title: MHCII.Hi_S56

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S56]


title: MHCII.Hi_S52

status: Public on Nov 05 2018

type: SRA

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

country: USA

institute: Harvard T. H. Chan School of Public Health

library_source: transcriptomic

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM for each gene (rows) in each cell (columns).

molecule: total RNA

organism: Mus musculus

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S52]

extract_protocol:
Full length RNAseq (SMART-Seq2)
This sample represents a single cell processed with SMART-Seq2 protocol.

tag: cell type

value: Lgr5-GFP mouse intestinal epithelial cells

tag: strain

tag: treatment

tag: time point

tag: genotype


title: MHCII.Hi_S5

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S5]


title: MHCII.Hi_S51

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S51]


title: MHCII.Hi_S48

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S48]


title: MHCII.Hi_S50

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S50]


title: MHCII.Hi_S47

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S47]


title: MHCII.Hi_S49

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S49]


title: MHCII.Hi_S55

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S55]


title: MHCII.Hi_S46

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S46]


title: MHCII.Hi_S45

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S45]


title: MHCII.Hi_S44

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S44]


title: MHCII.Hi_S42

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S42]


title: MHCII.Hi_S41

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S41]


title: MHCII.Hi_S43

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S43]


title: MHCII.Hi_S40

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S40]


title: MHCII.Hi_S6

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S6]


title: MHCII.Hi_S38

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S38]


title: MHCII.Hi_S4

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S4]


title: MHCII.Hi_S39

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S39]


title: MHCII.Hi_S34

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S34]


title: MHCII.Hi_S35

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S35]


title: MHCII.Hi_S33

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S33]


title: MHCII.Hi_S32

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S32]


title: MHCII.Hi_S36

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S36]


title: MHCII.Hi_S37

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S37]


title: MHCII.Hi_S31

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S31]


title: MHCII.Hi_S286

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S286]


title: MHCII.Hi_S282

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S282]


title: MHCII.Hi_S283

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S283]


title: MHCII.Hi_S29

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S29]


title: MHCII.Hi_S3

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S3]


title: MHCII.Hi_S285

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S285]


title: MHCII.Hi_S281

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S281]


title: MHCII.Hi_S278

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S278]


title: MHCII.Hi_S279

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S279]


title: MHCII.Hi_S284

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S284]


title: MHCII.Hi_S277

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S277]


title: MHCII.Hi_S280

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S280]


title: MHCII.Hi_S276

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S276]


title: MHCII.Hi_S275

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S275]


title: MHCII.Hi_S274

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S274]


title: MHCII.Hi_S273

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S273]


title: MHCII.Hi_S28

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S28]


title: MHCII.Low_S126

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Low_S126]


title: MHCII.Hi_S270

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S270]


title: MHCII.Hi_S271

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S271]


title: MHCII.Hi_S268

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S268]


title: MHCII.Hi_S272

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S272]


title: MHCII.Hi_S269

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S269]


title: MHCII.Hi_S266

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S266]


title: MHCII.Hi_S265

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S265]


title: MHCII.Hi_S27

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S27]


title: MHCII.Hi_S267

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S267]


title: MHCII.Hi_S264

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S264]


title: MHCII.Hi_S263

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S263]


title: MHCII.Hi_S30

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S30]


title: MHCII.Hi_S260

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S260]


title: MHCII.Hi_S261

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S261]


title: MHCII.Hi_S262

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S262]


title: MHCII.Hi_S26

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S26]


title: MHCII.Hi_S258

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S258]


title: MHCII.Hi_S257

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S257]


title: MHCII.Hi_S254

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S254]


title: MHCII.Hi_S253

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S253]


title: MHCII.Hi_S256

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S256]


title: MHCII.Hi_S252

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S252]


title: MHCII.Hi_S251

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S251]


title: MHCII.Hi_S25

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S25]


title: MHCII.Hi_S255

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S255]


title: MHCII.Hi_S247

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S247]


title: MHCII.Hi_S249

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S249]


title: MHCII.Hi_S245

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S245]


title: MHCII.Hi_S242

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S242]


title: MHCII.Hi_S241

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S241]


title: MHCII.Hi_S243

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S243]


title: MHCII.Hi_S24

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S24]


title: MHCII.Hi_S248

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S248]


title: MHCII.Hi_S240

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S240]


title: MHCII.Hi_S246

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S246]


title: MHCII.Hi_S250

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S250]


title: MHCII.Hi_S238

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S238]


title: MHCII.Hi_S239

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S239]


title: MHCII.Hi_S259

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S259]


title: MHCII.Hi_S235

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S235]


title: MHCII.Hi_S234

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S234]


title: MHCII.Hi_S231

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S231]


title: MHCII.Hi_S237

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S237]


title: MHCII.Hi_S232

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S232]


title: MHCII.Hi_S229

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S229]


title: MHCII.Hi_S228

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S228]


title: MHCII.Hi_S236

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S236]


title: MHCII.Hi_S226

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S226]


title: MHCII.Hi_S23

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S23]


title: MHCII.Hi_S225

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S225]


title: MHCII.Hi_S244

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S244]


title: MHCII.Hi_S222

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S222]


title: MHCII.Hi_S233

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S233]


title: MHCII.Hi_S220

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S220]


title: MHCII.Hi_S22

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S22]


title: MHCII.Hi_S224

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S224]


title: MHCII.Hi_S219

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S219]


title: MHCII.Hi_S218

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S218]


title: MHCII.Hi_S217

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S217]


title: MHCII.Hi_S216

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S216]


title: MHCII.Hi_S215

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S215]


title: MHCII.Hi_S214

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S214]


title: MHCII.Hi_S212

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S212]


title: MHCII.Hi_S211

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S211]


title: MHCII.Hi_S213

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S213]


title: MHCII.Hi_S21

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S21]


title: MHCII.Hi_S230

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S230]


title: MHCII.Hi_S207

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S207]


title: MHCII.Hi_S227

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S227]


title: MHCII.Hi_S209

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S209]


title: MHCII.Hi_S206

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S206]


title: MHCII.Hi_S204

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S204]


title: MHCII.Hi_S203

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S203]


title: MHCII.Hi_S202

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S202]


title: MHCII.Hi_S221

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S221]


title: MHCII.Hi_S200

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S200]


title: MHCII.Hi_S201

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S201]


title: MHCII.Hi_S2

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S2]


title: MHCII.Hi_S199

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S199]


title: MHCII.Hi_S190

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S190]


title: MHCII.Hi_S197

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S197]


title: MHCII.Hi_S195

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S195]


title: MHCII.Hi_S196

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S196]


title: MHCII.Hi_S189

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S189]


title: MHCII.Hi_S19

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S19]


title: MHCII.Hi_S20

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S20]


title: MHCII.Hi_S194

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S194]


title: MHCII.Hi_S210

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S210]


title: MHCII.Hi_S188

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S188]


title: MHCII.Hi_S208

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S208]


title: MHCII.Hi_S186

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S186]


title: MHCII.Hi_S205

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S205]


title: MHCII.Hi_S185

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S185]


title: MHCII.Hi_S181

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S181]


title: MHCII.Hi_S184

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S184]


title: MHCII.Hi_S182

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S182]


title: MHCII.Hi_S18

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S18]


title: MHCII.Hi_S180

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S180]


title: MHCII.Hi_S183

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S183]


title: MHCII.Hi_S198

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S198]


title: MHCII.Hi_S176

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S176]


title: MHCII.Hi_S178

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S178]


title: MHCII.Hi_S177

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S177]


title: MHCII.Hi_S193

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S193]


title: MHCII.Hi_S179

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S179]


title: MHCII.Hi_S170

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S170]


title: MHCII.Hi_S187

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S187]


title: MHCII.Hi_S171

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S171]


title: MHCII.Hi_S166

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S166]


title: MHCII.Hi_S17

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S17]


title: MHCII.Hi_S165

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S165]


title: MHCII.Hi_S167

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S167]


title: MHCII.Hi_S168

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S168]


title: MHCII.Hi_S223

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S223]


title: MHCII.Hi_S164

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S164]


title: MHCII.Hi_S175

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S175]


title: MHCII.Hi_S172

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S172]


title: MHCII.Hi_S174

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S174]


title: MHCII.Hi_S169

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S169]


title: MHCII.Hi_S163

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S163]


title: MHCII.Hi_S162

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S162]


title: MHCII.Hi_S173

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S173]


title: MHCII.Hi_S159

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S159]


title: MHCII.Hi_S161

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S161]


title: MHCII.Hi_S160

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S160]


title: MHCII.Hi_S158

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S158]


title: MHCII.Hi_S156

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S156]


title: MHCII.Hi_S155

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S155]


title: MHCII.Hi_S154

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S154]


title: MHCII.Hi_S153

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S153]


title: MHCII.Hi_S152

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S152]


title: MHCII.Hi_S157

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S157]


title: MHCII.Hi_S151

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S151]


title: MHCII.Hi_S150

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S150]


title: MHCII.Hi_S15

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S15]


title: MHCII.Hi_S148

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S148]


title: MHCII.Hi_S146

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S146]


title: MHCII.Hi_S145

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S145]


title: MHCII.Hi_S144

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S144]


title: MHCII.Hi_S140

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S140]


title: MHCII.Hi_S141

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S141]


title: MHCII.Hi_S142

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S142]


title: MHCII.Hi_S149

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S149]


title: MHCII.Hi_S147

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S147]


title: MHCII.Hi_S16

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S16]


title: MHCII.Hi_S137

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S137]


title: MHCII.Hi_S135

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S135]


title: MHCII.Hi_S139

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S139]


title: MHCII.Hi_S136

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S136]


title: MHCII.Hi_S134

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S134]


title: MHCII.Hi_S138

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S138]


title: MHCII.Hi_S133

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S133]


title: MHCII.Hi_S13

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S13]


title: MHCII.Hi_S130

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S130]


title: MHCII.Hi_S128

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S128]


title: MHCII.Hi_S127

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S127]


title: MHCII.Hi_S125

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S125]


title: MHCII.Hi_S124

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S124]


title: MHCII.Hi_S143

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S143]


title: MHCII.Hi_S122

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S122]


title: MHCII.Hi_S123

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S123]


title: MHCII.Hi_S120

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S120]


title: MHCII.Hi_S118

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S118]


title: MHCII.Hi_S117

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S117]


title: MHCII.Hi_S14

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S14]


title: MHCII.Hi_S12

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S12]


title: MHCII.Hi_S114

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S114]


title: MHCII.Hi_S116

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S116]


title: MHCII.Hi_S110

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S110]


title: MHCII.Hi_S119

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S119]


title: MHCII.Hi_S111

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S111]


title: MHCII.Hi_S115

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S115]


title: MHCII.Hi_S132

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S132]


title: MHCII.Hi_S131

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S131]


title: MHCII.Hi_S108

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S108]


title: MHCII.Hi_S112

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S112]


title: MHCII.Hi_S129

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S129]


title: MHCII.Hi_S107

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S107]


title: MHCII.Hi_S106

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S106]


title: MHCII.Hi_S105

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S105]


title: MHCII.Hi_S104

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S104]


title: MHCII.Hi_S103

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S103]


title: MHCII.Hi_S121

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S121]


title: MHCII.Hi_S101

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S101]


title: MHCII.Hi_S100

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S100]


title: MHCII.Hi_S10

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S10]


title: Ova_S287

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S287]

value: WT mouse intestinal epithelial cells

value: DQ-OVA

value: WT


title: Ova_S286

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S286]


title: Ova_S288

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S288]


title: MHCII.Hi_S1

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S1]


title: MHCII.Hi_S109

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S109]


title: MHCII.Hi_S113

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S113]


title: MHCII.Hi_S11

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S11]


title: Ova_S278

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S278]


title: Ova_S279

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S279]


title: Ova_S280

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S280]


title: Ova_S282

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S282]


title: Ova_S284

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S284]


title: Ova_S276

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S276]


title: Ova_S283

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S283]


title: Ova_S274

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S274]


title: Ova_S277

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S277]


title: MHCII.Hi_S102

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S102]


title: Ova_S273

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S273]


title: Ova_S268

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S268]


title: Ova_S272

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S272]


title: Ova_S270

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S270]


title: Ova_S267

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S267]


title: Ova_S271

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S271]


title: Ova_S265

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S265]


title: Ova_S281

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S281]


title: Ova_S285

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S285]


title: Ova_S262

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S262]


title: Ova_S260

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S260]


title: Ova_S266

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S266]


title: Ova_S258

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S258]


title: Ova_S251

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S251]


title: Ova_S254

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S254]


title: Ova_S252

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S252]


title: Ova_S264

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S264]


title: Ova_S261

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S261]


title: Ova_S263

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S263]


title: Ova_S275

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S275]


title: Ova_S257

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S257]


title: Ova_S269

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S269]


title: Ova_S259

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S259]


title: Ova_S250

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S250]


title: Ova_S248

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S248]


title: Ova_S249

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S249]


title: Ova_S256

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S256]


title: Ova_S253

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S253]


title: Ova_S246

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S246]


title: Ova_S247

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S247]


title: Ova_S245

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S245]


title: Ova_S244

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S244]


title: Ova_S241

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S241]


title: Ova_S242

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S242]


title: Ova_S243

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S243]


title: Ova_S240

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S240]


title: Ova_S238

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S238]


title: Ova_S239

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S239]


title: Ova_S255

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S255]


title: Ova_S237

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S237]


title: Ova_S235

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S235]


title: Ova_S234

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S234]


title: Ova_S233

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S233]


title: Ova_S232

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S232]


title: Ova_S231

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S231]


title: Ova_S230

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S230]


title: Ova_S225

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S225]


title: Ova_S228

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S228]


title: Ova_S223

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S223]


title: Ova_S222

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S222]


title: Ova_S221

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S221]


title: Ova_S229

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S229]


title: Ova_S227

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S227]


title: Ova_S226

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S226]


title: Ova_S220

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S220]


title: Ova_S217

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S217]


title: Ova_S224

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S224]


title: Ova_S218

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S218]


title: Ova_S219

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S219]


title: Ova_S216

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S216]


title: Ova_S212

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S212]


title: Ova_S213

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S213]


title: Ova_S209

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S209]


title: Ova_S211

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S211]


title: Ova_S208

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S208]


title: Ova_S214

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S214]


title: Ova_S236

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S236]


title: Ova_S210

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S210]


title: Ova_S207

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S207]


title: Ova_S206

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S206]


title: Ova_S205

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S205]


title: Ova_S203

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S203]


title: Ova_S204

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S204]


title: Ova_S198

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S198]


title: Ova_S196

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S196]


title: Ova_S201

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S201]


title: Ova_S200

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S200]


title: Ova_S194

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S194]


title: Ova_S195

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S195]


title: Ova_S197

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S197]


title: Ova_S193

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S193]


title: Ova_S199

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S199]


title: MHCII.Hi_S126

source_name: Primary intestinal epithelial cells from wild type mice, sorted on H2-Ab1 and Lgr5 [Fig.S2D] [MHCII.Hi_S126]


title: Ova_S202

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S202]


title: CytoOrgs_Th2

status: Public on Nov 01 2018

data_processing:
3' polyA RNA-seq
CellRanger 1.0
PCA (prcomp in R)
kNN-based graph clustering (R code)
Genome_build: mm10
Supplementary_files_format_and_content: 3' polyA RNA-seq. The expression levels for each gene (rows) in each single cell (column) in UMI counts as calculated using the CellRanger pipeline. Each column header provides the sequencing batch id, the cell barcode, and the cell type as identified by cluster analysis. Each ID is seperated by '_'

source_name: Intestinal organoid epithelial cells

extract_protocol:
3' polyA RNA seq
10X Genomics Chromium Prep

value: co-cultured with in vitro-differentiated Th2 cells

value: Wild-type


title: CytoOrgs_Treg

value: co-cultured with in vitro-differentiated Treg cells


title: CytoOrgs_Th1

value: co-cultured with in vitro-differentiated Th1 cells


title: CytoOrgs_Th17

value: co-cultured with in vitro-differentiated Th17 cells


title: CytoOrgs_IL17_Rep3

value: treated with 20 ng/ml IL-17A


title: Ova_S215

source_name: EpCAM+ DQ-Ova+ cultured intestinal epithelial cells from wild type mice [Fig. 2B] [Ova_S215]


title: CytoOrgs_IL17_Rep2


title: CytoOrgs_IL13_Rep2

value: treated with 20ng/ml IL-13


title: CytoOrgs_IL17_Rep1


title: CytoOrgs_IL10_Rep1

value: treated with 10ng/ml IL-10


title: CytoOrgs_IFNg_Rep2

value: treated with 0.5u/ml Interferon-gamma (IFNγ)


title: CytoOrgs_IFNg_Rep1


title: CytoOrgs_IL10_Rep2


title: CytoOrgs_ControlTcells


title: CytoOrgs_IL13_Rep1


title: CytoOrgs_ControlIL13


title: CytoOrgs_ControlCytokines_Rep1


title: CytoOrgs_ControlCytokines_Rep2


title: PreB_ped_2

status: Public on Oct 02 2018

city: Philadelphia

first: Andrei

last: Thomas-Tikhonenko

state: PA

address: 3501 Civic Center Blvd, CTRB 4056

department: Children's Hospital of Philadelphia

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
STAR version 020201 (--alignSJoverhangMin 8)
MAJIQ version 1.05
HTSeq version 0.6.0 (-m intersection-strict)
Genome_build: hg19
Supplementary_files_format_and_content: read counts per gene

organism: Homo sapiens

extract_protocol:
Mononuclear cells from fresh non-leukemic bone marrow specimens were purified via Ficoll gradient separation.  Bone marrow fractions were separated via flow cytometry directly into RLT lysis buffer. Total RNA was extracted using Qiagen Rneasy Micro spin columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: age (yrs)

tag: tissue

value: Bone Marrow

tag: purification

value: Ficoll gradient

tag: surface antigen


title: PreB_1

source_name: PreB

value: female


title: ProB_1

source_name: ProB


title: PreB_ped_1


title: TUMOR4

status: Public on Oct 21 2018

type: RNA

city: Madrid

first: Monica

last: Martinez-Fernandez

address: Avda Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5.5 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: Expression data were normalized, background-and batch corrected using the Guanine Cytosine Count Normalization (GCCN) and Signal Space Transformation (SST), and prior to summarizing using the Robust Multi-Array Average (RMA) algorithm implemented in the Affymetrix Expression Console software. In order to combine the different microarray data sets, possible batch effects were corrected by using the Bioconductor Combat package in R environment (Johnson et al., 2007)

label: biotin

source_name: Bladder, adeno-cre inoculated

label_protocol: cRNA is converted to biotinylated sense-strand DNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

extract_protocol: Extraction of total RNA was performed using miRNeasy FFPE kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: To induce tumor formation, mice were inoculated in the bladder with an adenovirus coding for Cre recombinase. To study the potential activity of Palbociclib+CDDP treatment in BC management, mice were treated with Cdk4/6 inhibitor daily 150 mg/kg intraperitoneally for 28 days plus a once per week 6 mg/kg dose of CDDP.

tag: background strain

value: FVB/N

value: bladder


title: PALBO1

source_name: Bladder, adeno-cre inoculated, Palbo+CDDP treated


title: M2

source_name: Metastasis

value: Metastatic tumor


title: PALBO2


title: TUMOR7


title: M4


title: TUMOR5


title: CT1

source_name: Bladder


title: M1


title: TUMOR6


title: TUMOR3


title: CT2


title: TUMOR2


title: PALBO-MET


title: M3


title: B6CASTF1.PRDM9hc.H3K4me3.Rep1

status: Public on Sep 28 2018

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

library_source: genomic

data_processing:
reads mapped to mm10 with bwa followed by stampy (see bam headers)
duplicates removed by samtools rmdup
reads filtered using samtools view -F12 -q1
paired-end coordinates converted to bed (in-house perl script)
fragment depth computed using bedtools genomecov (provided as supplementary bedgraph files)
force-calling of enrichment and haplotype calling performed using in-house R code (described in paper, hosted on website)
de novo broad peak calling using the method and code from Davies et al. Nature 2016
de novo narrow peak calling using the method and code from Altemose et al. eLife 2017
Genome_build: mm10
Supplementary_files_format_and_content: *FragmentDepth.B6CASTF1.PRDM9hc.H3K4me3.*.bedgraph.gz files are in bedGraph format and report the computed fragment depth at each base across the genome for each ChIP replicate and for the input control, used as input for de novo narrow peak calling.
Supplementary_files_format_and_content: GSE119727_H3K4me3.DeNovoPeaks_BroadPeakRegions.B6CASTF1.PRDM9hc.txt is a 3-column bed file listing broad peak regions with significant H3K4me3 enrichment (used for overlap comparisons in the manuscript).
Supplementary_files_format_and_content: GSE119727_H3K4me3.DeNovoPeaks.B6CASTF1.PRDM9hc.txt is a tab-delimited text file listing narrow peak regions with column descriptions in commented header (used for broad-scale analyses of H3K4me3 enrichment).
Supplementary_files_format_and_content: GSE119727_Filtered_PRDM9_Independent_BroadPeakRegions.bed is a 3-column bed file listing broad H3K4me3 peak regions determined to be potentially PRDM9-independent (using mice of different PRDM9 genotypes; see Davies et al. Nature 2016) and used for filtering out intersecting peaks in this study.

molecule: genomic DNA

source_name: whole adult testis

extract_protocol:
ChIP-seq was performed as previously described (Davies et al. Nature 2016) with several important modifications that increased ChIP stringency (noted here). Lysis was performed in 1% SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0, 2x protease inhibitors). Sonication was performed in a Bioruptor Twin sonication bath at 4°C for three 5-minute periods of 30s on, 30s off at high power. Sonicated lysates were diluted 1:10 in IP wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% Na deoxycholate, 2x Protease Inhibitor, filtered) instead of dilution buffer for antibody incubation. This yielded roughly 1 ng of ChIP DNA per testis.
Libraries were prepared using Illumina's TruSeq ChIP library preparation kit.

value: (C57BL/6J x CAST/Eij)F1

tag: prdm9 genotype

value: Humanized/CAST

tag: chip antibody

value: H3K4me3 (Abcam ab8580)

value: whole adult testis


title: CT6


title: CT4


title: MethylC-seq_P7_Kidney_EC_R2

status: Public on Sep 06 2018

city: Baltimore

first: Mark

middle: F

last: Sabbagh

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: MethylC-seq.bed.tar

data_processing:
Adaptor sequences were trimmed from sequencing reads using Cutadapt 1.11 with parameters -f fastq -q 20 -m 50 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. We further trimmed 10 bp from both 5’- and 3’- ends of both R1 and R2 reads with parameters -f fastq -u 10 -u -10 -m 30. Trimmed R1 and R2 reads were mapped to the mm10 reference genome as single-end reads using bismark 0.14.4 with parameter --bowtie2. --pbat option was used for mapping R1 reads. Mapped reads were sorted using Samtools 1.3 followed by removing duplicate reads using Picard 1.141 MarkDuplicates with parameter REMOVE_DUPLICATES=true. Reads were further filtered by MAPQ > 20 using samtools view with parameter -bhq20. Methylation level at each cytosine was summarized using call_methylated_sites from Methylpy package (https://github.com/yupenghe/methylpy/).
genome build: mm10
Supplementary_files_format_and_content: bed files (in tar archive on series record) and tar of chromosome-specific files with read counts.

source_name: P7 GFP-positive sorted cells from Kidney (vascular ECs)

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
DNA for MethylC-seq was prepared from GFP-positive FACS-sorted cells using the DNeasy Blood and Tissue kit (69504, QIAGEN).
DNA methylome libraries were prepared using a modified snmC-seq protocol adapted for bulk DNA samples (Luo et al., 2017). 20 ng of purified genomic DNA with 0.5% unmethylated lambda DNA spike-in (D1521, Promega) was bisulfite converted using the EZ DNA Methylation-Direct™ Kit (D5021, Zymo) following the product manual and was eluted in 10 µl M-Elution buffer. 9 µl converted DNA was mixed with 1 µl P5L_random oligo (5 µM, /5SpC3/TTCCCTACACGACGCTCTTCCGATCTNNNNNNNNN, IDT) followed by heat denaturing at 95°C for 3 min using a thermocycler. The samples were chilled on ice for 2 min and mixed with 10 µl enzyme mix containing 2 µl of Blue Buffer (B0110, Enzymatics), 1 µl of 10 mM dNTP (N0447L, NEB), 1 µl of Klenow exo- (50 U/µl, P7010-HC-L, Enzymatics) and 6 µl H2O. The samples were incubated using a thermocycler with the following program: 4°C for 5 min, ramp up to 25°C at 0.1°C/sec, 25°C for 5 min, ramp up to 37°C at 0.1°C/sec, 37°C for 60 min, 4°C. A 3 µl enzyme mix containing 2 µl of Exonuclease 1 (20U/µl, X8010L, Enzymatics) and 1 µl of Shrimp Alkaline Phosphatase (rSAP, M0371L, NEB) was added to the samples. The samples were incubated at 37°C for 30 min using a thermocycler. Samples were cleaned-up using 0.8x SPRI beads and eluted with 10 µl M-Elution buffer. Eluted samples were heated at 95°C for 3 min using a thermocycler and were chilled on ice for 2 min. Samples were mixed with 10.5 ul Adaptase master mix containing 2 ul Buffer G1, 2 ul Regent G2, 1.25 ul Reagent G3, 0.5 ul Enzyme G4, 0.5 ul Enzyme G5 and 4.25 ul M-Elution buffer (Accel-NGS Adaptase Module for Single Cell Methyl-Seq Library Preparation, 33096, Swift Biosciences). Samples were incubated at 37°C for 30 min, 95°C for 2 min and 4°C using a thermocycler. 1 µl 30 µM P5 indexing primer and 5 µl 10 µM P7 indexing primer and 25 µl KAPA HiFi HotStart ReadyMix, (KK2602, KAPA BIOSYSTEMS) were added into each sample followed by thermocycling using the following program - 95°C for 2 min, 98°C for 30 sec, 10 cycles of (98°C for 15 sec, 64°C for 30 sec, 72°C for 2min), 72°C for 5 min and then 4°C. PCR products were cleaned up using 0.8x SPRI beads twice. Methylome libraries were sequenced using an Illumina HiSeq 4000 instrument with 5% PhiX DNA spike-in.

tag: strain/genotype

tag: age

tag: Sex

value: Male

value: Kidney

tag: cell-type

value: Vascular endothelial cells


title: PALBO3


title: CT5


title: ProB_2


title: ProB_ped_1


title: ProB_ped_2


title: PreB_2


title: MethylC-seq_P7_Brain_EC_R2

description: MethylC-seq.bed.tar

source_name: P7 GFP-positive sorted cells from brain (vascular ECs)

value: Brain


title: B6CASTF1.PRDM9hc.Input

value: none (input)


title: MethylC-seq_P7_Lung_EC_R1

description: MethylC-seq.bed.tar

source_name: P7 GFP-positive sorted cells from Lung (vascular ECs)

value: Lung


title: B6CASTF1.PRDM9hc.H3K4me3.Rep2


title: 1000_element_library_plasmid

status: Public on Aug 27 2018

city: Cambridge

first: Frederic

middle: D

last: Sigoillot

state: MA

address: 181 Massachusetts Avenue

department: Chemical Biology and Therapeutics

institute: Novartis Institutes for Biomedical Research

data_processing:
Library strategy: CRISPR screen
Basecalls performed using Illumina bcl2fastq version 2.17.1
Sequenced reads were trimmed to barcode/CRISPR sequence and aligned by bowtie version 1.0.1.  For CRISPR reads, no mismatches were allowed during alignment.  For barcode reads, two mismatches were allowed.
Read counts were summarized using custom python scripts
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file with read counts

organism: synthetic construct

source_name: plasmid

extract_protocol:
Genomic DNA was isolated from the dissociated organoids using the QIAamp DNA Blood Maxi kit (#51194, Qiagen) and quantified using PicoGreen (P7589, Invitrogen) following the manufacturer’s instructions.
Illumina sequencing libraries were generated using PCR amplification with primers specific to the sequence of the genome of the lentiviral vector backbone. For each sample, 8 x 1 µg PCR reactions were performed in a volume of a 100µl each. For each reaction, a final concentration of 0.5 mM of each PCR primer (Integrated DNA Technologies), 0.5 mM dNTPs (#N8080261, Clontech) and 1x Titanium Taq and buffer (#639242, Clontech). The following conditions were used for PCR: 1x 98 °C for 5 min; 28x 95 °C for 15 s, 65 °C for 15 s, 72 °C for 30 s; 1x 72 °C for 5 min.


title: MethylC-seq_P7_Liver_EC_R2

description: MethylC-seq.bed.tar

source_name: P7 GFP-positive sorted cells from Liver (vascular ECs)

value: Liver


title: MethylC-seq_P7_Lung_EC_R2

description: MethylC-seq.bed.tar


title: 1000_element_library_sample_Day12_replicate1

source_name: Liver organoid

value: Liver organoid


title: MethylC-seq_P7_Liver_EC_R1

description: MethylC-seq.bed.tar


title: 1000_element_library_sample_Day12_replicate2


title: TUMOR1


title: MethylC-seq_P7_Brain_EC_R1

description: MethylC-seq.bed.tar


title: MethylC-seq_P7_Kidney_EC_R1

description: MethylC-seq.bed.tar


title: Take_rate_library_plasmid


title: Take_rate_library_sample_Day4


title: Take_rate_library_sample_Day12


title: 5503785

status: Public on Aug 24 2018

city: Little Rock

first: Brian

last: Walker

state: AR

address: 4301 W Markham St.

institute: University of Arkansas for Medical Sciences

description: Gene expresion data from newly diagnosed Multiple Myeloma patient

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on human GeneChip. U133 plus 2.0 chips are washed and stained further in affymetrix fluidics station

scan_protocol: Chips were scanned using the HG-U133 Plus 2.0 v2.2 on a Affymetrix Genechip scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: bone biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from200ng  total RNA

growth_protocol: Whole bone marrow biopsies were collected from patients with multiple myeloma, smoldering myeloma, MGUS and patients with MM that achieved a CR (sample collected within 6 months of CR achievement), as well as healthy donors. Frozen whole BM biopsies were ground in liquid nitrogen with a mortar and pestle before proceeding to RNA extraction.

extract_protocol: RNA extraction and isolation was performed with the AllPrep kit by Qiagen

tag: cell type

value: mixed/undefined or similar

tag: patient id

tag: patient group

value: TT

tag: sample type

value: RNBX-Random Biopsy

tag: molecular subgroup

value: PR

tag: gep70 score


title: 5514233

description: Gene expresion data from Normal patient

value: Normal

value: Normal Biopsy (NBX)

value: MF


title: 5511855


title: 5510892

description: Gene expresion data from Normal patient


title: 5511863

description: Gene expresion data from Normal patient


title: 5510127

value: HY


title: 5503787

description: Gene expresion data from newly diagnosed Smouldering patient

value: AMM


title: 5510115


title: 5505157


title: 5500053


title: 5500283


title: 5500273

description: Gene expresion data from Multiple Myeloma patient in CR

value: TT CR


title: 5500271


title: 5498745


title: 5500267


title: 5486989


title: 5486952


title: 5500040

value: LB


title: 5485245


title: 5498683


title: 5498743

value: MS


title: 5510120


title: 5492369


title: 5485244


title: 5500044


title: 5489072


title: 5486419


title: 5482662


title: 5482661


title: 5483297


title: 5482665


title: 5483299


title: 5481241


title: 5485243


title: 5483300


title: 5483298


title: 5494149


title: 5485262


title: 5482667


title: 5472692


title: 5483304


title: 5485761


title: 5472626


title: 5472620


title: 5472617


title: 5472619


title: 5472625


title: 5472616


title: 5481293


title: 5472667


title: 5470961


title: 5472615


title: 5471018

description: Gene expresion data from Normal patient


title: 5470960


title: 5470956


title: 5470958


title: 5470959


title: 5468576


title: 5470939


title: 5468578


title: 5468580


title: 5468559


title: 5468567


title: 5468568


title: 5470952


title: 5472614


title: 5468561


title: 5470953


title: 5468560


title: 5468581


title: 5468579


title: 5468577


title: 5468558


title: 5468121


title: 5461877


title: 5460468

description: Gene expresion data from Normal patient


title: 5468110


title: 5460505

description: Gene expresion data from Normal patient


title: 5460467

description: Gene expresion data from Normal patient


title: 5460465

description: Gene expresion data from Normal patient


title: 5460469

description: Gene expresion data from Normal patient


title: 5460466

description: Gene expresion data from Normal patient


title: 5460460

description: Gene expresion data from Normal patient


title: 5468112


title: 5460463

description: Gene expresion data from Normal patient


title: 5472623


title: 5460455

description: Gene expresion data from Normal patient


title: 5460452

description: Gene expresion data from Normal patient


title: 5460454

description: Gene expresion data from Normal patient


title: 5460464

description: Gene expresion data from Normal patient


title: 5460449

description: Gene expresion data from Normal patient


title: 5460459

description: Gene expresion data from Normal patient


title: 5460462

description: Gene expresion data from Normal patient


title: 5460456

description: Gene expresion data from Normal patient


title: 5460451

description: Gene expresion data from Normal patient


title: 5460457

description: Gene expresion data from Normal patient


title: 5460461

description: Gene expresion data from Normal patient


title: 5460450

description: Gene expresion data from Normal patient


title: 5453237


title: 5460448

description: Gene expresion data from Normal patient


title: 5459253


title: 5420531

description: Gene expresion data from Normal patient


title: 5338453


title: 5420532

description: Gene expresion data from Normal patient


title: 5370570


title: 5338450


title: 5453233


title: 5468113


title: 5427024


title: 5453208


title: 5420533

description: Gene expresion data from Normal patient


title: 5338451


title: 5338447


title: 5338038


title: 5420524

description: Gene expresion data from Normal patient


title: 5338445


title: 5338443


title: 5338448


title: 5338440


title: 5338436


title: 5338437


title: 5453210


title: 5337686


title: 5338039


title: 5338037


title: 5338449


title: 5337665


title: 5330401


title: 5337684


title: 5330287


title: 5330468


title: 5330471


title: 5330283


title: 5330280


title: 5337681


title: 5337676


title: 5337679


title: 5337664


title: 5337682


title: 5337663


title: 5330402


title: 5337683


title: 5330281


title: 5330389


title: 5328792


title: 5330403


title: 5330284


title: 5328777


title: 5330481


title: 5328788


title: 5337666


title: 5328789


title: 5328793


title: 5328790


title: 5328779


title: 5324998


title: 5295932


title: 5324999


title: 5269571


title: 5324996


title: 5293126


title: 5268027


title: 5249270


title: 5293121


title: 5328776


title: 5324997


title: 5240797

description: Gene expresion data from Normal patient


title: 5268016


title: 5293142


title: 5249456


title: 5240770


title: 5249304


title: 5325000


title: 5249183


title: 5196566


title: 5208580


title: 5196056


title: 5196058


title: 5240769


title: 5264881


title: 5193917


title: 5175419

description: Gene expresion data from newly diagnosed MGUS patient

value: MGUS


title: 5175418


title: 5178120


title: 5175414


title: 5175420


title: 5175412


title: 5175383


title: 5175382


title: 5175385


title: 5175410


title: 5175386


title: 5175413


title: 5175380


title: 5175416


title: 5175309


title: 5175377


title: 5175361


title: 5175381


title: 5175359


title: 5175311


title: 5175310


title: 5175379


title: 5175307


title: 5175305


title: 5175411


title: 5175302


title: 5175292


title: 5175286


title: 5175296


title: 5175301


title: 5175295


title: 5175287


title: 5175304


title: 5175298


title: 5175384


title: 5175308


title: 5175283


title: 5175299


title: 5175284


title: 5175288


title: 5175294


title: 5328791


title: 5175278


title: 5164563


title: 5156753


title: 5161145


title: 5161237


title: 5164576


title: 5175275


title: 5175281


title: 5168246


title: 5164434


title: 5175280


title: 5164574


title: 5154129


title: 5152752


title: 5175279


title: 5164427


title: 5159818


title: 5158840


title: 5149946


title: 5156662


title: 5149954


title: 5156279

description: Gene expresion data from Normal patient


title: 5161248


title: 5149933


title: 5149822

description: Gene expresion data from Normal patient


title: 5154155


title: 5149819

description: Gene expresion data from Normal patient


title: 5149782

description: Gene expresion data from Normal patient


title: 5149953


title: 5149804


title: 5115767


title: 5149931


title: 5175282


title: 5141545


title: 5149798


title: 5113585


title: 5115696


title: 5115731


title: 5105016


title: 5108794


title: 5115710


title: 5115705


title: 5079467

description: Gene expresion data from Normal patient


title: 5104869


title: 5067351


title: 5113612


title: 5079474


title: 5104349


title: 5115721


title: 5115768


title: 5104357


title: 5105015


title: 5076462


title: 5108757


title: 5113606


title: 5079463


title: 5059563


title: 5065910


title: 5059528


title: 5059561


title: 5059481


title: 5059480


title: 5059562


title: 5059467


title: 5059444


title: 5059486


title: 5059466


title: 5059476


title: 5059478


title: 5059431


title: 5059440


title: 5059479


title: 5059420


title: 5059423


title: 5059464


title: 5059439


title: 5059461


title: 5059435


title: 5059436


title: 5059395


title: 5059398


title: 5059397


title: 5059477


title: 5059434


title: 5059483


title: 5059402


title: 5059428


title: 5059396


title: 5059392


title: 5059386


title: 5059389


title: 5059394


title: 5059381


title: 5059388


title: 5059393


title: 5015417


title: 5059387


title: 5015424


title: 5015422


title: 5015427


title: 5015421


title: 5059390


title: 5059384


title: 5015420


title: 5015397


title: 5015411


title: 5059383


title: 5015398


title: 5015406


title: 5015399


title: 5015403


title: 5015374


title: 5015386


title: 5015377


title: 5015385


title: 5015394


title: 5015379


title: 5015412


title: 5015371


title: 5008691

description: Gene expresion data from Normal patient


title: 5007069


title: 5006989

description: Gene expresion data from Normal patient


title: 5006977

description: Gene expresion data from Normal patient


title: 5007076


title: 5008693

description: Gene expresion data from Normal patient


title: 5007003

description: Gene expresion data from Normal patient


title: 5006984

description: Gene expresion data from Normal patient


title: 5008653

description: Gene expresion data from Normal patient


title: 5007004

description: Gene expresion data from Normal patient


title: 5006992

description: Gene expresion data from Normal patient


title: 5008646

description: Gene expresion data from Normal patient


title: 5006975

description: Gene expresion data from Normal patient


title: 5008658

description: Gene expresion data from Normal patient


title: 5006999

description: Gene expresion data from Normal patient


title: 5006968

description: Gene expresion data from Normal patient


title: 5006971

description: Gene expresion data from Normal patient


title: 4850406


title: 4798688


title: 4568077


title: 5006961

description: Gene expresion data from Normal patient


title: 4733649


title: 5006969

description: Gene expresion data from Normal patient


title: 5006967

description: Gene expresion data from Normal patient


title: 4929112


title: 5006966

description: Gene expresion data from Normal patient


title: 5006974

description: Gene expresion data from Normal patient


title: 5006964

description: Gene expresion data from Normal patient


title: 4798094


title: 4568075


title: 5006973

description: Gene expresion data from Normal patient


title: 4568072


title: 4568059


title: 4562324


title: 4399511


title: 4396363

description: Gene expresion data from Normal patient


title: 4562271


title: 4568073


title: 4568069


title: 4389000


title: 4338241


title: 4388998


title: 4396367


title: 4562322


title: 4399509


title: 4338217


title: 4338247


title: 4294646


title: 4338222


title: 4294647


title: 4388996


title: 4389001


title: 4399508


title: 4338226


title: 4294669


title: 4389005


title: 4287330


title: 4287324


title: 4287332


title: 4396360

description: Gene expresion data from Normal patient


title: 4338233


title: 4269132


title: 4287307


title: 4269137


title: 4287306


title: 4269134


title: 4269140


title: 4287321


title: 4396362

description: Gene expresion data from Normal patient


title: 4568074


title: 4262184


title: 4266496


title: 4262057


title: 4262188


title: 4287374


title: 4266575


title: 4242423


title: 4262055


title: 4262067


title: 4262056


title: 4266501


title: 4250050


title: 4257207


title: 4262173


title: 4262181


title: 4396359

description: Gene expresion data from Normal patient


title: 4239447


title: 4232099


title: 4234334


title: 4237295


title: 4235646


title: 4214753


title: 4214660


title: 4214700


title: 4188809


title: 4214781


title: 4214750


title: 4232101


title: 4188805


title: 4152291

description: Gene expresion data from Normal patient


title: 4161903

description: Gene expresion data from Normal patient


title: 4188824


title: 4188820


title: 4214714


title: 4152281

description: Gene expresion data from Normal patient


title: 4152284

description: Gene expresion data from Normal patient


title: 4152277

description: Gene expresion data from Normal patient


title: 4103794


title: 4188832


title: 4219465


title: 4088976


title: 4188806


title: 4112689


title: 4151672


title: 4068745


title: 4068720


title: 4088942


title: 4063768


title: 4068724


title: 4068769


title: 4068691


title: 4063686


title: 4068716


title: 4063700


title: 4063727


title: 4063748


title: 4057812


title: 4088972


title: 4039427


title: 4063701


title: 4088938


title: 4037792


title: 4037788


title: 4057777


title: 4039275


title: 4013966


title: 4088974


title: 4028735


title: 4020138


title: 4006010


title: 4039520


title: 4002373


title: 4002385


title: 4002363


title: 4002387


title: 4002397


title: 3975081


title: 4002382


title: 4088940


title: 3975075


title: 4002383


title: 3975069


title: 3975065


title: 4002392


title: 4037785


title: 3972086


title: 3972151


title: 3972078


title: 3975077


title: 3972112


title: 3958897


title: 3972199


title: 3972084


title: 3972081


title: 3972070


title: 3946709


title: 3958886


title: 3946667


title: 3958895


title: 3958783


title: 3946613


title: 3945084


title: 3945960


title: 3957307


title: 3945933


title: 3941877


title: 3972080


title: 3946623


title: 3945858


title: 3945861


title: 3958896


title: 3931639


title: 3931574


title: 3945952


title: 3928511


title: 3917926


title: 3928504


title: 3928489


title: 3917903


title: 3912274


title: 3768728


title: 3912198


title: 3928513


title: 3768766


title: 3768397


title: 3912239


title: 3912209


title: 3928472


title: 3917932


title: 3768370


title: 3911188


title: 3848532


title: 3912221


title: 3911190


title: 3902696


title: 3903644


title: 3749037


title: 3903713


title: 3902569


title: 3749036


title: 4003233


title: 4003314


title: 3749001


title: 3654588


title: 3665454


title: 3451341


title: 3451337


title: 3654585


title: 3413946


title: 3574564


title: 3413988


title: 3620526


title: 3414025


title: 3562410


title: 3402650


title: 3401682


title: 3464845


title: 3413987


title: 3572612


title: 3401689


title: 3401694


title: 3389410


title: 3389411


title: 3654522


title: 3385119


title: 3413938


title: 3401678


title: 3402652


title: 3383965


title: 3401683


title: 3385134


title: 3383966


title: 3383919


title: 3383963


title: 3383922


title: 3376555


title: 3376544


title: 3383918


title: 3276055


title: 3375549


title: 3376557


title: 3376547


title: 3376454


title: 3376528


title: 3376455


title: 3375567


title: 3376539


title: 3376469


title: 3375608


title: 3375570


title: 3375566


title: 3917911


title: 3375607


title: 3256188


title: 3375514


title: 3256175


title: 3256140


title: 2950147


title: 2674685


title: 2950149


title: 2753312


title: 3375569


title: 2744914


title: 3169346


title: 2730123


title: 2664690


title: 2664702


title: 2664537


title: 2626785


title: 2664747


title: 2626783


title: 2664542


title: 2442856


title: 2644669


title: 2439742


title: 2511723


title: 2579562


title: 2579565


title: 2654047


title: 2439743


title: 2484039


title: 2439726


title: 2664574


title: 2439711


title: 2579566


title: 2439683


title: 2458435

description: Gene expresion data from Normal patient


title: 2511699


title: 2579567


title: 2381558

description: Gene expresion data from Normal patient


title: 2439741


title: 2626735


title: 2439717


title: 2579563


title: 2381530


title: 2159763


title: 2381529


title: 2380441


title: 2381485


title: 2159663


title: 2159661


title: 2096287


title: 2096284


title: 2159680


title: 2111410


title: 2380426


title: 2380418


title: 2091537


title: 2381533


title: 2380415


title: 2159667


title: 2159756


title: 2159677


title: 2159678


title: 2037598


title: 2081889


title: 2037659


title: 2059139


title: 2059154


title: 2043052


title: 2037640


title: 2380434


title: 2037563


title: 2037582


title: 2037554


title: 2037577


title: 2037565


title: 2037386


title: 2037380


title: 2037384


title: 2037562


title: 2037382


title: 2036552


title: 2037512


title: 2159679


title: 2037551


title: 2037338


title: 2036433


title: 2037560


title: 2036551


title: 2036555


title: 2009084


title: 2009128


title: 2009193


title: 2036583


title: 2009127


title: 2037367


title: 2037351


title: 2037238


title: 2009077


title: 2081900


title: 2037336


title: 1973091


title: 1914543


title: 1902563


title: 1914535


title: 1951407


title: 1991822


title: 1884286


title: 1884296


title: 1923377


title: 1951413


title: 1884288


title: 1914537


title: 1880232


title: 1902562


title: 1884294


title: 1914541


title: 1914542


title: 1914539


title: 1884251


title: 1880235


title: 1923347


title: 1914538


title: 1884291


title: 1876975


title: 1914530


title: 1876936


title: 1876971


title: 1880237


title: 1884298


title: N402Barcode_722-518

status: Public on Jul 12 2018

city: Stanford

first: Yuan

last: Xue

address: 318 Campus Drive

institute: Stanford University

data_processing:
Read alignment, STAR, 2.5.0a,  –outSAMstrandField intronMotif --runThreadN {threads} --outFileNamePrefix {wdir} --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outReadsUnmapped Fastx --clip3pAdapterSeq CTGTCTCTTATACACATCT --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1; gene count, htseq-count, 0.10.0, -s no -t exon -r pos -f bam -i Parent -m intersection-strict
Genome_build: schistosoma_mansoni.PRJEA36577.WBPS9.genomic.fa.gz. See text file on Series record with full link to genome.
Supplementary_files_format_and_content: Comma-separated values of normalized gene count (tpm) matrix where rows are genes and columns are sample names.

molecule: polyA RNA

organism: Schistosoma mansoni

source_name: Schistosoma mansoni stem cells

extract_protocol:
Smart-seq2 protocol, which lysed cells with Triton X-100
Nextera XT DNA

value: stem cells

tag: mouse strain with s. mansoni

value: Swiss  Webster NR-21963

tag: worm age

value: 2.5 weeks


title: E12.5-1

status: Public on Jun 21 2018

city: Xiamen

last: Miao

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

country: China

institute: Huaqiao University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: RPKM

source_name: E12.5_cerebral cortex

extract_protocol:
The RNAs for RNA-seq from three E12.5 mouse cerebral cortices, were extracted by TRIzol (Invitrogen, USA) according to manufacturer’s instructions.Ribosome RNA (rRNA) was removed from the total RNA using Epicentre Ribo-Zero™ rRNA Removal Kit (Epicentre, Madison, Wisconsin, USA), and the remaining RNA was collected and purified
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype/variation

value: wild type

tag: development stage

tag: tissue

value: Cerebral cortex


title: E12.5-3


title: 1876916

value: mixed/undefined or similar

value: TT


title: 1787852

value: RNBX-Random Biopsy

value: PR


title: 1753637


title: 1735476


title: 1884297


title: 1869206


title: 1787844


title: 1737328


title: 1705322


title: E12.5-2


title: 1869164


title: Patient 36_Neuroendocrine tissue

status: Public on Jun 18 2018

city: Cusano Milanino

first: Francesca

last: Pecori Giraldi

state: Milan

address: via Zucchi 18

department: Neuroendocrinology Research Laboratory

country: Italy

institute: Istituto Auxologico Italiano

description: Patient 36

hyb_protocol: Biotinylated cDNA is annealed to assay oligonucleotides and bound to streptavidin conjugated paramagnetic particles. After oligo hybridization, mis-hybridized and non-hybridized oligo are washed away.(Illumina WG-DASL HT Assay protocol)

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data matrix was obtained from 40 patients and 20818 genes, AVG signal was normalized using quantile normalization
Data normalization was obtained using Genome Studio Software (Illumina)

label: biotinylated- primers

source_name: pituitary tissue_microadenoma

label_protocol: Biotinylated cDNA were obtained using biotinylated primers in the reverse transcription reaction according the WG-DASL HT Assay (Illumina protocol)

extract_protocol: RNA was extracted with Recover All Total Nucleic Acid isolation specific for FFPE tissues (Life Technologies) in accordance with the kit protocol. RNA quantity was detected using IMPLEN NanoPhotometer, while RNA quality measuring gene expression of RPL13A as suggested in literature.

tag: pathology

value: Cushing's disease

value: Patient 36

tag: size of the tumor

value: microadenoma

value: ACTH-secreting pituitary adenomas

tag: storage

value: formalin-fixed paraffin-embedded

tag: usp8 variant status

value: USP8 wildtype


title: 1696135

value: MF


title: Patient 35_Neuroendocrine tissue

description: Patient 35

value: Patient 35

tag: age

value: USP8 variant


title: 1737306

tag: cell type

value: MGUS


title: 1753889

tag: patient id


title: 1787843

tag: patient group

value: MS


title: Patient 37_Neuroendocrine tissue

description: Patient 37

value: Patient 37


title: Patient 33_Neuroendocrine tissue

description: Patient 33

value: Patient 33


title: Patient 38_Neuroendocrine tissue

description: Patient 38

value: Patient 38


title: Patient 34_Neuroendocrine tissue

description: Patient 34

value: Patient 34


title: Patient 40_Neuroendocrine tissue

description: Patient 40

value: Patient 40


title: 1737325

value: mixed/undefined or similar

tag: sample type

value: RNBX-Random Biopsy

value: PR


title: 1691768

tag: molecular subgroup


title: Patient 39_Neuroendocrine tissue

description: Patient 39

value: Cushing's disease

value: Patient 39

value: microadenoma


title: 1704902

tag: gep70 score


title: Patient 31_Neuroendocrine tissue

description: Patient 31

value: Patient 31

value: ACTH-secreting pituitary adenomas

value: formalin-fixed paraffin-embedded

value: USP8 wildtype


title: Patient 30_Neuroendocrine tissue

description: Patient 30

value: Patient 30


title: Patient 29_Neuroendocrine tissue

description: Patient 29

value: Patient 29


title: Patient 25_Neuroendocrine tissue

description: Patient 25

value: Patient 25


title: Patient 28_Neuroendocrine tissue

description: Patient 28

value: Patient 28


title: Patient 26_Neuroendocrine tissue

description: Patient 26

value: Patient 26


title: Patient 15_Neuroendocrine tissue

description: Patient 15

value: Patient 15


title: Patient 24_Neuroendocrine tissue

description: Patient 24

value: Patient 24


title: Patient 23_Neuroendocrine tissue

description: Patient 23

value: Patient 23


title: Patient 18_Neuroendocrine tissue

description: Patient 18

source_name: pituitary tissue_macroadenoma

value: Patient 18

value: macroadenoma


title: Patient 27_Neuroendocrine tissue

description: Patient 27

value: Cushing's disease

value: Patient 27

value: USP8 variant


title: Patient 20_Neuroendocrine tissue

description: Patient 20

value: Patient 20

value: microadenoma


title: Patient 16_Neuroendocrine tissue

description: Patient 16

value: Patient 16

value: ACTH-secreting pituitary adenomas

value: formalin-fixed paraffin-embedded


title: Patient 17_Neuroendocrine tissue

description: Patient 17

value: Patient 17


title: Patient 22_Neuroendocrine tissue

description: Patient 22

value: Patient 22


title: Patient 13_Neuroendocrine tissue

description: Patient 13

value: Patient 13

value: USP8 wildtype


title: Patient 14_Neuroendocrine tissue

description: Patient 14

value: Patient 14


title: Patient 8_Neuroendocrine tissue

description: Patient 8

value: Patient 8


title: Patient 7_Neuroendocrine tissue

description: Patient 7

value: Patient 7


title: Patient 9_Neuroendocrine tissue

description: Patient 9

value: Patient 9


title: Patient 6_Neuroendocrine tissue

description: Patient 6

value: Patient 6

value: macroadenoma


title: Patient 10_Neuroendocrine tissue

description: Patient 10

value: Cushing's disease

value: Patient 10


title: Patient 4_Neuroendocrine tissue

description: Patient 4

value: Patient 4


title: Patient 21_Neuroendocrine tissue

description: Patient 21

value: Patient 21

value: microadenoma


title: Patient 11_Neuroendocrine tissue

description: Patient 11

value: Patient 11

value: ACTH-secreting pituitary adenomas


title: Patient 2_Neuroendocrine tissue

description: Patient 2

value: Patient 2

value: formalin-fixed paraffin-embedded


title: Patient 5_Neuroendocrine tissue

description: Patient 5

value: Patient 5


title: Patient 3_Neuroendocrine tissue

description: Patient 3

value: Patient 3

value: USP8 wildtype


title: Patient 12_Neuroendocrine tissue

description: Patient 12

value: Patient 12


title: Patient 1_Neuroendocrine tissue

description: Patient 1

value: Patient 1


title: Patient 32_Neuroendocrine tissue

description: Patient 32

value: Patient 32


title: bladder tumour 1453

status: Public on Jun 15 2018

city: Leeds

first: Margaret

middle: A

last: Knowles

state: West Yorkshire

address: Becket Street

department: LICAP

country: United Kingdom

institute: University of Leeds

hyb_protocol: Microarrays were washed and stained using the Affymetrix GeneChip® Hybridization, Wash, and Stain Kit according to manufacturer’s instructions using the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip® 7G microarray scanner.

data_processing: Data QC was analysed using Affymetrix® Expression Console™ Software samples were normalised using RMA.

source_name: fresh frozen bladder tumour tissue

label_protocol: Total RNA was amplified using the Affymetrix GeneChip® WT PLUS Reagent Kit according to manufacturer’s instructions. The resulting cDNA was quantified using OD (NanoDrop). The cDNA was normalised and hybridised onto Affymetrix Human Transcriptome 2.0 microarrays for 16 hours at 45°C.

extract_protocol: Total RNA was extracted from fresh frozen tissue samples comprising at least 70% tumour using an RNeasy  Plus Micro Kit (Qiagen). The protocol for fibrous tissue was followed with the inclusion of an on-column DNase digestion step

tag: tumour stage

value: Ta


title: bladder tumour 1467


title: bladder tumour 1361


title: bladder tumour 1474


title: bladder tumour 1335


title: bladder tumour 1440


title: bladder tumour 1307


title: bladder tumour 1436


title: Patient 19_Neuroendocrine tissue

description: Patient 19

value: Patient 19

value: macroadenoma


title: bladder tumour 1142


title: bladder tumour 1063


title: bladder tumour 1213


title: bladder tumour 1313


title: bladder tumour 1167


title: bladder tumour 1117


title: bladder tumour 1177


title: bladder tumour 1283


title: bladder tumour 1058


title: bladder tumour 1038


title: bladder tumour 865


title: bladder tumour 1144


title: bladder tumour 1017


title: bladder tumour 933


title: bladder tumour 934


title: bladder tumour 1385


title: bladder tumour 1305


title: bladder tumour 1387


title: bladder tumour 894


title: bladder tumour 1273


title: UPR Perturb-seq experiment guide barcodes (gemgroup 8)

status: Public on Dec 15 2016

city: San Francisco

first: Thomas

last: Norman

institute: UCSF

description:
Guide barcode reads
read length: Read 1: 98, Index read 1 (i7): 14, Index read 2 (i5): 8, Read 2: 10
Custom paired end, all 4 reads informative

data_processing:
BAM files were generated directly from raw Illumina BCL files using 10X Genomics Cellranger version 1.1 with default paramaters (cellranger demux)
Gene-barcode matrices were determined using 10X Genomics Cellranger version 1.1 with default parameters (cellranger run)
Guide barcode identities were determined as described in the paper.
Genome_build: hg19
Supplementary_files_format_and_content: BAM files were generated by cellranger and contain raw reads for single-cell RNAseq, including cell identity, UMI information, and gemgroup id (referred to in guide barcode filenames). Gene-barcode matrices are the UMI-collapsed counts of these reads, representing counts of molecules per cell as determined and filtered by cellranger. These are provided in the format outputted by cellranger: the matrix itself is in matrix market exchange format, with the rows (cell barcodes) and columns (gene identities) labels given in TSV format as described in the cellranger documentation. Guide barcodes were specifically amplified from the RNAseq libraries and sequenced to higher coverage, and then identities were called as discussed in the paper.

source_name: K562 cells

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev A

tag: cell line


title: UPR Perturb-seq experiment guide barcodes (gemgroup 7)


title: UPR Perturb-seq experiment guide barcodes (gemgroup 9)


title: UPR Perturb-seq experiment guide barcodes (gemgroup 6)


title: Hi-C D0 ES

status: Public on Jun 07 2018

first: Chen-Yu

last: Wang

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
In situ Hi-C: Each end of the read-pairs was aligned separately as single-end reads to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02 and allele-specificity was assigned. The single-end alignments were joined to generate a Hi-C summary file.
Genome_build: mm9
Hi-C: Allele-resolved Hi-C data were presented as Hi-C summary file (file names ending with '.summary.txt'), where the first 7 columns represent read names, chromosome for read 1, positions for read 1 (5' end of read), strand of read 1 (+ or -), chromosome for read 2, positions for read 2 (5' end of read), and strand of read 2 (+ or -), respectively. WT1, WT clone 1. KO1, Smchd1-/- clone 1. rep1, replicate 1. rep2, replicate 2. cas, cas-specific reads. mus, mus-specific reads. comp, all reads. Two biological replicates were pooled and principle component analysis was performed on pooled Hi-C data at 200-kb resolution using HiTC. PC1 values were presented as bedGraph files (file names ending with '.PC1.bedGraph'). WT1, WT clone 1. KO1, Smchd1-/- clone 1. D0, undifferentiated ES cells. D4, day4 differentiated embryoid bodies. D7, day7 differentiated embryoid bodies. Xa, PC1 values derived from Xcas reads (WT1, KO1, D4, and D7) or all reads mapped to the X (D0). Xi, Xmus reads. To match sequencing depths, 50% reads from WT1 rep1 and KO1 rep1 Hi-C summary files were randomly sampled to generate down-sampled Hi-summary files and PC1 profiles (file names starting with 'Downsampled'). We also reanalyzed published undifferentiated female ES cells Hi-C data (GSE72697: GSM1868575). Reads were aligned to the mm9 genome using bowtie2 and the PC1 values of the X chromosome at 200-kb resolution were similarly derived using total X chromosomal reads (Giorgetti.D0.HiC.Xa.comp.PC1.bedGraph). Insulation scores were computed using iteratively corrected Hi-C contact matrices at 40-kb resolution as described (Giorgetti et al., 2016) and summarized in X_chromosome.insulation_score.txt.

source_name: mouse embryonic stem cells

growth_protocol: ES cell–derived neural progenitor cell clones were cultured on poly-L-ornithine (0.001%) and laminin (1μg/ml) coated plates with N2 media (DMEM/F-12, GlutaMAX™ supplement, 1X N2 supplement, 1X B27 supplement, 1X Pen/Strep) supplemented with FGF2 (20ng/ml), EGF (20ng/ml), laminin (1μg/ml), and heparin (10μg/ml). Undifferentiated ES cells were grown on 0.2% gelatin-coated plates with N2B27 media (mixture of 500ml DMEM/F12 media, 500ml Neurobasal media, 5ml N2 supplement, 10ml B27 supplement, 10ml Pen/Strep, 5ml GlutaMAX, and 2ml 55mM β-mercaptoethanol) supplemented with 1μM PD0325901, 3μM CHIR-99021, and 1000U/ml LIF. Embryoid bodies (EBs) were grown with differentiation media (DMEM, high glucose, GlutaMAX supplement, pyruvate, 15% Hyclone FBS, 25mM HEPES pH 7.2-7.5, 1X MEM non-essential amino acids, 1X Pen/Strep, 0.1mM β-mercaptoethanol) in suspension (D4 EBs) or on gelatin-coated plates (D7 EBs).

extract_protocol:
Total RNA was extracted using standard Trizol protocol. ChIP/CHART-enriched and input DNA were extracted with phenol:chloroform.
RNA-seq libraries were generated by dUTP-mediated directional RNA-seq based on NEBNext Ultra directional RNA library preparation protocol. ChIP-seq and Hi-C libraries were generated by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina. CHART-seq libraries were generated by NEBNext Ultra DNA Library Prep Kit for Illumina.

value: mouse embryonic stem cells

tag: genotype

value: WT


title: Hi-C D4 EB


title: UPR Perturb-seq experiment guide barcodes (gemgroup 10)


title: bladder tumour 675


title: bladder tumour 672


title: UPR Perturb-seq experiment guide barcodes (gemgroup 3)


title: bladder tumour 578


title: Hi-C D7 EB


title: UPR Perturb-seq experiment guide barcodes (gemgroup 4)


title: UPR Perturb-seq experiment guide barcodes (gemgroup 1)


title: bladder tumour 811


title: Epistasis experiment guide barcodes (gemgroup 3)


title: Epistasis experiment guide barcodes (gemgroup 2)


title: Pilot TF experiment cells

description:
Single-cell RNAseq data
read length: Read 1: 98, Index read 1 (i7): 14, Index read 2 (i5): 8, Read 2: 10
Custom paired end, all 4 reads informative


title: UPR Perturb-seq experiment guide barcodes (gemgroup 5)


title: Epistasis experiment guide barcodes (gemgroup 1)


title: Epistasis experiment cells


title: Pilot TF experiment guide barcodes


title: bladder tumour 239


title: UPR Perturb-seq experiment guide barcodes (gemgroup 2)


title: UPR Perturb-seq experiment cells


title: bladder tumour 494


title: bladder tumour 1214


title: Tomato field sample showing disease symptoms

status: Public on Dec 31 2013

city: Beijing

first: Yongjiang

last: Zhang

institute: Chinese Academy of Inspection and Quarantine

hyb_protocol: Cy3-labeled DNA fragments, pre-heated for 10 min at 80 oC, were added to the microarray for hybridization for 16 hr at 42 oC. Slides were washed for 4 min at 42 oC with 2x SSC, 0.2% SDS and then washed for 4 min at 42 oC with 0.2x SSC.

scan_protocol: The microarrays were scanned with LuxScan 3.0 (CapitalBio, China). Microarray images acquisition and signal analysis were performed using LuxScan 3.0 software.

data_processing: The signal intensity of the probes was corrected by subtracting background intensity from the feature intensity. The value in the sample table is the mean signal intensity of the replicated spots.

organism: unclassified viroids

label_protocol: First-strand reverse transcription to cDNA was initiated with a nonamer random primer. The amplified cDNA product was purified with the NucleotideSpin Extract II (MN, Germany). Cy3-dCTP was incorporated into the purified cDNA product with nonamer random primer using the Klenow fragment of DNA polymerase I.

extract_protocol: Total RNA was extracted from plant samples using TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's protocols. RNA was purified using the NucleotideSpin® RNA clean-up (MN, Duren, Germany).

tag: genus

value: unknown


title: Chrysanthemum field sample showing disease symptoms