title: gng_p9_d9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e10

status: Public on Mar 23 2018

type: SRA

city: Cambridge

first: Shristi

last: Pandey

address: 16 Divinity Ave

department: Molecular and Cellular Biology

country: USA

institute: Harvard University

description: HHKCVBGXY.RSEM.genes

library_source: transcriptomic

data_processing:
Reads were aligned to a reference genome (Zv10 ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: Zv10
Supplementary_files_format_and_content: text file with tab delimiters

molecule: total RNA

organism: Danio rerio

source_name: Danio Rerio, 10days post fertilization

extract_protocol:
Dissociated brains were FAC sorted into 96 well plates(single cells) containing lysis buffer
Smart-seq2 (Picelli et al., Nature Methods, 2014)

tag: genotype

tag: tissue

value: brain

tag: cell type

value: 10days post fertilization habenula


title: gng_p9_d7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d10

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c8

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c10

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_e12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b8

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b7

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_c6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_d11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b11

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a9

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b10

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a5

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a4

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a2

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h6

description: HHKCVBGXY.RSEM.genes


title: gng_p9_b5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h1

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h3

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h12

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_h11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g1

description: HHKCVBGXY.RSEM.genes


title: gng_p9_a11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g3

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_g11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f3

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f1

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_f9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e3

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e1

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_e11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d3

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d1

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c1

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b1

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b10

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_d11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b3

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_c3

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a7

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a6

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a5

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a4

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a11

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a2

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h8

description: HHKCVBGXY.RSEM.genes


title: gng_p8_b8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h9

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g12

description: HHKCVBGXY.RSEM.genes


title: gng_p8_a10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_g10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_h5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_f1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_d10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_e12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b10

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a7

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b11

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a4

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a6

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a5

description: HHKCVBGXY.RSEM.genes


title: gng_p7_c2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a8

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a1

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a3

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h9

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a12

description: HHKCVBGXY.RSEM.genes


title: gng_p7_a11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h2

description: HHKCVBGXY.RSEM.genes


title: gng_p7_b3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_h11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_g4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_f10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_e12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_d11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b10

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b11

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a7

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a8

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a4

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a5

description: HHKCVBGXY.RSEM.genes


title: gng_p6_c3

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a9

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a6

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a2

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b12

description: HHKCVBGXY.RSEM.genes


title: gng_p6_a1

description: HHKCVBGXY.RSEM.genes


title: gng_p6_b3

description: HHKCVBGXY.RSEM.genes


title: gng_p4_h7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g4

description: HGJMWBGXY.RSEM.genes


title: gng_p6_a10

description: HHKCVBGXY.RSEM.genes


title: gng_p4_g3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g7

description: HGJMWBGXY.RSEM.genes


title: gng_p6_a11

description: HHKCVBGXY.RSEM.genes


title: gng_p4_g6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_h2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_g11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_f2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_d12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_e10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b11

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_b12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a7

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a6

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a8

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_c9

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a4

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a3

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a12

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a5

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a2

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a1

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a10

description: HGJMWBGXY.RSEM.genes


title: gng_p4_a11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_h1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_g6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_e10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_f12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_d12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b7

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b1

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b12

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a3

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a2

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h6

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a11

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a10

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a12

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h8

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b5

description: HGJMWBGXY.RSEM.genes


title: gng_p3_b6

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h5

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h4

description: HGJMWBGXY.RSEM.genes


title: gng_p3_c10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h2

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h3

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h12

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g9

description: HGJMWBGXY.RSEM.genes


title: gng_p3_a7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g8

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g6

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g5

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g4

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g3

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_h1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g2

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g12

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_g10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f6

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f8

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f5

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f4

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f3

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f2

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f12

description: HGJMWBGXY.RSEM.genes


title: Urso_3

type: RNA

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Fluorescent targets were hybridized to Human Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: The slides were scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by Genepix 4.1 software (Molecular Devices, Sunnyvale, CA, USA). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 0 or control probes. Spots that pass aforementioned criteria were normalized by R program in the limma package.

organism: Homo sapiens

source_name: HepG2 cells

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNAs were extracted using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: HepG2 cells were treated with 25 μM glycyrrhizin, silymarin, or ursodeoxycholic acid.

tag: cell line

value: Hepatocarcinoma cell line HepG2

tag: agent

value: Urso


title: Urso_2


title: Gly_3

value: Gly


title: Urso_1


title: Gly_2


title: Mock_1

value: Ctrl


title: gng_p2_e8

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e6

description: HGJMWBGXY.RSEM.genes


title: Sil_1

value: Sil


title: gng_p2_e7

description: HGJMWBGXY.RSEM.genes


title: Sil_3


title: Gly_1


title: Sil_2


title: Mock_3


title: gng_p2_e5

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e4

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e2

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e3

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e12

description: HGJMWBGXY.RSEM.genes


title: Mock_2


title: gng_p2_e11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_f10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d8

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d6

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d5

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d4

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d2

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d3

description: HGJMWBGXY.RSEM.genes


title: gng_p2_e10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d12

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c8

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_d7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c6

description: HGJMWBGXY.RSEM.genes


title: Tum pDC PBS 1

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw counts measurements

organism: Mus musculus

source_name: tumor pDC PBS

extract_protocol:
Tumor were excised, digested and tumor-associated plasmacytoid and conventional dendritic cells were FACS-sorted. They were collected in RNAprotect Cell Reagent (Qiagen). RNA was isolated using RNeasy Plus Micro kit (Qiagen)
cDNA libraries were constructed by the Genomic platform of the University of Geneva as followed: the SMARTer™ Ultra Low RNA kit from Clontech was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 1 ng of total RNA. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina.Pools of 10 libraries were loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

tag: strain background

tag: genotype/variation

value: wild type

tag: age

value: 10 weeks

tag: injected with

value: PBS

value: tumor-associated plasmacytoid dendritic cells (pDC)


title: Tum pDC PBS 4


title: Tum pDC PBS 2


title: Tum pDC CpG-B 4

source_name: tumor pDC CpG-B

value: CpG-B


title: gng_p2_c5

description: HGJMWBGXY.RSEM.genes


title: Tum pDC PBS 3


title: gng_p2_c4

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c3

description: HGJMWBGXY.RSEM.genes


title: Tum pDC CpG-B 3


title: gng_p2_c2

description: HGJMWBGXY.RSEM.genes


title: Tum pDC CpG-B 1


title: gng_p2_c12

description: HGJMWBGXY.RSEM.genes


title: Tum pDC CpG-B 2


title: Tum cDC PBS 3

source_name: tumor cDC PBS

value: conventional dendritic cells


title: Tum cDC PBS 2


title: gng_p2_b9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_c1

description: HGJMWBGXY.RSEM.genes


title: Tum cDC PBS 1


title: gng_p2_c10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b8

description: HGJMWBGXY.RSEM.genes


title: Tum cDC CpG-B 2

source_name: tumor cDC CpG-B


title: Tum cDC CpG-B 1


title: gng_p2_b6

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b7

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b5

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b4

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b12

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b2

description: HGJMWBGXY.RSEM.genes


title: Tum cDC CpG-B 3


title: gng_p2_b11

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b10

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b3

description: HGJMWBGXY.RSEM.genes


title: gng_p2_b1

description: HGJMWBGXY.RSEM.genes


title: gng_p2_a9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_a8

description: HGJMWBGXY.RSEM.genes


title: gng_p2_a7

description: HGJMWBGXY.RSEM.genes


title: 2011-369 RNA121

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling Illumina CASAVA v1.8.2
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The sequencing reads were processed by MAP-RSeq v.1.2 workflow [1], the Mayo Bioinformatics Core pipeline. The alignment in MAPRseq was performed with TopHat 2.0.6 and the gene counts was obtained using HTSeq-count v0.5.3p9
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file includes raw gene counts

source_name: corneal endothelium

extract_protocol: RNA libraries were prepared using TruSeq RNA  Sample Prep Kit v2 (Illumina, San Diego, CA). Briefly, poly(A)  mRNA was purified from total RNA using oligo(dT) magnetic  beads, fragmented at 95 °C for 8 min, eluted from the beads, and  primed for first-strand cDNA synthesis using SuperScript III  reverse transcriptase and random primers (Invitrogen). Second-  strand cDNA synthesis was performed using DNA polymerase  I and RNase H, and double-stranded cDNA was purified  using a single AMPure XP bead cleanup step (Agencourt,  Danvers, MA). The cDNA ends were repaired and phosphorylated  using Klenow fragment, T4 polymerase, and T4 polynucleotide  kinase, followed by a single AMPure XP bead cleanup  step. The blunt-ended cDNAs were modified to include a single  3 -adenylate residue using Klenow exo  (3  to 5  exo ), and  paired-end DNA adaptors (Illumina) with a single T base overhang  at the 3 -end were ligated to the A-tailed cDNA population.  Unique indexes, included in the standard TruSeq kits (12-  Set A and 12-Set B), were incorporated at the adaptor ligation  step for multiplex sample loading on the flow cells. The resulting  constructs were purified by two consecutive AMPure XP  bead cleanup steps and enriched by 12 cycles of PCR using  primers included in TruSeq RNA Sample Prep Kit v2. Libraries  were loaded onto paired-end flow cells at concentrations of  8–10 pM to generate cluster densities of 700,000/mm2 using  cBot and cBot Paired-end Cluster Kit v3 (Illumina) following  the manufacturer’s standard protocol. The flow cells were  sequenced as 51   2 paired-end reads on an Illumina HiSeq  4000 system using TruSeq SBS Sequencing Kit v3 and SCS  v1.4.8 data collection software.

tag: group

value: FECD with expansion

tag: batch

tag: re

value: RE+


title: 2011-395 RNA142

value: FECD NO expansion

value: RE-


title: 2011-392 RNA124


title: 2011-491 RNA167


title: 2011-344 RNA114


title: 2011-492 RNA166


title: 2011-573 RNA193


title: 2011-414 RNA141


title: 2011-398 RNA87


title: 2253 RNA27


title: 2011-553 RNA183


title: gng_p2_a6

description: HGJMWBGXY.RSEM.genes

value: brain


title: 2011-313 RNA 120

description: RNA 120


title: gng_p2_a4

description: HGJMWBGXY.RSEM.genes

value: 10days post fertilization habenula


title: gng_p2_a5

description: HGJMWBGXY.RSEM.genes


title: 4827 RNA102


title: 2011-353 RNA112


title: 2011-096 RNA111


title: gng_p2_a3

description: HGJMWBGXY.RSEM.genes


title: 2255 RNA28


title: gng_p2_a12

description: HGJMWBGXY.RSEM.genes


title: 2286 RNA90


title: gng_p2_a11

description: HGJMWBGXY.RSEM.genes


title: 2011-359 RNA100


title: gng_p2_a10

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h7

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h4

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h3

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h5

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h8

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h9

description: HGJMWBGXY.RSEM.genes


title: gng_p2_a1

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h2

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h6

description: HGJMWBGXY.RSEM.genes


title: DC_1

city: Wuhan

first: Xiang

last: Li

state: Hubei

address: No.152 Luoyu Road

department: School of Chemistry

country: China

institute: Central China Normal University

description:
DC_1
FPKM_DU145_RWPE-1.txt

data_processing:
Through in-house perl scripts, clean reads were obtained from raw reads (FASTQ) by removing low quality, adapter-related and polyy-N reads. Q20, Q30, and GC content of the clean reads were also calculated.
Remaining paired-end clean reads were aligned to the reference genome (GRCh38) using HISAT aligner .
After calculating the reads numbers mapped to each gene by HTSeq, we estimated gene expression levels via Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Differential expression analysis of two different groups was performed using the DESeq R package, which was based on a model of negative binomial distribution.
The resulting P-values were adjusted by the Benjamini and Hochberg’s approach to control the false discovery rate. When the adjusted P-values of genes were less than 0.05, them were assigned as differentially expressed.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Prostate

extract_protocol:
Total RNA extraction was performed using Trizol (Invitrogen, 15596026). Then, 3 µg RNA per sample was used as input material, and sequencing libraries were generated by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, E7530S) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: treatment

value: control

value: carcinoma

value: Prostate


title: RL_3

description:
RL_3
FPKM_DU145_RWPE-1.txt

value: treated with LD100

value: normal


title: DC_3

description:
DC_3
FPKM_DU145_RWPE-1.txt


title: RC_2

description:
RC_2
FPKM_DU145_RWPE-1.txt


title: RC_1

description:
RC_1
FPKM_DU145_RWPE-1.txt


title: DL_2

description:
DL_2
FPKM_DU145_RWPE-1.txt


title: RC_3

description:
RC_3
FPKM_DU145_RWPE-1.txt


title: DL_1

description:
DL_1
FPKM_DU145_RWPE-1.txt


title: RL_2

description:
RL_2
FPKM_DU145_RWPE-1.txt


title: DC_2

description:
DC_2
FPKM_DU145_RWPE-1.txt


title: gng_p2_a2

description: HGJMWBGXY.RSEM.genes


title: RL_1

description:
RL_1
FPKM_DU145_RWPE-1.txt


title: gng_p1_h1

description: HGJMWBGXY.RSEM.genes


title: DL_3

description:
DL_3
FPKM_DU145_RWPE-1.txt


title: gng_p1_h12

description: HGJMWBGXY.RSEM.genes


title: S_2

description:
S_2
FPKM_HeLa.txt

source_name: Cervix

value: HeLa

value: SOD1 knockdown

value: adenocarcinoma

value: Cervix


title: gng_p1_h11

description: HGJMWBGXY.RSEM.genes


title: S_1

description:
S_1
FPKM_HeLa.txt


title: S_3

description:
S_3
FPKM_HeLa.txt


title: gng_p1_g9

description: HGJMWBGXY.RSEM.genes


title: L_2

description:
L_2
FPKM_HeLa.txt


title: L_3

description:
L_3
FPKM_HeLa.txt


title: gng_p1_g7

description: HGJMWBGXY.RSEM.genes


title: gng_p1_g8

description: HGJMWBGXY.RSEM.genes


title: gng_p1_h10

description: HGJMWBGXY.RSEM.genes


title: L_1

description:
L_1
FPKM_HeLa.txt


title: gng_p1_g6

description: HGJMWBGXY.RSEM.genes


title: gng_p1_g5

description: HGJMWBGXY.RSEM.genes


title: C_2

description:
C_2
FPKM_HeLa.txt


title: gng_p1_g11

description: HGJMWBGXY.RSEM.genes


title: gng_p1_g3

description: HGJMWBGXY.RSEM.genes


title: gng_p1_g2

description: HGJMWBGXY.RSEM.genes


title: gng_p1_g12

description: HGJMWBGXY.RSEM.genes


title: C_1

description:
C_1
FPKM_HeLa.txt


title: gng_p1_g4

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f9

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (no SM) Experiment 2 [AGH81_08]

city: Bethesda

first: Yashpal

last: Rawal

state: Maryland

address: 6 Center Dr., Bldg 6, Room 233

department: 1Laboratory of Gene Regulation and Development

institute: NICHD-NIH

description:
Biological replicate 2
Lengths used in .bw files:  Range: 50 - 200 bp

library_source: genomic

data_processing:
Sequencing data were mapped to the S. cerevisiae reference genome sacCer3, using bowtie2 (Langmead and Salzberg, Nature Methods, 2012) with parameters "-X 1000 --very-sensitive. Duplicate reads were removed using the samtools rmdup command, and unique reads with the length between 50-300 bp or 50-200 bp were size-selected in R.
IGV tracks (UCSC bigWig format) with the genome-wide occupancy profiles were generated in R using the rtracklayer package. The occupancy profiles were normalized such that the average occupancy for every chromosome is 1.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files containing the normalized occupancy profiles

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.5 to 0.6) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol: The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: antibody

value: anti-H3 histone antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: strain

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4 HIS3MX6::PTET-STH1

value: Formaldehyde-fixed and MNase digested

tag: growth protocol

value: no SM


title: IP: H3 (no SM) Experiment 1 [AGH81_07]

description:
Biological replicate 1
Lengths used in .bw files:  Range: 50 - 200 bp

tag: genotype


title: IP: H3 (no SM) Experiment 1 [AGH81_04]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 HIS3MX6::PTET-STH1


title: IP: H3 (no SM) Experiment 6 [AGH87_10]

description:
Biological replicate 6
Lengths used in .bw files:  Range: 50 - 200 bp


title: IP: H3 (no SM) Experiment 5 [AGH87_09]

description:
Biological replicate 5
Lengths used in .bw files:  Range: 50 - 200 bp


title: IP: H3 (no SM) Experiment 4 [AGH87_02]

description:
Biological replicate 4
Lengths used in .bw files:  Range: 50 - 200 bp

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4


title: IP: H3 (no SM) Experiment 4 [AGH87_04]


title: IP: H3 (no SM) Experiment 2 [AGH81_06]


title: IP: H3 (no SM) Experiment 3 [AGH87_03]

description:
Biological replicate 3
Lengths used in .bw files:  Range: 50 - 200 bp


title: gng_p1_g10

description: HGJMWBGXY.RSEM.genes

tag: tissue

value: brain

tag: cell type

value: 10days post fertilization habenula


title: IP: H3 (no SM) Experiment 2 [AGH81_03]


title: gng_p1_f8

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (no SM) Experiment 1 [AGH81_02]


title: C_3

description:
C_3
FPKM_HeLa.txt

tag: cell line

value: control


title: gng_p1_f7

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 5 [AGH73_08]

value: +SM


title: IP: H3 (+SM) Experiment 3 [AGH68_11]


title: gng_p1_f4

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f5

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f6

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f3

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 2 [AGH68_10]


title: gng_p1_g1

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 6 [AGH73_09]


title: gng_p1_f11

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f2

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f12

description: HGJMWBGXY.RSEM.genes


title: gng_p1_f1

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 4 [AGH68_12]


title: IP: H3 (no SM) Experiment 3 [AGH87_01]


title: gng_p1_e9

description: HGJMWBGXY.RSEM.genes


title: gng_p1_e8

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 4 [AGH73_07]


title: gng_p1_f10

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 1 [AGH68_07]


title: IP: H3 (+SM) Experiment 2 [AGH68_08]


title: IP: H3 (+SM) Experiment 5 [AGH73_12]


title: gng_p1_e7

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 1 [AGH68_09]


title: gng_p1_e6

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 3 [AGH73_06]


title: IP: H3 (+SM) Experiment 5 [AGH73_10]


title: IP: H3 (+SM) Experiment 4 [AGH73_05]


title: gng_p1_e2

description: HGJMWBGXY.RSEM.genes


title: gng_p1_e1

description: HGJMWBGXY.RSEM.genes


title: gng_p1_e12

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 2 [AGH68_06]


title: gng_p1_e4

description: HGJMWBGXY.RSEM.genes


title: gng_p1_e3

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 3 [AGH73_03]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: gng_p1_e11

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 2 [AGH68_04]


title: gng_p1_d9

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (no SM) Experiment 4 [AGH73_02]


title: IP: H3 (+SM) Experiment 1 [AGH68_03]


title: gng_p1_e10

description: HGJMWBGXY.RSEM.genes


title: gng_p1_d8

description: HGJMWBGXY.RSEM.genes


title: gng_p1_e5

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (no SM) Experiment 3 [AGH73_01]


title: IP: H3 (no SM) Experiment 2 [AGH68_02]


title: gng_p1_d7

description: HGJMWBGXY.RSEM.genes


title: gng_p1_d6

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (no SM) Experiment 1 [AGH68_01]


title: gng_p1_d5

description: HGJMWBGXY.RSEM.genes


title: gng_p1_d4

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 3 [AGH73_04]


title: IP: Rpb3 (+SM) Experiment 3 [AGH51_10]

description:
Biological replicate 3
Lengths used in .bw files:  Range: 50 - 300 bp

value: anti-Rpb3 antibody

value: NeoClone

value: Formaldehyde-fixed and sonicated


title: gng_p1_d3

description: HGJMWBGXY.RSEM.genes


title: IP: Rpb3 (+SM) Experiment 2 [AGH51_09]

description:
Biological replicate 2
Lengths used in .bw files:  Range: 50 - 300 bp


title: gng_p1_d2

description: HGJMWBGXY.RSEM.genes


title: IP: Rpb3 (+SM) Experiment 1 [AGH51_02]

description:
Biological replicate 1
Lengths used in .bw files:  Range: 50 - 300 bp


title: IP: Rpb3 (+SM) Experiment 1 [AGH51_01]


title: IP: H3 (+SM) Experiment 1 [AGH68_05]


title: gng_p1_d1

description: HGJMWBGXY.RSEM.genes


title: gng_p1_d11

description: HGJMWBGXY.RSEM.genes


title: gng_p1_d12

description: HGJMWBGXY.RSEM.genes


title: gng_p1_c9

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 3 [AGH63_09]

value: anti-H2B histone antibody


title: gng_p1_d10

description: HGJMWBGXY.RSEM.genes


title: gng_p1_c8

description: HGJMWBGXY.RSEM.genes


title: gng_p1_c7

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 2 [AGH63_08]


title: IP: H2B (+SM) Experiment 3 [AGH63_06]


title: gng_p1_c6

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 2 [AGH63_05]


title: IP: H2B (+SM) Experiment 1 [AGH63_07]


title: IP: H2B (+SM) Experiment 1 [AGH63_04]


title: gng_p1_c5

description: HGJMWBGXY.RSEM.genes


title: gng_p1_c4

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 5 [AGH48_08]


title: IP: Rpb3 (+SM) Experiment 3 [AGH51_06]


title: IP: H2B (+SM) Experiment 6 [AGH48_09]


title: IP: H2B (+SM) Experiment 4 [AGH48_07]


title: IP: Rpb3 (+SM) Experiment 2 [AGH51_05]


title: gng_p1_c2

description: HGJMWBGXY.RSEM.genes


title: gng_p1_c3

description: HGJMWBGXY.RSEM.genes


title: gng_p1_c1

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 2 [AGH60_12]

description:
Biological replicate 5
Lengths used in .bw files:  Range: 50 - 300 bp


title: gng_p1_c12

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 3 [AGH45_10]

description:
Biological replicate 6
Lengths used in .bw files:  Range: 50 - 300 bp


title: gng_p1_c11

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 3 [AGH62_11]


title: gng_p1_b9

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 1 [AGH60_04]


title: gng_p1_c10

description: HGJMWBGXY.RSEM.genes


title: gng_p1_b7

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (+SM) Experiment 2 [AGH45_03]


title: gng_p1_b8

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 3 [AGH67_12]


title: gng_p1_b6

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 2 [AGH67_11]


title: gng_p1_b5

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 3 [AGH67_9]


title: gng_p1_b3

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 2 [AGH67_8]


title: IP: H2B (no SM) Experiment 3 [AGH67_6]


title: IP: H2B (no SM) Experiment 1 [AGH67_10]


title: IP: H2B (+SM) Experiment 1 [AGH60_11]

description:
Biological replicate 4
Lengths used in .bw files:  Range: 50 - 300 bp


title: IP: H2B (no SM) Experiment 1 [AGH67_7]


title: gng_p1_b4

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 1 [AGH67_4]


title: gng_p1_b2

description: HGJMWBGXY.RSEM.genes


title: gng_p1_b10

description: HGJMWBGXY.RSEM.genes


title: gng_p1_b12

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 2 [AGH67_5]


title: gng_p1_b11

description: HGJMWBGXY.RSEM.genes


title: IP: H2B (no SM) Experiment 2 [AGH45_01]


title: IP: H2B (no SM) Experiment 3 [AGH45_02]


title: IP: H2B (no SM) Experiment 1 [AGH60_02]


title: gng_p1_b1

description: HGJMWBGXY.RSEM.genes


title: IP: H3 (+SM) Experiment 1 [AGH54_01]


title: IP: H3 (+SM) Experiment 2 [AGH54_02]


title: IP: H3 (+SM) Experiment 1 [AGH50_01]


title: 2011-291 RNA79

value: FECD NO expansion

value: RE-


title: IP: H3 (+SM) Experiment 2 [AGH54_03]

value: anti-H3 histone antibody

value: Abcam


title: IP: H3 (+SM) Experiment 3 [AGH50_06]


title: 2011-038 RNA20


title: IP: H3 (+SM) Experiment 2 [AGH59_02]


title: IP: H3 (+SM) Experiment 3 [AGH62_05]


title: IP: H3 (+SM) Experiment 3 [AGH62_08]


title: IP: H3 (+SM) Experiment 2 [AGH62_03]


title: 6004 RNA19

value: FECD with expansion

value: RE+


title: 2011-024 RNA16


title: IP: H3 (+SM) Experiment 1 [AGH59_01]


title: IP: H3 (+SM) Experiment 1 [AGH58_04]


title: IP: H3 (no SM) Experiment 3 [AGH57_9]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 HIS3MX6::PTET-STH1

value: no SM


title: IP: H3 (+SM) Experiment 3 [AGH50_10]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4 HIS3MX6::PTET-STH1


title: IP: H3 (no SM) Experiment 3 [AGH57_6]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4


title: IP: H3 (no SM) Experiment 1 [AGH57_7]


title: IP: H3 (no SM) Experiment 1 [AGH57_4]


title: IP: H3 (no SM) Experiment 2 [AGH57_5]


title: IP: H3 (no SM) Experiment 2 [AGH57_8]


title: IP: H3 (no SM) Experiment 1 [AGH57_10]


title: IP: H3 (no SM) Experiment 2 [AGH62_01]


title: IP: H3 (no SM) Experiment 1 [AGH58_02]


title: IP: H3 (no SM) Experiment 3 [AGH62_02]


title: 2011-020 RNA10


title: 2011-041 RNA15


title: IP: H3 (no SM) Experiment 3 [AGH57_12]


title: IP: H3 (no SM) Experiment 2 [AGH57_11]


title: NPCs cocultured with ASCs 1

city: Shanghai

first: Zhihua Han

last: Han

state: Please select region, state or province

address: Xin Songjiang Road 650

department: Orthopedic Traumatology, Shanghai Trauma and Emergency Center

institute: Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University

description: Gene expression data and ncRNAs data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: degenerate nucleus pulposus derived cells

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: NPCs were isolated and cultured in Dulbecco’s modified Eagle’s medium/F12 medium containing 10% fetal bovine serum (FBS) in 37°, 5% CO2 incubator. The medium was changed every 2-3 days.

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

treatment_protocol: Both ASCs and NPCs at passage 3 were co-cultured using non-direct cell-cell contact coculturing system for 7 days

value: nucleus pulposus

tag: passage

value: passage 3


title: NPCs only 3

description: Gene expression data and ncRNAs data

source_name: degenerate nucleus pulposus derived cells cocultured with adipose derived stem cells


title: NPCs only 1

description: Gene expression data and ncRNAs data


title: KO7-ear

city: Chapel Hill

first: Zhi

last: Liu

state: NC

address: 4157 Genome Sciences Building, CB#2360

department: Dermatology

institute: University of North Carolina at Chapel Hill

hyb_protocol: not provided

scan_protocol: Microarray images were processed using Agilent Feature Extractor according to manufacturer-supplied protocols

data_processing: 'gProcessedSignal' value was used from the raw output of the Agilent Feature Extraction software.  This value is LOWESS normalized and contains additional filtering to control for negative control spike-ins, dome bias, and other common events during data collection.

source_name: total skin RNA from NC16A deficient mouse

label_protocol: not provided

extract_protocol: RNA was extrated using commercial kits ( Qiagen Rneasy) following manufacturer protocol. RNA purity and concentration was measured with Nanodrop.

value: ear


city: Philadelphia

first: Markus

middle: Daniel

last: Lacher

state: PA

address: 2929 Arch Street, 4th floor

department: R&D

institute: BriaCell Therapeutics Corp.

description:
RES Lot II cryo_S1.AVG_Signal
SV-BR-1-GM_Research sample type_cells from cryovial lysed without culturing_biological replicate 1 (from different cryovial than replicate 2)

hyb_protocol: The biotinylated antisense RNA was then hybridized onto HumanHT-12 v4 Expression BeadChip arrays (Illumina) and thereafter stained with Cy3-streptavidin.

scan_protocol: Fluorescent signal intensities were acquired on an iScan array scanner (Illumina).

data_processing:
Non-normalized average signal intensities and detection p-values were calculated for each Sentrix array separately using GenomeStudio (Illumina). The 22 samples were run on 3 BeadChip arrays  (2 samples on 100896670114, 8 samples on 101064350130, 12 samples on 200123510079), with Sentrix arrays 100896670114 and 101064350130 also loaded with 10 and 4, respectively, samples not shown here. Expression levels of all 22 samples  were quantile-normalized using the IlluminaNormalizer version 2 (beta) module of GenePattern using the public server portal (http://www.broadinstitute.org/cancer/software/genepattern/) (Reich et al., Nat Genet (2006) 38(5):500-1).
Non-normalized values are average signal intensities and p-values as obtained separately for each Sentrix Array using GenomeStudio V2011.1 (Illumina). Normalized  values are quantile-normalized expression levels as obtained via the IlluminaNormalizer version 2 (beta) module of GenePattern using the public server portal (http://www.broadinstitute.org/cancer/software/genepattern/) (Reich et al., Nat Genet (2006) 38(5):500-1). No p-values were calculated for the normalized expression data.

label_protocol: RNA was amplified as antisense RNA and biotinylated using the Illumina™ TotalPrep™-96 RNA Amplification Kit (Thermo Fisher Scientific).

growth_protocol: SV-BR-1-GM cells were either lysed after cryopreservation without a culturing step or were cultured in RPMI-1640 supplemented with 10% FBS and GlutaMAX.

extract_protocol: SV-BR-1-GM cells were lysed in RLT Buffer and RNA extracted using the RNeasy Mini kit (Qiagen).

value: clinically effective GM-CSF-secreting human breast cancer cell line


title: Mm_colon_Colitis_CsA_rep10

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description:
Gene expression data in colon from DSS-induced colitis female mouse, CsA treatment
CSA10

hyb_protocol: 100 ng of total RNA was used for hybridization of Affymetrix GeneChip® Mouse Gene 2.0 ST Arrays according to manufacturer's instructions (Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays – P/N 703147 Rev. 3). Labeled samples were injected into Affymetrix arrays and hybridized at 45°C and 60 rpm for 16 h in an Affymetrix Hybridization Oven. Arrays were later stained and washed in the Affymetrix GeneChip Fluidic Station 450.

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

data_processing:
GeneChip data was processed and analyzed using R/Bioconductor packages. Data were summarized (w.r.t. core meta-probeset annotations and AFFX control probes, probes grouped to the level of transcripts) and quantile-normalized (background computed from antigenomic probes) using RMA algorithm from XPS package using the following parameters: xps::rma(normalize=TRUE, option=transcript, background=antigenomic, exonlevel=metacore+affx, params = list(16384, 0.0, 1.0, 10, 0.01, 1)).
MoGene-2_0-st.pgf
MoGene-2_0-st.mps
In the data table, 'null' denotes the filtered-out values.

source_name: Colon from DSS-induced colitis female mouse, CsA treatment

label_protocol: Total RNA was used to synthesize double-stranded cDNA tagged with a T7 promoter sequence. The double-stranded cDNA was subsequently used as a template for in vitro transcription with T7 RNA polymerase producing cRNA. Single-stranded cDNA was synthesized by reverse transcription of cRNA and treated with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognized the unnatural dUTP residues and broke the DNA strand. DNA was labelled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix proprietary DNA Labelling Reagent that is covalently linked to biotin.

growth_protocol: Female C57BL/6JOlaHsd mice (Harlan, Italy) were obtained at 7 weeks of age and acclimatized for at least one week before entering the study. Mice were housed in groups of 5 mice per cage (Ehret, Germany; 825 cm2 floor space) in standard controlled environmental conditions (22±1°C room temperature and 55±10 relative humidity) with a 12-h light/dark cycle on bedding material (Lignocel ¾, Germany) at Medical experimental centre (Ljubljana, Slovenia) and received standard rodent diet (Altromin 1324, Germany) and drinking water ad libitum.

extract_protocol: Mice were euthanized by CO2 overdosing and spleen and the entire colon (from ceacum to the anus) were removed. Each colon was measured (wet length) and then divided into three parts; the distal and proximal parts were taken for histological evaluation and the middle part was used for RNA extraction. Colon samples for RNA extraction were cut into two parts, snap-frozen in liquid nitrogen and stored at -80 °C until used. Tissue was homogenized in 1000 µl of TRI Reagent (Sigma) and total RNA was isolated according to the manufacturer's instructions. RNA quantity and quality were assessed with Agilent 2100 Bioanalyzer instrument, all samples isolated fulfilled the minimum requirements (OD260/280 and OD230/280>1.8) for microarray hybridization.

treatment_protocol: Colitis was induced by the addition of DSS (3% DSS; TdB Consultancy AB, Uppsala Sweden, molecular mass 40 kDa) dissolved in the drinking water for 5 consecutive days. The DSS solutions were made freshly every morning. Cyclosporine (CsA) 25mg/kg (Sandimmun Neoral, Novartis Pharma GmbH, Germany from 100 mg/ml) was suspended in 2% methocel solution and administered orally daily from day 1 to day 15 in an administration volume of 10 ml/kg (according to Sann et al, 2013). Intragastric tube of probiotic mixture of 1x10e9 L930BB and 1x10e9 IM386 strains suspended in 100 μl saline solution was administered prior the addition of DSS and then simultaneously with DSS.

value: colon, middle part

value: ~11 weeks

tag: disease

value: Colitis

tag: Sex

value: F

value: CsA


title: KO1-ear


title: Mm_colon_Colitis_CsA_rep09

description:
Gene expression data in colon from DSS-induced colitis female mouse, CsA treatment
CSA09

tag: age


title: KO2-ear


description:
CP Lot VIII cryo_S3.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_cells from cryovial lysed without culturing_biological replicate 3 (from different cryovial than replicates 1 and 2)


description:
CP Lot VIII cryo_S1.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_cells from cryovial lysed without culturing_biological replicate 1 (from different cryovial than replicates 2 and 3)


description:
CP Lot VIII culture_3d_S3_Flask B.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 4-day culture_biological replicate 3-2 (from different cryovial than replicates 1-1, 1-2, 2-1, and 2-2; and from different culture dish than replicate 3-1)


description:
RES Lot II cryo_S2.AVG_Signal
SV-BR-1-GM_Research sample type_cells from cryovial lysed without culturing_biological replicate 2 (from different cryovial than replicate 1)


title: Mm_colon_Colitis_CsA_rep07

description:
Gene expression data in colon from DSS-induced colitis female mouse, CsA treatment
CSA07


title: WT3-ear

source_name: total skin RNA from NC16A sufficient mouse


title: Mm_colon_Colitis_CsA_rep04

description:
Gene expression data in colon from DSS-induced colitis female mouse, CsA treatment
CSA04


title: NPCs cocultured with ASCs 3

description: Gene expression data and ncRNAs data


description:
CP Lot VIII culture_3d_S2_Flask B.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 4-day culture_biological replicate 2-2 (from different cryovial than replicates 1-1, 1-2, 3-1, and 3-2; and from different culture dish than replicate 2-1)


description:
CP Lot VIII culture_3d_S2_Flask A.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 4-day culture_biological replicate 2-1 (from different cryovial than replicates 1-1, 1-2, 3-1, and 3-2; and from different culture dish than replicate 2-2)


title: WT2-ear


title: Mm_colon_Colitis_Probiotic_rep07

description:
Gene expression data in colon from DSS-induced colitis female mouse, probiotic treatment
PDP07

source_name: Colon from DSS-induced colitis female mouse, probiotic treatment

value: Probiotic


description:
CP Lot VIII cryo_S2.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_cells from cryovial lysed without culturing_biological replicate 2 (from different cryovial than replicates 1 and 3)


title: Mm_colon_Colitis_Probiotic_rep08

description:
Gene expression data in colon from DSS-induced colitis female mouse, probiotic treatment
PDP08


title: WT1-ear


title: NPCs only 2

description: Gene expression data and ncRNAs data


title: NPCs cocultured with ASCs 2

description: Gene expression data and ncRNAs data


description:
CP Lot VIII culture_3d_S3_Flask A.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 4-day culture_biological replicate 3-1 (from different cryovial than replicates 1-1, 1-2, 2-1, and 2-2; and from different culture dish than replicate 3-2)


description:
CP Lot VIII culture_3d_S1_Flask B.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 4-day culture_biological replicate 1-2 (from different cryovial than replicates 2-1, 2-2, 3-1, and 3-2; and from different culture dish than replicate 1-1)


description:
CP Lot VIII culture_3d_S1_Flask A.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 4-day culture_biological replicate 1-1 (from different cryovial than replicates 2-1, 2-2, 3-1, and 3-2; and from different culture dish than replicate 1-2)


description:
CP Lot VIII culture_1d_S3.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 2-day culture_biological replicate 3 (from different cryovial than replicates 1 and 2)


description:
CP Lot VIII culture_1d_S1.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 2-day culture_biological replicate 1 (from different cryovial than replicates 2 and 3)


title: Mm_colon_Healthy_Probiotic_rep04

description:
Gene expression data in colon from healthy female mouse, probiotic treatment
Pro04

source_name: Colon from healthy female mouse, probiotic treatment

value: Healthy


description:
CP Lot VIII culture_1d_S2.AVG_Signal
SV-BR-1-GM_Lot VIII (Master Cell Bank 2)_from 2-day culture_biological replicate 2 (from different cryovial than replicates 1 and 3)


title: M_Rheb1-/-_2

city: Tianjin

first: wang

last: xiaomin

state: Tianjin

address: Institute of Hematology and Blood Diseases Hospital, Tianjin 300020, China.

institute: Institute of Hematology and Blood Diseases Hospital,Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Gene expression for myeloid cells of Rheb1-/-mouse
M_V2

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

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.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: myeloid cells,Rheb1-/-mouse,replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)/TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Myeloid progenitor,Hematopoietic stem cells and myeloid cells isolated from the Rheb1fl/fl mice which were crossed with Vav1-cre mice to generate Vav1-cre; Rheb1fl/fl mice (Rheb-/-, specific Rheb1 deletion in the hematopoietic system).

value: myeloid cells


title: Mm_colon_Colitis_Probiotic_rep03

description:
Gene expression data in colon from DSS-induced colitis female mouse, probiotic treatment
PDP03


title: M_Rheb1-/-_1

description:
Gene expression for myeloid cells of Rheb1-/-mouse
M_V1

source_name: myeloid cells,Rheb1-/-mouse,replicate 1


description:
CP Lot IV 4p culture_S1.AVG_Signal
SV-BR-1-GM_Lot IV plus 4 passages_from culture_biological replicate 1 (from different cryovial than replicate 2)


title: Mm_colon_Colitis_Probiotic_rep05

description:
Gene expression data in colon from DSS-induced colitis female mouse, probiotic treatment
PDP05


title: Mm_colon_Healthy_Probiotic_rep07

description:
Gene expression data in colon from healthy female mouse, probiotic treatment
Pro07


description:
CP Lot IV 4p cryo_S1.AVG_Signal
SV-BR-1-GM_Lot IV_cells from cryovial lysed without culturing_biological replicate 1 (from different cryovial than replicate 2)


title: M_wildtype_3

description:
Gene expression for myeloid cells of wild type mouse
M_R3

source_name: myeloid cells,wild type mouse,replicate 3

value: wild type


title: Mm_colon_Healthy_Probiotic_rep06

description:
Gene expression data in colon from healthy female mouse, probiotic treatment
Pro06


title: Mm_colon_Healthy_Probiotic_rep05

description:
Gene expression data in colon from healthy female mouse, probiotic treatment
Pro05


title: M_Rheb1-/-_3

description:
Gene expression for myeloid cells of Rheb1-/-mouse
M_V3

source_name: myeloid cells,Rheb1-/-mouse,replicate 3


title: Mm_colon_Colitis_None_rep10

description:
Gene expression data in colon from DSS-induced colitis female mouse, no treatment
DSS10

source_name: Colon from DSS-induced colitis female mouse, no treatment


description:
CP Lot IV culture_S1_Dish B.AVG_Signal
SV-BR-1-GM_Lot IV_from culture_biological replicate 1 (from same cryovial as replicate 2 but different culture dish)

source_name: SV-BR-1-GM_Lot IV_from culture


description:
CP Lot IV culture_S1_Dish D.AVG_Signal
SV-BR-1-GM_Lot IV_from culture_biological replicate 2 (from same cryovial as replicate 1 but different culture dish)


description:
CP Lot IV 4p cryo_S2.AVG_Signal
SV-BR-1-GM_Lot IV_cells from cryovial lysed without culturing_biological replicate 2 (from different cryovial than replicate 1)


description:
CP Lot IV 4p culture_S2.AVG_Signal
SV-BR-1-GM_Lot IV plus 4 passages_from culture_biological replicate 2 (from different cryovial than replicate 1)


title: Mm_colon_Colitis_None_rep07

description:
Gene expression data in colon from DSS-induced colitis female mouse, no treatment
DSS07


title: HSC_wildtype

description:
Gene expression for Hematopoietic stem cells of wild type mouse
HSC_R

source_name: Hematopoietic stem cells,wild type mouse,replicate 1

value: Hematopoietic stem cells


title: M_wildtype_2

description:
Gene expression for myeloid cells of wild type mouse
M_R2

source_name: myeloid cells,wild type mouse,replicate 2


title: Mm_colon_Colitis_None_rep06

description:
Gene expression data in colon from DSS-induced colitis female mouse, no treatment
DSS06


title: GMP_Rheb1-/-_3

description:
Gene expression for Myeloid progenitor of Rheb1-/-mouse
GMP_V3

value: Myeloid progenitor


title: HSC_Rheb1-/-

description:
Gene expression for Hematopoietic stem cells of Rheb1-/-mouse
HSC_V

source_name: Hematopoietic stem cells,Rheb1-/-mouse,replicate 1


description:
MCB cryo_S1R1.AVG_Signal
SV-BR-1-GM_Master Cell Bank 1_cells from cryovial lysed without culturing_technical replicate 1 (same RNA as replicate 2)


description:
MCB cryo_S1R2.AVG_Signal
SV-BR-1-GM_Master Cell Bank 1_cells from cryovial lysed without culturing_technical replicate 2 (same RNA as replicate 1)


title: GMP_Rheb1-/-_2

description:
Gene expression for Myeloid progenitor of Rheb1-/-mouse
GMP_V2


title: M_wildtype_1

description:
Gene expression for myeloid cells of wild type mouse
M_R1

source_name: myeloid cells,wild type mouse,replicate 1


title: Rat at C1, biological rep1 [miRNA-4_0]

first: Guojun

last: Guo

address: 1277# Jiefang Avenue

department: Hand Surgery

institute: Union Hospital of Tongji medical college, Huazhong University of Science & Technology

description:
C1_miRNA-4_0
miRNA expression data from DRG in normal control rat.

hyb_protocol: The labeled RNA were hybridized for 16 hr at 60 rpm at 48C on Affymetrix miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: Raw data files were analyzed by using Affymetrix Expression Console with the default miRNA array settings. Raw data were processed and normalized on basis of organism rat using RMA-DABG algorithm.

organism: Rattus norvegicus

source_name: DRG, normal SD rat

label_protocol: About 1ug total RNA were polyA tailed and labeled with FlashTag™ Biotin HSR Labeling Kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Rats were kept in cages where commercial rat feed and water were available ad libitum, and the room condition was kept at 23±1℃ temperature, 40% humidity, and 12 hours day and night cycle.

extract_protocol: Total RNA was extracted using miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Healthy male SD rats (180-220g) were randomly divided into diabetic and control groups. The diabetic group (D group) rats were induced by a single intraperitoneal injection of STZ at a dose of 65mg/kg body weight, and the control group (C group) rats received an equal volume of vehicle (citrate buffer) alone. One week later, non-fasting blood glucose levels were measured, and the diabetic groups rats with glucose levels less than 16.7 mM were excluded. 8 weeks after induction, withdrawal threshold of the hind paws were tested to assess diabetic peripheral neuropathy. Then the DRG tissues were collected, immediately immersed in RNAlater reagent, and stored as instructed before RNA extraction. For each rat, bilateral L3-L6 DRGs were collected and pooled together as one single sample, and three diabetic rats and three control rats were chosen randomly for microarray analysis.

tag: strain/background

value: Sprague-Dawley

tag: gender

value: male

tag: disease state

value: control

value: dorsal root ganglia (DRG)


title: Rat at C3, biological rep3 [miRNA-4_0]

description:
C3_miRNA-4_0
miRNA expression data from DRG in normal control rat.


title: Mm_colon_Colitis_None_rep05

description:
Gene expression data in colon from DSS-induced colitis female mouse, no treatment
DSS05

tag: treatment


title: Mm_colon_Healthy_None_rep04

description:
Gene expression data in colon from healthy female mouse, no treatment
Sal04

source_name: Colon from healthy female mouse, no treatment


title: Mm_colon_Healthy_None_rep06

description:
Gene expression data in colon from healthy female mouse, no treatment
Sal06


title: GMP_wildtype_3

description:
Gene expression for Myeloid progenitor of wild type mouse
GMP_R3

source_name: Myeloid progenitor,wild type mouse,replicate 3


title: Rat at D2, biological rep2 [miRNA-4_0]

description:
D2_miRNA-4_0
miRNA expression data from DRG in STZ-induced diabetic rat.

source_name: DRG, diabetic rat

value: diabetic


title: Rat at D1, biological rep1 [miRNA-4_0]

description:
D1_miRNA-4_0
miRNA expression data from DRG in STZ-induced diabetic rat.


title: Mm_colon_Healthy_None_rep07

description:
Gene expression data in colon from healthy female mouse, no treatment
Sal07


title: Mm_colon_Healthy_None_rep02

description:
Gene expression data in colon from healthy female mouse, no treatment
Sal02


title: Ba/F3_control

city: Kobe

first: Kei

last: Enomoto

state: Hyogo

address: Chuo-ku, Minatojima-Minamimachi

country: Japan

institute: ASUBIO PHARMA CO., LTD.

description: Gene expression of Ba/F3 (control)

hyb_protocol: 1.65 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K v2 (G4846A) 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 immediately after washing on the Agilent DNA Microarray Scanner (G2505CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalization was achieved using Agilent GeneSpring GX version12.1 as follows. First, signal intensities less than 1.0 were set to 1.0. Then, each chip was normalized to the 75th percentile of the measurements taken from that chip. Finally the normalized intensities were log2-transformed.

source_name: Ba/F3, control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cells using the TRIzol Plus RNA Purification System (Invitrogen) following the manufacturer's recommendations. Purified RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: clone id


title: GMP_wildtype_1

description:
Gene expression for Myeloid progenitor of wild type mouse
GMP_R1

source_name: Myeloid progenitor,wild type mouse,replicate 1


title: GMP_wildtype_2

description:
Gene expression for Myeloid progenitor of wild type mouse
GMP_R2

source_name: Myeloid progenitor,wild type mouse,replicate 2


title: Rat at C2, biological rep2 [miRNA-4_0]

description:
C2_miRNA-4_0
miRNA expression data from DRG in normal control rat.


title: Ba/F3_#BEB1

description: Gene expression of Ba/F3 (#BEB1)

source_name: Ba/F3, #BEB1

value: derived from Ba/F3


title: HUVEC2+DMSO +stretch

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
n3_DMSO_plus
Gene expression data from stretched Human umbilical vein endothelial cells (HUVECs) treated with DMSO

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HUVEC+DMSO +stretch

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

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were freshly isolated from individual umbilical cords and grown on collagen I-bonded BioFlex® plates (Flexcell International) and exposed to biomechanical stretch (15%, 0.5 Hz) for 6 hours.

extract_protocol: RNA was isolated and processed for DNA microarray analysis according to manufacturers’ instructions

treatment_protocol: HUVECs were exposed to Glycyrrhetinic acid (40 μM) or DMSO as solvent control and exposed to biomechanical stretch for 6 hours.

tag: donor id

value: donor 2

value: biomechanically stretched HUVEC

tag: exposed to

value: DMSO as solvent control

tag: batch


title: Rat at D3, biological rep3 [miRNA-4_0]

description:
D3_miRNA-4_0
miRNA expression data from DRG in STZ-induced diabetic rat.


title: GMP_Rheb1-/-_1

description:
Gene expression for Myeloid progenitor of Rheb1-/-mouse
GMP_V1


title: HUVEC2+G40 +stretch

description:
n3_G40
Gene expression data from stretched Human umbilical vein endothelial cells (HUVECs) treated with Glycyrrhetinic acid

source_name: HUVEC+G40 +stretch

value: Glycyrrhetinic acid (40 μM)


title: HUVEC1+G40 +stretch

description:
n1_G40
Gene expression data from stretched Human umbilical vein endothelial cells (HUVECs) treated with Glycyrrhetinic acid

value: donor 1


title: HUVEC1+DMSO +stretch

description:
n1_DMSO_plus
Gene expression data from stretched Human umbilical vein endothelial cells (HUVECs) treated with DMSO


title: tR(CCU)J_37

city: Stanford

first: Chuan

state: CA

address: 327 Campus Drive

department: Biology

institute: Stanford University

description: 3 replicates of amplicon sequencing

data_processing:
Only perfectly matched fully overlapping paired-end reads were used in estimating genotype frequencies.
The change in relative genotype frequency during the competition was used to estimate the fitness of each genotype relative to the wild-type.
The fitness of a genotype is calculated by averaging the fitness among biological replicates.
We focused on 23,284 genotypes with read counts ≥ 100 before the competition.
Supplementary_files_format_and_content: Fitness for 23284 variant across 4 environments

source_name: cell culture

extract_protocol:
Gentra Puregene Yeast/Bact. Kit
PCR amplification using KAPA HiFi HotStart DNA Polymerase to add adaptors

tag: strain

tag: generation

tag: environment

value: 37°C in YPD


title: HUVEC3+DMSO +stretch

description:
n4_DMSO_plus
Gene expression data from stretched Human umbilical vein endothelial cells (HUVECs) treated with DMSO

value: donor 3

tag: cell type


title: High-fat diet, biological replicate 1

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity > 8.5 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer following the manufacturer's instructions. On completion of the fragmentation reaction,55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100µl were hybridized to Agilent-026655 Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed according to manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were normalized using Bioconductor and limma package. Briefly, background subtraction was performed using the normexp correction with an offset=50, then signals were normalized using quantile normalization. Control spots were suppressed as low signal or saturating spots. Replicates were averaged. Statistical analysis was performed on 28,061 probes.

source_name: beta pancreatic cells from mouse submitted to high-fat diet

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amp Labeling One Color kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: beta pancreatic cells

value: high-fat diet


title: High-fat diet, biological replicate 4


title: HUVEC3+G40 +stretch

description:
n4_G40
Gene expression data from stretched Human umbilical vein endothelial cells (HUVECs) treated with Glycyrrhetinic acid


title: High-fat diet, biological replicate 3


title: High-fat diet, biological replicate 2


title: rat at C2, biological rep2 [RTA-1_0]

description:
C2_RTA-1_0
lncRNA and mRNA expression data from DRG in normal control rat.

hyb_protocol: Following fragmentation, 5.5 ug of ss DNA were hybridized for 16 hr at 45C on GeneChip Rat Transcriptome 1.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus Reagent Kit Manual, Affymetrix).

tag: tissue


title: tR(CCU)J_DMSO

description: 3 replicates of amplicon sequencing

value: 30°C in YPD with 3% DMSO


title: tR(CCU)J_30C

description: 5 replicates of amplicon sequencing

value: 30°C in the rich medium YPD


title: tR(CCU)J_T0

description: 2 replicates of amplicon sequencing

value: starting population


title: rat at C3, biological rep3 [RTA-1_0]

description:
C3_RTA-1_0
lncRNA and mRNA expression data from DRG in normal control rat.

value: Sprague-Dawley

value: male


title: tR(CCU)J_23C

description: 5 replicates of amplicon sequencing

value: 23°C in YPD


title: D9FD76F2

status: Public on Mar 22 2018

type: genomic

city: Paris

first: Nathalie

last: Clément

address: 26 rue d'Ulm

institute: Institut Curie

hyb_protocol: For each sample, 700 ng of tumor and normal DNA were labeled and co-hybridized to the NimbleGen arrays according to the manufacturer’s protocol.  After ethanol-coprecipitation with 210µg of Human Cot-1 DNA (Invitrogen, Cergy (Invitrogen, Cergy Pontoise, France), resuspension in hybridization buffer (50% formamide), denaturation at 95°C for 10 minutes and pre-hybridization at 37°C for 90 minutes, probes were cohybridized on aCGH. The aCGH slide was previously preblocked with a buffer containing 2.6mg succinic anhydride/118ml N-methyl-2-pyrrolidinone/32ml sodium tetraborate decahydrate, pH 8.0 for BAC array.       .

scan_protocol: Arrays were washed and then scanned on a GenePix 4000B scanner using GenePix 6.0 Software for Nimblegen array.  The aCGH developed in the laboratory contains 3342 sequence-validated BACs including 340 localized on 1p and 29 on 19q. After washing, arrays were scanned using a 4000B scan.

data_processing:
Raw data in .pair file format were normalized and processed using the NimbleScan v2.5 Software (Roche NimbleGen) to obtain data with a resolution of 100 kb. The data were then visualized with SignalMap v1.9 (Roche NimbleGen) before analysis. For .gpr files, image analysis was performed with Genepix 5.1 software (Axon) and ratios of Cy5/Cy3 signals were determined for BAC array.
The data included in the processed data files (.txt files) are: normalized log2 ratio (Cy5/Cy3) representing test/reference. The Log2 ratio values can also be found in the .gpr files in the column "Log Ratio (635/532). The  "RATIO_CORRECTED" column in the processed data for the Nimblegen arrays is identical to the "RATIO_CORRECTED" column in the *raw.txt files.

source_name: tumor DNA

label_protocol: For each sample, 700 ng of tumor and normal DNA  (from normal tissue from healthy donor) were labeled and co-hybridized to the NimbleGen arrays according to the manufacturer’s protocol. Tumor DNAs were labeled by the random priming method with cyanine-5 and using the same procedure, we labeled control DNAs (from control tissue from healthy donor)with cyanine-3  for homemade bacterial artificial chromosome (BAC)-arrays.

extract_protocol: Total DNA extracted using Trizol following manufacturer's instructions

value: Neuroblastoma

tag: tumor inss stage

tag: tumor inrg stage

tag: gender (1=male; 2=female)

tag: mycn status (0=non amplified, 1= amplified)

tag: age (days) at diagnosis

tag: relapse/progression (0=no, 1= yes)

tag: time from diagnosis to event or last follow up (days)

tag: patient status (0=alive, 1= dead)

tag: time from diagnosis to death or last follow up (days)

source_name: Normal reference DNA

tag: control type

value: normal tissue (blood) from healthy donor


title: D1581A8B


title: 711D5429


title: 429193D0


title: F52A687A


title: Control diet, biological replicate 4

source_name: beta pancreatic cells from mouse submitted to chow diet

tag: strain/background

tag: treatment

value: control diet


title: rat at C1, biological rep1 [RTA-1_0]

description:
C1_RTA-1_0
lncRNA and mRNA expression data from DRG in normal control rat.

tag: gender

tag: disease state

value: control

value: dorsal root ganglia (DRG)


title: 9DC568F6


title: B184BECD


title: rat at D3, biological rep3 [RTA-1_0]

description:
D3_RTA-1_0
lncRNA and mRNA expression data from DRG in STZ-induced diabetic rat.

value: diabetic


title: Control diet, biological replicate 2


title: 7AE356D8


title: rat at D2, biological rep2 [RTA-1_0]

description:
D2_RTA-1_0
lncRNA and mRNA expression data from DRG in STZ-induced diabetic rat.


title: 5A58BC39


title: rat at D1, biological rep1 [RTA-1_0]

description:
D1_RTA-1_0
lncRNA and mRNA expression data from DRG in STZ-induced diabetic rat.


title: sGCL-inner

city: Kyoto

first: Tetsuya

last: Imura

address: kamigyo-ku, kajiicho 465

department: Pathology

institute: Kyoto Prefectural University of Medicine

description: Gene expression of senile inner granule cell layer

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent) using the Mouse GE 4x44K Microarray Kit v2 (GPL11202). Washing and staining of the arrays were performed according to the manufacturer’s recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B). Scanned image files were inspected for artifacts and then analyzed.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 9.5.3). We applied quantile-normalization to the log2-transformed intensity values as a method for between-array normalization.

source_name: inner region of the dentate granule cell layer_20-24-month-old

label_protocol: Cy3 labeled cRNA was prepared from 0.6 ug RNA using  the WT-Ovation Pico RNA Amplification System (Nugen), One Color protocol (Agilent 5190-2305) and the Agilent One color RNA Spike-In Kit (Agilent 5188-5252) following the manufacturer's standard protocols.

growth_protocol: Congenic C57Bl6J wilt type mice were used in this study.

extract_protocol: RNA was isolated from the LCM samples directly captured into the RLT lysis buffer of the RNAeasy Nano kit (Qiagen). The quality was checked using a Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Mice at the age of eithe 3-month-old  or 20-24-month-old  were sacrificed. Brains were immediately removed and embedded in OCT compound, and coronal hippocampal sections (20 μm) were cut, mounted onto membrane-coated slides. Laser capture microdissection was performed using the MMI CellCut.

tag: strain

value: female

tag: age

value: inner granule cell layer


title: yGCL-outer

description: Gene expression of young outer granule cell layer

source_name: outer region of the dentate granule cell layer_3-month-old

tag: tissue

value: outer granule cell layer


title: Control diet, biological replicate 1

tag: cell type

value: beta pancreatic cells


title: sGCLi-outer

description: Gene expression of senile outer granule cell layer

source_name: outer region of the dentate granule cell layer_20-24-month-old


title: Control diet, biological replicate 3


title: 888C0D0F

tag: tumor inss stage

tag: tumor inrg stage


title: yGCL-inner

description: Gene expression of young inner granule cell layer

source_name: inner region of the dentate granule cell layer_3-month-old


title: B3BD7135

tag: gender (1=male; 2=female)

tag: mycn status (0=non amplified, 1= amplified)


title: A955675A

tag: age (days) at diagnosis

tag: relapse/progression (0=no, 1= yes)


title: 0F8B21F3

tag: time from diagnosis to event or last follow up (days)

tag: patient status (0=alive, 1= dead)