title: AF32.96

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

description:
Sample 384
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

data_processing:
The quality of the data was assessed using FastQC and MultiQC.
The reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate).
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters), only uniquely mapped reads were used.
Cells with fewer than 3m reads total were discarded from further analysis.
Raw expression levels were normalized with sctransform.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: raw.csv contains raw gene counts.
Supplementary_files_format_and_content: normalized.csv contains cells sctransform-normalized expression levels of cells that passed QC.

source_name: Primed pluripotent stem cells

growth_protocol: FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX.

extract_protocol:
Cells were directly sorted into each well of 96-well plate filled with 2.3 µl of lysis buffer (1 unit/µl of SUPERaseIN RNase inhibitor (Invitrogen), 0.2% Triton X) by BD FACSAria Fusion (BD Biosciences).
Libraries were prepared by Smart-seq2 (Illumina) followed by previously described (Picelli et al., 2014).

tag: cell line

tag: cell type

value: Pluripotent stem cells

tag: condition

value: Primed


title: KO_AL_002

status: Public on Dec 04 2020

type: SRA

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

country: USA

institute: Princeton University

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome assembly mm10.GRCm38.
Alignment was done with HISAT2 v2.1.0 with default parameters including splice sites obtained from gene annotations
Gene annotations from GENCODE vM17 were used for all analysis
Uniquely aligned reads were extracted using grep with parameters “-v 'NH:i:[2-9]'” and SAMtools v1.3.138, with parameters “view -h -F 4 -q 20 -b” and sorted and indexed using SAMtools.
Reads in genes were counted using Rsubread v1.28.1.
Differential gene expression between any pair of samples was assessed using DESeq2 v1.18.1, using default FDR adjustment of p-values for multiple hypothesis testing.
Genome_build: mm10.GRCm38.
Supplementary_files_format_and_content: csv with results of pairwise differential expression analysis and normalized read counts

molecule: total RNA

organism: Mus musculus

source_name: CD44+ OT-I T cells from D6 LCMV-OVA infected host

growth_protocol: Recipient mice were fed ad libitum or fasted

extract_protocol:
Samples were double sorted into Trizol
RNA libraries were prepared for sequencing using SMARTer amplification (TAKARA) and standard Illumina protocols

treatment_protocol: Recipient mice were infected with LCMV- OVA and fasted for 24h on d5 post-infection beginning at 6pm

tag: tissue

value: Spleen

tag: strain

tag: genotype

value: FXR KO

tag: host absorptive state

value: Fed Ad libitum (AL)


title: KO_AL_001


title: AF32.94

country: United Kingdom

description:
Sample 382
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.93

description:
Sample 381
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: KO_Fs_003

value: Fasted for 24h on D5 post-infection (Fs)


title: AF32.95

description:
Sample 383
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.91

description:
Sample 379
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.90

description:
Sample 378
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.88

description:
Sample 376
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.85

description:
Sample 373
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.82

description:
Sample 370
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.89

description:
Sample 377
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.87

description:
Sample 375
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.81

description:
Sample 369
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.77

description:
Sample 365
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.83

description:
Sample 371
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.80

description:
Sample 368
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.78

description:
Sample 366
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.84

description:
Sample 372
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.76

description:
Sample 364
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.74

description:
Sample 362
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.75

description:
Sample 363
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.79

description:
Sample 367
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.71

description:
Sample 359
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.72

description:
Sample 360
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.73

description:
Sample 361
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.69

description:
Sample 357
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.68

description:
Sample 356
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.64

description:
Sample 352
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.86

description:
Sample 374
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.62

description:
Sample 350
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.66

description:
Sample 354
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.61

description:
Sample 349
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.65

description:
Sample 353
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.67

description:
Sample 355
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.92

description:
Sample 380
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.58

description:
Sample 346
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.57

description:
Sample 345
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.59

description:
Sample 347
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.56

description:
Sample 344
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.63

description:
Sample 351
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.70

description:
Sample 358
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.54

description:
Sample 342
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.55

description:
Sample 343
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.50

description:
Sample 338
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.48

description:
Sample 336
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.53

description:
Sample 341
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.52

description:
Sample 340
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.47

description:
Sample 335
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.49

description:
Sample 337
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.60

description:
Sample 348
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.44

description:
Sample 332
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.46

description:
Sample 334
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.51

description:
Sample 339
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.45

description:
Sample 333
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.43

description:
Sample 331
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.42

description:
Sample 330
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.39

description:
Sample 327
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.41

description:
Sample 329
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.40

description:
Sample 328
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.38

description:
Sample 326
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.36

description:
Sample 324
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.35

description:
Sample 323
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.33

description:
Sample 321
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.32

description:
Sample 320
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.30

description:
Sample 318
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.29

description:
Sample 317
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.28

description:
Sample 316
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.27

description:
Sample 315
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.26

description:
Sample 314
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.21

description:
Sample 309
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.22

description:
Sample 310
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.24

description:
Sample 312
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.25

description:
Sample 313
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.23

description:
Sample 311
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.18

description:
Sample 306
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.19

description:
Sample 307
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.17

description:
Sample 305
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.15

description:
Sample 303
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.13

description:
Sample 301
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.34

description:
Sample 322
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.14

description:
Sample 302
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.37

description:
Sample 325
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.9

description:
Sample 297
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.8

description:
Sample 296
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.31

description:
Sample 319
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.7

description:
Sample 295
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.10

description:
Sample 298
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.12

description:
Sample 300
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.5

description:
Sample 293
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.4

description:
Sample 292
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.3

description:
Sample 291
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.1

description:
Sample 289
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.2

description:
Sample 290
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.96

description:
Sample 288
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.20

description:
Sample 308
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.95

description:
Sample 287
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.94

description:
Sample 286
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.93

description:
Sample 285
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.91

description:
Sample 283
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.90

description:
Sample 282
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.92

description:
Sample 284
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.16

description:
Sample 304
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.89

description:
Sample 281
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.88

description:
Sample 280
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.11

description:
Sample 299
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.87

description:
Sample 279
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.85

description:
Sample 277
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.84

description:
Sample 276
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.83

description:
Sample 275
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.81

description:
Sample 273
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.80

description:
Sample 272
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.79

description:
Sample 271
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.77

description:
Sample 269
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.82

description:
Sample 274
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.78

description:
Sample 270
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.76

description:
Sample 268
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AF32.6

description:
Sample 294
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.75

description:
Sample 267
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.74

description:
Sample 266
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.71

description:
Sample 263
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.72

description:
Sample 264
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.73

description:
Sample 265
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.70

description:
Sample 262
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.69

description:
Sample 261
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.68

description:
Sample 260
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.65

description:
Sample 257
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.66

description:
Sample 258
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.64

description:
Sample 256
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.63

description:
Sample 255
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.62

description:
Sample 254
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.61

description:
Sample 253
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.86

description:
Sample 278
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.60

description:
Sample 252
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.59

description:
Sample 251
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.58

description:
Sample 250
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.57

description:
Sample 249
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.55

description:
Sample 247
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.56

description:
Sample 248
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.54

description:
Sample 246
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.52

description:
Sample 244
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.51

description:
Sample 243
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.53

description:
Sample 245
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.49

description:
Sample 241
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.48

description:
Sample 240
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.47

description:
Sample 239
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.46

description:
Sample 238
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.45

description:
Sample 237
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.50

description:
Sample 242
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.44

description:
Sample 236
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.42

description:
Sample 234
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.67

description:
Sample 259
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.40

description:
Sample 232
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.39

description:
Sample 231
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.38

description:
Sample 230
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.41

description:
Sample 233
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.36

description:
Sample 228
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.32

description:
Sample 224
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.33

description:
Sample 225
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.34

description:
Sample 226
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.35

description:
Sample 227
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.31

description:
Sample 223
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.43

description:
Sample 235
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.30

description:
Sample 222
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.29

description:
Sample 221
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.28

description:
Sample 220
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.27

description:
Sample 219
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.26

description:
Sample 218
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.24

description:
Sample 216
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.22

description:
Sample 214
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.37

description:
Sample 229
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.25

description:
Sample 217
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.21

description:
Sample 213
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.23

description:
Sample 215
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.19

description:
Sample 211
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.18

description:
Sample 210
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.17

description:
Sample 209
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.16

description:
Sample 208
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.14

description:
Sample 206
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.13

description:
Sample 205
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.15

description:
Sample 207
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.12

description:
Sample 204
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.9

description:
Sample 201
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.5

description:
Sample 197
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.8

description:
Sample 200
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.7

description:
Sample 199
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.4

description:
Sample 196
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.6

description:
Sample 198
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.1

description:
Sample 193
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.2

description:
Sample 194
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.96

description:
Sample 192
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

source_name: Formative pluripotent stem cells

value: Formative


title: 5ar2.95

description:
Sample 191
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.91

description:
Sample 187
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.92

description:
Sample 188
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.90

description:
Sample 186
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.87

description:
Sample 183
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.88

description:
Sample 184
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.86

description:
Sample 182
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.81

description:
Sample 177
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.84

description:
Sample 180
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.11

description:
Sample 203
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.89

description:
Sample 185
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.83

description:
Sample 179
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.85

description:
Sample 181
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.93

description:
Sample 189
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.80

description:
Sample 176
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.10

description:
Sample 202
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.79

description:
Sample 175
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.3

description:
Sample 195
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.78

description:
Sample 174
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.77

description:
Sample 173
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.74

description:
Sample 170
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.73

description:
Sample 169
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.76

description:
Sample 172
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.75

description:
Sample 171
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.72

description:
Sample 168
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.70

description:
Sample 166
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.94

description:
Sample 190
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.69

description:
Sample 165
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.71

description:
Sample 167
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.82

description:
Sample 178
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.67

description:
Sample 163
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.66

description:
Sample 162
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.60

description:
Sample 156
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.62

description:
Sample 158
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.63

description:
Sample 159
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.58

description:
Sample 154
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.54

description:
Sample 150
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.65

description:
Sample 161
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.57

description:
Sample 153
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.56

description:
Sample 152
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.55

description:
Sample 151
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: AFX6.20

description:
Sample 212
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.59

description:
Sample 155
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.53

description:
Sample 149
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.52

description:
Sample 148
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.51

description:
Sample 147
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.50

description:
Sample 146
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.44

description:
Sample 140
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.46

description:
Sample 142
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.45

description:
Sample 141
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.48

description:
Sample 144
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.49

description:
Sample 145
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.42

description:
Sample 138
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.41

description:
Sample 137
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.43

description:
Sample 139
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.68

description:
Sample 164
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.64

description:
Sample 160
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.40

description:
Sample 136
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.61

description:
Sample 157
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.39

description:
Sample 135
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.38

description:
Sample 134
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.36

description:
Sample 132
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.33

description:
Sample 129
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.35

description:
Sample 131
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.34

description:
Sample 130
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.30

description:
Sample 126
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.37

description:
Sample 133
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.28

description:
Sample 124
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.29

description:
Sample 125
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.47

description:
Sample 143
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.26

description:
Sample 122
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.25

description:
Sample 121
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.27

description:
Sample 123
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.24

description:
Sample 120
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.21

description:
Sample 117
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.20

description:
Sample 116
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.18

description:
Sample 114
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.23

description:
Sample 119
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.19

description:
Sample 115
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.15

description:
Sample 111
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.17

description:
Sample 113
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.14

description:
Sample 110
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.13

description:
Sample 109
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.12

description:
Sample 108
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.11

description:
Sample 107
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.32

description:
Sample 128
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.10

description:
Sample 106
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.7

description:
Sample 103
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.5

description:
Sample 101
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.1

description:
Sample 97
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.6

description:
Sample 102
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.3

description:
Sample 99
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.2

description:
Sample 98
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.4

description:
Sample 100
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.96

description:
Sample 96
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.22

description:
Sample 118
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HD-MY-Z_39h

city: Berlin

first: Nikolai

last: Genov

state: Berlin

address: Invalidenstraße 110

country: Germany

institute: Humboldt University Berlin/Charite Medical University Berlin

data_processing:
Isoform quantification with Salmon
Genome_build: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary_files_format_and_content: Salmon Isoform Quantification Files (.sf)

organism: Homo sapiens

source_name: HD-MY-Z Cell Line

growth_protocol: Cells were maintained in DMEM low glucose supplemented with 10% FBS, 1x Penicillin/Streptomycin and 2 mM Ultraglutamine

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol
mRNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the low sample protocol guidelines
Samples were sequenced on an Illumina NextSeq 500 platform (paired-end 75 bp reads) by standard methods.

treatment_protocol: Cells were synchronised by medium change. Samples were collected starting 12 h after synchronisation in 3-h intervals for 30 h

value: HD-MY-Z

tag: time point


title: 5ar2.16

description:
Sample 112
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.94

description:
Sample 94
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.8

description:
Sample 104
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.93

description:
Sample 93
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HD-MY-Z_33h


title: HD-MY-Z_30h


title: 5ar1.95

description:
Sample 95
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.92

description:
Sample 92
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar2.31

description:
Sample 127
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HD-MY-Z_42h


title: HD-MY-Z_27h


title: HD-MY-Z_36h


title: HD-MY-Z_24h


title: HD-MY-Z_21h


title: 5ar2.9

description:
Sample 105
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.90

description:
Sample 90
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.89

description:
Sample 89
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.91

description:
Sample 91
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.88

description:
Sample 88
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HD-MY-Z_18h


title: 5ar1.87

description:
Sample 87
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HD-MY-Z_15h


title: 5ar1.86

description:
Sample 86
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.85

description:
Sample 85
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_42h

source_name: L-1236 Cell Line


title: L-1236_39h


title: 5ar1.84

description:
Sample 84
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_36h


title: 5ar1.83

description:
Sample 83
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_33h


title: 5ar1.82

description:
Sample 82
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_30h


title: L-1236_27h


title: 5ar1.79

description:
Sample 79
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.80

description:
Sample 80
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_21h


title: 5ar1.78

description:
Sample 78
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_18h


title: L-1236_15h


title: 5ar1.77

description:
Sample 77
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.76

description:
Sample 76
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: L-1236_12h


title: 5ar1.75

description:
Sample 75
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: LCL-HO_39h

source_name: LCL-HO Cell Line

value: LCL-HO


title: 5ar1.73

description:
Sample 73
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: LCL-HO_42h


title: HD-MY-Z_12h


title: LCL-HO_36h


title: 5ar1.72

description:
Sample 72
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.70

description:
Sample 70
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: LCL-HO_33h


title: LCL-HO_30h


title: 5ar1.81

description:
Sample 81
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: LCL-HO_27h


title: L-1236_24h


title: 5ar1.71

description:
Sample 71
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.69

description:
Sample 69
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.68

description:
Sample 68
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.67

description:
Sample 67
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: LCL-HO_21h


title: LCL-HO_15h


title: LCL-HO_24h


title: LCL-HO_18h


title: 5ar1.65

description:
Sample 65
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.64

description:
Sample 64
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.74

description:
Sample 74
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: Aim2-/- iTreg 24 hour_rep4

city: Chapel Hill

first: Zengli

last: Guo

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Raw counts of TGF-beta induced Treg cells

data_processing:
RNA-seq libraries sequenced using the 50bp single-end protocol via the BGISEQ-500 sequencer per the manufacturer’s protocol.
After filtering of adaptors and low quality reads, clean reads (>26 Million reads per sample) are mapped to mouse reference genome using HISAT /Bowtie2 tool. Mapping results are stored in BAM files using SAMtools.
Total read counts in gene level were summarized using featureCounts function in the Rsubread in R environment, with the R package biomaRt for gene and transcripts mapping.
The differential expression (DE) genes were analyzed by DESeq2 package with default setting using total read counts as input, and the adjusted p value (padj) less than 0.05.
Genome_build: mm10

source_name: CD4+ T cells  from Spleen

growth_protocol: For in vivo islolated Treg cells, CD4+CD25+ Treg cells from WT and Aim2 knockout mice were isolated by FACS.  For TGF-beta induced Treg cells, CD4 T cells from  WT and Aim2 knockout mice were isolated by MACS.

extract_protocol:
Total RNA of all the Treg cells was extracted by using the Direct-zol miniprep kit (Zymo Research, R2060)
The RNA samples were firstly enriched by Oligo(dT) magnetic beads  and used to construct BGISEQ-500 libraries.

treatment_protocol: For in vivo islolated Treg cells, CD4+CD25+ Treg cellswere stimulated by anti-CD3 and anti-CD28 antibodies in the presence of IL2 (500 U/ml) for indicated time. For TGF-beta induced Treg cells, CD4 T cells were stimulated by anti-CD3 and anti-CD28 antibodies in the presence of IL2 (40 u/ml) and TGF-beta (2 ng/ml) for 24 hours.

tag: age

value: 8-12 weeks

value: Aim2 knockout

tag: treatment

value: anti-CD3/CD28, IL-2 and TGF-beta for 24 hours


title: MV411_10uM_SR0813_R3

city: La Jolla

first: Michael

last: Erb

state: CA

address: 10650 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

description: 3' mRNA-seq after 4 hour 10 µM SR0813 treatment

data_processing:
Sequences were aligned and count tables with CPM normaliztion were generated using SLAMdunk (https://t-neumann.github.io/slamdunk/) with the -q option.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file matrix with CPM values for each sample.

source_name: acute myeloid leukemia

growth_protocol: MV4;11 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin.

extract_protocol:
Total RNA was isolated with Qiagen Rneasy Mini Kit.
3' mRNA libraries were prepared with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Cat. No. 015) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 1 or 10 µM SR-0813 or DMSO for 4 hours.

value: 10 microM SR-0813


title: LCL-HO_12h


title: Aim2-/- iTreg 24 hour_rep2


title: Aim2-/- iTreg 24 hour_rep1


title: MV411_10uM_SR0813_R2


title: 5ar1.63

description:
Sample 63
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.62

description:
Sample 62
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: MV411_10uM_SR0813_R1


title: 5ar1.61

description:
Sample 61
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: MV411_1uM_SR0813_R3

description: 3' mRNA-seq after 4 hour 1 µM SR0813 treatment

value: 1 microM SR-0813


title: WT iTreg 24 hour_rep4

value: wild type


title: MV411_1uM_SR0813_R2


title: 5ar1.66

description:
Sample 66
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.59

description:
Sample 59
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.60

description:
Sample 60
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: WT iTreg 24 hour_rep2


title: WT iTreg 24 hour_rep3


title: MV411_1uM_SR0813_R1


title: 5ar1.58

description:
Sample 58
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: WT iTreg 24 hour_rep1


title: Aim2-/- iTreg 24 hour_rep3


title: 5ar1.57

description:
Sample 57
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: MV411_DMSO_R3

description: 3' mRNA-seq after 4 hour 0.1% DMSO treatment

value: 0.1percent DMSO


title: Aim2-/- Treg 24 hour_rep4

description: Raw counts of in vivo isolated Treg cells

source_name: CD4+CD25+ Treg from Spleen

value: anti-CD3/CD28 and IL-2 for 24 hours


title: MV411_DMSO_R2


title: Aim2-/- Treg 24 hour_rep3


title: 5ar1.56

description:
Sample 56
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

value: Pluripotent stem cells


title: MV411_DMSO_R1


title: Aim2-/- Treg 24 hour_rep2


title: MV411_10uM_SR0813_ENL

description: Chromatin IP against ENL with 10 µM SR-0813 treatment

library_source: genomic

data_processing:
Sequenced reads were aligned to HG19 reference genome with bowtie2 using default parameters except for 'k -1'.
Alignment files were sorted and indexed with Samtools -sort and -index.
Peaks were called using MACS (1.4.2) with p-val = 1e-7 cutoff used and MV411_Input sample used as input.
Bedgraphs were made from bams using Bedtools genomecov with -bg option.
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in bedgraph format.

molecule: genomic DNA

growth_protocol: MV4;11 cells were cultured in RPMI supplemented with 20% FBS, penicillin, and streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared with Takara ThruPLEX® DNA-Seq Kit (Cat. No. R400674) according to manufacturer's instructions.

tag: chip antibody

value: ENL (Cell Signaling Technology, #14893S)


title: 5ar1.53

description:
Sample 53
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: WT Treg 24 hour_rep4


title: MV411_1uM_SR0813_ENL

description: Chromatin IP against ENL with 1 µM SR-0813 treatment


title: MV411_DMSO_ENL

description: Chromatin IP against ENL with DMSO treatment


title: 5ar1.52

description:
Sample 52
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: MV411_Input

description: Input sample for background measurement


title: WT Treg 24 hour_rep2


title: 5ar1.51

description:
Sample 51
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: WT Treg 24 hour_rep3


title: 5ar1.50

description:
Sample 50
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: SORT1_HEPG2_BAC47M16_RNA_REP3

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: STARR-seq library from BAC reporter-derived mRNA

data_processing:
Library strategy: STARR-seq
Basecalls performed using CASAVA version 1.8
Paired-end reads were aligned to custom references corresponding to BAC coverage using bowtie2 v2.2.5.
Alignment BAMs were parsed for alignment position and strand using samtools v 1.8 and a custom PERL script resulting in a BED file of stranded fragments
Genome_build: GRCh38
Supplementary_files_format_and_content: BED files

source_name: transfected plasmid reporter

growth_protocol: All cells were grown according to ATCC instructions.

extract_protocol:
For the HTT locus experiments, RNA was extracted using the Total RNA Purification Kit (Norgen) and mRNA isolated using DynaBeads poly-A Selection Kit (Invitrogen). RNA samples were treated with DynaBeads poly-A Selection Kit (Invitrogen) to remove DNA contamination. DNA was purified using the DNEasy Kit (Qiagen).  For the SORT1 locus experiments, both DNA and RNA were isolated using the Qiagen Allprep kit (Qiagen). From total RNA, mRNA was purified using using the mRNA Mini Kit (Oligotex). RNA samples were treated with DynaBeads poly-A Selection Kit (Invitrogen) to remove DNA contamination.
RNA samples were subject to reverse transcription using a gene specific primer targeting reporter RNA.  Both harvested transfected DNA and cDNA were amplified via PCR using reporter specific primers.  Sequencing adaptors were added by further PCR in separate round.

treatment_protocol: Cells were transfected with STARR-seq libraries using Fugene (Promega) or Lipofectamine PLUS (Invitrogen).  Cell were grown for 48 hours prior to harvesting.

tag: library type

value: STARR-seq transcript RNA

tag: bac ids


title: WT Treg 24 hour_rep1


title: SORT1_HEPG2_BAC47M16_RNA_REP2


title: 5ar1.55

description:
Sample 55
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.54

description:
Sample 54
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: Aim2-/- Treg 24 hour_rep1


title: Aim2-/- Treg 0 hour_rep4

value: anti-CD3/CD28 and IL-2 for 0 hour


title: 5ar1.49

description:
Sample 49
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.48

description:
Sample 48
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: Aim2-/- Treg 0 hour_rep3


title: SORT1_HEPG2_BAC47M16_RNA_REP1


title: SORT1_HEPG2_BAC47M16_DNA_REP3

description: STARR-seq library from BAC transfected DNA

value: STARR-seq transfected DNA


title: 5ar1.47

description:
Sample 47
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.46

description:
Sample 46
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: SORT1_HEPG2_BAC47M16_DNA_REP1


title: SORT1_HEPG2_BAC47M16_DNA_REP2


title: 5ar1.45

description:
Sample 45
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: Aim2-/- Treg 0 hour_rep1

description: Raw counts of in vivo isolated Treg cells


title: Aim2-/- Treg 0 hour_rep2


title: WT Treg 0 hour_rep4


title: SORT1_HEPG2_BAC463O24_RNA_REP3


title: 5ar1.44

description:
Sample 44
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: WT Treg 0 hour_rep3


title: SORT1_HEPG2_BAC463O24_RNA_REP2


title: WT Treg 0 hour_rep2


title: 5ar1.43

description:
Sample 43
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: WT Treg 0 hour_rep1


title: SORT1_HEPG2_BAC463O24_RNA_REP1


title: 5ar1.42

description:
Sample 42
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: SORT1_HEPG2_BAC463O24_DNA_REP3


title: 5ar1.41

description:
Sample 41
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: SORT1_HEPG2_BAC463O24_DNA_REP1


title: DGRP_892_M_T14_R2

city: Bethesda

first: Susan

middle: T

last: Harbison

state: MD

address: 10 Center Drive, Bldg. 10, Rm. 7D13

department: Center for Systems Biology

institute: National Heart Lung and Blood Institute

description:
ASA0143
DGRP_892, Male, CT14, Replicate 2

data_processing:
Quality Control (QC) of FASTQ files were assessed using FastQC toolkit (v0.11.5) using default parameters (http://www.bioinformatics.babraham. ac.uk/projects/fastqc). Paired-end reads were aligned against the Drosophila melanogaster reference genome (dmel.r6.16) (dos Santos et al., 2015) using STAR (v2.5.3a) alignment software with the following parameters “--twopassMode basic --sjdbOverhang 75”(Dobin et al., 2013).We used featureCounts (v1.5.2) to compute gene-level read counts using only uniquely mapped reads with setting “-p -s 2” (paired-end, reverse- stranded) (Liao et al., 2013; Liao et al., 2014). We used the trimmed mean of M-values (TMM) normalization method to normalize raw read counts (Robinson and Oshlack, 2010).
Using the ERCC spike-in reads, we noted a bias in the data according to the date of the sequencing run. We removed this batch effect in our dataset from TMM-normalized reads using the ComBat function in the sva R package (Leek and Storey, 2007).
Genome_build: dmel.r6.16
Supplementary_files_format_and_content: There are two supplemental files. The first file (Circadian RNA-Seq raw read counts.csv) contains the raw read counts per gene for all 144 samples; the second file (Circadian RNA-Seq TMM normalized counts.csv contains the batch-corrected TMM-normalized read counts per gene for all 144 samples. Both files are in a .csv format.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Head

growth_protocol: Flies were grown under standard culture (cornmeal-sucrose-agar medium, 25°C, 60-75% relative humidity) and lighting conditions (12-hour light: dark cycle) (LD). Five virgin males and five females of each line were used to set up w1118; Canton-S B and DGRP_892 cultures in an LD incubator. We collected 24-separate-sex vials with 150 virgin males and 150 virgin females in each vial per genotype/replicate.

extract_protocol:
Samples were randomized and extracted in groups of 12. For each RNA sample, 150 heads were placed in Omni-ruptor tubes (Omni International, Kennesaw, GA) with 4 RNase/DNase-free metal beads (Omni International, Kennesaw, GA) and homogenized in 1 ml TRIzol (Thermo Fisher Scientific, Grand Island, NY) using an Omni-bead ruptor with the following settings: Speed, 5.65 m/s; Time, 20 sec; Duration, 30 sec; Cycles, 2. Homogenates were incubated at room temperature for 5 minutes. 200 µl of chloroform (Mallinckrodt Baker, Center Valley, PA) were added to each tube; samples were then mixed by shaking for 15 seconds, incubated at room temperature for 3 minutes, and centrifuged at 4°C, 12,000 x g for 15 minutes. The 500-µl aqueous phase was transferred to new tubes and RNA was further purified using the PureLink RNA Mini Kit (Life Technologies, Carlsbad, CA) with on-column DNase treatment, according to the manufacturer’s instructions. Purified total RNA was eluted in 60 µl of water and stored at -80°C. RNA was quantified by NanoDrop 8000 (Thermo Fisher Scientific, Grand Island, NY) and quality verified by BioAnalyzer 2100 using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA).
First, we added 0.02 µl ERCC Spike-In Control Mix 1 (Life Technologies, Carlsbad, CA) to 1 µg total RNA. Poly(A)-selected stranded mRNA libraries were constructed using Illumina TruSeq Stranded mRNA Sample Prep Kits (Illumina, San Diego, CA) per the manufacturer’s instructions except that PCR amplification was performed for 10 cycles rather than 15 to minimize the risk of over-amplification. Unique barcode adapters were applied to each library; dual indices were used. Libraries were pooled for sequencing and sequenced on multiple lanes of a HiSeq4000 using version 4 chemistry to achieve a minimum of 12 million 76-bp read pairs. Sequences were processed using RTA version 1.18.64 and CASAVA 1.8.2 (Illumina, San Diego, CA).

treatment_protocol: Half of the flies were light-entrained in an incubator with a 12:12 LD cycle for 3 days and the other half was entrained in an incubator with a reverse LD cycle for 3 days. Both groups of flies were then transferred to a common incubator kept in constant darkness (DD). After 3 days in DD, flies were flash-frozen on dry ice every 2 hours starting at circadian time (CT02/CT12). Flies were decapitated on dry ice for RNA extraction. We replicated this procedure three times to produce 144 RNA samples (3 biological replicates, 2 sexes, 2 genotypes and 12 time points).

tag: developmental stage

value: Adult

tag: Sex

value: Male

value: Head

tag: timepoint

tag: replicate


title: 5ar1.40

description:
Sample 40
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

tag: cell line

value: Formative


title: SORT1_HEPG2_BAC463O24_DNA_REP2

tag: cell type


title: CSB_F_T18_R3

description:
ASA0142
Canton-S B, Female, CT18, Replicate 3

value: Female


title: HTT_K562_RNA_REP3

description: STARR-seq library from BAC pool reporter-derived mRNA


title: CSB_F_T8_R1

description:
ASA0144
Canton-S B, Female, CT08, Replicate 1


title: 5ar1.39

description:
Sample 39
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

tag: condition


title: 5ar1.38

description:
Sample 38
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: DGRP_892_F_T8_R2

description:
ASA0141
DGRP_892, Female, CT08, Replicate 2

tag: tissue


title: HTT_K562_RNA_REP2


title: 8255

type: genomic

city: Jena

first: Ainash

last: Childebayeva

state: thuringia

address: Kahlaische Strasse 10

department: Archaeogenetics

institute: Max Planck Institute for the Science of Human History

hyb_protocol: University of Michigan Epigenomics Core

scan_protocol: University of Michigan Epigenomics Core

data_processing:
Data was processed using the pipeline in Childebayeva A. et al. 2020. Genome-wide epigenetic signatures of adaptive developmental plasticity in the andes. Genome Biol Evol.
Beta values were normalized using preprocessQuantile (minfi) and ChampBMIQ (ChAMP) functions

source_name: born high altitude, current high altitude

label_protocol: not provided

extract_protocol: Qiagen Dneasy blood kit

value: whole blood

tag: group


title: 8247


title: 8104


title: 8100


title: HTT_K562_RNA_REP1


title: CSB_M_T4_R3

description:
ASA0140
Canton-S B, Male, CT04, Replicate 3

tag: strain


title: DGRP_892_M_T24_R2

description:
ASA0139
DGRP_892, Male, CT24, Replicate 2


title: 8226


title: 8108


title: 8259


title: 8245


title: 8250


title: 8093


title: 5ar1.37

description:
Sample 37
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8221


title: 5ar1.36

description:
Sample 36
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HTT_K562_DNA

description: STARR-seq library from BAC pool transfected DNA


title: 8117


title: HTT_HEPG2_RNA_REP3


title: 8109


title: 5ar1.35

description:
Sample 35
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: DGRP_892_M_T12_R2

description:
ASA0138
DGRP_892, Male, CT12, Replicate 2


title: 5ar1.34

description:
Sample 34
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: CSB_F_T18_R1

description:
ASA0137
Canton-S B, Female, CT18, Replicate 1


title: HTT_HEPG2_RNA_REP2


title: DGRP_892_F_T8_R3

description:
ASA0136
DGRP_892, Female, CT08, Replicate 3


title: HTT_HEPG2_RNA_REP1


title: 5ar1.32

description:
Sample 32
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8091


title: CSB_M_T14_R2

description:
ASA0135
Canton-S B, Male, CT14, Replicate 2


title: 5ar1.31

description:
Sample 31
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8089


title: 8075


title: HTT_HEPG2_DNA


title: 5ar1.30

description:
Sample 30
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HTT_BE2C_RNA_REP2

description: STARR-seq library from BAC pool reporter-derived mRNA


title: 8071


title: DGRP_892_M_T6_R3

description:
ASA0133
DGRP_892, Male, CT06, Replicate 3


title: 5ar1.29

description:
Sample 29
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8096


title: 8065


title: 8078


title: HTT_BE2C_RNA_REP1


title: DGRP_892_M_T18_R2

description:
ASA0132
DGRP_892, Male, CT18, Replicate 2


title: 5ar1.28

description:
Sample 28
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: CSB_F_T8_R2

description:
ASA0131
Canton-S B, Female, CT08, Replicate 2


title: HTT_BE2C_DNA


title: 5ar1.27

description:
Sample 27
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HTT_A549_RNA_REP3


title: 8067


title: CSB_F_T22_R2

description:
ASA0129
Canton-S B, Female, CT22, Replicate 2


title: DGRP_892_F_T18_R1

description:
ASA0130
DGRP_892, Female, CT18, Replicate 1


title: 5ar1.25

description:
Sample 25
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.33

description:
Sample 33
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: DGRP_892_M_T6_R2

description:
ASA0128
DGRP_892, Male, CT06, Replicate 2


title: 5ar1.26

description:
Sample 26
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HTT_A549_RNA_REP2


title: CSB_M_T10_R1

description:
ASA0127
Canton-S B, Male, CT10, Replicate 1


title: HTT_A549_RNA_REP1


title: 5ar1.24

description:
Sample 24
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HTT_A549_DNA

description: STARR-seq library from BAC pool transfected DNA


title: 8080


title: 8061


title: 5ar1.23

description:
Sample 23
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: DGRP_892_M_T14_R3

description:
ASA0126
DGRP_892, Male, CT14, Replicate 3


title: DGRP_892_F_T20_R2

description:
ASA0134
DGRP_892, Female, CT20, Replicate 2


title: CSB_F_T12_R2

description:
ASA0125
Canton-S B, Female, CT12, Replicate 2


title: HIVWT250_2_S23

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Campus

institute: University of Warwick

description: processed data file: HIV_Counts.csv

data_processing:
Read and adapter trimming was carried out using TrimGalore! v0.4.3 with Cutadept v0.4.3 using default settings
RNA-seq reads were mapped to the human genome (GRCh38.p12, Gencode primary annotation) and the respective (HBB WT/mut and HIV-1 WT/mut) transgenic sequence using STAR v2.5.3a
Counts per gene were calculated using LiBiNorm in htseq-count compatible mode with the following parameters: --format=bam --minaqual=10 --stranded=reverse –mode=intersection-strict
Normalized counts per gene were generated using DESeq2 v1.22.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Comma delineated files containing normalised counts for each sample

source_name: HEK293 Flp-In T-Rex cells singly integrated tetracycline-inducible HIV-1-env gene

extract_protocol:
RNA samples were prepared using the RNeasy Mini kit (Qiagen)
RNAseq libraries were prepared using 500 ng of total input RNA and the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (E7760L), along with the NEBNext® rRNA Depletion Kit (E6310L) and NEBNext® Multiplex Oligos for Illumina Set 1 and 2 (E7335, E7500)

value: Flp-In T-REx HEK293

tag: genotype/variation

value: Singly integrated tetracycline-inducible HIV-1-env gene (wild-type)

value: Tetracycline


title: 8094


title: HIVWT250_1_S22

description: processed data file: HIV_Counts.csv


title: DGRP_892_F_T16_R3

description:
ASA0124
DGRP_892, Female, CT16, Replicate 3


title: 5ar1.21

description:
Sample 21
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.20

description:
Sample 20
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: CSB_F_T22_R3

description:
ASA0123
Canton-S B, Female, CT22, Replicate 3


title: 8060


title: HIVWT0_3_S21

description: processed data file: HIV_Counts.csv

value: Control


title: 5ar1.22

description:
Sample 22
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HIVWT0_2_S20

description: processed data file: HIV_Counts.csv


title: HTT_BE2C_RNA_REP3

description: STARR-seq library from BAC pool reporter-derived mRNA


title: DGRP_892_F_T16_R2

description:
ASA0122
DGRP_892, Female, CT16, Replicate 2


title: 8038


title: 8034


title: 5ar1.18

description:
Sample 18
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: DGRP_892_F_T6_R3

description:
ASA0120
DGRP_892, Female, CT06, Replicate 3


title: HIVPA250_3_S10

description: processed data file: HIV_Counts.csv

value: Singly integrated tetracycline-inducible HIV-1-env gene with mutation in poly(A) signal


title: CSB_M_T8_R3

description:
ASA0121
Canton-S B, Male, CT08, Replicate 3


title: 5ar1.16

description:
Sample 16
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HIVWT0_1_S19

description: processed data file: HIV_Counts.csv


title: HIVPA250_2_S9

description: processed data file: HIV_Counts.csv


title: 8058


title: 8020


title: 5ar1.15

description:
Sample 15
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: CSB_M_T14_R3

description:
ASA0118
Canton-S B, Male, CT14, Replicate 3


title: 8027


title: HIVPA250_1_S8

description: processed data file: HIV_Counts.csv


title: HIVWT250_3_S24

description: processed data file: HIV_Counts.csv


title: 8015


title: CSB_F_T6_R3

description:
ASA0117
Canton-S B, Female, CT06, Replicate 3


title: 5ar1.19

description:
Sample 19
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HIVPA0_3_S7

description: processed data file: HIV_Counts.csv


title: 8016


title: 8010


title: CSB_M_T2_R1

description:
ASA0116
Canton-S B, Male, CT02, Replicate 1


title: 8017


title: HIVPA0_2_S6

description: processed data file: HIV_Counts.csv


title: 5ar1.12

description:
Sample 12
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: DGRP_892_M_T10_R1

description:
ASA0115
DGRP_892, Male, CT10, Replicate 1


title: HIVPA0_1_S5

description: processed data file: HIV_Counts.csv


title: 5ar1.14

description:
Sample 14
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8025


title: CSB_M_T2_R3

description:
ASA0114
Canton-S B, Male, CT02, Replicate 3


title: 5ar1.17

description:
Sample 17
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.13

description:
Sample 13
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8013


title: 8007


title: 5ar1.11

description:
Sample 11
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.10

description:
Sample 10
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HBBWT250_2_S15

description: processed data file: HBB_Counts.csv

source_name: HEK293 Flp-In T-Rex cells singly integrated tetracycline-inducible β-globin gene

value: Singly integrated tetracycline-inducible beta-globin gene (wild-type)


title: 1294

source_name: born high altitude, current low altitude


title: 5ar1.9

description:
Sample 9
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

value: Pluripotent stem cells


title: DGRP_892_M_T22_R1

description:
ASA0113
DGRP_892, Male, CT22, Replicate 1


title: CSB_M_T20_R1

description:
ASA0112
Canton-S B, Male, CT20, Replicate 1


title: DGRP_892_F_T14_R2

description:
ASA0119
DGRP_892, Female, CT14, Replicate 2


title: 5ar1.8

description:
Sample 8
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 8006


title: 1286


title: 1296


title: DGRP_892_F_T2_R3

description:
ASA0110
DGRP_892, Female, CT02, Replicate 3


title: HBBWT0_2_S11

description: processed data file: HBB_Counts.csv


title: 5ar1.7

description:
Sample 7
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.6

description:
Sample 6
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: HBBWT0_1_S3

description: processed data file: HBB_Counts.csv


title: HBBWT0_3_S12

description: processed data file: HBB_Counts.csv


title: DGRP_892_M_T20_R1

description:
ASA0108
DGRP_892, Male, CT20, Replicate 1


title: DGRP_892_F_T2_R1

description:
ASA0111
DGRP_892, Female, CT02, Replicate 1


title: 1280


title: 1289


title: 1293


title: 1281

source_name: born low altitude, current low altitude


title: DGRP_892_M_T2_R3

description:
ASA0109
DGRP_892, Male, CT02, Replicate 3


title: HBBWT250_1_S4

description: processed data file: HBB_Counts.csv


title: HBBPA250_3_S18

description: processed data file: HBB_Counts.csv

value: Singly integrated tetracycline-inducible beta-globin gene with mutation in poly(A) signal


title: HBBWT250_3_S16

description: processed data file: HBB_Counts.csv


title: DGRP_892_F_T24_R3

description:
ASA0107
DGRP_892, Female, CT24, Replicate 3


title: 1276


title: DGRP_892_F_T14_R1

description:
ASA0106
DGRP_892, Female, CT14, Replicate 1


title: 5ar1.5

description:
Sample 5
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.1

description:
Sample 1
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.3

description:
Sample 3
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: 5ar1.2

description:
Sample 2
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv


title: CSB_M_T18_R2

description:
ASA0105
Canton-S B, Male, CT18, Replicate 2


title: HBBPA0_3_S14

description: processed data file: HBB_Counts.csv


title: DGRP_892_M_T8_R2

description:
ASA0104
DGRP_892, Male, CT08, Replicate 2


title: HBBPA0_2_S13

description: processed data file: HBB_Counts.csv


title: 1270


title: CSB_M_T10_R2

description:
ASA0103
Canton-S B, Male, CT10, Replicate 2


title: HBBPA0_1_S2

description: processed data file: HBB_Counts.csv


title: input.FS.2

data_processing:
The quality of the data was assessed using FastQC and MultiQC
The reads were aligned using bwa mem v0.7.10-r789 (default parameters) and BAM files sorted with samtools v1.9
MT, X, Y chromosomes and scaffolds were removed from BAM files
Peaks were called using macs2 v2.2.6 (-f BAMPE -q 0.05)
Genome browser tracks were created using deepTools bamCoverage v3.3.1 (--binSize 5 -of bigwig)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Bigwig tracks, created after removal of MT, X, Y chromosomes and scaffolds

growth_protocol: ES cells were cultured in 2iL, FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX

extract_protocol:
Chromatin was cross-linked with 1% formaldehyde for 10 minutes at RT and quenched with 125 mM Glycine for 5 minutes at RT with rotation. After cell pellets were lysed, sonication was performed for 16 cycle on High setting, 30sec ON/30 sec OFF cycle by Bioruptor (Diagnode), 2x107 cells per 300 µl in Bioruptor tube (Diagnode). 10% inputs were collected for the later library construction. Chromatin was immunoprecipitated with 2 µg of each antibodies and 20 µl of Protein G Dynabeads (Invitrogen) were used against 3x106 cells. After the washes, DNA was eluted and each samples were treated with 2.5 µg/ml RNase A at 37˚C for 30 minutes followed by 87.5 µg/ml Proteinase K at 55˚C for 1 hour. DNA was purified with PCR clean-up kit (Qiagen).
Libraries were prepared by NEXTflex Rapid DNA-Seq Kit 2.0 bundle with 96 HT barcodes (ParkinElmer).

tag: histone mark

value: input

value: Rep 2


title: input.FS.1

value: Rep 1


title: 1275


title: DGRP_892_M_T6_R1

description:
ASA0102
DGRP_892, Male, CT06, Replicate 1

value: Adult


title: B128-2A

city: London

first: Paul

last: Kelly

state: UK

address: Turner Street

department: Immunobiology

institute: Blizard Institute Barts & The London School of Medicine

data_processing:
Reads were filtered by removing reads with adaptor sequence, reads with >10% unknown bases, and reads with >50% quality <=5.
Bowtie read alignment
RSEM (Li B and Dewey C N.,2011) computes maximum likelihood abundance estimates using the Expectation-Maximization (EM) algorithm for its statistical model,including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.
Genome_build: not stated in BGI report
Supplementary_files_format_and_content: Excel spreadsheet with FPKM values for each gene and sample

source_name: Biopsy 2 of 2

extract_protocol:
Intestinal biopsies were flash-frozen in liquid N2, then extracted using Trizol and RNA-easy minikits. RNA was transported to BGI, then quality checked using an Agilent 2100 bioanalyser. RNA was treated with Dnase, then mRNA enriched using oligo-dT beads
Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. Then the first strand of cDNA was synthesized using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. Double strand cDNA was purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used to qualify and quantify of the sample library.

value: Intestinal biopsy


title: input.ES.2

value: Naive


title: DGRP_892_F_T10_R2

description:
ASA0101
DGRP_892, Female, CT10, Replicate 2

value: Head


title: B128-1A

source_name: Biopsy 1 of 2


title: input.ES.1


title: B125-2A


title: CSB_M_T2_R2

description:
ASA0100
Canton-S B, Male, CT02, Replicate 2

value: Male


title: input.AFX.2

value: Primed


title: DGRP_892_F_T10_R1

description:
ASA0099
DGRP_892, Female, CT10, Replicate 1

value: Female


title: B125-1A


title: B122-2A


title: 1254

value: whole blood


title: 1239


title: input.AFX.1


title: 1260


title: input.AF.2


title: DGRP_892_F_T20_R3

description:
ASA0097
DGRP_892, Female, CT20, Replicate 3


title: 1248


title: B122-1A


title: 1238


title: 1255


title: 1232


title: H3K27Ac.FS.2

value: Formative


title: CSB_F_T20_R3

description:
ASA0095
Canton-S B, Female, CT20, Replicate 3


title: B106-2A


title: B114-1A

source_name: 2 biopsies together


title: 1237


title: H3K27Ac.FS.1


title: CSB_F_T22_R1

description:
ASA0098
Canton-S B, Female, CT22, Replicate 1


title: CSB_M_T16_R1

description:
ASA0096
Canton-S B, Male, CT16, Replicate 1


title: 1227


title: 1267


title: CSB_F_T4_R1

description:
ASA0094
Canton-S B, Female, CT04, Replicate 1


title: 5ar1.4

description:
Sample 4
Smart-seq2 scRNA-seq, PE, 101bp reads.
raw.csv
normalized.csv

source_name: Formative pluripotent stem cells


title: H3K27Ac.ES.2


title: CSB_M_T20_R3

description:
ASA0093
Canton-S B, Male, CT20, Replicate 3


title: DGRP_892_M_T16_R2

description:
ASA0092
DGRP_892, Male, CT16, Replicate 2


title: 1211


title: B106-1A


title: H3K27Ac.AFX.2


title: 1210


title: HBBPA250_2_S17

description: processed data file: HBB_Counts.csv

value: Flp-In T-REx HEK293

value: Tetracycline


title: HBBPA250_1_S1

description: processed data file: HBB_Counts.csv


title: DGRP_892_F_T12_R3

description:
ASA0091
DGRP_892, Female, CT12, Replicate 3


title: 1222


title: 1230


title: B097-2A


title: 1196


title: B094-1A


title: H3K27Ac.AFX.1


title: H3K27Ac.AF.2


title: B097-1A


title: CSB_F_T16_R3

description:
ASA0089
Canton-S B, Female, CT16, Replicate 3


title: B089-2A


title: 1184


title: B089-1A


title: H3K27Ac.AF.1


title: H3K27me3.FS.2


title: DGRP_892_M_T4_R1

description:
ASA0087
DGRP_892, Male, CT04, Replicate 1


title: CSB_M_T22_R3

description:
ASA0090
Canton-S B, Male, CT22, Replicate 3


title: 1189


title: input.AF.1


title: H3K27me3.FS.1


title: CSB_F_T2_R3

description:
ASA0086
Canton-S B, Female, CT02, Replicate 3


title: B085-1A


title: 1183


title: H3K27me3.ES.2


title: CSB_F_T10_R3

description:
ASA0085
Canton-S B, Female, CT10, Replicate 3


title: B075-2A


title: CSB_M_T8_R1

description:
ASA0084
Canton-S B, Male, CT08, Replicate 1


title: B075-1A


title: H3K27Ac.ES.1


title: CSB_M_T24_R1

description:
ASA0083
Canton-S B, Male, CT24, Replicate 1


title: H3K27me3.AFX.2


title: CSB_F_T14_R3

description:
ASA0082
Canton-S B, Female, CT14, Replicate 3


title: H3K27me3.AFX.1


title: DGRP_892_M_T16_R3

description:
ASA0088
DGRP_892, Male, CT16, Replicate 3


title: 1175


title: 1204


title: B068-1A


title: 1194


title: H3K27me3.AF.1


title: B065-2A


title: CSB_F_T8_R3

description:
ASA0081
Canton-S B, Female, CT08, Replicate 3


title: H3K4me3.FS.2


title: B065-1A


title: DGRP_892_F_T12_R2

description:
ASA0080
DGRP_892, Female, CT12, Replicate 2


title: DGRP_892_M_T4_R3

description:
ASA0079
DGRP_892, Male, CT04, Replicate 3


title: B062-2A


title: 1167


title: 1150


title: 1169


title: H3K4me3.FS.1


title: H3K4me3.ES.2


title: DGRP_892_M_T14_R1

description:
ASA0078
DGRP_892, Male, CT14, Replicate 1


title: B062-1A


title: B094-2A


title: H3K4me3.ES.1


title: 1134


title: 1146


title: B061-1A


title: 1159


title: B061-2A


title: H3K4me3.AFX.1


title: DGRP_892_M_T2_R1

description:
ASA0075
DGRP_892, Male, CT02, Replicate 1


title: B085-2A


title: B068-2A


title: B060-2A


title: 1147


title: CSB_F_T18_R2

description:
ASA0076
Canton-S B, Female, CT18, Replicate 2


title: CSB_F_T10_R1

description:
ASA0077
Canton-S B, Female, CT10, Replicate 1


title: DGRP_892_F_T20_R1

description:
ASA0074
DGRP_892, Female, CT20, Replicate 1


title: B060-1A


title: DGRP_892_F_T2_R2

description:
ASA0073
DGRP_892, Female, CT02, Replicate 2


title: 1170


title: B058-2A


title: 1132


title: 1130


title: H3K4me1.FS.2


title: DGRP_892_F_T6_R1

description:
ASA0072
DGRP_892, Female, CT06, Replicate 1


title: B058-1A


title: H3K4me3.AFX.2


title: H3K4me1.FS.1


title: B053-2A


title: CSB_M_T24_R2

description:
ASA0071
Canton-S B, Male, CT24, Replicate 2


title: H3K4me1.ES.2


title: 1126


title: H3K4me3.AF.1


title: B053-1A


title: 1125


title: DGRP_892_F_T22_R1

description:
ASA0070
DGRP_892, Female, CT22, Replicate 1


title: H3K4me1.ES.1


title: CSB_M_T12_R3

description:
ASA0069
Canton-S B, Male, CT12, Replicate 3


title: H3K27me3.ES.1


title: B044-2A


title: DGRP_892_M_T16_R1

description:
ASA0068
DGRP_892, Male, CT16, Replicate 1


title: B044-1A


title: H3K4me1.AFX.2


title: CSB_M_T18_R1

description:
ASA0067
Canton-S B, Male, CT18, Replicate 1


title: H3K4me1.AFX.1


title: B043-2A


title: 1120


title: H3K4me3.AF.2


title: H3K4me1.AF.2


title: B043-1A


title: 1108


title: B040-2A


title: CSB_M_T8_R2

description:
ASA0065
Canton-S B, Male, CT08, Replicate 2


title: 1123


title: 1113


title: WT.AFX.2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

data_processing:
Reads were quality-trimmed using TrimGalore!, and reads shorter than 15 nt were discarded. Reads were aligned to the mouse reference genome (mm10) using bowtie with parameters "-m1 -v1 --best --strata -X 2000 --trim3 1". Duplicates were removed using Picard tools. Moreover, reads shorter than one nucleosome length were discarded, and an offset of 4 nts was introduced.  Peaks were called with MACS2 and parameters "--nomodel --shift -55 --extsize 110 --broad -g mm --broad-cutoff 0.1".
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peaks

extract_protocol:
50,000 cells were collected and washed with ice-cold PBS once then lysed in the buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL). The nuclear pellets were collected and Tn5 tagmentation were performed with Illumina Nextera kit.  (FC-121-1030)
Library construction were performed with Illumina Nextera kit.  (FC-121-1030)

tag: culture condition

value: EpiSCs cultured in AFX

tag: cell types

value: EpiSC

tag: passage


title: 1112


title: B040-1A


title: 1133


title: B032-2A


title: CSB_M_T12_R2

description:
ASA0063
Canton-S B, Male, CT12, Replicate 2


title: WT.GFP_LOW.cell_2.2

value: EpiLCs were induced from ES cells in AF supplemented with KSR for 2 days. GFP-low fraction were sorted.

value: EpiLC


title: B032-1A


title: CSB_M_T6_R3

description:
ASA0062
Canton-S B, Male, CT06, Replicate 3


title: WT.GFP_LOW.cell_2.1


title: DGRP_892_M_T10_R2

description:
ASA0061
DGRP_892, Male, CT10, Replicate 2


title: 1107


title: B031-2A


title: 1092


title: WT.GFP_LOW.cell_1.2


title: DGRP_892_M_T24_R1

description:
ASA0060
DGRP_892, Male, CT24, Replicate 1


title: WT.AFX.1


title: B031-1A


title: WT.GFP_LOW.cell_1.1


title: CSB_F_T24_R1

description:
ASA0059
Canton-S B, Female, CT24, Replicate 1


title: 1089


title: B030-2A


title: 1093


title: 1085


title: WT.ES.2

value: ES cells were cultured in 2iL

value: ESC


title: B030-1A


title: WT.ES.1


title: DGRP_892_M_T24_R3

description:
ASA0057
DGRP_892, Male, CT24, Replicate 3

value: Adult


title: B025-2A

value: Intestinal biopsy


title: ES [E14IV-C_p20]

data_processing:
trimmed using trim_galore using the “--paired” option
aligned to the mouse mm10 genome using tophat2 v2.1.0
Genes quantified using Featurecounts v1.5.0 and ensembl release 86
Genome_build: mm10
Supplementary_files_format_and_content: Gene raw counts

source_name: mES cells

growth_protocol: mES cells are cultued in 2iL, mFS cells are cultured in A3X or A3XR medium and mEpiSC were cultured in AF or AFX medium

extract_protocol:
Cells were lysed in Trizol and total RNAs are prepared by PureLink RNA Mini Kit
NEXTflex Rapid Directional RNA-seq Kit were used


title: DGRP_892_M_T8_R3

description:
ASA0066
DGRP_892, Male, CT08, Replicate 3


title: 1096


title: H3K4me1.AF.1

value: Rep 1


title: B025-1A


title: 1104


title: DGRP_892_M_T10_R3

description:
ASA0064
DGRP_892, Male, CT10, Replicate 3

value: Head


title: 1065


title: CSB_M_T4_R1

description:
ASA0055
Canton-S B, Male, CT04, Replicate 1

value: Male


title: ES [E14IV-C_p15]


title: B010-2A


title: DGRP_892_M_T20_R3

description:
ASA0054
DGRP_892, Male, CT20, Replicate 3


title: DGRP_892_F_T6_R2

description:
ASA0056
DGRP_892, Female, CT06, Replicate 2


title: B010-1A


title: ES [E14IV-C_p13]


title: B007-2A


title: CSB_M_T22_R1

description:
ASA0053
Canton-S B, Male, CT22, Replicate 1


title: ES [E14IV-C_p12]


title: DGRP_892_M_T12_R1

description:
ASA0052
DGRP_892, Male, CT12, Replicate 1


title: DGRP_892_F_T22_R3

description:
ASA0058
DGRP_892, Female, CT22, Replicate 3


title: AFX [AFX6_p8]

source_name: mEpiSC

value: EpiSCs

value: AFX


title: B007-1A


title: AFX [AFX6_p5]


title: 1077

value: whole blood


title: B005-2A


title: 1056


title: H3 ip, replicate 4

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Image analysis was performed with Illumina RTA 1.18.61. Basecalling was performed with illumina bcl2fastq 1.8.3.
Primary analysis pipeline was run with CASAVA 1.8.2.
Reads were aligned to sacCer3 from UCSC using bowtie2 version 2.1.0 with -k 1.
Data was read into R 3.1.0 for visualization and analysis.
rpm (reads per million) normalized bigWig files were generated in R by taking the running mean (101-base window) of the reads per million mapped reads.
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig format files of 101-base smoothed rpm values.

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells were grown in 200 ml YPD media at 30°C until OD600 of 0.5-0.7.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody

value: H3 (Abcam, ab1791)


title: AFX [AFX6_p12]


title: 1060


title: 1058


title: H3 ip, replicate 3


title: B005-1A


title: AF [AF32_p15]

value: AF


title: 1083


title: CSB_M_T12_R1

description:
ASA0049
Canton-S B, Male, CT12, Replicate 1


title: B004-2A


title: AF [AF32_p14]


title: 1045


title: CSB_F_T2_R2

description:
ASA0048
Canton-S B, Female, CT02, Replicate 2

value: Female


title: H3 ip, replicate 1


title: B004-1A


title: H3 ip, replicate 2


title: AF [AF32_p13]


title: CSB_M_T6_R1

description:
ASA0047
Canton-S B, Male, CT06, Replicate 1


title: B003-2A


title: H3pt11 ip, replicate 4

value: H3pt11 (Abcam, ab5168)


title: AXR2 [5ar3_p5]

source_name: mFS cells

value: Formative Stem Cells


title: DGRP_892_F_T24_R1

description:
ASA0046
DGRP_892, Female, CT24, Replicate 1


title: CSB_F_T12_R3

description:
ASA0050
Canton-S B, Female, CT12, Replicate 3


title: H3pt11 ip, replicate 3


title: 1049


title: CSB_F_T24_R2

description:
ASA0045
Canton-S B, Female, CT24, Replicate 2


title: B003-1A


title: 1021


title: CSB_F_T2_R1

description:
ASA0051
Canton-S B, Female, CT02, Replicate 1


title: 1038


title: AXR2 [5ar3_p12]


title: B002-1A


title: CSB_F_T16_R2

description:
ASA0044
Canton-S B, Female, CT16, Replicate 2


title: AXR1 [5ar1_p14]


title: B002-2A


title: DGRP_892_F_T14_R3

description:
ASA0043
DGRP_892, Female, CT14, Replicate 3


title: H3pt11 ip, replicate 1


title: H3pt11 ip, replicate 2


title: TRL_2015_010c-007: Thymus DP 4+ 8+ 3+

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

data_processing:
CircRNAs were detected and quantified by CirComPara v0.6.3 using 6 backsplice detection methods (CIRI2 v2.0.2; Findcirc v1.2; CIRCexplorer2 v2.3.3 combined to each of BWA, STAR, and TopHat2 alignments and DCC v0.4.6) and default parameters, which selected only the circRNAs detected by two or more methods.   Version of other software tools included in CirComPara: Bowtie2 v2.2.9, BWA v0.7.15-r1140, STAR v2.6.1d, Segemehl v0.3.4, and TopHat2 v2.1.0 with Bowtie v1.1.2.  CirComPara preprocessed raw reads with Trimmomatic v0.38 to remove residual adapters and select reads by quality and length. Read linear mapping to the human genome was performed with HISAT2 v2.0.4 . CirComPara implements circular to linear ratio as described in. CirComPara’s non-default parameters used for analyses:   Adapter sequence = Trimmomatic file TruSeq3-PE.fa;   PREPROCESSOR = Trimmomatic,   TOGGLE_TRANSCRIPTOME_RECONSTRUCTION = 'False'; LINEAR_EXPRESSION_METHODS = 'stringtie';   CIRCRNA_METHODS = "dcc, ciri, circexplorer2_star, findcirc, circexplorer2_bwa, circexplorer2_tophat";   PREPROCESSOR_PARAMS = "MAXINFO:40:0.5 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:30 MINLEN:50 AVGQUAL:30";   HISAT2_EXTRA_PARAMS = "--rna-strandness RF ";   STRINGTIE_PARAMS = '--rf';   BWA_PARAMS = ['-T', '19', '-c', '1'];   TOPHAT_PARAMS = ['--zpacker', 'pigz', '--max-multihits', '1'];   STAR_PARAMS = ['--outFilterMultimapNmax', '1', '--outSJfilterOverhangMin', '15', '15', '15', '15', '--alignSJoverhangMin', '15', '--alignSJDBoverhangMin', '15', '--seedSearchStartLmax', '30', '--outFilterScoreMin', '1', '--outFilterMatchNmin', '1', '--outFilterMismatchNmax', '2', '--chimSegmentMin', '15', '--chimScoreMin', '15', '--chimScoreSeparation', '10', '--chimJunctionOverhangMin', '15'];   MIN_READS = 2;   MIN_METHODS = 2;   DCC_EXTRA_PARAMS = ['-fg', '-M', '-F', '-Nr', 1, 1];   FINDCIRC_EXTRA_PARAMS = ['--best-qual', '40'];   FIX_READ_HEADER = 'True'    CircRNA annotation and all analyses were based on the Ensembl GRCh38 human genome and annotation v93. Loci without annotated genes and expressing one circRNA or more circRNAs (overlapping or not far than 5000 nt) defined new loci, called “circClusters”. CircRNAs were considered detected if presenting a raw counts at least 5 in at least one sample. Subsequently, only circRNAs expressed in all samples of at least one T-cell maturation stage and with average expression in the three highest quarters were kept. CircRNAs expression was  normalized with variance stabilizing transformation method.
Genome_build: GRCh38
Supplementary_files_format_and_content: backsplice read count table. The first six columns describe circRNA features in relation to the host gene, then per sample circRNA expression levels are reported

source_name: Human postnatal thymus

extract_protocol:
Total RNA was extracted with QIAzol reagent (QIAgen) and precipitated with isopropanol.
RNA libraries were prepared with the TruSeq Stranded Total RNA Ribo-Zero Gold kit.

value: Thymus

tag: cell population

tag: donor


title: ribozero_set2_lane2_prg1n4357_rep3

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

description: ribo-zero total RNA

data_processing:
ChIP-seq data mapping was done with BWA. RNA-seq data setes were mapped via STAR.
ChIP peak calling was done with MACS2 and linear enrichment was obtained with MACS2 bdgcmp function.
RNA-seq counting over genes and transposons was done with featureCounts.
Differential analysis of genes was performed via DEseq2 in Rstudio.
Log2 and Z-score transformation of ChIP-seq data was performed via custom scripts in Rstudio.
Genome_build: ce11
Supplementary_files_format_and_content: bw: big wigle format contains log2 or Z-score for ChIP-seq libraries per replicate.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: animals were grown at 20C, on HB101 E. coli seeded NGM plates.

extract_protocol:
All RNA samples were collected with Trizol and treated with Dnase I.
for polyA selected total RNA and ChIP-seq libraries, NEB-NEXT Ultra for Illumina was used. For, ribo-zero depleted total RNA libraries, NEB-NEXT Ultra II Directional for Illumina was used. For small-RNA-seq, Illumina TRU-SEQ was ued.

treatment_protocol: For ChIP, extracts were fixed with 1% FA.

value: whole animal

tag: selection/treatment

value: ribo-zero depletion


title: CSB_M_T4_R2

description:
ASA0042
Canton-S B, Male, CT04, Replicate 2

tag: developmental stage

tag: Sex

tag: timepoint


title: AXR1 [5ar1_p12]


title: 1063


title: TRL_2015_010c-006: Thymus DP 4+ 8+ 3-


title: ribozero_set2_lane1_prg1n4357_rep3

description: ribo-zero total RNA


title: 1030


title: AXR1 [5ar1_p10]


title: CSB_M_T24_R3

description:
ASA0041
Canton-S B, Male, CT24, Replicate 3

tag: replicate


title: TRL_2015_010c-003: Thymus CD34+ 4+


title: AXR2 [5ar3_p4]


title: 1013


title: ribozero_set2_lane2_prg1n4357_rep2

description: ribo-zero total RNA


title: 1022


title: ribozero_set2_lane1_prg1n4357_rep2

description: ribo-zero total RNA


title: E6.0 [E6_2]

source_name: mouse epiblast

growth_protocol: FS cells were cultured in A3XR, AF cells were cultured in AF and AFX cells were cultured in AFX

extract_protocol: cells and epiblasts were prepared PicoPure RNA Isolation kit

treatment_protocol: 1,000 cells were collected from in vitro cells and each epiblast were collected individually

value: E6.5 epiblast


title: ribozero_set2_lane2_prg1n4357_rep1

description: ribo-zero total RNA


title: E6.0 [E6_3]


title: TRL_2015_010c-002: Thymus CD34+ 4- 1+


title: E6.0 [E6_1]


title: 1023


title: DGRP_892_F_T4_R1

description:
ASA0040
DGRP_892, Female, CT04, Replicate 1

source_name: Head

value: Adult


title: ribozero_set2_lane1_prg1n4357_rep1

description: ribo-zero total RNA


title: DGRP_892_F_T18_R2

description:
ASA0038
DGRP_892, Female, CT18, Replicate 2


title: 1024


title: DGRP_892_M_T2_R2

description:
ASA0037
DGRP_892, Male, CT02, Replicate 2


title: TRL_2015_010-020: Thymus CD34+ 4+


title: E5.5 [E5.5_3]

value: E5.5 epiblast


title: 1017


title: ribozero_set2_lane2_wt_rep3

description: ribo-zero total RNA


title: E5.5 [E5.5_2]


title: DGRP_892_M_T22_R3

description:
ASA0036
DGRP_892, Male, CT22, Replicate 3


title: TRL_2015_010-025: Thymus CD34+ 4- 1-


title: DGRP_892_F_T10_R3

description:
ASA0039
DGRP_892, Female, CT10, Replicate 3


title: TRL_2015_010c-001: Thymus CD34+ 4- 1-


title: 1012


title: 1004


title: ribozero_set2_lane1_wt_rep3

description: ribo-zero total RNA


title: TRL_2015_010-021: Thymus CD34+ 4- 1+


title: E5.5 [E5.5_1]


title: CSB_F_T10_R2

description:
ASA0035
Canton-S B, Female, CT10, Replicate 2


title: ribozero_set2_lane2_wt_rep2

description: ribo-zero total RNA


title: X2015_010C-018: Thymus DP 4+ 8+ 3+


title: E5.0 [E5.0_4]

value: E5.0 epiblast


title: X2015_010C-017: Thymus DP 4+ 8+ 3-


title: E5.0 [E5.0_2]


title: CSB_M_T22_R2

description:
ASA0034
Canton-S B, Male, CT22, Replicate 2

value: Head


title: CSB_F_T20_R1

description:
ASA0033
Canton-S B, Female, CT20, Replicate 1


title: ribozero_set2_lane1_wt_rep2

description: ribo-zero total RNA


title: X2015_010C-014: Thymus CD34+ 4+


title: DGRP_892_F_T16_R1

description:
ASA0032
DGRP_892, Female, CT16, Replicate 1


title: ribozero_set2_lane2_wt_rep1

description: ribo-zero total RNA


title: X2015_010C-013: Thymus CD34+ 4- 1+


title: CSB_F_T14_R1

description:
ASA0031
Canton-S B, Female, CT14, Replicate 1


title: X2015_010C-012: Thymus CD34+ 4- 1-


title: DGRP_892_M_T18_R1

description:
ASA0030
DGRP_892, Male, CT18, Replicate 1

value: Male


title: 5dep_smallRNA_rescue_rep3

description: 5dependent smalRNAs

value: oxidation treatment


title: AFX [E14_AFX_p15]

value: EpiSCs

value: AFX


title: AFX [E14_AFX_p16]


title: 5dep_smallRNA_rescue_rep2

description: 5dependent smalRNAs


title: DGRP_892_F_T18_R3

description:
ASA0029
DGRP_892, Female, CT18, Replicate 3


title: AFX [E14_AFX_p14]


title: CSB_M_T6_R2

description:
ASA0028
Canton-S B, Male, CT06, Replicate 2


title: AF [E14_AF_p16]


title: CSB_F_T14_R2

description:
ASA0027
Canton-S B, Female, CT14, Replicate 2


title: AF [E14_AF_p15]


title: 3h fresh media rep3

city: Brookings

first: Nicholas

middle: C.

last: Butzin

state: SD

address: 1224 Medary Ave.

institute: South Dakota State University

data_processing:
Fastq files were aligned to NC_000913.3 and the plasmid p24KmNB82 using Geneious v. 11.0.3.
Raw read counts were calculated using 'calculate expression tool' in Geneious v. 11.0.3
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Table with raw read counts for every gene and sample; comma separated values

organism: Escherichia coli

source_name: 3h fresh media

growth_protocol: Cultures were grown in modified MMB+ media, which consists of the following: K2HPO4 (10.5 mg/ml), KH2PO4 (4.5 mg/ml), (NH4)2SO4 (2.0 mg/ml), C6H5Na3O7 (0.5 mg/ml), NaCl (1.0 mg/ml), 2 mM MgSO4 x 7H2O, 100 µM CaCl2, thiamine (10 µg/ml), 0.5% glycerol, amino acids (40 µg/ml) and kanamycin (25 µg/ml)

extract_protocol:
Samples were treated with Tween (0.2%) and chloramphenicol (5 µg/ml) then immediately filtered out of solution and resuspended in lysis buffer containing 25 mM Tris pH 8.0, 25 mM NH4Cl, 10 mM MgOAc, 0.8 % Triton X-100, 0.1 U/µL RNase-free DNase I, 1 U/μL. Then immediately frozen in liquid nitrogen and stored at -80 C.  Frozen pellets were thawed on ice and centrifuged for 20 minutes at 16,000 x g at 4 °C with 0.3% Sodium Deoxychorate to pellet particulate matter. The supernatant was then removed and RNA was column purified (Qiagen miRNeasy cat. No. 217004) before removing rRNA (Invitrogen RiboMinus cat no. K155004) Superase-In, ~60 U/µl ReadyLyse Lysozyme, 1.55 mM Chloramphenicol, and 17 μΜ 5′-guanylyl imidodiphosphate (GMPPNP).
cDNA libraries were prepared and multiplexed according to manufacturer's protocols: NEBNext Ultra II cat no. E7103S. Libraries were then pooled and sequenced by Illumina HiSeq paired-end sequencing.

treatment_protocol: Stationary phase cultures were diluted 1/100 into fresh MMB+ media and collected after three hours. Ampicillin treated cultures also contained 100 ug/ml ampicillin

tag: plasmid

tag: treatment


title: 5dep_smallRNA_rescue_rep1

description: 5dependent smalRNAs

tag: tissue


title: 3h amp media rep2

source_name: 3h fresh media with ampicillin

tag: strain

value: ampicillin


title: 5dep_smallRNA_rpb9mj261_rep2

description: 5dependent smalRNAs


title: ribozero_set2_lane1_wt_rep1

description: ribo-zero total RNA


title: 5dep_smallRNA_rpb9mj261_rep1

description: 5dependent smalRNAs


title: 3h amp media rep1


title: FS2 [5cdr2_p16]


title: AF [E14_AF_p14]

value: AF


title: CSB_F_T4_R2

description:
ASA0026
Canton-S B, Female, CT04, Replicate 2

value: Female


title: 5dep_smallRNA_rpb9mj261_rep3

description: 5dependent smalRNAs


title: E5.0 [E5.0_1]


title: 3h fresh media rep1


title: 5dep_smallRNA_wildtype_rep3

description: 5dependent smalRNAs


title: DGRP_892_M_T12_R3

description:
ASA0024
DGRP_892, Male, CT12, Replicate 3


title: CSB_F_T20_R2

description:
ASA0025
Canton-S B, Female, CT20, Replicate 2


title: Stationary rep3

source_name: Stationary phase cells


title: DGRP_892_M_T8_R1

description:
ASA0023
DGRP_892, Male, CT08, Replicate 1


title: 3h amp media rep3


title: 5dep_smallRNA_wildtype_rep2

description: 5dependent smalRNAs


title: Stationary rep2


title: 5dep_smallRNA_wildtype_rep1

description: 5dependent smalRNAs


title: FS1 [5cdr1_p18]


title: Stationary rep1


title: DGRP_892_M_T18_R3

description:
ASA0021
DGRP_892, Male, CT18, Replicate 3


title: smallRNA_rescue_rep3

description: 5independent smalRNAs

value: pyrophosphatase treatment


title: 3h fresh media rep2


title: smallRNA_rescue_rep2

description: 5independent smalRNAs


title: NFATc3MTG_rep3

city: Guangzhou

first: Si-Jia

last: Liang

state: Guangdong

address: 74 Zhongshan 2 Rd

department: Pharmacology

country: China

institute: Zhongshan School of Medicine, Sun Yat-Sen University

data_processing:
Quality control.Clean datas were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data  through custom perl  and python scripts
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Known miRNA alignment.Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA.
Target gene of miRNA  was predicted by psRobot_tar inmiRanda (Enright et al, 2003) .
miRNA expression levels were estimated by TPM (transcript per million).
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: ensembl 97
Supplementary_files_format_and_content: miRNA expression read counts were included in excel file with TPM value.

source_name: Peritoneal macrophages

growth_protocol: Isolated peritoneal macrophages were cultured in DMEM with 10% FBS, 1% HEPES, and 1% penicillin/streptomycin for 24 h.

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.).

treatment_protocol: Untreated

tag: cell type

value: Untreated

tag: age

value: 10 weeks

tag: gender

value: male


title: FS1 [5cdr1_p11]

tag: cell types

value: Formative Stem Cells

tag: culture condition


title: FS1 [5cdr1_p10]


title: NFATc3MTG_rep2


title: smallRNA_rpb9mj261_rep3

description: 5independent smalRNAs

value: whole animal


title: CSB_M_T10_R3

description:
ASA0020
Canton-S B, Male, CT10, Replicate 3

value: Adult


title: smallRNA_rescue_rep1

description: 5independent smalRNAs


title: FS2 [5cdr2_p13]


title: CSB_M_T16_R3

description:
ASA0018
Canton-S B, Male, CT16, Replicate 3


title: CSB_F_T16_R1

description:
ASA0019
Canton-S B, Female, CT16, Replicate 1


title: FS2 [5cdr2_p12]


title: NFATc3MTG_rep1


title: smallRNA_rpb9mj261_rep2

description: 5independent smalRNAs


title: Wild-type_rep3


title: ES.1

source_name: ES p16

value: ES cells were cultured in 2iL

value: ESC

tag: passage


title: ES.3


title: ES.2


title: CSB_F_T12_R1

description:
ASA0017
Canton-S B, Female, CT12, Replicate 1

value: Head


title: DGRP_892_M_T20_R2

description:
ASA0016
DGRP_892, Male, CT20, Replicate 2

value: Male


title: smallRNA_rpb9mj261_rep1

description: 5independent smalRNAs


title: Wild-type_rep2


title: E33.3

source_name: EpiSC (AFX)2 p16

value: EpiSCs  cultured in AFX

value: EpiSC


title: smallRNA_wildtype_rep3

description: 5independent smalRNAs


title: CSB_F_T4_R3

description:
ASA0022
Canton-S B, Female, CT04, Replicate 3


title: E33.2


title: Wild-type_rep1


title: CSB_M_T20_R2

description:
ASA0015
Canton-S B, Male, CT20, Replicate 2


title: smallRNA_wildtype_rep2

description: 5independent smalRNAs


title: E33.1


title: smallRNA_wildtype_rep1

description: 5independent smalRNAs