen according to manufacturer's instructions

treatment_protocol: HEY cells were transfected  (Lipofectamine 2000 -Invitrogen, Inc.) with mir-429 and a negative control micro-RNA (Ambion, Inc.)

value: HEY cell line

tag: transfection

tag: time point


title: nc HEY cells transfected with synthetic mirna at T144, biological rep3

description: Gene expression data from HEY cells at 144hr synthetic mirna transfection

source_name: HEY cells after 144hr of synthetic mirna transfection

value: synthetic mirna


title: nc HEY cells transfected with synthetic mirna at T48, biological rep1

description: Gene expression data from HEY cells at 48hr synthetic mirna transfection

source_name: HEY cells after 48hr of synthetic mirna transfection


title: nc HEY cells transfected with mir-429 at T48, biological rep3


title: nc HEY cells transfected with mir-429 at T48, biological rep1


title: HEY cells at T0, biological rep1

description: Gene expression data from HEY cells before transfection

source_name: HEY cells before transfection


title: nc HEY cells transfected with synthetic mirna at T144, biological rep2


title: nc HEY cells transfected with mir-429 at T144, biological rep1

description: Gene expression data from HEY cells at 144hr mir-429 transfection

source_name: HEY cells after 144hr of mir-429 transfection


title: nc HEY cells transfected with mir-429 at T24, biological rep1

description: Gene expression data from HEY cells at 24hr mir-429 transfection

source_name: HEY cells after 24hr of mir-429 transfection


title: nc HEY cells transfected with mir-429 at T24, biological rep3


title: nc HEY cells transfected with mir-429 at T144, biological rep2


title: nc HEY cells transfected with mir-429 at T144, biological rep3


title: nc HEY cells transfected with synthetic mirna at T144, biological rep1


title: nc HEY cells transfected with mir-429 at T24, biological rep2


title: Etoposide-treated TF1a cells, biological rep2

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from human AML cell line TF1a in vitro cultured with Etoposide for 6 days in ordinary culture medium

hyb_protocol: All steps of sense cDNA synthesis, fragmentation and hybridization were performed according to the manufacturer protocol (GeneAtlasR WT Expression Kit User Manual). To ensure optimum fragmentation the resulted fragmented sense cDNA was assessed using Agilent 2100 Bioanalyzer. The resulted fragmented whole transcript sense target was hybridized to Human Gene 2.1 Array Strips that have been designed with a median of 21 unique probes for each transcript. All steps of hybridization, washing, and scanning were carried out automatically by the GeneAtlasR microarray system (Affymetrix).

data_processing: The raw CEL files were normalized using the RMA background correction.

growth_protocol: TF1a cells were cultured in 10% FCS RPMI medium before counting and harvesting into RLT buffer for total RNA extraction.

extract_protocol: RNA was extracted and purified by using QIAamp RNA kits (52304; Qiagen) with DNase treatment according to the manufacturers’ instructions.

treatment_protocol: TF1a cells were cultured with or without TGFB1, rapamycin or etoposide for the indicated time point

tag: cell type

value: Acute Myeloid Leukaemia cells


title: HEY cells at T0, biological rep3


title: HEY cells at T0, biological rep2


title: nc HEY cells transfected with synthetic mirna at T24, biological rep1

description: Gene expression data from HEY cells at 24hr synthetic mirna transfection

source_name: HEY cells after 24hr of synthetic mirna transfection


title: nc HEY cells transfected with synthetic mirna at T24, biological rep3


title: nc HEY cells transfected with synthetic mirna at T48, biological rep2


title: nc HEY cells transfected with synthetic mirna at T48, biological rep3


title: nc HEY cells transfected with synthetic mirna at T24, biological rep2


title: recurrent prostate cancer sample #38

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: Labeled RNAs were heat denatured and hybridized to Agilent microarray at 55o C for 20 hr.

scan_protocol: After hybridization, slides were immediately washed and scanned in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA). Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images.

data_processing: Data were normalized by quantile normalization, using Bioconductor 2.10 with R version 2.15.

source_name: primary prostate cancer

label_protocol: 100 ng of total RNA from each sample were labeled with Cy3 by using Agilent miRNA labeling kit following manufacturer’s instructions.

extract_protocol: RNA was extracted using TRIzol (Invitrogen, San Diego, CA) method following the manufacturer’s protocol.

value: prostate cancer

tag: recurrence status

value: recurrent


title: recurrent prostate cancer sample #42


title: recurrent prostate cancer sample #39


title: recurrent prostate cancer sample #43


title: recurrent prostate cancer sample #35


title: TGFB1+Rapamycin-treated TF1a cells, biological rep2

description: Gene expression data from human AML cell line TF1a in vitro cultured with TGFB1+Rapamycin for 3 days in ordinary culture medium

scan_protocol: All steps of sense cDNA synthesis, fragmentation and hybridization were performed according to the manufacturer protocol (GeneAtlasR WT Expression Kit User Manual). To ensure optimum fragmentation the resulted fragmented sense cDNA was assessed using Agilent 2100 Bioanalyzer. The resulted fragmented whole transcript sense target was hybridized to Human Gene 2.1 Array Strips that have been designed with a median of 21 unique probes for each transcript. All steps of hybridization, washing, and scanning were carried out automatically by the GeneAtlasR microarray system (Affymetrix).


title: recurrent prostate cancer sample #41


title: TGFB1+Rapamycin-treated TF1a cells, biological rep3

label_protocol: All steps of sense cDNA synthesis, fragmentation and hybridization were performed according to the manufacturer protocol (GeneAtlasR WT Expression Kit User Manual). To ensure optimum fragmentation the resulted fragmented sense cDNA was assessed using Agilent 2100 Bioanalyzer. The resulted fragmented whole transcript sense target was hybridized to Human Gene 2.1 Array Strips that have been designed with a median of 21 unique probes for each transcript. All steps of hybridization, washing, and scanning were carried out automatically by the GeneAtlasR microarray system (Affymetrix).


title: recurrent prostate cancer sample #33


title: recurrent prostate cancer sample #31


title: recurrent prostate cancer sample #40


title: Etoposide-treated TF1a cells, biological rep1


title: Rapamycin-treated TF1a cells, biological rep2

description: Gene expression data from human AML cell line TF1a in vitro cultured with Rapamycin for 3 days in ordinary culture medium


title: Etoposide-treated TF1a cells, biological rep3


title: Rapamycin-treated TF1a cells, biological rep1


title: TGFB1-treated TF1a cells, biological rep2

description: Gene expression data from human AML cell line TF1a in vitro cultured with TGFB1 for 3 days in ordinary culture medium


title: Untreated TF1a cells, biological rep2

description: Gene expression data from human AML cell line TF1a in ordinary culture medium

source_name: Untreated TF1a cells, biological rep2


title: Untreated TF1a cells, biological rep1

source_name: Untreated TF1a cells, biological rep1


title: Untreated TF1a cells, biological rep3

source_name: Untreated TF1a cells, biological rep3


title: recurrent prostate cancer sample #37


title: recurrent prostate cancer sample #26


title: recurrent prostate cancer sample #36


title: TGFB1+Rapamycin-treated TF1a cells, biological rep1


title: TGFB1-treated TF1a cells, biological rep3


title: Rapamycin-treated TF1a cells, biological rep3


title: recurrent prostate cancer sample #34


title: recurrent prostate cancer sample #24


title: TGFB1-treated TF1a cells, biological rep1


title: recurrent prostate cancer sample #25


title: recurrent prostate cancer sample #22


title: B6_BAT_011

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

country: Germany

institute: Deutsches Institut für Ernährungsforschung

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: B6 mice in brown adipose tissue on HFD

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from murine tissue using TRIzol™ reagent (Invitrogen, Germany). From parental NZO and B6 mice (6 weeks of age), samples of gonadal white adipose tissue (gWAT), brown adipose tissue (BAT), and skeletal muscle were aliquoted for RNA extraction. The procedure was carried out according to manufacturer’s instructions. RNA quality was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) and the manufacturer’s instructions were followed to measure RNA integrity (RIN). Samples with RIN values >8 were subsequently selected for microarray analysis.

treatment_protocol: Mice were fed a high fat diet (45%, fat, Research Diets)

tag: strain

tag: gender

value: male

value: brown adipose tissue


title: non-recurrent prostate cancer sample #39

value: non-recurrent


title: recurrent prostate cancer sample #21


title: non-recurrent prostate cancer sample #38


title: recurrent prostate cancer sample #32


title: non-recurrent prostate cancer sample #36


title: recurrent prostate cancer sample #28


title: B6_quad_015

source_name: B6 mice in skeletal muscle on HFD

value: skeletal muscle


title: recurrent prostate cancer sample #27


title: B6_BAT_015


title: B6_BAT_009


title: B6_quad_011


title: B6_BAT_010


title: recurrent prostate cancer sample #23


title: Cell_40d_50ppm_rec_replicate 1

city: Nanjing

first: Junkang

last: Wu

state: Jiangsu

address: 2 Sipailou Street

department: Energy and environment

country: China

institute: Southeast University

description: Gene expression after 40-d exposure to 50ppm TiO2 NPs

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent N. europaea ATCC 19718 Microarrays (8x15K, Agilent Technologies) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37 °C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Present (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance  (P≤0.05, Fold-change ≥ 2.0) .were identified through Volcano Plot filtering.

organism: Nitrosomonas europaea ATCC 19718

source_name: Cell, 40d, 50ppm, rec

label_protocol: Sample labeling were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, USA) on the Agilent Array platform. Fluorescent cRNA was produced and labeled with Cy3-UTP using Quick Amp Labeling Kit, One-Color (Agilent Technologies, Inc., Palo Alto, CA, USA). The labeled cRNAs were then purified with RNeasy Mini Kit. The concentrations of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) before hybridization onto the N. europaea ATCC 19718 Microarray (8x15K, Agilent Technologies).

growth_protocol: N. europaea (ATCC 19718) cells were continuously cultured in a chemostat bioreactor with a 3 L working volume (hydraulic retention time: 2.2 d) at 25 °C in the dark. The dissolved oxygen (DO) concentration was maintained at (2.0 ± 0.2) mg/L by aeration of filter-sterilized air. The pH in the reactor was controlled at (7.45 ± 0.05) by automatic addition of saturated sterile NaHCO3 solution with a Meller pH controller (Taiwang, China). The cultivation medium containing 10 mM (NH4)2SO4 was the same as described before (Yu et al., 2015).

extract_protocol: The cells were collected by centrifuging 40 mL sample at 13,000 rpmm for 10 min. The pellet was immediately re-suspended in 1 mL Trizol solution (Invitrogen, Carlsbad, CA, USA) and stored at -80 °C. The total RNA was extracted with RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality control was accessed by electrophoresis on a denaturing agarose gel before microarray hybridization.

treatment_protocol: TiO2 NPs at 50 mg NPs/L were added into both the fresh meidum and the chemostat reactor to explore their long-term effects on N. europaea. Cell cultures were withdrew from reactor for Microarry analysis before NP treatment and after 12-d and 40-d exposure.

tag: stress

value: 50 ppm TiO2 NPs

tag: time


title: Cell_40d_50ppm_rec_replicate 2


title: Cell_12d_50ppm_exp_replicate 3

description: Gene expression after 12-d exposure to 50ppm TiO2 NPs

source_name: Cell, 12d, 50ppm, exp


title: Cell_12d_50ppm_exp_replicate 2


title: non-recurrent prostate cancer sample #37


title: Cell_40d_50ppm_rec_replicate 3


title: NZO_BAT_003

source_name: NZO mice in brown adipose tissue on HFD

value: NZO/HiBomDife


title: non-recurrent prostate cancer sample #33


title: NZO_BAT_011


title: NZO_BAT_007


title: NZO_BAT_009


title: non-recurrent prostate cancer sample #34


title: non-recurrent prostate cancer sample #31_2


title: B6_quad_009


title: Cell_12d_50ppm_exp_replicate 1


title: Cell_0d_0ppm_con_replicate 3

description: Gene expression of normal cells

source_name: Cell, 0d, 0ppm, con

value: control


title: non-recurrent prostate cancer sample #35


title: B6_quad_010


title: NZO_quad_003

source_name: NZO mice in skeletal muscle on HFD


title: non-recurrent prostate cancer sample #31


title: NZO_quad_007


title: Cell_0d_0ppm_con_replicate 2

description: Gene expression of normal cells


title: Cell_0d_0ppm_con_replicate 1

description: Gene expression of normal cells


title: non-recurrent prostate cancer sample #30


title: non-recurrent prostate cancer sample #29


title: NZO_quad_009


title: B6_gWAT_009

source_name: B6 mice in gonadal white adipose tissue on HFD

value: gonadal white adipose tissue


title: non-recurrent prostate cancer sample #28


title: non-recurrent prostate cancer sample #27


title: NZO_quad_011


title: NIH3T3-H3.3T32IGFP-UnInfect

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka

department: Medical Institute of Bioregulation, Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
processed data file:
countMatrix_GENCODEvM9_3T3RNAseq_inclMut.txt.gz

data_processing:
The raw sequence reads were aligned to mouse genome (GRCm38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained for ChIP-seq/ATAC-seq analysis.
The matrices of read counts on gencode genes (release M9) were generated using featureCounts (version 1.5.0-p3). For ATAC-seq, the option of featureCounts: -B -C -P -d 20 -D 150, were used to extract subnucleosomal fraction.
The coverage tracks of ATAC-seq (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.txt files include tab-delimited read count matrices

growth_protocol: NIH3T3 cells were infected with retrovirus expressing MyoD.

extract_protocol: Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 15 cycles. Following PCR amplification, the libraries were purified using a Qiagen MinElute kit.

treatment_protocol: Total RNA was isolated and reversed-transcribed with PrimeScript Reverse Transcriptase (Takara Bio Inc.) and an oligo dT primer.

tag: cell line


title: B6_gWAT_011


title: NIH3T3-H3.3T32IGFP-0h


title: NIH3T3-H3.3T32IGFP-48h


title: NIH3T3-H3.3S57AGFP-24h


title: NIH3T3-H3.3S57AGFP-48h


title: NIH3T3-H3.3T32IGFP-24h


title: non-recurrent prostate cancer sample #25


title: B6_gWAT_015


title: non-recurrent prostate cancer sample #22


title: non-recurrent prostate cancer sample #24


title: non-recurrent prostate cancer sample #26


title: NZO_gWAT_003

source_name: NZO mice in gonadal white adipose tissue on HFD


title: non-recurrent prostate cancer sample #21


title: NZO_gWAT_007


title: B6_gWAT_010


title: NIH3T3-H3.3S57AGFP-UnInfect


title: NZO_gWAT_009


title: non-recurrent prostate cancer sample #23


title: NZO_gWAT_012


title: ATAC-C2C12-WT-72h-lot2

description:
processed data file:
countMatrix_GENCODEvM9_C2C12ATAC_subNuc20-150_exonUp2k.txt.gz

library_source: genomic

molecule: genomic DNA

growth_protocol: C2C12 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60%–70% confluence. Differentiated cells were transferred to DMEM containing 2% horse serum upon reaching confluence.

treatment_protocol: 50,000 sorted cells were centrifuged at 800 × g for 5 min, followed by a wash using 500 µl of cold PBS and centrifugation at 800 × g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 min using a refrigerated centrifuge. Next, the pellet was resuspended in the transposase reaction mix (10 µl of 2× TAPS+DMF buffer, 1.5 µl transposase (in house) and 8.5 µl nuclease-free water). The transposition reaction was carried out for 30 min at 37°C and immediately placed on ice. Directly afterwards, the sample was purified using a Qiagen MinElute kit.


title: ATAC-C2C12-WT-G-lot1


title: ATAC-C2C12-WT-G-lot2


title: ATAC-C2C12-WT-72h-lot1


title: ATAC-C2C12-H3mm7KO-G-lot1


title: NIH3T3-H3.3S57AGFP-0h


title: THP-1(Single-Crosslinking)

city: Wuhan

first: Ping

last: Hong

state: Hubei

address: No.1,Shizishan Street

department: college of informatics

institute: Huazhong Agricultural University

description: THP-1 cell lines single cross-linking DLO Hi-C data

data_processing:
ChIA-PET Tool used for linker filtering
Two end of interacted fragments were seperated by the command awk
Two end of interacted fragments were separately mapped to hg19 by bwa v0.7.12-r1039 with the parameter -n 0, and then unique mapping reads were conserved
Samtools v1.2 was used to transfer the sam format to bed format
Two end bed format files were combined to bedpe file by a perl script
Redundancies and same fragment interactions were discard by perl scripts
The bedpe format file sorted by the command sort
The sorted file transferred to matrix by a python script
The matrix normalized by ICE
Locations of topologically associated domains (TADs) were computed using the scripts provided by Dixon et al. 2012 (PMID: 22495300)
Genome_build: hg19
Supplementary_files_format_and_content: The THP-1_HindIII.TADs.bed, THP-1_BglII.TADs.bed and THP-1_MseI.TADs.bed contain the coordinates of TADs

source_name: peripheral blood monocyte cells

growth_protocol: K562 (ATCC, CCL-243) and THP-1 (ATCC, TIB-202) cells were grown in RPMI-1640 with 10% FBS.

extract_protocol: Follow DLO Hi-C library construction protocol. Cells were double cross-linked with EGS and formaldehyde and then digested with a restriction enzyme. The digested chromatins were divided into two tubes, ligated with different 20-bp half linkers by the simultaneous digestion and ligation, and subsequently mixed for in-gel proximity ligation. The ligated DNA was purified and digested by MmeI, which released specific 80-bp DLO Hi-C DNA fragments. These DLO Hi-C DNA fragments were ligated with Illumina adapters and subjected to high-throughput sequencing

treatment_protocol: Without treatment

value: peripheral blood monocyte cells


title: ATAC-C2C12-H3mm7KO-72h-lot2


title: K562

description: K562 cell lines DLO Hi-C data

source_name: human erythroleukemic cell line

value: human erythroleukemic cell line


title: ATAC-C2C12-H3mm7KO-24h-lot1


title: ATAC-C2C12-H3mm7KO-24h-lot2


title: ATAC-C2C12-H3mm7KO-72h-lot1


title: ATAC-C2C12-WT-24h-lot2


title: ATAC-C2C12-WT-24h-lot1


title: ATAC-C2C12-H3mm7KO-G-lot2


title: piglet pig milk replacer with sialyllactose rep9

city: Beijing

first: yujie

last: shi

address: No.5 building No.5 Road Dijin

institute: Nestle research center- Beijing hub

description: Gene expression data from piglet retina of pig milk replacer with sialyllactose

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000 7G system.

data_processing: The data were analyzed with Expression console software using Robust Multichip Average(RMA) as normalization method.

label: Biotin

organism: Sus scrofa

source_name: piglet retina, pig milk replacer with sialyllactose, postnatal day 38

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Three-day-old male domestic piglets (Sus scrofa, Landrace×Large White cross) were purchased from a commercial piggery in Xiamen City, China and randomly placed in the 2 groups. All animals were kept in the temperature-controlled environment with a 12-h light (08:00~20:00) and a 12-h dark (20:00~08:00) cycle. The home pens contained a “nest” (a rubber tire covered with a clean towel), a heat lamp over the nest and an identical woody toy hang in the home pen. All facilities (including home pens and behavior room) were monitored for 24-h. The feeding time was fixed as 8:00, 13:00, 18:00, 22:30, with an extra 50mL milk/pig supplied at the last feeding.

extract_protocol: The extraction of total RNA was performed using Agencourt RNAdvance tissue kit according to the manufacturer's instructions.

treatment_protocol: Pig retina samples were collected after sacrifice and immediately stored in liquid nitrogen tank until RNA extraction.

value: Domestic pig (Landrace x Large White)

value: retina

tag: age

value: postnatal day 38

tag: treatment group

value: sialyllactose supplement group


title: piglet pig milk replacer with sialyllactose rep5


title: piglet pig milk replacer with sialyllactose rep8


title: piglet pig milk replacer rep9

description: Gene expression data from piglet retina of pig milk replacer

source_name: piglet retina, pig milk replacer, postnatal day 38

value: control group feeding basal level


title: Th-05

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

institute: NAR Center, Inc. & Genoplan, Inc.

description: thymus_5 from male BALB/c mouse (six weeks old)

hyb_protocol: After cleaning and fragmentation, a total of fifty cDNA samples from each of 10 different tissues collected from the five mice were hybridized using the Mouse gene 1.0 ST array for 16 h.

scan_protocol: After washing and staining with streptavidin phycoerythrin solution and antibody solution, images were obtained by capturing the fluorescence intensity using a GMS 418 Array Scanner.

data_processing: Microarray data were uploaded using GenPlexTM v3.0 (Istech Inc., Korea) and GeneSpring GX 7.3 software (Agilent Technology) and normalized with RMA. Further statistical analyses were performed primarily using tools included in GenPlex and GeneSpring GX 7.3. Functional annotation of genes was performed per the Gene Ontology™ Consortium (http://www.geneontology.org/index.shtml). Gene classification was based on searches using the GeneCards (http://www.genecards.org/), BioCarta (http://www.biocarta.com/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline (http://www.ncbi.nlm.nih.gov/) databases.

source_name: thymus

label_protocol: cDNA was synthesized from total RNA (100 ng) using a T7 oligomer and Superscript RT II kit, and cDNA was purified with a QIAquick PCR Purification Kit. Next, biotin-labeled cRNA was synthesized using an Affymetrix RNA transcription labeling kit.

growth_protocol: The mice were housed in an auto-controlled pathogen-free animal room at 22 ± 2°C under a 12:12 h light/dark cycle, and they were provided with commercial pellets and tap water ad libitum for five weeks. The mice were sacrificed by complete blood collection via the inferior vena cava under anesthesia with ether. The spleen, liver, left kidney, left testis, stomach, thymus, lung, heart, brain, and left rectus femoris muscle were removed in that order and then stored in RNAlater solution at -20°C. Experiments were designed and performed in strict accordance with the Guide for the Care and Use of Laboratory Animals (8TH edition, NIH update 2011) and approved by the Institutional Animal Care and Use Committee of Daejeon University (Animal ethical clearance number: DJUARB 2016-034 to 6).

extract_protocol: Total RNA was extracted using the RNeasy midi kit according to the manufacturer's instructions. RNA quality and concentration were assessed using an Agilent Bioanalyzer 2100 and a NanoDrop ND-1000 spectrophotometer, respectively. The absorbance ratio at 260:280 nm for all samples was >1.8 and the RIN value was >8. The integrity of RNA samples was also ascertained by the presence of distinct 28S and 18S ribosomal RNA bands in agarose gels after electrophoretic resolution.

value: six weeks old

value: BALB/c


title: Th-01

description: thymus_1 from male BALB/c mouse (six weeks old)

value: male


title: St-03

description: stomach_3 from male BALB/c mouse (six weeks old)

source_name: stomach


title: St-04

description: stomach_4 from male BALB/c mouse (six weeks old)


title: piglet pig milk replacer with sialyllactose rep7


title: St-05

description: stomach_5 from male BALB/c mouse (six weeks old)


title: Raptinal_B

city: Urbana

first: Kathryn

last: Partlow

address: 1301 West Gregory Drive

institute: University of Illinois, Urbana-Champaign

hyb_protocol: 10 ug of biotinylated shRNA target was hybridized to Affymetrix GeneChip using the manufacturer’s standard protocols.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: The CEL files were processed with System Biosciences' GeneNet™ siRNA Library Data Analysis Software (ver. 5 -06.28.10), which outputs raw probe-level values for only the 216,351 probes that can be used to interrogate the 27-bp siRNA sequences. GeneNet only outputs the siRNA sense sequence and the probe set ID for each raw probe value, but not the individual probe ID. The individual probe IDs were obtained by matching the raw probe-level values + probe set IDs using R (v 3.1.2) and the affy package (1.44.0). The original output from GeneNet with the siRNA sequences plus the matching probe IDs are in the supplementary file GeneNet_Annotation.xlsx.

source_name: MIA PaCa-2 pancreatic cancer cell line (ATCC CRL-1420), 1.25-1.8 micromolar Raptinal treatment, 20 days, biological replicate B

label_protocol: 5 ug RNA was reverse transcribed using specific GNF/GNH primers and M-MLV Reverse Transcriptase. Following RT, shRNA inserts from cDNA were PCR amplified with GNF/GNH forward and reverse primers, followed by a second round of PCR using GNF/GNH nested reverse primers and forward biotinylated primers. Amplicons were confirmed by gel electrophoresis and products were cleaned using QIAquick PCR cleanup columns. The sense non-biotinylated strand was removed with a Lambda Exonuclease treatment, checked by gel electrophoresis and cleaned again with the QIAquick columns.

growth_protocol: DMEM media with 10% FBS and 1% Penicillin-Streptomycin

extract_protocol: Total RNA exraction was performed from 8 million cells per sample using the Qiagen Rneasy kit, without on-column DNAse treatment. Quality of total RNA was determined by Agilent Bioanalyzer.

treatment_protocol: Cells were transduced with GeneNet Human 50K Plasmid siRNA Library in pSIF1-H1-copGFP vector (200,000 shRNA constructs targeting 47,400 transcripts) at MOI of 0.5-0.7. After 24 hours, the media was replaced and the cells expanded for 72 hours, after which treatment with Raptinal (1.5 µM, 2 biological replicates) or DMSO was commenced. After every 2-3 days of drug treatment, cells were allowed to recover in drug-free medium and three rounds of treatment (1.25-1.8 µM Raptinal) were performed over 20 days with cell passaging on a scale sufficient to maintain >100 fold library representation.

value: MIA PaCa-2

value: human pancreatic cancer cell line

tag: treatment

value: Raptinal


title: St-02

description: stomach_2 from male BALB/c mouse (six weeks old)


title: piglet pig milk replacer with sialyllactose rep3


title: piglet pig milk replacer with sialyllactose rep6


title: piglet pig milk replacer with sialyllactose rep2


title: Th-02

description: thymus_2 from male BALB/c mouse (six weeks old)


title: Control

source_name: MIA PaCa-2 pancreatic cancer cell line (ATCC CRL-1420), DMSO treated, 20 days

value: DMSO (vehicle)


title: Th-04

description: thymus_4 from male BALB/c mouse (six weeks old)


title: Th-03

description: thymus_3 from male BALB/c mouse (six weeks old)


title: Raptinal_A

source_name: MIA PaCa-2 pancreatic cancer cell line (ATCC CRL-1420), 1.25-1.8 micromolar Raptinal treatment, 20 days, biological replicate A


title: Sp-04

description: spleen_4 from male BALB/c mouse (six weeks old)

source_name: spleen


title: piglet pig milk replacer rep6


title: St-01

description: stomach_1 from male BALB/c mouse (six weeks old)


title: piglet pig milk replacer with sialyllactose rep1


title: piglet pig milk replacer rep8


title: Sp-05

description: spleen_5 from male BALB/c mouse (six weeks old)


title: piglet pig milk replacer rep7


title: piglet pig milk replacer with sialyllactose rep4


title: piglet pig milk replacer rep5


title: piglet pig milk replacer rep4


title: Sp-02

description: spleen_2 from male BALB/c mouse (six weeks old)


title: Sp-01

description: spleen_1 from male BALB/c mouse (six weeks old)


title: Ki-05

description: kidney_5 from male BALB/c mouse (six weeks old)

source_name: kidney


title: piglet pig milk replacer rep2


title: Ki-04

description: kidney_4 from male BALB/c mouse (six weeks old)


title: piglet pig milk replacer rep3

description: Gene expression data from piglet retina of pig milk replacer


title: piglet pig milk replacer rep1


title: Ki-02

description: kidney_2 from male BALB/c mouse (six weeks old)


title: BxPC-3 rep1 [miRNA]

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

hyb_protocol: According to mfg protocol; 16 hour incubation in GeneChip Hybridisation Oven 640 (48°C for miRNA 3.0 arrays). Washing and Staining according to mfg protocol on GeneChip Fluidics Station  450.

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing:
After scanning, CEL files were processed using the Affymetrix MiRNA QC TOOL.
miRNA-3_0.probe_list.20120906.txt
miRNA-3_0-st-v1.annotations.20140513.csv

source_name: CDX

label_protocol: 1 μg of total RNA was used for labeling with FlashTag® Biotin HSR Kit (Genisphare).

growth_protocol: Mice were housed in Macrolon® type II or III cages, soiled with bedding, in groups of 3 or 7-10 at 21.5 ± 1.5 °C temperature and 55 ± 10 % humidity in a 12h/12h light/dark cycle. Standardized diet and autoclaved tap water were provided ad libitum. Subcutaneous microchips implanted under isoflurane anesthesia were used for identification.

extract_protocol: RNA was extracted from cryo-sections of xenograft tumors using TRIzol® (Life Technologies) and purified using a miRNeasy Mini kit (Qiagen).

treatment_protocol: For efficacy studies, 1 x 10^7 MIA PaCa-2 or 1 x 10^6 BxPC-3 cells (with Matrigel® 50:50) were injected subcutaneously into the right flank of female BomTac:NMRI-Foxn1nu mice (age 6 weeks, 24-30 g); Taconic, Denmark). Mice were randomized according to tumor volume when tumors had reached diameters of 6-8 mm. BI 853520 suspended in 1 mol/L HCl and diluted with 0.5 % Natrosol® was administered intragastrally at 10 ml/kg once daily (n = 7 for BxPC-3 and n = 10 for MIA PaCa-2). Natrosol-treated animals served as vehicle controls (n = 10). Tumor diameters were measured three times weekly using a caliper and volumes were calculated according to the formula tumor volume = length*diameter2*π/6.

tag: organ derivation

value: Pancreas


title: Sp-03

description: spleen_3 from male BALB/c mouse (six weeks old)


title: SK-OV-3 rep1 [miRNA]

value: Ovary


title: BxPC-3 rep2 [miRNA]


title: Li-03

description: liver_3 from male BALB/c mouse (six weeks old)

source_name: liver


title: SK-OV-3 rep2 [miRNA]


title: Li-01

description: liver_1 from male BALB/c mouse (six weeks old)


title: PANC-1 rep1 [miRNA]


title: SK-OV-3 rep3 [miRNA]


title: Li-02

description: liver_2 from male BALB/c mouse (six weeks old)


title: Ki-03

description: kidney_3 from male BALB/c mouse (six weeks old)


title: Lu-04

description: lung_4 from male BALB/c mouse (six weeks old)

source_name: lung


title: Li-05

description: liver_5 from male BALB/c mouse (six weeks old)


title: PC-3 rep2 [miRNA]

value: Prostate


title: PANC-1 rep2 [miRNA]


title: Ki-01

description: kidney_1 from male BALB/c mouse (six weeks old)


title: NCI-H2110 rep2 [miRNA]

value: Lung


title: NCI-H2110 rep3 [miRNA]


title: Lu-05

description: lung_5 from male BALB/c mouse (six weeks old)


title: Li-04

description: liver_4 from male BALB/c mouse (six weeks old)


title: Lu-03

description: lung_3 from male BALB/c mouse (six weeks old)


title: Mu-05

description: muscle_5 from male BALB/c mouse (six weeks old)

source_name: muscle


title: MIA PaCa-2 rep2 [miRNA]


title: MIA PaCa-2 rep3 [miRNA]


title: TOV-21G rep1 [miRNA]


title: Lu-02

description: lung_2 from male BALB/c mouse (six weeks old)


title: PC-3 rep1 [miRNA]


title: TOV-21G rep2 [miRNA]


title: MIA PaCa-2 rep1 [miRNA]


title: He-02

description: heart_2 from male BALB/c mouse (six weeks old)

source_name: heart


title: Mu-03

description: muscle_3 from male BALB/c mouse (six weeks old)


title: HCC-461 rep2 [miRNA]


title: AsPC-1 rep2 [miRNA]


title: Mu-02

description: muscle_2 from male BALB/c mouse (six weeks old)


title: He-05

description: heart_5 from male BALB/c mouse (six weeks old)


title: Lu-01

description: lung_1 from male BALB/c mouse (six weeks old)


title: AsPC-1 rep1 [miRNA]


title: He-04

description: heart_4 from male BALB/c mouse (six weeks old)


title: Mu-01

description: muscle_1 from male BALB/c mouse (six weeks old)


title: A-498 rep3 [miRNA]

value: Kidney


title: A-498 rep1 [miRNA]


title: A-498 rep2 [miRNA]


title: He-01

description: heart_1 from male BALB/c mouse (six weeks old)


title: He-03

description: heart_3 from male BALB/c mouse (six weeks old)


title: Mu-04

description: muscle_4 from male BALB/c mouse (six weeks old)


title: HCC-461 rep1 [miRNA]


title: Te-04

description: testis_4 from male BALB/c mouse (six weeks old)

source_name: testis


title: Hs 746T rep3 [miRNA]

value: Stomach

value: Hs 746T


title: Hs 746T rep2 [miRNA]


title: NCI-H2122 rep3 [miRNA]


title: Hs 746T rep1 [miRNA]


title: Te-05

description: testis_5 from male BALB/c mouse (six weeks old)


title: Te-02

description: testis_2 from male BALB/c mouse (six weeks old)


title: Te-01

description: testis_1 from male BALB/c mouse (six weeks old)


title: Calu-6 rep3 [miRNA]


title: Ce-03

description: cerebrum_3 from male BALB/c mouse (six weeks old)

source_name: cerebrum


title: Calu-6 rep2 [miRNA]


title: NCI-H2122 rep1 [miRNA]


title: Ce-01

description: cerebrum_1 from male BALB/c mouse (six weeks old)


title: Ce-02

description: cerebrum_2 from male BALB/c mouse (six weeks old)


title: WT neuron PR50 - 3

city: Boston

first: Nicholas

middle: J

last: Kramer

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: WT_neurons_PR50_vs_GFP_resultsOrderedDF.csv

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: hg38 for human samples, mm10 for mouse samples
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: primary cortical neuron cultures

extract_protocol:
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

value: PR50 Lenti

tag: experiment grouping

value: Experiment 3


title: LoVo rep1 [miRNA]

value: Colon/Rectum

value: LoVo


title: Calu-6 rep1 [miRNA]


title: WT neuron PR50 - 2


title: SW480 rep1 [miRNA]


title: SW480 rep2 [miRNA]


title: WT neuron PR50 - 1


title: Ce-04

description: cerebrum_4 from male BALB/c mouse (six weeks old)

value: six weeks old

value: BALB/c


title: LoVo rep2 [miRNA]


title: NCI-H2122 rep2 [miRNA]


title: Ce-05

description: cerebrum_5 from male BALB/c mouse (six weeks old)

value: male


title: Suz12_sh_H3K27me3

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were mapped to mm10 genome using bowtie2-2.3.2
Duplicates were removed by picard-tools-2.10.2 (Broad Institute)
Enriched regions were identified with hiddenDomain-2.3, defalt parameters.
Genome_build: mm10

source_name: F9 cells

growth_protocol: F9 cells were grown om 0.1% gelatin coated plates and subcultured every 48 hours.

extract_protocol:
Cells were crosslinked, sonicated and protein were immunoprecipitated by antibodies.
DNA libraries were constructed by standard illumina protocol.

treatment_protocol: F9 cells were treated with 1uM RA for 3 days.

tag: tisse

value: Testis

value: Embryonal carcinoma

value: Epithelial


title: WT neuron Ctl - 3

value: GFP Control Lenti


title: Te-03

description: testis_3 from male BALB/c mouse (six weeks old)


title: WT neuron Ctl - 2


title: Ezh2_sh_H3K27me3

tag: disease


title: WT neuron Ctl - 1


title: Eed_sh_H3K27me3

tag: morpology


title: abdominal aortic aneurysm sample#47

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

description: sample#47-abdominal_aortic_aneurysms-ruptured-large

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and background substraction and log2 transformed using limma package for R (Bioconductor).

source_name: Abdominal aortic aneurysm (human infrarenal aneurysmatic aortic wall)

label_protocol: cRNA was prepared  using the TargetAmp™- Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, Madison, WI, USA).

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: infrarenal aortic wall

tag: group of aortic aneurysms

value: ruptured abdominal aortic aneurysms (rAAA)

tag: diameter of aortic aneurysms

value: large size abdominal aortic aneurysms


title: abdominal aortic aneurysm sample#45

description: sample#45-abdominal_aortic_aneurysms-ruptured-large


title: pp_rep2

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: Gene expression data from iPS derived pancreatic precursor cells, biological replicate 2

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression data were RMA normalized using the oligo package (version 1.38.0)

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen)

growth_protocol: XM001 iPSCs were cultured on 1:100 diluted Matrigel (BD Biosciences) in mTeSR™1 medium (Stem Cell Technologies). At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) followed by incubation with 1× TrypLE Select Enzyme (Life Technology) for 3–5 min at 37 °C. Single cells were rinsed with mTeSR™1 medium, and spun at 1,000 rpm for 3 min. The resulting cell pellet was resuspended in mTeSR™1 medium supplemented with 10 μM Y-27632 (Sigma-Aldrich) and the single cell suspension was seeded at ~1.0 × 105 cells/cm² on Matrigel-coated surfaces. Cultures were fed every day with mTeSR™1 medium and differentiation was initiated 48 h following seeding, resulting in ~90% starting confluency.

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol: XM001 iPSCs plated on 1:100 diluted Matrigel were first rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) and then cultured in RPMI 1640 medium (Invitrogen) further supplemented with 1.2 g/L sodium bicarbonate (Sigma), 0.2% ESC-qualified FBS (Life Technologies), 100 ng/mL Activin-A (R&D Systems), and 20 ng/mL of Wnt3A (R&D Systems) for day 1 only. For the next 2 days, cells were cultured in RPMI with 0.5% FBS, 1.2g/L sodium bicarbonate and 100 ng/mL Activin-A ; Cells were rinsed with 1× DPBS (without Mg2+ and Ca2+) once and then exposed to DMEM-F12 (Life Technologies) medium further supplemented with 2 g/L sodium bicarbonate, 2% FBS and 50 ng/mL of FGF7 (R&D Systems) for 3 days; Cultures were maintained for 4 days in DMEM-HG medium (Life Technologies) supplemented with 0.25 µM SANT-1 (Sigma-Aldrich), 2 µM retinoic acid (RA; Sigma-Aldrich), 100 ng/mL of Noggin (R&D Systems), and 1% B27 (Invitrogen).

tag: cell type

value: iPS derived pancreatic precursor cells


title: TMX2 (PR50) - 3

description: SafePR50_vs_TMX2PR50-ExpDiff (neurons).csv

value: TMX2 sgRNAs (+PR50 lenti)

value: Experiment 2


title: abdominal aortic aneurysm sample#48

description: sample#48-abdominal_aortic_aneurysms-ruptured-large


title: abdominal aortic aneurysm sample#43

description: sample#43-abdominal_aortic_aneurysms-ruptured-large


title: iPS_rep2

description: Gene expression data from iPS cells, biological replicate 2

scan_protocol: According to the Affymetrix expression protocol

source_name: iPS cells, biological replicate 2

value: iPS cells


title: TMX2 (PR50) - 2


title: D3_H3K27me3


title: abdominal aortic aneurysm sample#41

description: sample#41-abdominal_aortic_aneurysms-ruptured-large


title: abdominal aortic aneurysm sample#46

description: sample#46-abdominal_aortic_aneurysms-ruptured-large


title: iPS_rep1

description: Gene expression data from iPS cells, biological replicate 1

source_name: iPS cells, biological replicate 1


title: D3_Ezh2


title: TMX2 (PR50) - 1


title: pp_rep1

description: Gene expression data from iPS derived pancreatic precursor cells, biological replicate 1


title: abdominal aortic aneurysm sample#44

description: sample#44-abdominal_aortic_aneurysms-ruptured-large


title: abdominal aortic aneurysm sample#42

description: sample#42-abdominal_aortic_aneurysms-ruptured-large


title: abdominal aortic aneurysm sample#40

description: sample#40-abdominal_aortic_aneurysms-ruptured-large


title: D0_H3K27me3


title: NCI-H2110 rep1 [miRNA]

value: Lung


title: Safe (PR50) - 3

value: Control sgRNAs (+PR50 lenti)


title: Safe (PR50) - 2


title: Safe (PR50) - 1


title: abdominal aortic aneurysm sample#38

description: sample#38-abdominal_aortic_aneurysms-elective-large

value: elective stable abdominal aortic aneurysms (eAAA)


title: Ctrl_sh_H3K27me3


title: D0_Ezh2


title: abdominal aortic aneurysm sample#37

description: sample#37-abdominal_aortic_aneurysms-elective-large


title: abdominal aortic aneurysm sample#39

description: sample#39-abdominal_aortic_aneurysms-elective-large


title: Day14-Uninjured-WT-rep2

description:
processed data file:
countMatrix_CELSeq_MuscleInjury.txt.gz

source_name: Injured TA muscle from wild-type mouse

growth_protocol: Muscle injury was induced by the intramuscular injection of 100 ul CTX.

extract_protocol: Libraries were prepared according to the protocol described in Hashimshony, T. et al. (Genome Biol. 2016).

treatment_protocol: At days 5 and 14 after cardiotoxin injection, cryosections of injured (left leg) and uninjured (right) tibialis anterior muscle were prepared from H3mm7+/+ and H3mm7-/- mice.

tag: genotype/variation

value: wild-type

value: Injured TA muscle


title: Day14-Uninjured-WT-rep1


title: abdominal aortic aneurysm sample#35

description: sample#35-abdominal_aortic_aneurysms-elective-large