title: CB pre-cDC_S281

description: CB pre-cDC_S281


title: CB pre-cDC_S279

status: Public on Nov 15 2016

type: SRA

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

country: USA

institute: The Rockefeller University

description: CB pre-cDC_S279

library_source: transcriptomic

data_processing:
Raw sequencing data were processed as previously described (Shalek et al., 2014). Briefly, short sequencing reads were aligned to the UCSC hg19 transcriptome and were also used as input in RSEM v 1.2.1 to quantify gene expression levels (transcripts per million; TPM) for all UCSC hg19 genes in all samples.
We filtered out cells from our dataset where we detected less than 1,000 unique genes per cell. All genes that were not detected in at least 1% of all our single cells were discarded, leaving 20,869 genes for all further analyses. Data were log transformed (log TPM+1) for all downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of gene expression estimates across good quality samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Cord Blood pre-cDCs

extract_protocol: cDNA from each sample was prepared using the SMART-Seq 2 protocol (Picelli et al., 2013).

tag: cell type

value: CB pre-cDC

value: cord blood pre-conventional dendritic cells (cDCs)


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description: CB pre-cDC_S278


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description: CB pre-cDC_S277


title: CB pre-cDC_S280

description: CB pre-cDC_S280


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description: CB pre-cDC_S276


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description: CB pre-cDC_S273


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description: CB pre-cDC_S267


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description: CB pre-cDC_S286


title: CB pre-cDC_S266

description: CB pre-cDC_S266


title: CB pre-cDC_S263

description: CB pre-cDC_S263


title: CB pre-cDC_S262

description: CB pre-cDC_S262


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description: CB pre-cDC_S282


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description: CB pre-cDC_S259


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description: CB pre-cDC_S260


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description: CB pre-cDC_S255


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description: CB pre-cDC_S249


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description: CB pre-cDC_S264


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description: CB pre-cDC_S245


title: CB pre-cDC_S242

description: CB pre-cDC_S242


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description: CB pre-cDC_S240


title: CB pre-cDC_S241

description: CB pre-cDC_S241


title: CB pre-cDC_S235

description: CB pre-cDC_S235


title: CB pre-cDC_S238

description: CB pre-cDC_S238


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description: CB pre-cDC_S236


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description: CB pre-cDC_S239


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description: CB pre-cDC_S233


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description: CB pre-cDC_S237


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description: CB pre-cDC_S227


title: CB pre-cDC_S229

description: CB pre-cDC_S229


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title: CB pre-cDC_S247

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title: CB pre-cDC_S225

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description: CB pre-cDC_S228


title: CB pre-cDC_S224

description: CB pre-cDC_S224


title: CB pre-cDC_S222

description: CB pre-cDC_S222


title: CB pre-cDC_S231

description: CB pre-cDC_S231


title: CB pre-cDC_S244

description: CB pre-cDC_S244


title: CB pre-cDC_S220

description: CB pre-cDC_S220


title: CB pre-cDC_S221

description: CB pre-cDC_S221


title: CB pre-cDC_S243

description: CB pre-cDC_S243


title: CB pre-cDC_S219

description: CB pre-cDC_S219


title: CB pre-cDC_S218

description: CB pre-cDC_S218


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title: CB pre-cDC_S217

description: CB pre-cDC_S217


title: CB pre-cDC_S215

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title: CB pre-cDC_S206

description: CB pre-cDC_S206


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title: CB pre-cDC_S207

description: CB pre-cDC_S207


title: CB pre-cDC_S213

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description: CB pre-cDC_S209


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description: CB pre-cDC_S199


title: CB pre-cDC_S202

description: CB pre-cDC_S202


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description: CB pre-cDC_S201


title: CB pre-cDC_S203

description: CB pre-cDC_S203


title: CB pre-cDC_S196

description: CB pre-cDC_S196


title: CB pre-cDC_S195

description: CB pre-cDC_S195


title: CB pre-cDC_S192

description: CB pre-cDC_S192


title: CB pre-cDC_S193

description: CB pre-cDC_S193


title: CB pre-cDC_S191

description: CB pre-cDC_S191


title: CB pre-cDC_S190

description: CB pre-cDC_S190


title: CB pre-cDC_S189

description: CB pre-cDC_S189


title: CB pre-cDC_S188

description: CB pre-cDC_S188


title: CB pre-cDC_S186

description: CB pre-cDC_S186


title: CB pre-cDC_S187

description: CB pre-cDC_S187


title: CB pre-cDC_S185

description: CB pre-cDC_S185


title: CB pre-cDC_S297

description: CB pre-cDC_S297


title: CB pre-cDC_S200

description: CB pre-cDC_S200


title: CB pre-cDC_S183

description: CB pre-cDC_S183


title: CB pre-cDC_S182

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title: CB pre-cDC_S181

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title: CB pre-cDC_S180

description: CB pre-cDC_S180


title: CB pre-cDC_S204

description: CB pre-cDC_S204


title: CB pre-cDC_S198

description: CB pre-cDC_S198


title: CB pre-cDC_S178

description: CB pre-cDC_S178


title: CB pre-cDC_S176

description: CB pre-cDC_S176


title: CB pre-cDC_S179

description: CB pre-cDC_S179


title: CB pre-cDC_S172

description: CB pre-cDC_S172


title: CB pre-cDC_S171

description: CB pre-cDC_S171


title: CB pre-cDC_S194

description: CB pre-cDC_S194


title: CB pre-cDC_S175

description: CB pre-cDC_S175


title: CB pre-cDC_S173

description: CB pre-cDC_S173


title: CB pre-cDC_S169

description: CB pre-cDC_S169


title: CB pre-cDC_S174

description: CB pre-cDC_S174


title: CB pre-cDC_S168

description: CB pre-cDC_S168


title: CB pre-cDC_S167

description: CB pre-cDC_S167


title: CB pre-cDC_S166

description: CB pre-cDC_S166


title: CB pre-cDC_S165

description: CB pre-cDC_S165


title: CB pre-cDC_S163

description: CB pre-cDC_S163


title: CB pre-cDC_S164

description: CB pre-cDC_S164


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description: CB pre-cDC_S162


title: CB pre-cDC_S161

description: CB pre-cDC_S161


title: CB pre-cDC_S160

description: CB pre-cDC_S160


title: CB pre-cDC_S159

description: CB pre-cDC_S159


title: CB pre-cDC_S158

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title: CB pre-cDC_S157

description: CB pre-cDC_S157


title: CB pre-cDC_S152

description: CB pre-cDC_S152


title: CB pre-cDC_S153

description: CB pre-cDC_S153


title: CB pre-cDC_S150

description: CB pre-cDC_S150


title: CB pre-cDC_S151

description: CB pre-cDC_S151


title: CB pre-cDC_S155

description: CB pre-cDC_S155


title: CB pre-cDC_S170

description: CB pre-cDC_S170


title: CB pre-cDC_S149

description: CB pre-cDC_S149


title: CB pre-cDC_S147

description: CB pre-cDC_S147


title: CB pre-cDC_S156

description: CB pre-cDC_S156


title: CB pre-cDC_S146

description: CB pre-cDC_S146


title: CB pre-cDC_S145

description: CB pre-cDC_S145


title: CB pre-cDC_S144

description: CB pre-cDC_S144


title: CB pre-cDC_S148

description: CB pre-cDC_S148


title: CB pre-cDC_S143

description: CB pre-cDC_S143


title: CB pre-cDC_S139

description: CB pre-cDC_S139


title: CB pre-cDC_S141

description: CB pre-cDC_S141


title: CB pre-cDC_S138

description: CB pre-cDC_S138


title: CB pre-cDC_S140

description: CB pre-cDC_S140


title: CB pre-cDC_S137

description: CB pre-cDC_S137


title: CB pre-cDC_S135

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title: CB pre-cDC_S134

description: CB pre-cDC_S134


title: CB pre-cDC_S154

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title: CB pre-cDC_S133

description: CB pre-cDC_S133


title: CB pre-cDC_S129

description: CB pre-cDC_S129


title: CB pre-cDC_S130

description: CB pre-cDC_S130


title: CB pre-cDC_S127

description: CB pre-cDC_S127


title: CB pre-cDC_S126

description: CB pre-cDC_S126


title: CB pre-cDC_S125

description: CB pre-cDC_S125


title: CB pre-cDC_S120

description: CB pre-cDC_S120


title: CB pre-cDC_S117

description: CB pre-cDC_S117


title: CB pre-cDC_S142

description: CB pre-cDC_S142


title: CB pre-cDC_S123

description: CB pre-cDC_S123


title: CB pre-cDC_S118

description: CB pre-cDC_S118


title: CB pre-cDC_S124

description: CB pre-cDC_S124


title: CB pre-cDC_S177

description: CB pre-cDC_S177


title: CB pre-cDC_S116

description: CB pre-cDC_S116


title: CB pre-cDC_S112

description: CB pre-cDC_S112


title: CB pre-cDC_S115

description: CB pre-cDC_S115


title: CB pre-cDC_S113

description: CB pre-cDC_S113


title: CB pre-cDC_S111

description: CB pre-cDC_S111


title: CB pre-cDC_S114

description: CB pre-cDC_S114


title: CB pre-cDC_S110

description: CB pre-cDC_S110


title: CB pre-cDC_S132

description: CB pre-cDC_S132


title: CB pre-cDC_S108

description: CB pre-cDC_S108


title: CB pre-cDC_S107

description: CB pre-cDC_S107


title: CB pre-cDC_S131

description: CB pre-cDC_S131


title: CB pre-cDC_S128

description: CB pre-cDC_S128


title: CB pre-cDC_S106

description: CB pre-cDC_S106


title: CB pre-cDC_S105

description: CB pre-cDC_S105


title: CB pre-cDC_S104

description: CB pre-cDC_S104


title: CB pre-cDC_S103

description: CB pre-cDC_S103


title: CB pre-cDC_S102

description: CB pre-cDC_S102


title: CB pre-cDC_S99

description: CB pre-cDC_S99


title: CB pre-cDC_S100

description: CB pre-cDC_S100


title: CB pre-cDC_S98

description: CB pre-cDC_S98


title: CB pre-cDC_S101

description: CB pre-cDC_S101


title: CB pre-cDC_S96

description: CB pre-cDC_S96


title: CB pre-cDC_S122

description: CB pre-cDC_S122


title: CB pre-cDC_S95

description: CB pre-cDC_S95


title: CB pre-cDC_S94

description: CB pre-cDC_S94


title: CB pre-cDC_S93

description: CB pre-cDC_S93


title: CB pre-cDC_S92

description: CB pre-cDC_S92


title: CB pre-cDC_S91

description: CB pre-cDC_S91


title: CB pre-cDC_S109

description: CB pre-cDC_S109


title: CB pre-cDC_S90

description: CB pre-cDC_S90


title: CB pre-cDC_S89

description: CB pre-cDC_S89


title: CB pre-cDC_S88

description: CB pre-cDC_S88


title: CB pre-cDC_S87

description: CB pre-cDC_S87


title: CB pre-cDC_S84

description: CB pre-cDC_S84


title: CB pre-cDC_S86

description: CB pre-cDC_S86


title: CB pre-cDC_S83

description: CB pre-cDC_S83


title: CB pre-cDC_S82

description: CB pre-cDC_S82


title: CB pre-cDC_S79

description: CB pre-cDC_S79


title: CB pre-cDC_S80

description: CB pre-cDC_S80


title: CB pre-cDC_S97

description: CB pre-cDC_S97


title: CB pre-cDC_S81

description: CB pre-cDC_S81


title: CB pre-cDC_S76

description: CB pre-cDC_S76


title: CB pre-cDC_S77

description: CB pre-cDC_S77


title: CB pre-cDC_S75

description: CB pre-cDC_S75


title: CB pre-cDC_S74

description: CB pre-cDC_S74


title: CB pre-cDC_S73

description: CB pre-cDC_S73


title: CB pre-cDC_S72

description: CB pre-cDC_S72


title: CB pre-cDC_S70

description: CB pre-cDC_S70


title: CB pre-cDC_S68

description: CB pre-cDC_S68


title: CB pre-cDC_S67

description: CB pre-cDC_S67


title: CB pre-cDC_S69

description: CB pre-cDC_S69


title: CB pre-cDC_S66

description: CB pre-cDC_S66


title: CB pre-cDC_S85

description: CB pre-cDC_S85


title: CB pre-cDC_S65

description: CB pre-cDC_S65


title: CB pre-cDC_S64

description: CB pre-cDC_S64


title: CB pre-cDC_S63

description: CB pre-cDC_S63


title: CB pre-cDC_S62

description: CB pre-cDC_S62


title: CB pre-cDC_S61

description: CB pre-cDC_S61


title: CB pre-cDC_S60

description: CB pre-cDC_S60


title: CB pre-cDC_S59

description: CB pre-cDC_S59


title: CB pre-cDC_S78

description: CB pre-cDC_S78


title: CB pre-cDC_S58

description: CB pre-cDC_S58


title: CB pre-cDC_S121

description: CB pre-cDC_S121


title: CB pre-cDC_S57

description: CB pre-cDC_S57


title: CB pre-cDC_S56

description: CB pre-cDC_S56


title: CB pre-cDC_S119

description: CB pre-cDC_S119


title: CB pre-cDC_S55

description: CB pre-cDC_S55


title: CB pre-cDC_S53

description: CB pre-cDC_S53


title: CB pre-cDC_S71

description: CB pre-cDC_S71


title: CB pre-cDC_S52

description: CB pre-cDC_S52


title: CB pre-cDC_S50

description: CB pre-cDC_S50


title: CB pre-cDC_S54

description: CB pre-cDC_S54


title: CB pre-cDC_S49

description: CB pre-cDC_S49


title: CB pre-cDC_S48

description: CB pre-cDC_S48


title: CB pre-cDC_S51

description: CB pre-cDC_S51


title: CB pre-cDC_S47

description: CB pre-cDC_S47


title: CB pre-cDC_S45

description: CB pre-cDC_S45


title: CB pre-cDC_S46

description: CB pre-cDC_S46


title: CB pre-cDC_S43

description: CB pre-cDC_S43


title: CB pre-cDC_S42

description: CB pre-cDC_S42


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description: CB pre-cDC_S39


title: CB pre-cDC_S40

description: CB pre-cDC_S40


title: CB pre-cDC_S38

description: CB pre-cDC_S38


title: CB pre-cDC_S44

description: CB pre-cDC_S44


title: CB pre-cDC_S37

description: CB pre-cDC_S37


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title: CB pre-cDC_S41

description: CB pre-cDC_S41


title: CB pre-cDC_S33

description: CB pre-cDC_S33


title: CB pre-cDC_S34

description: CB pre-cDC_S34


title: CB pre-cDC_S32

description: CB pre-cDC_S32


title: CB pre-cDC_S31

description: CB pre-cDC_S31


title: CB pre-cDC_S28

description: CB pre-cDC_S28


title: CB pre-cDC_S30

description: CB pre-cDC_S30


title: CB pre-cDC_S29

description: CB pre-cDC_S29


title: CB pre-cDC_S27

description: CB pre-cDC_S27


title: CB pre-cDC_S26

description: CB pre-cDC_S26


title: CB pre-cDC_S23

description: CB pre-cDC_S23


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description: CB pre-cDC_S24


title: CB pre-cDC_S25

description: CB pre-cDC_S25


title: CB pre-cDC_S21

description: CB pre-cDC_S21


title: CB pre-cDC_S22

description: CB pre-cDC_S22


title: CB pre-cDC_S20

description: CB pre-cDC_S20


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title: CB pre-cDC_S19

description: CB pre-cDC_S19


title: CB pre-cDC_S17

description: CB pre-cDC_S17


title: CB pre-cDC_S15

description: CB pre-cDC_S15


title: CB pre-cDC_S35

description: CB pre-cDC_S35


title: CB pre-cDC_S16

description: CB pre-cDC_S16


title: CB pre-cDC_S14

description: CB pre-cDC_S14


title: CB pre-cDC_S11

description: CB pre-cDC_S11


title: CB pre-cDC_S12

description: CB pre-cDC_S12


title: CB pre-cDC_S13

description: CB pre-cDC_S13


title: CB pre-cDC_S9

description: CB pre-cDC_S9


title: CB pre-cDC_S7

description: CB pre-cDC_S7


title: CB pre-cDC_S10

description: CB pre-cDC_S10


title: CB pre-cDC_S6

description: CB pre-cDC_S6


title: CB pre-cDC_S4

description: CB pre-cDC_S4


title: CB pre-cDC_S1

description: CB pre-cDC_S1


title: CD141+ cDC_S86

description: CD141+ cDC_S86

source_name: Blood Dendritic Cells

value: CD141+ cDC

value: primary human conventional dendritic cells (cDCs)


title: CB pre-cDC_S184

description: CB pre-cDC_S184


title: CB pre-cDC_S3

description: CB pre-cDC_S3


title: CD141+ cDC_S83

description: CD141+ cDC_S83


title: CD141+ cDC_S85

description: CD141+ cDC_S85


title: CD141+ cDC_S81

description: CD141+ cDC_S81


title: CD141+ cDC_S84

description: CD141+ cDC_S84


title: CD141+ cDC_S82

description: CD141+ cDC_S82


title: CD141+ cDC_S80

description: CD141+ cDC_S80


title: CD141+ cDC_S78

description: CD141+ cDC_S78


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description: CD141+ cDC_S79


title: CD141+ cDC_S77

description: CD141+ cDC_S77


title: CB pre-cDC_S8

description: CB pre-cDC_S8


title: CD141+ cDC_S75

description: CD141+ cDC_S75


title: CD141+ cDC_S76

description: CD141+ cDC_S76


title: CD141+ cDC_S74

description: CD141+ cDC_S74


title: CD141+ cDC_S72

description: CD141+ cDC_S72


title: CB pre-cDC_S5

description: CB pre-cDC_S5


title: CD141+ cDC_S68

description: CD141+ cDC_S68


title: CD141+ cDC_S70

description: CD141+ cDC_S70


title: CD141+ cDC_S67

description: CD141+ cDC_S67


title: CD141+ cDC_S69

description: CD141+ cDC_S69


title: CB pre-cDC_S2

description: CB pre-cDC_S2


title: CD141+ cDC_S71

description: CD141+ cDC_S71


title: CD141+ cDC_S66

description: CD141+ cDC_S66


title: CD141+ cDC_S87

description: CD141+ cDC_S87


title: CD141+ cDC_S65

description: CD141+ cDC_S65


title: CD141+ cDC_S64

description: CD141+ cDC_S64


title: CD141+ cDC_S63

description: CD141+ cDC_S63


title: CD141+ cDC_S62

description: CD141+ cDC_S62


title: CD141+ cDC_S60

description: CD141+ cDC_S60


title: CD141+ cDC_S58

description: CD141+ cDC_S58


title: CD141+ cDC_S61

description: CD141+ cDC_S61


title: CD141+ cDC_S56

description: CD141+ cDC_S56


title: CD141+ cDC_S57

description: CD141+ cDC_S57


title: CD141+ cDC_S54

description: CD141+ cDC_S54


title: CD141+ cDC_S51

description: CD141+ cDC_S51


title: CD141+ cDC_S50

description: CD141+ cDC_S50


title: CD141+ cDC_S49

description: CD141+ cDC_S49


title: CD141+ cDC_S73

description: CD141+ cDC_S73


title: CD141+ cDC_S46

description: CD141+ cDC_S46


title: CD141+ cDC_S43

description: CD141+ cDC_S43


title: CD141+ cDC_S42

description: CD141+ cDC_S42


title: CD141+ cDC_S44

description: CD141+ cDC_S44


title: CD141+ cDC_S48

description: CD141+ cDC_S48


title: CD141+ cDC_S45

description: CD141+ cDC_S45


title: CD141+ cDC_S40

description: CD141+ cDC_S40


title: CD141+ cDC_S41

description: CD141+ cDC_S41


title: CD141+ cDC_S38

description: CD141+ cDC_S38


title: CD141+ cDC_S39

description: CD141+ cDC_S39


title: CD141+ cDC_S59

description: CD141+ cDC_S59


title: CD141+ cDC_S36

description: CD141+ cDC_S36


title: CD141+ cDC_S34

description: CD141+ cDC_S34


title: CD141+ cDC_S37

description: CD141+ cDC_S37


title: CD141+ cDC_S55

description: CD141+ cDC_S55


title: CD141+ cDC_S33

description: CD141+ cDC_S33


title: CD141+ cDC_S31

description: CD141+ cDC_S31


title: CD141+ cDC_S35

description: CD141+ cDC_S35


title: CD141+ cDC_S32

description: CD141+ cDC_S32


title: CD141+ cDC_S30

description: CD141+ cDC_S30


title: CD141+ cDC_S29

description: CD141+ cDC_S29


title: CD141+ cDC_S53

description: CD141+ cDC_S53


title: CD141+ cDC_S52

description: CD141+ cDC_S52


title: CD141+ cDC_S47

description: CD141+ cDC_S47


title: CD141+ cDC_S26

description: CD141+ cDC_S26


title: CD141+ cDC_S27

description: CD141+ cDC_S27


title: CD141+ cDC_S24

description: CD141+ cDC_S24


title: CD141+ cDC_S25

description: CD141+ cDC_S25


title: CD141+ cDC_S23

description: CD141+ cDC_S23


title: CD141+ cDC_S22

description: CD141+ cDC_S22


title: CD141+ cDC_S21

description: CD141+ cDC_S21


title: CD141+ cDC_S19

description: CD141+ cDC_S19


title: CD141+ cDC_S16

description: CD141+ cDC_S16


title: CD141+ cDC_S18

description: CD141+ cDC_S18


title: CD141+ cDC_S17

description: CD141+ cDC_S17


title: CD141+ cDC_S14

description: CD141+ cDC_S14


title: CD141+ cDC_S13

description: CD141+ cDC_S13


title: CB pre-cDC_S136

description: CB pre-cDC_S136


title: treg_tumor_patient16

city: New York

first: Catherine

last: Konopacki

state: NY

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw reads were trimmed and clipped for quality control in Trimmomatic v0.32 with standard settings to remove low-quality reads and adaptor contamination.
Trimmed reads were aligned to human genome using TopHat2 v2.0.11 implementing Bowtie2 v2.2.2 with default settings.
Read alignments were sorted with SAMtools v0.1.19 before being counted to genomic features using HTSeq v0.6.1p1
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values files including a matrix of raw counts of sequencing reads for all genes

molecule: total RNA

source_name: Regulatory T cells

growth_protocol: Samples were collected from adult treatment-naïve women undergoing surgery for primary breast cancer. All samples were obtained after informed consent and approval from the Institutional Review Board (IRB) at Memorial Sloan Kettering Cancer Center. Normal breast parenchyma (NBP) was obtained from patients undergoing contralateral prophylactic mastectomies. Peripheral blood mononuclear cells (PBMCs) were obtained from patients prior to their surgical procedures and from buffy coats obtained from the New York Blood Center (NYBC). All cells were utilized immediately ex vivo.

extract_protocol:
Iontorrent Ion ChIP-Seq Kit with end-repair process
Cells were sorted directly into Trizol LS (ThermoFisher) and stored at -80°C prior to RNA extraction. RNA was extracted and quantified and identical quantities of RNA from each sample were subjected to SMARTer amplification with 12-16 round of PCR was performed.

treatment_protocol: Breast tumors and NBP were minced and enzymatically digested using Liberase TL for 20 minutes at 37C. The digested tissues were then passed through a 100uM filter and washed twice with FACS buffer prior to surface staining. PBMC were enriched for CD4 T cells through negative selection with RosetteSep antibody cocktails and washed twice with FACS buffer prior to surface staining. Lymphocytes were stained at 1 x 106 cells per ml for 20 minutes following Fc receptor blockade (BioLegend). Definitions used for cell sorting were as follows, conventional CD4+ T cells: CD45+CD3+CD4+CD8-CD25-, Treg cells: CD45+CD3+CD4+CD8-CD127-CD25high. Tissue Treg cells were largely of an activated phenotype and in order to provide a fair comparison to their blood counterparts blood Treg cells were defined as CD45+CD3+CD4+CD8-CD45RO+CD127-CD25high. , while resting Treg cells were defined as CD45+CD3+CD4+CD8-CD45RA+CD127-CD25high. Post sort purity was checked following every sort and was routinely > 95% pure for the sorted populations.

tag: tissue

value: breast tumor

value: Regulatory T cells

tag: cell activation

tag: cell category

value: activated


title: CD141+ cDC_S8

description: CD141+ cDC_S8


title: CD141+ cDC_S9

description: CD141+ cDC_S9


title: treg_tumor_patient15


title: CD141+ cDC_S10

description: CD141+ cDC_S10


title: treg_tumor_patient14


title: CD141+ cDC_S12

description: CD141+ cDC_S12


title: treg_PBMC_patient20

value: PBMC


title: CD141+ cDC_S7

description: CD141+ cDC_S7


title: CD141+ cDC_S28

description: CD141+ cDC_S28


title: treg_naive_PBMC_patient20

value: naïve


title: CD141+ cDC_S5

description: CD141+ cDC_S5


title: treg_naive_PBMC_patient19


title: treg_PBMC_patient19


title: CD141+ cDC_S4

description: CD141+ cDC_S4


title: CD141+ cDC_S6

description: CD141+ cDC_S6


title: CD141+ cDC_S20

description: CD141+ cDC_S20


title: treg_PBMC_patient18


title: CD141+ cDC_S3

description: CD141+ cDC_S3


title: CD141+ cDC_S15

description: CD141+ cDC_S15


title: treg_naive_PBMC_patient18


title: treg_naive_PBMC_patient17


title: CD141+ cDC_S2

description: CD141+ cDC_S2


title: treg_PBMC_patient17


title: tconv_tumor_patient16

source_name: Conventional CD4 T cells

value: Conventional CD4 T cells


title: CD1c+ cDC_S77

description: CD1c+ cDC_S77

value: CD1c+ cDC


title: tconv_tumor_patient15


title: CD1c+ cDC_S76

description: CD1c+ cDC_S76


title: tconv_tumor_patient13


title: CD1c+ cDC_S75

description: CD1c+ cDC_S75


title: tconv_tumor_patient14


title: CD1c+ cDC_S74

description: CD1c+ cDC_S74


title: CD141+ cDC_S11

description: CD141+ cDC_S11


title: CD1c+ cDC_S73

description: CD1c+ cDC_S73


title: tconv_tumor_patient12


title: tconv_naive_PBMC_patient18


title: CD1c+ cDC_S70

description: CD1c+ cDC_S70


title: CD1c+ cDC_S69

description: CD1c+ cDC_S69


title: tconv_naive_PBMC_patient17


title: CD1c+ cDC_S71

description: CD1c+ cDC_S71


title: CD1c+ cDC_S72

description: CD1c+ cDC_S72


title: Sud_WT_9

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

description: ribosomal RNA depleted

data_processing:
Samples were sequenced on the Illumina HiSeq2500, and basecalling was performed using the provided Illumina software.
Reads were trimmed by passing parameters ‘--adapters adapters.fa --adapter-trim-end RIGHT --length-dist --threads 12 --adapter-min-overlap 7 --max-uncalled 250 --min-read-length 25 --nolength-dist’ to FLEXBAR version 2x4, where the file adapters.fa listed the sequences ‘AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT’ and ‘AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’.
Reads were then were aligned to the mouse genome (mm9/NCBI build 37) using TopHat2 version 2.0.8, with annotations provided by Ensembl version 67.
TopHat was passed parameters ‘--library-type fr-firststrand,’ to accommodate stranded reads.
Exon-exon junction counts were obtained by parsing the ‘junctions.bed’ file produced by TopHat.
Gene counts were determined by excluding secondary read alignments from the BAM files (using samtools view –F 0x0100) and processing the resulting reads using HTseq5 version 0.5.4p1 (with parameters: mode intersection-strict; minaqual 1; stranded reverse; type exon; idattr gene_id).
Genome_build: mm9
Supplementary_files_format_and_content: "merged-final.tsv" file includes raw counts of reads spanning splice junctions for all samples. "mouse-s34f-sud-gene-count-matrix-sanitized.tsv" includes raw counts of reads spanning genes for all samples.

organism: Mus musculus

source_name: bulk bone marrow cells

extract_protocol:
RNA was extracted from bone marrow cells using the Qiagen miRNeasy kit.  Genomic DNA was removed by Turbo DNA free (Ambion).
Ribosomal RNA was removed using Ribozero (Epicenter).  cDNA preparation and generation of stranded libraries was performed with the TruSeq Stranded Total RNA Sample Prep kit (Illumina).

treatment_protocol: rtTA-dependent transgene induction occurred for 7 days using doxycycline chow (625 ppm).  Mice were transplanted with transgenic donor bone marrow cells, and engraftment was allowed for >6 weeks prior to transgene induction.  Sudemycin D6 treatment occurred via IV drug infusions, which occurred through an intrajugular catheter placed in each mouse.  Sudemycin D6 drug infusions were performed for the last 5 days of the 7 days of transgene induction.

tag: genotype

value: U2AF1(WT)/rtTA doxycycline-inducible transgenic mice

tag: treatment

value: Sudemycin D6 treatment

tag: tissue source

value: bone marrow


title: Sud_WT_8

description: ribosomal RNA depleted


title: CD1c+ cDC_S67

description: CD1c+ cDC_S67


title: CD1c+ cDC_S68

description: CD1c+ cDC_S68


title: Sud_WT_6

description: ribosomal RNA depleted


title: CD141+ cDC_S1

description: CD141+ cDC_S1


title: CD1c+ cDC_S66

description: CD1c+ cDC_S66


title: CD1c+ cDC_S64

description: CD1c+ cDC_S64


title: Veh_WT_4

description: ribosomal RNA depleted

value: Vehicle treatment


title: Veh_WT_5

description: ribosomal RNA depleted


title: CD1c+ cDC_S65

description: CD1c+ cDC_S65


title: tconv_PBMC_patient18


title: Veh_WT_3

description: ribosomal RNA depleted


title: CD1c+ cDC_S63

description: CD1c+ cDC_S63


title: Veh_WT_2

description: ribosomal RNA depleted


title: CD1c+ cDC_S62

description: CD1c+ cDC_S62


title: CD1c+ cDC_S60

description: CD1c+ cDC_S60


title: Sud_WT_10

description: ribosomal RNA depleted


title: CD1c+ cDC_S61

description: CD1c+ cDC_S61


title: Sud_WT_12

description: ribosomal RNA depleted


title: CD1c+ cDC_S59

description: CD1c+ cDC_S59


title: Veh_WT_1

description: ribosomal RNA depleted


title: tconv_PBMC_patient17


title: Sud_MUT_9

description: ribosomal RNA depleted

value: U2AF1(S34F)/rtTA doxycycline-inducible transgenic mice


title: CD1c+ cDC_S57

description: CD1c+ cDC_S57


title: CD1c+ cDC_S56

description: CD1c+ cDC_S56


title: Veh_MUT_7

description: ribosomal RNA depleted


title: CD1c+ cDC_S58

description: CD1c+ cDC_S58


title: CD1c+ cDC_S55

description: CD1c+ cDC_S55


title: Sud_MUT_6

description: ribosomal RNA depleted


title: Sud_MUT_2

description: ribosomal RNA depleted


title: Veh_MUT_3

description: ribosomal RNA depleted


title: CD1c+ cDC_S54

description: CD1c+ cDC_S54


title: CD1c+ cDC_S53

description: CD1c+ cDC_S53


title: Sud_MUT_12

description: ribosomal RNA depleted


title: CD1c+ cDC_S52

description: CD1c+ cDC_S52


title: Sud_MUT_10

description: ribosomal RNA depleted


title: CD1c+ cDC_S51

description: CD1c+ cDC_S51


title: CD1c+ cDC_S50

description: CD1c+ cDC_S50


title: Veh_MUT_1

description: ribosomal RNA depleted


title: CD1c+ cDC_S48

description: CD1c+ cDC_S48


title: CD1c+ cDC_S49

description: CD1c+ cDC_S49


title: Bcas2-Control

city: Beijing

first: Wenbo

last: Liu

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of zoology

data_processing:
For each cDNA library, 5G base pairs (raw data) were generated by Illumina Hi-Seq 2500.
After base composition and quality tests were passed, we removed the adapter sequence, and sequences with a high content of unknown bases (unknown bases more than 10%) or low quality reads.
Paired-end clean reads were mapped to the mouse reference genome using Tophat2 v2.0.9 software according to the standard protocol.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene id and RPKM value

source_name: P9 testes

growth_protocol: All mice were maintained under specific-pathogen-free (SPF) conditions in compliance with the guidelines of the Animal Care and Use Committee of the Institute of Zoology at the Chinese Academy of Sciences (CAS).

extract_protocol:
Total RNA was extracted from whole testes using Trizol reagent (Invitrogen, 15596-026) following the manufacturer’s instructions. After removing the residual genomic DNA with the DNase I Kit (Promega, M6101), 500 ng of total RNA was reverse-transcribed into cDNAs using the PrimeScript RT Reagent Kit (TaKaRa, RR037A) according to the manufacturer’s protocol.
A total amount of 2 mg of RNA per sample was used to prepare cDNA libraries, which were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations.

treatment_protocol: Testes samples were collected from 9-day-old control and Bcas2F/-;Vasa-Cre mice.

tag: strain

tag: age

tag: genotype/variation

value: control

value: testes


title: Bcas2-Fv


title: CD1c+ cDC_S47

description: CD1c+ cDC_S47


title: CD1c+ cDC_S46

description: CD1c+ cDC_S46


city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
MTP, DOX, and BRM combined pretreatment replicate 3
MDB3

data_processing:
Basecalls and quality scores performed using RTA 1.18.61 and Fastq files generated from reads passing chastity filtering.
Illumina adapters were trimmed using Trimmomatic with the following setting: ILLUMINACLIP:<ADAPTERS FILE>:2:30:10:1:TRUE
The reference assembly GRCm38.p3 with transcript annotation Ensembl v78 was used for alignment and quantitation. Transcript quantitation was accomplished by streaming read alignment from Bowtie2 (Langmead and Salzberg, 2012) to eXpress (Roberts and Pachter, 2013; Roberts et al., 2013).  Bowtie2 alignment settings were used as previously described (Roberts et al., 2013) and eXpress setting –r-stranded was used for directional transcript analysis.  Bias corrected effective counts were used for downstream normalization and differential expression analysis.
Read alignments used for viewing in Integrated Genomics Viewer (IGV) (Thorvaldsdottir et al., 2013) were performed using a 2-step alignment strategy employing TopHat2 (Kim et al., 2013) splice junction mapper keeping the alignment with the best alignment score.  Reads were first aligned to the annotation GTF prior to aligning to the genome reference assembly using the default settings with the exception of the following options: -g 1 –library-type fr-firststrand –G <gtf file>.
FPKM from eXpress were used to filter the effective counts from eXpress prior to normalizing the data via library size correction using the TMM method within the R package edgeR. Prior to normalization, transcripts showing at least 1 FPKM in all replicates of any group were kept for further analysis. Design matrices were created for defining groups. Differential expression (DE) was analyzed by Iimma v3.22.3 that employed the Iimma voom function for estimating dispersion [36]. DE statistics were obtained by moderated t-test, Enhanced Bayes, and Benjamini-Hochberg calculations, yielding P values, F and B-statistics, and false discovery rates (FDRs), respectively.  The DE filter was set for transcripts with FPKM fold changes of more than 2 and an FDR of less than 5%.
Genome_build: GRCm38.p3 with Ensembl v78
Supplementary_files_format_and_content:
DE_combined.txt; Significant differential expression results from the combined pretreatment experiment.
DE_mono.txt; Significant differential expression results from the mono pretreatment experiment.
eXpress_counts_combined.txt; Quantitation output from eXpress of effective counts from the combined pretreatment experiment.
eXpress_counts_mono.txt; Quantitation output from eXpress of effective counts from the mono pretreatment experiment.
eXpress_fpkm_combined.txt; Quantitation output from eXpress of fpkm values from the combined pretreatment experiment.
eXpress_fpkm_mono.txt; Quantitation output from eXpress of fpkm values from the mono pretreatment experiment.
normalized_fpkm_combined.txt; TMM normalized fpkm values from the combined pretreatment experiment.
normalized_fpkm_mono.txt; TMM normalized fpkm values from the mono pretreatment experiment.

source_name: MTP, DOX, and BRM combined pretreatment

extract_protocol:
Trizol was used to isolated the RNAs from the mouse retinas.
Illumina TruSeq Stranded mRNA Sample Preparation Kit (Part# RS-122-2101)
mRNA pull down, chemical RNA fragmentation, dUTP method for strandedness

treatment_protocol: Abca4-/-Rdh8-/- mice were expsoed to bright light with or without indicated drug treatment. The retinas were harvested 24 hours after bright light exposure. The retinas from Abca4-/-Rdh8-/- mice without bright light exposure were also included as controls. Monotreatment and combined treamtment experiments were performed and analyzed separately.

tag: strain background

value: 4- to 6-weeks

tag: drug

value: MTP, DOX, BRM

tag: light exposure

value: light exposure

value: neural retina

tag: index/adapter 1

tag: requested sequencing type-depth


title: CD1c+ cDC_S45

description: CD1c+ cDC_S45

value: primary human conventional dendritic cells (cDCs)


description:
MTP, DOX, and BRM combined pretreatment replicate 2
MDB2


title: CD1c+ cDC_S44

description: CD1c+ cDC_S44


title: Veh_MUT_5

description: ribosomal RNA depleted


description:
MTP, DOX, and BRM combined pretreatment replicate 1
MDB1


title: CD1c+ cDC_S43

description: CD1c+ cDC_S43


title: CD1c+ cDC_S42

description: CD1c+ cDC_S42


description:
light exposure, combined pretreatment experiment, replicate 3
LC3

value: DMSO


description:
BRM, MTP and TAM combined pretreatment replicate 1
BMT1

source_name: BRM, MTP and TAM combined pretreatment

value: BRM, MTP, TAM


title: CD1c+ cDC_S41

description: CD1c+ cDC_S41


title: CD1c+ cDC_S40

description: CD1c+ cDC_S40


title: CD1c+ cDC_S39

description: CD1c+ cDC_S39


title: CD1c+ cDC_S38

description: CD1c+ cDC_S38


description:
no light exposure control, combined pretreatment experiment, replicate 3
CC3

value: no light exposure


description:
light exposure, combined pretreatment experiment, replicate 2
LC2


description:
BRM, MTP and TAM combined pretreatment replicate 2
BMT2


title: CD1c+ cDC_S37

description: CD1c+ cDC_S37


title: Veh_MUT_11

description: ribosomal RNA depleted


description:
no light exposure control, combined pretreatment experiment, replicate 2
CC2


title: CD1c+ cDC_S35

description: CD1c+ cDC_S35


description:
no light exposure control, combined pretreatment experiment, replicate 1
CC1


title: CD1c+ cDC_S36

description: CD1c+ cDC_S36


description:
BRM, MTP and TAM combined pretreatment replicate 3
BMT3


title: DOX mono pretreatment replicate 2

description:
DOX mono pretreatment replicate 2
D2

source_name: DOX mono pretreatment

value: DOX


title: CD1c+ cDC_S34

description: CD1c+ cDC_S34

value: CD1c+ cDC


title: CD1c+ cDC_S33

description: CD1c+ cDC_S33


title: TAM mono pretreatment replicate 2

description:
TAM mono pretreatment replicate 2
T2

source_name: TAM mono pretreatment

value: TAM


title: CD1c+ cDC_S30

description: CD1c+ cDC_S30


title: TAM mono pretreatment replicate 1

description:
TAM mono pretreatment replicate 1
T1


title: CD1c+ cDC_S31

description: CD1c+ cDC_S31


title: TAM mono pretreatment replicate 3

description:
TAM mono pretreatment replicate 3
T3


description:
light exposure, combined pretreatment experiment, replicate 1
LC1


title: MTP mono pretreatment replicate 2

description:
MTP mono pretreatment replicate 2
M2

source_name: MTP mono pretreatment

value: MTP


title: MTP mono pretreatment replicate 3

description:
MTP mono pretreatment replicate 3
M3


title: CD1c+ cDC_S27

description: CD1c+ cDC_S27


title: CD1c+ cDC_S28

description: CD1c+ cDC_S28


title: CD1c+ cDC_S29

description: CD1c+ cDC_S29


title: MTP mono pretreatment replicate 1

description:
MTP mono pretreatment replicate 1
M1


title: CD1c+ cDC_S26

description: CD1c+ cDC_S26


title: CD1c+ cDC_S25

description: CD1c+ cDC_S25


title: BRM mono pretreatment replicate 2

description:
BRM mono pretreatment replicate 2
B2

source_name: BRM mono pretreatment

value: BRM


title: BRM mono pretreatment replicate 1

description:
BRM mono pretreatment replicate 1
B1


title: CD1c+ cDC_S24

description: CD1c+ cDC_S24


title: DOX mono pretreatment replicate 3

description:
DOX mono pretreatment replicate 3
D3


title: BRM mono pretreatment replicate 3

description:
BRM mono pretreatment replicate 3
B3


title: DOX mono pretreatment replicate 1

description:
DOX mono pretreatment replicate 1
D1


description:
light exposure, mono pretreatment experiment, replicate 2
LM2


title: CD1c+ cDC_S22

description: CD1c+ cDC_S22


title: CD1c+ cDC_S21

description: CD1c+ cDC_S21


title: CD1c+ cDC_S23

description: CD1c+ cDC_S23


description:
light exposure, mono pretreatment experiment, replicate 1
LM1


title: CD1c+ cDC_S32

description: CD1c+ cDC_S32


description:
no light exposure control, mono pretreatment experiment, replicate 3
CM3


title: CD1c+ cDC_S19

description: CD1c+ cDC_S19


title: CD1c+ cDC_S18

description: CD1c+ cDC_S18


description:
no light exposure control, mono pretreatment experiment, replicate 2
CM2


description:
no light exposure control, mono pretreatment experiment, replicate 1
CM1


title: CD1c+ cDC_S17

description: CD1c+ cDC_S17


title: CD1c+ cDC_S16

description: CD1c+ cDC_S16


title: CD1c+ cDC_S14

description: CD1c+ cDC_S14


title: Treatment 2 rep 2

description: NIH3T3 P23H-opsin/GFP cells treated with compound 2

data_processing:
Basecalls and quality scores performed using RTA 1.18.61 and Fastq files generated from reads passing chastity filtering.
Illumina adapters were trimmed using Trimmomatic with the following setting: ILLUMINACLIP:<ADAPTERS FILE>:2:30:10:1:TRUE
The reference assembly GRCm38.p3 with transcript annotation Ensembl v78 was used for alignment and quantitation. Transcript quantitation was accomplished by streaming read alignment from Bowtie2 (Langmead and Salzberg, 2012) to eXpress (Roberts and Pachter, 2013; Roberts et al., 2013).  Bowtie2 alignment settings were used as previously described (Roberts et al., 2013) and eXpress setting –r-stranded was used for directional transcript analysis.  Bias corrected effective counts were used for downstream normalization and differential expression analysis.
Read alignments used for viewing in Integrated Genomics Viewer (IGV) (Thorvaldsdottir et al., 2013) were performed using a 2-step alignment strategy employing TopHat2 (Kim et al., 2013) splice junction mapper keeping the alignment with the best alignment score.  Reads were first aligned to the annotation GTF prior to aligning to the genome reference assembly using the default settings with the exception of the following options: -g 1 –library-type fr-firststrand –G <gtf file>.
FPKM from eXpress were used to filter the effective counts from eXpress prioir to normalizing the data via library size correction using the TMM method within the R package edgeR. Prior to normalization, transcripts showing at least 1 FPKM in all replicates of any group were kept for further analysis. Design matrices were created for defining groups. Differential expression (DE) was analyzed by Iimma v3.22.3 that employed the Iimma voom function for estimating dispersion [36]. DE statistics were obtained by moderated t-test, Enhanced Bayes, and Benjamini-Hochberg calculations, yielding P values, F and B-statistics, and false discovery rates (FDRs), respectively.  The DE filter was set for transcripts with FPKM fold changes of more than 2 and an FDR of less than 5%.
Genome_build: GRCm38.p3 with Ensembl v78
Supplementary_files_format_and_content: Quantitation output from eXpress of effective counts.
Supplementary_files_format_and_content: Quantitation output from eXpress of fpkm values.
Supplementary_files_format_and_content: TMM normalized fpkm values.
Supplementary_files_format_and_content: Significant differential expression results from OPSIN versus WT.
Supplementary_files_format_and_content: Significant differential expression results from P23H versus WT.
Supplementary_files_format_and_content: Significant differential expression results from P23H versus OPSIN.
Supplementary_files_format_and_content: Significant differential expression results from T1 versus P23H.

source_name: NIH3T3 cells (P23H-Opsin/GFP)

growth_protocol: Each cell line was cultured at 37° C with 5% CO2 in Dulbecco's modified Eagle's medium (DMEM; Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS, Hyclone), 100 units/mL penicillin, 100 μg/mL streptomycin, and 2.92 μg/mL L-glutamine (Hyclone). The three cell lines were cultured to the same passage to achieve 90% confluence in a 50 mm culture dish before subsequent treatments.

extract_protocol:
Cells were lysed with TRIzol (1 mL/dish, Thermo Fisher Scientific, Grand Island, NY, USA) after 24 h of treatment, and total RNA was extracted from each sample according to the TRIzol reagent manual.
Illumina TruSeq Stranded mRNA Sample Preparation Kit (Part# RS-122-2101)
mRNA pull down, chemical RNA fragmentation, dUTP method for strandedness

treatment_protocol: Five cell assay conditions were arranged: 1) NIH3T3(GFP) cells were treated with 0.05% DMSO, labeled as WT; 2) NIH3T3(WT-opsin/GFP) cells were treated with 0.05% DMSO, labeled as OPSIN; 3) NIH3T3(P23H-opsin/GFP) cells were treated with 0.05% DMSO, labeled as P23H; 4) NIH3T3(P23H-opsin/GFP) cells were treated with 5 µM of compound 1 (an isoquinoline-2(3H)-hexanamide), labeled as T1; 5) NIH3T3(P23H-opsin/GFP) cells were treated with 10 µM of compound 2 (4-(5-chlorothiophen-2-yl)furan-2(5H)-one), labeled as T2

tag: background

value: Swiss albino

tag: tissue type

value: Embryonic fibroblast

value: compound 2

tag: age/passage/timepoint

value: passage 5

tag: assay


title: CD1c+ cDC_S15

description: CD1c+ cDC_S15

tag: cell type


title: CD1c+ cDC_S13

description: CD1c+ cDC_S13


title: Treatment 1 rep 3

description: NIH3T3 P23H-opsin/GFP cells treated with compound 1

value: compound 1


title: Treatment 1 rep 2


title: CD1c+ cDC_S12

description: CD1c+ cDC_S12


description:
light exposure, mono pretreatment experiment, replicate 3
LM3

value: 4- to 6-weeks

tag: tissue


title: Treatment 1 rep 1


title: CD1c+ cDC_S10

description: CD1c+ cDC_S10


title: P23H_opsin control rep 3

description: NIH3T3 P23H-opsin/GFP cells treated with 0.05% DMSO


title: CD1c+ cDC_S11

description: CD1c+ cDC_S11


title: CD1c+ cDC_S9

description: CD1c+ cDC_S9


title: P23H_opsin control rep 2


title: P23H_opsin control rep 1


title: WT_opsin control rep 2

description: NIH3T3 WT-opsin/GFP cells treated with 0.05% DMSO

source_name: NIH3T3 cells (WT-Opsin/GFP)


title: WT_opsin control rep 1


title: CD1c+ cDC_S7

description: CD1c+ cDC_S7


title: CD1c+ cDC_S6

description: CD1c+ cDC_S6


title: CD1c+ cDC_S5

description: CD1c+ cDC_S5


title: CD1c+ cDC_S8

description: CD1c+ cDC_S8


title: WT_opsin control rep 3


title: Treatment 2 rep 3


title: NIH3T3 control rep 2

description: NIH3T3 cells treated with 0.05% DMSO

source_name: NIH3T3 cells (GFP)


title: NIH3T3 control rep 3

description: NIH3T3 cells treated with 0.05% DMSO


title: CD1c+ cDC_S4

description: CD1c+ cDC_S4


title: CD1c+ cDC_S1

description: CD1c+ cDC_S1


title: Treatment 2 rep 1


title: CordBlood preDCs-CD172a+ Rep4

city: Sao Paulo

first: Israel

middle: Tojal da

last: Silva

state: SP

address: Tagua, 440

country: Brazil

institute: HOSPITAL A C CAMARGO

data_processing:
alignment with STAR 2.4.1d (default settings)
Gene expression counts generated with htseq-count version 0.6.0
Genome_build: hg19
Supplementary_files_format_and_content: the processed data files includes the refGene gene symbol and counts

source_name: Cord Blood

extract_protocol:
RNA was extracted and column-purified using the Arcturus PicoPure RNA Isolation kit (Applied Biosystems). Genomic DNA was removed by on-column digest with DNAse I (Qiagen), according to the PicoPure RNA Isolation kit manual
RNA libraries were prepared using the SMARTer Ultra Low Input RNA for Sequencing kit (Clontech Laboratories) followed with Nextera XT DNA Library Prep kit (Illumina).  Libraries were sequenced by 75-bp single-end reading on a NextSeq 500 sequencer (Illumina)

value: Cord Blood


title: CordBlood preDCs-CD172a+ Rep3


title: treg_tumor_patient8

extract_protocol:
Illumina TruSeq paired-end library preparation following manufacturer's protocols
Cells were sorted directly into Trizol LS (ThermoFisher) and stored at -80°C prior to RNA extraction. RNA was extracted and quantified and identical quantities of RNA from each sample were subjected to SMARTer amplification with 12-16 round of PCR was performed.

value: breast tumor

value: Regulatory T cells

tag: cell activation

tag: cell category

value: activated

tag: barcode

value: CAAAAG


title: NIH3T3 control rep 1

description: NIH3T3 cells treated with 0.05% DMSO

tag: treatment

value: DMSO


title: CordBlood preDCs-CD172a+ Rep2


title: treg_tumor_patient5

value: CGATGT


title: treg_tumor_patient1

value: GTCCGC


title: CordBlood preDCs-CD172a- Rep4


title: CordBlood preDCs-CD172a+ Rep1


title: treg_NBP_patient9

value: NBP

value: CAGGCG


title: CD1c+ cDC_S2

description: CD1c+ cDC_S2

value: CD1c+ cDC

value: primary human conventional dendritic cells (cDCs)


title: CordBlood preDCs-CD172a- Rep3


title: wild type epithelium CTB023

first: Tomasz

middle: Boguslaw

last: Owczarek

address: 1130 St. Nicolas Av.

department: Hematology and Oncology

institute: Columbia University

data_processing:
A TruSeq RNA Sample Prep Kit v2 (Illumina) was used for library preparation followed by sequencing (30 million reads, single end) on an Illumina HiSeq 2500. Paired-end reads were mapped to mouse genome build M4 using STAR aligner. Raw gene counts were determined using featureCounts then normalized and variance-stabilized using DESeq2 package (Bioconductor) in R-system v3.1.1 (The R Foundation for Statistical Computing, ISBN 3-900051-07-0).
Genome_build: M4

source_name: bladder tissue

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2500 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: Tumor induction was achieved by injection of an adenovirus expressing Cre-recombinase (Adeno-Cre) into the bladder lumen. Ultrasound imaging using a Vevo 2100® Imaging System (Visual Sonics, Toronto, Ontario, Canada) was performed to detect bladder tumors, as well as to measure tumor volume using 3D imaging. For drug treatment studies, cisplatin (Sigma-Aldrich; Catalog #479306) was dissolved in phosphate-buffered saline (PBS) and freshly made solution or vehicle (PBS) was administered once weekly via IP at 4 mg/kg

tag: Sex

value: f

tag: age (months)

tag: genotype

tag: rin


title: wild type epithelium CTB025

value: m


title: treg_NBP_patient8

value: CACCGG


title: CordBlood preDCs-CD172a- Rep2


title: TKO treated with cisplatin (4mg/kg) CTB018

value: Arff/f; p53f/f; Ptenf/f


title: wild type epithelium CTB027


title: wild type epithelium CTB020


title: CD1c+ cDC_S3

description: CD1c+ cDC_S3


title: TKO treated with cisplatin (4mg/kg) CTB019


title: treg_NBP_patient7

value: ATGAGC


title: wild type epithelium CTB026


title: CordBlood preDCs-CD172a- Rep1

value: Cord Blood


title: treg_NBP_patient4

value: CTTGTA


title: TKO treated with cisplatin (4mg/kg) CTB017


title: TKO treated with cisplatin (4mg/kg) CTB016


title: Blood BDCA-3hiDCs Rep4

source_name: Blood

value: Blood


title: CD1c+ cDC_S20

description: CD1c+ cDC_S20

source_name: Blood Dendritic Cells


title: TKO treated with cisplatin (4mg/kg) CTB015


title: DKO treated with cisplatin (4mg/kg) CTB014

value: Arf+/+; p53f/f; Ptenf/f


title: treg_NBP_patient3

source_name: Regulatory T cells

value: Regulatory T cells

value: activated

value: TAGCTT


title: DKO treated with cisplatin (4mg/kg) CTB013


title: treg_NBP_patient2

value: CCGTCC


title: Blood BDCA-3hiDCs Rep3


title: DKO treated with cisplatin (4mg/kg) CTB012


title: DKO treated with cisplatin (4mg/kg) CTB011


title: tconv_tumor_patient9

source_name: Conventional CD4 T cells

value: breast tumor

value: Conventional CD4 T cells

value: CACTCA


title: Blood BDCA-3hiDCs Rep2


title: TKO treated with vehicle (PBS) CTB010


title: tconv_tumor_patient8

value: CAACTA


title: Blood BDCA-1+DCs Rep4


title: TKO treated with vehicle (PBS) CTB009


title: DKO treated with vehicle (PBS) CTB005

value: f


title: Blood BDCA-1+DCs Rep3


title: tconv_tumor_patient5

value: TGACCA


title: TKO treated with vehicle (PBS) CTB008


title: TKO treated with vehicle (PBS) CTB007


title: tconv_tumor_patient6

value: ACTGAT


title: Blood BDCA-1+DCs Rep2


title: DKO treated with vehicle (PBS) CTB006


title: DKO treated with vehicle (PBS) CTB003

value: m


title: DKO treated with vehicle (PBS) CTB004


title: tconv_tumor_patient4

value: CAGATC


title: DKO treated with vehicle (PBS) CTB002


title: Blood BDCA-1+DCs Rep1


title: BPDCN Patient-1 ATAC-Seq

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

library_source: genomic

data_processing:
ATAC-Seq Analysis
Calculation Method: ATAC-Seq libraries were sequenced on the High-Output Next-Seq flow cell (Illumina, 150 cycles, paired end 2 x 75 bp). To generate ATAC-Seq genome browser tracks, the reads were aligned to the human genome hg18 by Bowtie with default parameters. An in-house peak calling script was used to scan the read peaks on the alignment file with following criteria: maximum read mismatch <=4, minimum read depth >=3, bin size 25 bp, read extension 200 bp. Statistically significant peaks were selected based on a p value <= 10(6) (Poisson distribution probability) and saved in the standard WIG format for visualization in the genome browser. To perform the ATAC-Seq cluster analysis, reads were aligned to human genome hg18 by Bowtie software with mismatches up to 2 nucleotides, and extended 100 bp in each direction from the 5' start. The frequencies of aligned reads in every 100-bp-bins of chromosome regions were further summarized by an in-house script. Only the bins with the depth greater than 15 reads were used for further analysis.
Library strategy:  ATAC-Seq
Supplementary_files_format_and_content: wig file
Genome_build: hg18

molecule: genomic DNA

source_name: BPDCN Patient-1

extract_protocol:
Nuclei Extraction Protocol
Other: Cells were harvested and 50,000 cells were pelleted by centrifugation for 10' at 500g. Media was removed and pelleted cells were resuspended directly in room-temperature lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.5% IGEPAL CA-630). A second centrifugation (10', 500g) isolated the nuclei.
Isolated nuclei were tagmented in 50 ul transposase reaction mix (25 uL 2X TD buffer, 10 uL transposase (Nextera DNA Library Prep Kit, Illumina) and 15 uL nuclease-free water). The transposition reaction incubated for 30 min in a 37C water bath, and then purified with the Qiagen MinElute kit. Following purification, the tagmented DNA was amplified. Depending on the sample, 8-10 total PCR cycles were necessary. After PCR amplification, the ATAC-Seq libraries were purified with the Qiagen MinElute kit and further cleaned-up with Agencourt AMPure XP beads (Beckman Coulter) at a sample to beads ratio of 1 : 1.75.

value: primary PBMCs from BPDCN-Patients

tag: disease state

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN)

tag: individual

value: Patient 1


title: Mbd2KD_Mbd2FLAG_ChIP

city: Pittsburgh

first: Sarah

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Single-end fastq reads were split by barcode adapter sequences, adapter sequences were removed, and reads were mapped to the mm9 genome using bowtie, allowing up to three mismatches. Aligned reads were processed in HOMER (Heinz et al., 2010). Genome browser tracks (bedGraph files) were generated from mapped reads using the “makeUCSCfile” command. Peaks were called using the “findPeaks” command after reads were mapped. Peaks were called individually from replicate datasets and those peaks enriched in both datasets were retained. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), intermediate CpG promoters (ICPs, defined in (Weber et al., 2007)), low methylated regions (LMRs, from (Stadler et al., 2011)), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, Mbd3 peaks (peaks called from both EGFP KD Mbd3 ChIP-seq libraries using HOMER) and Mbd2 peaks (peaks called from both EGFP KD Mbd2 ChIP-seq libraries using HOMER). After anchoring data over reference sites, aggregation plots were generated by averaging data obtained from biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: Mbd2KD, Mbd2FLAG, ChIP, murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol: Cells were fixed, washed with PBS, and pelleted. After resuspention and incubation with Lysis buffers 1 (50 mM HEPES KOH pH 7.6, 140 mM NaC, 1 mM EDTA, 10% (w/v) glycerol, 0.5% NP-40, 0.25% Triton X100) l and 2, pellets were sheared in Lysis buffer 2  (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for sonication in a Bioruptor. Sheared chromatin was incubated at 4°C overnight with protein G magnetic beads (NEB) pre-blocked and coupled with anti-Flag M2 (Sigma F1804). Magnetic beads were washed, material was eluted at 65°C on a thermomixer, and the eluent was incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μL elution buffer (20 mM Tris-HCl pH 8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS) and treated similarly. Samples were treated with RNaseA/T1 (Ambion) followed by proteinase K (Ambion) and then PCI extracted. Ethanol precipitated ChIP-enriched DNA was then used for library construction or as a template for qPCR reactions. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection

tag: cell line

value: E14 (endogenous Mbd2 C-terminally tagged with 6XHIS+3XFLAG immediately before the stop codon)

value: ESC

tag: genotype/variation

value: Mbd2 knockdown

tag: chip antibody

value: anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035)


title: Mbd3KD_Mbd2FLAG_ChIP

source_name: Mbd3KD, Mbd2FLAG, ChIP, murine embryonic stem cells

value: Mbd3 knockdown


title: tconv_tumor_patient2

value: breast tumor

value: activated

value: ATGTCA


title: tconv_tumor_patient10

value: Conventional CD4 T cells

value: CGTACG


title: EGFPKD_Mbd2FLAG_ChIP

source_name: EGFPKD, Mbd2FLAG, ChIP, murine embryonic stem cells

value: EGFP knockdown


title: Mbd2KD_Mbd3FLAG_ChIP

source_name: Mbd2KD, Mbd3FLAG, ChIP, murine embryonic stem cells

value: E14 (endogenous Mbd3abc C-terminally tagged with 6XHIS+3XFLAG immediately before the stop codon)


title: cDCs Donor-2 ATAC-Seq

source_name: cDCs Donor-2

value: conventional dendritic cells (cDCs)

value: Donor 2


title: Untagged_Mbd2FLAG_ChIP

source_name: Untagged, Mbd2FLAG, ChIP, murine embryonic stem cells

value: control


title: pDCs Donor-2 ATAC-Seq

source_name: pDCs Donor-2

value: normal plasmacytoid dendritic cells (pDCs)


title: Blood BDCA-3hiDCs Rep1

value: Blood


title: Mbd3KD_Mbd3FLAG_ChIP

source_name: Mbd3KD, Mbd3FLAG, ChIP, murine embryonic stem cells


title: tconv_tumor_patient1

value: GTGAAA


title: Untagged_Mbd3FLAG_ChIP

source_name: Untagged, Mbd3FLAG, ChIP, murine embryonic stem cells

value: ESC


title: pDCs Donor-1 ATAC-Seq

source_name: pDCs Donor-1

value: Donor 1


title: cDCs Donor-1 ATAC-Seq

source_name: cDCs Donor-1


title: tconv_NBP_patient9

value: NBP

value: CATGGC


title: EGFPKD_Mbd3FLAG_ChIP

source_name: EGFPKD, Mbd3FLAG, ChIP, murine embryonic stem cells

value: anti-Flag M2 (Sigma, catalog# F1804, lot# 080M6035)


title: MOLM-14 ATAC-Seq

value: acute myeloid leukemia (AML) cell line

value: acute myeloid leukemia (AML)


title: Mbd2KD_hMeDIP_rep1

description: hMeDIP-Seq

data_processing:
Single-end fastq reads were split by barcode adapter sequences, adapter sequences were removed, and reads were mapped to the mm9 genome using bowtie, allowing up to three mismatches. Aligned reads were processed in HOMER (Heinz et al., 2010). Genome browser tracks (bedGraph files) were generated from mapped reads using the “makeUCSCfile” command. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), intermediate CpG promoters (ICPs, defined in (Weber et al., 2007)), low methylated regions (LMRs, from (Stadler et al., 2011)), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, Mbd3 peaks (peaks called from both EGFP KD Mbd3 ChIP-seq libraries using HOMER) and Mbd2 peaks (peaks called from both EGFP KD Mbd2 ChIP-seq libraries using HOMER). After anchoring data over reference sites, aggregation plots were generated by averaging data obtained from biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: murine embryonic stem cells

extract_protocol: Genomic DNA was isolated from ES cells by resuspending cells in ES cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 10 mM NaCL, 0.5% sarkosyl), treating with RNase A, and incubating with 1 μg/μL proteinase K overnight at 55°C. DNA was cleaned through PCI extraction and isopropanol precipitation. Genomic DNA was then diluted to 20 ug/mL in TE buffer and sonicated in a Bioruptor (UCD-200) on low for 20 minutes with intervals of 15 seconds on/15 seconds off at 4°C. Sheared DNA (ranging in size from 200-600 bp) was prepared for deep sequencing and further processing by end-repaired, A-tailed, and adaptor-ligated with DNA purification through PCI extraction and ethanol precipitation between each step. 1.5 μg of prepared DNA was diluted in TE buffer up to 450 μL, denatured for 10 minutes at 95°C and immediately transferred to ice for 10 minutes. Denatured DNA was then incubated with 50 μL 10X DNA IP buffer (100 mM Na-HPO4 pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and 1.5 μL anti-5hmC (Active Motif 39791) overnight at 4°C with constant rotation. 40 μL of magnetic beads (anti-rabbit IgG for 5hmC, Life Technologies) were pre-blocked with BSA and then resuspended in DNA IP buffer. Beads were then added to the DNA/antibody mixture and incubated for 2 hours at 4°C with constant rotation. Beads were then washed three times with 700 μL 1X DNA IP buffer and DNA was eluted from the beads by incubating at 50°C on a thermomixer with 250 μL 1X DNA IP buffer and 4 μL proteinase K (20 μg/μL) for 3 hours. DNA from IP samples were cleaned through PCI extraction and ethanol precipitation. DNA was PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR. Each library was size-selected on a 1% agarose gel, its concentration determined using a Qubit (Thermo), and the integrity was confirmed by Topo-cloning a portion and sequencing ~10 fragments from each library. Libraries were sequenced on an Illumina HiSeq2000 using single-end sequencing at the UMass Medical School deep sequencing core facility. Resulting fastq sequences were processed and analyzed using the HOMER software.

treatment_protocol: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection.

tag: antibody


title: Mbd2KD_hMeDIP_rep2

description: hMeDIP-Seq


title: tconv_NBP_patient7

value: Conventional CD4 T cells

value: activated

value: ATTCCT


title: DKO treated with vehicle (PBS) CTB001

source_name: bladder tissue

value: f

value: Arf+/+; p53f/f; Ptenf/f


title: tconv_tumor_patient3

value: breast tumor

value: GATCAG


title: Dnmt1KD_hMeDIP_rep2

description: hMeDIP-Seq


title: HL-60 ATAC-Seq


title: Mbd3KD_hMeDIP_rep1

description: hMeDIP-Seq


title: tconv_NBP_patient4

value: ATCACG


title: Cal-1 ATAC-Seq

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN) cell line


title: EGFPKD_hMeDIP_rep2

description: hMeDIP-Seq


title: tconv_NBP_patient3

value: GGCTAC


title: EGFPKD_hMeDIP_rep1

description: hMeDIP-Seq


title: BPDCN Patient 30

description: Processed data in Series supplementary file RNA-Seq_FFPE_BPDCN_Normalized.xls

data_processing:
RNA-Seq Analysis (NextSeq)
Calculation Method: Pair-end sequencing was performed on a NextSeq 500 sequencer with v2 sequencing reagents (2x76bp reads). To calculate Digital Gene Expression values, the pair-end reads were aligned to hg19 genome with STAR software. The total number of reads within each gene was counted using HTSeq software. Once the total number of reads within each gene was counted, we generated for each sample the 90% trimmed mean of the read counts (average of the read counts for the middle 90% of genes in that sample). We then normalized all counts in a given sample by dividing by the samples trimmed mean and multiplying by 500. Genes with normalized counts less than 1 were set equal to one. Finally we log2 transformed the normalized counts to generate the final gene expression values.
Supplementary_files_format_and_content: Excel spread sheet of log2 transformed normalized counts
Genome_build: hg19

source_name: BPDCN Patient 30

extract_protocol:
AllPrep DNA/RNA FFPE Kit
Other: Total RNA from FFPE samples was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN) according to the manufacturer's instructions.
Smear analysis of the FFPE RNA was performed on the Agilent Bioanalyzer with the Agilent RNA 6000 Nano Kit. Only samples whose RNA was not excessively degraded (DV200 >30%) were used to generate FFPE RNA-Seq libraries with the TruSeq RNA Access kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Other: Biopsies were embedded in paraffin blocks after formalin fixation (FFPE). RNA was extracted with the AllPrep DNA/RNA FFPE Kit (QIAGEN). Smear analysis of the FFPE RNA was performed on the Agilent Bioanalyzer with the Agilent RNA 6000 Nano Kit. Only samples whose RNA was not excessively degraded (DV200 >30%) were used to generate FFPE RNA-Seq libraries.

value: plasmacytoid dendritic cells (pDCs)

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: Patient 30


title: Dnmt1KD_hMeDIP_rep1

description: hMeDIP-Seq


title: PHN Patient 13

source_name: PHN Patient 13

value: dendritic cells

value: unclassified primitive hematopoietic neoplasms (PHN)

value: Patient 13


title: cd177postreg_tumor_patient6

source_name: Regulatory T cells

value: Regulatory T cells

value: GAGTGG


title: cd177postreg_tumor_patient4

value: activated

value: ACAGTG


title: INPUT_hMeDIP_rep2

description: hMeDIP-Seq

extract_protocol: Genomic DNA was isolated from ES cells by resuspending cells in ES cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 10 mM NaCL, 0.5% sarkosyl), treating with RNase A, and incubating with 1 μg/μL proteinase K overnight at 55°C. DNA was cleaned through PCI extraction and isopropanol precipitation. Genomic DNA was then diluted to 20 ug/mL in TE buffer and sonicated in a Bioruptor (UCD-200) on low for 20 minutes with intervals of 15 seconds on/15 seconds off at 4°C. Sheared DNA (ranging in size from 200-600 bp) was prepared for deep sequencing and further processing by end-repaired, A-tailed, and adaptor-ligated with DNA purification through PCI extraction and ethanol precipitation between each step. 1.5 μg of prepared DNA was diluted in TE buffer up to 450 μL, denatured for 10 minutes at 95°C and immediately transferred to ice for 10 minutes. 1.5 μg of prepared DNA was stored for input samples. Input samples were diluted up to 250 μL with DNA IP buffer and treated with 4 μL proteinase K (20 μg/μL) for 3 hours. DNA from input samples were cleaned through PCI extraction and ethanol precipitation. DNA was PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR. Each library was size-selected on a 1% agarose gel, its concentration determined using a Qubit (Thermo), and the integrity was confirmed by Topo-cloning a portion and sequencing ~10 fragments from each library. Libraries were sequenced on an Illumina HiSeq2000 using single-end sequencing at the UMass Medical School deep sequencing core facility. Resulting fastq sequences were processed and analyzed as described for ChIP-seq libraries using the HOMER software.

treatment_protocol:
One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection
esiRNA transient transfection with lipofectamine 2000.


title: Mbd3KD_hMeDIP_rep2

description: hMeDIP-Seq


title: INPUT_hMeDIP_rep1

description: hMeDIP-Seq

extract_protocol: Genomic DNA was isolated from ES cells by resuspending cells in ES cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 10 mM NaCL, 0.5% sarkosyl), treating with RNase A, and incubating with 1 μg/μL proteinase K overnight at 55°C. DNA was cleaned through PCI extraction and isopropanol precipitation. Genomic DNA was then diluted to 20 ug/mL in TE buffer and sonicated in a Bioruptor (UCD-200) on low for 20 minutes with intervals of 15 seconds on/15 seconds off at 4°C. Sheared DNA (ranging in size from 200-600 bp) was prepared for deep sequencing and further processing by end-repaired, A-tailed, and adaptor-ligated with DNA purification through PCI extraction and ethanol precipitation between each step. 1.5 μg of prepared DNA was diluted in TE buffer up to 450 μL, denatured for 10 minutes at 95°C and immediately transferred to ice for 10 minutes. 1.5 μg of prepared DNA was stored for input samples. Input samples were diluted up to 250 μL with DNA IP buffer and treated with 4 μL proteinase K (20 μg/μL) for 3 hours. DNA from input samples were cleaned through PCI extraction and ethanol precipitation. DNA was PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR. Each library was size-selected on a 1% agarose gel, its concentration determined using a Qubit (Thermo), and the integrity was confirmed by Topo-cloning a portion and sequencing ~10 fragments from each library. Libraries were sequenced on an Illumina HiSeq2000 using single-end sequencing at the UMass Medical School deep sequencing core facility. Resulting fastq sequences were processed and analyzed using the HOMER software.


title: Gen2.2 ATAC-Seq


title: cd177postreg_tumor_patient3

value: TTAGGC


title: BPDCN Patient 27

source_name: BPDCN Patient 27

value: Patient 27


title: BPDCN Patient 29

source_name: BPDCN Patient 29

value: Patient 29


title: Mbd2KD_MeDIP_rep2

extract_protocol: Genomic DNA was isolated from ES cells by resuspending cells in ES cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 10 mM NaCL, 0.5% sarkosyl), treating with RNase A, and incubating with 1 μg/μL proteinase K overnight at 55°C. DNA was cleaned through PCI extraction and isopropanol precipitation. Genomic DNA was then diluted to 20 ug/mL in TE buffer and sonicated in a Bioruptor (UCD-200) on low for 20 minutes with intervals of 15 seconds on/15 seconds off at 4°C. Sheared DNA (ranging in size from 200-600 bp) was prepared for deep sequencing and further processing by end-repaired, A-tailed, and adaptor-ligated with DNA purification through PCI extraction and ethanol precipitation between each step. 1.5 μg of prepared DNA was diluted in TE buffer up to 450 μL, denatured for 10 minutes at 95°C and immediately transferred to ice for 10 minutes. Denatured DNA was then incubated with 50 μL 10X DNA IP buffer (100 mM Na-HPO4 pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and 1.5 μL anti-5mC (Eurogentec BI-MECY) overnight at 4°C with constant rotation. 40 μL of magnetic beads (anti- mouse IgG for 5mC, Life Technologies) were pre-blocked with BSA and then resuspended in DNA IP buffer. Beads were then added to the DNA/antibody mixture and incubated for 2 hours at 4°C with constant rotation. Beads were then washed three times with 700 μL 1X DNA IP buffer and DNA was eluted from the beads by incubating at 50°C on a thermomixer with 250 μL 1X DNA IP buffer and 4 μL proteinase K (20 μg/μL) for 3 hours. DNA from IP samples were cleaned through PCI extraction and ethanol precipitation. DNA was PCR amplified with KAPA HiFi polymerase using 16 cycles of PCR. Each library was size-selected on a 1% agarose gel, its concentration determined using a Qubit (Thermo), and the integrity was confirmed by Topo-cloning a portion and sequencing ~10 fragments from each library. Libraries were sequenced on an Illumina HiSeq2000 using single-end sequencing at the UMass Medical School deep sequencing core facility. Resulting fastq sequences were processed and analyzed using the HOMER software.


title: Mbd2KD_MeDIP_rep1


title: tconv_NBP_patient8

source_name: Conventional CD4 T cells

value: NBP

value: Conventional CD4 T cells

value: CACGAT


title: cd177postreg_tumor_patient10

value: breast tumor

value: GTGGCC


title: cd177postreg_tumor_patient2

value: AGTCAA


title: PB_gdT_rep3

city: Kyoto

first: Takuya

last: Maeda

state: Kyoto

address: 53 Kawahara-cho Shogoin Sakyo-ku

department: Department of Immunology

country: Japan

institute: Institute for Frontier Medical Science, Kyoto University

data_processing:
Basecalls performed using CASAVA
Sequence alignment performed using our in-house pipelines (Genomon Fusion).
Fragments per kilobase of exon per million fragments mapped (FPKM) was calculated for Refseq genes and then log-transformed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: γδ T cells

extract_protocol:
Total RNA was isolated using an RNeasy Plus Mini Kit (QIAGEN)
Libraries for RNA-sequence were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: gdT

tag: cell derivation

value: Peripheral blood

tag: stimulation method

value: CD3/28 beads with IL-7 and IL-15

tag: days after stimulation


title: BPDCN Patient 14

source_name: BPDCN Patient 14

tag: cell type

value: plasmacytoid dendritic cells (pDCs)

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: Patient 14


title: PB_gdT_rep1


title: cd177negtreg_tumor_patient6

tag: tissue

value: Regulatory T cells

tag: cell activation

tag: cell category

value: activated

value: GGTAGC


title: tconv_NBP_patient2

tag: barcode

value: GTAGAG


title: Mbd3KD_MeDIP_rep1


title: Mbd3KD_MeDIP_rep2


title: BPDCN Patient 8

source_name: BPDCN Patient 8

value: Patient 8


title: PB_CD8ab_rep3

source_name: CD8αβ T cells


title: SKM-1 FFPE RNA-Seq

source_name: SKM-1 FFPE

treatment_protocol: Other: Cell lines were embedded in paraffin blocks after formalin fixation (FFPE) and used as a compare/contrast control.

value: acute myeloid leukemia (AML) cell line

value: acute myeloid leukemia (AML)


title: PB_CD8ab_rep1


title: Dnmt1KD_MeDIP_rep1


title: MOLM-14 FFPE RNA-Seq

source_name: MOLM-14 FFPE


title: Dnmt1KD_MeDIP_rep2


title: HL-60 FFPE RNA-Seq

source_name: HL-60 FFPE


title: EGFPKD_MeDIP_rep2


title: cd177negtreg_tumor_patient2

value: AGTTCC


title: PB_gdT_rep2


title: PB_CD8aa_rep3

source_name: CD8αα T cells


title: PB_CD8aa_rep2


title: EGFPKD_MeDIP_rep1


title: Gen2.2 FFPE RNA-Seq

source_name: Gen2.2 FFPE

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN) cell line


title: BPDCN Patient 19

source_name: BPDCN Patient 19

value: Patient 19


title: cd177negtreg_tumor_patient10

value: breast tumor

value: GTTTCG


title: Cal-1 FFPE RNA-Seq

source_name: Cal-1 FFPE


title: IMR90-siNup153-RNAseq-r2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
RNA-Seq of siNup153 treated IMR90 cells replicate 2
processed data file: fpkm.txt.gz
strand specific polyA+ RNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the human genome (hg19) using bowtie2 (v2.1.0) for DamID, ChIP-seq, and DNase-Seq. In the case of DNase-seq reads, 3' adapter sequences needed to be removed (starting with AGTCGTGATGTTCGTATGCCGTCTTC). STAR (v2.2.0c) was used for RNA-Seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.  DamID reads were further removed if the read was not preceeded by a GATC in the genome (read starting immediately after the GATC).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser. DamID peaks for Nup153 and Nup93 were found by merging replicates and using the findPeaks program in HOMER with the following options "-style histone -o auto -size 2500 -minDist 2500 -tbp 0 -inputtbp 0 -fragLength 1 -inputFragLength 1 -F 2 -C 0 -ntagThreshold 100" using the GFP DamID experiments as background. LBR-defined LADs are much more broad than other features and were defined by first creating a log2 normalized bedGraph of LBR-DamID vs. GFP-DamID smoothed over a range of 100 kb, then taking defining enriched regions with a log2 ratio greater 0.30.  Regions within 200 kb were merged to larger domains, and finally only regions greater than 200kb in size were considered as TADs to avoid noise. ChIP-Seq peaks were founding using the findPeaks program in HOMER using the paramter "-style histone" to find broad peaks for H3K4me3 and H3K9me2 peaks or "-style super" to find super enhancers from H3K27ac peaks using input as background.  CTCF peaks were found using the parameter "-style factor".    DNase-Seq peaks were found using HOMER findPeaks using the option "-style dnase".  For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: hg19
Supplementary_files_format_and_content: BED file Columns: (1) chr (2) start (3) end (4) peakName (5) peak score (6) strand.  FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-) FPKM for each experiment

growth_protocol: U2OS cells were cultured in DMEM (Gibco), 10% FBS. IMR90 cells in DMEM 20% FBS supplemented with nonessential aminoacids (Gibco) and low oxygen conditions (3%).

extract_protocol:
RNA-Seq: RNA was extracted using Trizol (Ambion) and column purified using RNeasy kit (Qiagen).
RNA-Seq strand-specific polyA+ libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: RNAi mediated gene silencing was performed using the following oligos (Invitrogen): control (Luc; 5’ UAUGCAGUUGCUCUCCAGC), Nup153 (5’-ACAUUUGGUAGAGUCUGCCUU) and Nup93 (5’-GCGCUAAUUUACUACUGCA) and delivered using siLenFect (Bio-Rad). For DamID-Seq experiments, the heat shock promoter, ecodam tag and RFC.1 region of the pLgw EcoDam-V5-RFC1 vector (a kind gift of Dr. Bas Van Steensel) was cloned into the polylinker of the pMSCV-puro vector yielding pMSCV-ED-puro.  Subsequently, cDNAs (GFP, Nup153, LBR, mNup93) were inserted using the Gateway cloning system (Thermofisher) and the final product was used to transduce the cells. 48 hours after transduction, puromycin (1μg/ml) was added to select transduced cells.

tag: RNAi

value: Nup153 RNAi

tag: damid tagged factor

tag: antibody source


title: IMR90-siNup153-RNAseq-r1

description:
RNA-Seq of siNup153 treated IMR90 cells replicate 1
processed data file: fpkm.txt.gz
strand specific polyA+ RNA


title: INPUT_MeDIP_rep2

source_name: murine embryonic stem cells


title: LMP2_CD8ab_rep3

value: Regenerated from LMP2 T-iPSCs

value: LCL pulsed with LMP2 peptide with IL-7 and IL-21


title: INPUT_MeDIP_rep1


title: Mbd3abcKO_Dnmt1ChIP_rep2

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Dnmt1 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: Untreated Mbd3abc KO E14 ES cells

value: E14 with Mbd3abc KO generated using CRISPR/Cas9


title: cd177negtreg_tumor_patient4

value: GCCAAT


title: IMR90-siCtrl-RNAseq-r2

description:
RNA-Seq of siControl treated IMR90 cells replicate 2
processed data file: fpkm.txt.gz
strand specific polyA+ RNA

value: Control RNAi


title: cd177negtreg_tumor_patient3

value: Regulatory T cells

value: activated

value: ACTTGA


title: PB_CD8ab_rep2

value: Peripheral blood

value: CD3/28 beads with IL-7 and IL-15


title: LMP2_CD8ab_rep2


title: IMR90-siCtrl-RNAseq-r1

description:
RNA-Seq of siControl treated IMR90 cells replicate 1
processed data file: fpkm.txt.gz
strand specific polyA+ RNA


title: Gen2.2 JQ1 RNA Pol2

description: No additional information.

data_processing:
BRD4 and RNA Pol2 ChIP-Seq Analyses
Calculation Method: For BRD4 and RNA Pol2 ChIP-Seq analyses, 36 bp sequence tags were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. A maximum of two mismatches was allowed for each read. For each gene, a representative RefSeq was defined based on the RNA Pol2 ChIP-Seq data. In the case of multiple RefSeq deriving from alternative promoter usage, the RefSeq with highest RNA Pol2 promoter density (-+ 500 bp from TSS) was selected. In the case of multiple RefSeq sharing the same promoter but differing for exon composition, the RefSeq with the overall highest RNA Pol2 density was selected. Promoter peaks were defined as peaks whose apex was located within a -+ 2Kb window from a representative TSS. Upstream binding peaks were defined as peaks whose apex was located within a -15Kb to -2Kb window from the TSS. Gene body binding peaks were defined as peaks whose apex was located in a window starting at +2Kb from the TSS and ending with the end of the RefSeq. When multiple peaks were associated with the same representative RefSeq, the peak with the highest apex was used for further analyses. To compare the results of two experiments, ChIP-Seq data were normalized by total tags count.
Supplementary_files_format_and_content: wig file
Genome_build: hg18

source_name: Gen2.2 JQ1 RNA Pol2

growth_protocol:
Gen2.2 Growth Protocol
Other: Gen2.2 cells were cultured in RPMI 1640 medium supplemented with non-essential amino acids, sodium pyruvate, penicillin/streptomycin and 10% fetal bovine serum. The mouse MS-5 stromal feeder cell line was used to support growth of Gen2.2 cells. All cell lines were maintained in a humidified, 5% CO2 incubator at 37C.

extract_protocol:
RNA Pol2 Antibody Extraction
Other: For “Super-enhancer” ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of total RNA Pol2 antibody (Covance, 8WG16). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

treatment_protocol:
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 12 hours
In-vitro treatment: 1x10(8) exponentially growing cells were treated for 12 hours with 250 nM JQ1.

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells

tag: disease state


title: LMP2_CD8ab_rep1


title: siNup93-RNAseq-r2

description:
RNA-Seq of siNup93 treated U2OS cells replicate 2
processed data file: fpkm.txt.gz
strand specific polyA+ RNA

value: Nup93 RNAi


title: Dnmt1KO_Dnmt1ChIP

data_processing:
Single-end fastq reads were split by barcode adapter sequences, adapter sequences were removed, and reads were mapped to the mm9 genome using bowtie, allowing up to three mismatches. Aligned reads were processed in HOMER (Heinz et al., 2010). Genome browser tracks (bedGraph files) were generated from mapped reads using the “makeUCSCfile” command. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), intermediate CpG promoters (ICPs, defined in (Weber et al., 2007)), low methylated regions (LMRs, from (Stadler et al., 2011)), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, Mbd3 peaks (peaks called from both EGFP KD Mbd3 ChIP-seq libraries using HOMER) and Mbd2 peaks (peaks called from both EGFP KD Mbd2 ChIP-seq libraries using HOMER). After anchoring data over reference sites, aggregation plots were generated.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

treatment_protocol: Untreated Dnmt1 KO E14 ES cells

value: E14 with Dnmt1 KO generated using CRISPR/Cas9


title: LMP2_CD8aa_rep3

value: LCL pulsed with LMP2 peptide with IL-2 and IL-7


title: siNup93-RNAseq-r1

description:
RNA-Seq of siNup93 treated U2OS cells replicate 1
processed data file: fpkm.txt.gz
strand specific polyA+ RNA


title: WT_Dnmt1ChIP

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4C overnight with constant rotation. Dnmt1 antibody (bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000

treatment_protocol: Untreated WT E14 ES cells


title: PB_CD8aa_rep1


title: LMP2_CD8aa_rep2


title: Gen2.2 DMSO BRD4

description: No additional information.

source_name: Gen2.2 DMSO BRD4

extract_protocol:
BRD4 Antibody Extraction
Other: For “Super-enhancer” ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of BRD4 antibody (Bethyl, Cat No. A301-985A). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

treatment_protocol:
Agent: DMSO (Dimethyl sulfoxide)
Treatment time: 12 hours
In-vitro treatment: 1x10(8) exponentially growing cells were treated for 12 hours with DMSO.

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm)


title: WT_INPUT_Dnmt1ChIP

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples.  Input DNA was diluted with 170 μl elution buffer and incubated at 65°C overnight to reverse crosslinking. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: Gen2.2 DMSO IgG Control

description: No additional information.

source_name: Gen2.2 DMSO IgG Control

extract_protocol:
IgG Control Extraction
Other: For "Super-enhancer" ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of Negative Control antibody (anti-Flag-M2, Sigma). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.


title: Tet1ci_Mbd3ChIP_rep2

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Mbd3 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: Untreated Tet1c.i. E14 ES cells

value: E14 with two point mutations in catalytic domain of Tet1


title: Gen2.2 JQ1 BRD4

description: No additional information.

source_name: Gen2.2 JQ1 BRD4


title: LMP2_CD8aa_rep1


title: Gen2.2 DMSO RNA Pol2

description: No additional information.

source_name: Gen2.2 DMSO RNA Pol2


title: IMR90-Input-ChIPseq

description:
Input ChIP-seq sample
processed data file: none

extract_protocol:
ChIP-seq: cells were cross-linked with 1% formaldehyde at room temperature for 10 min and neutralized with 0.125 M glycine. After sonication,chromatin was incubated with 5–10 μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Dynabeads M280 sheep-anti-rabbit IgG or sheep-anti-mouse IgG (Invitrogen). Subsequently, immuno-complexes were washed, decorsslinked and DNA was purified by QIAquick Spin columns (Qiagen).
ChIP-Seq and DamID-Seq libraries were generated using the TruSeq ChIP sample Prep kit (Illumina) or the Kapa Hyper Prep Kit for Illumina Platforms followed by Illumina sequencing.


title: siCtrl-RNAseq-r2

description:
RNA-Seq of siControl treated U2OS cells replicate 2
processed data file: fpkm.txt.gz
strand specific polyA+ RNA


title: siCtrl-RNAseq-r1

description:
RNA-Seq of siControl treated U2OS cells replicate 1
processed data file: fpkm.txt.gz
strand specific polyA+ RNA


title: Cal-1 JQ1 IgG Control

description: No additional information.

source_name: Cal-1 JQ1 IgG Control

growth_protocol:
Cal-1 Growth Protocol
Other: Cal-1 cells were cultured in RPMI-1640 medium supplemented with penicillin/streptomycin and 10% fetal bovine serum (Tet tested, Atlanta Biologicals). All cell lines were maintained in a humidified, 5% CO2 incubator at 37C.


title: Cal-1 JQ1 BRD4

description: No additional information.

source_name: Cal-1 JQ1 BRD4