title: Sample 943_E7.5_Plate15_G01


title: Sample 954_E7.5_Plate15_G12

status: Public on Sep 30 2019

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HiSat270 (v2.1.0) using options --dta --sp 1000,1000 --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Genome_build: GRCm38
Supplementary_files_format_and_content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID

molecule: total RNA

organism: Mus musculus

source_name: Early embryo

extract_protocol:
Single-cells were sorted either manually (E4.5, E5.5) or using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing.
Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

tag: strain

tag: developmental stage


title: Sample 937_E7.5_Plate15_F07


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title: Sample 808_E7.5_Plate14_C10


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title: Sample 538_E7.5_Plate11_E02


title: Sample 535_E7.5_Plate11_D11


title: Sample 534_E7.5_Plate11_D10


title: Sample 533_E7.5_Plate11_D09


title: Sample 532_E7.5_Plate11_D08


title: Sample 531_E7.5_Plate11_D07


title: Sample 530_E7.5_Plate11_D06


title: Sample 529_E7.5_Plate11_D05


title: Sample 528_E7.5_Plate11_D04


title: Sample 526_E7.5_Plate11_D02


title: Sample 524_E7.5_Plate11_C12


title: Sample 525_E7.5_Plate11_D01


title: Sample 706_E7.5_Plate13_C04


title: Sample 523_E7.5_Plate11_C11


title: Sample 516_E7.5_Plate11_C03


title: Sample 514_E7.5_Plate11_C01


title: Sample 519_E7.5_Plate11_C07


title: Sample 510_E7.5_Plate11_B08


title: Sample 513_E7.5_Plate11_B12


title: Sample 517_E7.5_Plate11_C04


title: Sample 515_E7.5_Plate11_C02


title: Sample 512_E7.5_Plate11_B11


title: Sample 536_E7.5_Plate11_D12


title: Sample 521_E7.5_Plate11_C09


title: Sample 520_E7.5_Plate11_C08


title: Sample 508_E7.5_Plate11_B06


title: Sample 518_E7.5_Plate11_C05


title: Sample 522_E7.5_Plate11_C10


title: Sample 503_E7.5_Plate11_B01


title: Sample 505_E7.5_Plate11_B03


title: Sample 500_E7.5_Plate11_A10


title: Sample 501_E7.5_Plate11_A11


title: Sample 506_E7.5_Plate11_B04


title: Sample 507_E7.5_Plate11_B05


title: Sample 527_E7.5_Plate11_D03


title: Sample 502_E7.5_Plate11_A12


title: Sample 497_E7.5_Plate11_A07


title: Sample 496_E7.5_Plate11_A06


title: Sample 504_E7.5_Plate11_B02


title: Sample 498_E7.5_Plate11_A08


title: Sample 511_E7.5_Plate11_B09


title: Sample 509_E7.5_Plate11_B07


title: Sample 495_E7.5_Plate11_A05


title: Sample 494_E7.5_Plate11_A04


title: Sample 486_E4.5-5.5_new_Plate3_H06


title: Sample 488_E4.5-5.5_new_Plate3_H08


title: Sample 493_E7.5_Plate11_A03


title: Sample 487_E4.5-5.5_new_Plate3_H07


title: Sample 490_E4.5-5.5_new_Plate3_H12


title: Sample 499_E7.5_Plate11_A09


title: Sample 483_E4.5-5.5_new_Plate3_G11


title: Sample 477_E4.5-5.5_new_Plate3_F11


title: Sample 479_E4.5-5.5_new_Plate3_G02


title: Sample 478_E4.5-5.5_new_Plate3_F12


title: Sample 484_E4.5-5.5_new_Plate3_G12


title: Sample 473_E4.5-5.5_new_Plate3_F06


title: Sample 482_E4.5-5.5_new_Plate3_G05


title: Sample 480_E4.5-5.5_new_Plate3_G03


title: Sample 472_E4.5-5.5_new_Plate3_F05


title: Sample 481_E4.5-5.5_new_Plate3_G04


title: Sample 485_E4.5-5.5_new_Plate3_H01


title: Sample 471_E4.5-5.5_new_Plate3_F04


title: Sample 470_E4.5-5.5_new_Plate3_F03


title: Sample 476_E4.5-5.5_new_Plate3_F10


title: Sample 469_E4.5-5.5_new_Plate3_E11


title: Sample 474_E4.5-5.5_new_Plate3_F08


title: Sample 475_E4.5-5.5_new_Plate3_F09


title: Sample 468_E4.5-5.5_new_Plate3_E08


title: Sample 467_E4.5-5.5_new_Plate3_E07


title: Sample 492_E7.5_Plate11_A02


title: Sample 491_E7.5_Plate11_A01


title: Sample 489_E4.5-5.5_new_Plate3_H11


title: Sample 466_E4.5-5.5_new_Plate3_E06


title: Sample 464_E4.5-5.5_new_Plate3_D12


title: Sample 461_E4.5-5.5_new_Plate3_D09


title: Sample 462_E4.5-5.5_new_Plate3_D10


title: Sample 463_E4.5-5.5_new_Plate3_D11


title: Sample 460_E4.5-5.5_new_Plate3_D08


title: Sample 458_E4.5-5.5_new_Plate3_D06


title: Sample 459_E4.5-5.5_new_Plate3_D07


title: Sample 457_E4.5-5.5_new_Plate3_D04


title: Sample 456_E4.5-5.5_new_Plate3_D03


title: Sample 455_E4.5-5.5_new_Plate3_D02


title: Sample 453_E4.5-5.5_new_Plate3_C12


title: Sample 446_E4.5-5.5_new_Plate3_C02


title: Sample 450_E4.5-5.5_new_Plate3_C09


title: Sample 445_E4.5-5.5_new_Plate3_C01


title: Sample 443_E4.5-5.5_new_Plate3_B11


title: Sample 448_E4.5-5.5_new_Plate3_C06


title: Sample 454_E4.5-5.5_new_Plate3_D01


title: Sample 451_E4.5-5.5_new_Plate3_C10


title: Sample 449_E4.5-5.5_new_Plate3_C08


title: Sample 444_E4.5-5.5_new_Plate3_B12


title: Sample 447_E4.5-5.5_new_Plate3_C03


title: Sample 442_E4.5-5.5_new_Plate3_B10


title: Sample 441_E4.5-5.5_new_Plate3_B08


title: Sample 440_E4.5-5.5_new_Plate3_B06


title: Sample 439_E4.5-5.5_new_Plate3_B05


title: Sample 438_E4.5-5.5_new_Plate3_B04


title: Sample 437_E4.5-5.5_new_Plate3_A11


title: Sample 436_E4.5-5.5_new_Plate3_A09


title: Sample 435_E4.5-5.5_new_Plate3_A08


title: Sample 434_E4.5-5.5_new_Plate3_A05


title: Sample 433_E4.5-5.5_new_Plate3_A03


title: Sample 452_E4.5-5.5_new_Plate3_C11


title: Sample 425_E4.5-5.5_new_Plate1_H04


title: Sample 426_E4.5-5.5_new_Plate1_H05


title: Sample 429_E4.5-5.5_new_Plate1_H10


title: Sample 431_E4.5-5.5_new_Plate1_H12


title: Sample 430_E4.5-5.5_new_Plate1_H11


title: Sample 418_E4.5-5.5_new_Plate1_G05


title: Sample 422_E4.5-5.5_new_Plate1_G12


title: Sample 423_E4.5-5.5_new_Plate1_H01


title: Sample 417_E4.5-5.5_new_Plate1_G04


title: Sample 420_E4.5-5.5_new_Plate1_G10


title: Sample 421_E4.5-5.5_new_Plate1_G11


title: Sample 419_E4.5-5.5_new_Plate1_G06


title: Sample 410_E4.5-5.5_new_Plate1_F08


title: Sample 409_E4.5-5.5_new_Plate1_F07


title: Sample 414_E4.5-5.5_new_Plate1_F12


title: Sample 413_E4.5-5.5_new_Plate1_F11


title: Sample 411_E4.5-5.5_new_Plate1_F09


title: Sample 412_E4.5-5.5_new_Plate1_F10


title: Sample 432_E4.5-5.5_new_Plate3_A01


title: Sample 408_E4.5-5.5_new_Plate1_F06


title: Sample 407_E4.5-5.5_new_Plate1_F05


title: Sample 415_E4.5-5.5_new_Plate1_G01


title: Sample 428_E4.5-5.5_new_Plate1_H07


title: Sample 424_E4.5-5.5_new_Plate1_H03


title: Sample 427_E4.5-5.5_new_Plate1_H06


title: Sample 416_E4.5-5.5_new_Plate1_G02


title: Sample 404_E4.5-5.5_new_Plate1_F01


title: Sample 406_E4.5-5.5_new_Plate1_F04


title: Sample 403_E4.5-5.5_new_Plate1_E12


title: Sample 401_E4.5-5.5_new_Plate1_E07


title: Sample 400_E4.5-5.5_new_Plate1_E06


title: Sample 395_E4.5-5.5_new_Plate1_D09


title: Sample 396_E4.5-5.5_new_Plate1_D10


title: Sample 394_E4.5-5.5_new_Plate1_D08


title: Sample 397_E4.5-5.5_new_Plate1_D12


title: Sample 393_E4.5-5.5_new_Plate1_D07


title: Sample 392_E4.5-5.5_new_Plate1_D06


title: Sample 391_E4.5-5.5_new_Plate1_D04


title: Sample 387_E4.5-5.5_new_Plate1_C10


title: Sample 388_E4.5-5.5_new_Plate1_C12


title: Sample 390_E4.5-5.5_new_Plate1_D02


title: Sample 386_E4.5-5.5_new_Plate1_C07


title: Sample 405_E4.5-5.5_new_Plate1_F02


title: Sample 385_E4.5-5.5_new_Plate1_C06


title: Sample 389_E4.5-5.5_new_Plate1_D01


title: Sample 383_E4.5-5.5_new_Plate1_C01


title: Sample 379_E4.5-5.5_new_Plate1_B05


title: Sample 382_E4.5-5.5_new_Plate1_B10


title: Sample 380_E4.5-5.5_new_Plate1_B06


title: Sample 377_E4.5-5.5_new_Plate1_B03


title: Sample 378_E4.5-5.5_new_Plate1_B04


title: Sample 381_E4.5-5.5_new_Plate1_B09


title: Sample 376_E4.5-5.5_new_Plate1_A10


title: Sample 402_E4.5-5.5_new_Plate1_E10


title: Sample 398_E4.5-5.5_new_Plate1_E01


title: Sample 375_E4.5-5.5_new_Plate1_A06


title: Sample 374_E4.5-5.5_new_Plate1_A01


title: Sample 372_E7.5_Plate1_H8


title: Sample 373_E7.5_Plate1_H9


title: Sample 371_E7.5_Plate1_H7


title: Sample 399_E4.5-5.5_new_Plate1_E04


title: Sample 370_E7.5_Plate1_H6


title: Sample 368_E7.5_Plate1_H4


title: Sample 384_E4.5-5.5_new_Plate1_C04


title: Sample 369_E7.5_Plate1_H5


title: Sample 465_E4.5-5.5_new_Plate3_E05


title: Sample 367_E7.5_Plate1_H2


title: Sample 366_E7.5_Plate1_H1


title: Sample 364_E7.5_Plate1_H11


title: Sample 361_E7.5_Plate1_G8


title: Sample 362_E7.5_Plate1_G9


title: Sample 365_E7.5_Plate1_H12


title: Sample 363_E7.5_Plate1_H10


title: Sample 358_E7.5_Plate1_G5


title: Sample 357_E7.5_Plate1_G4


title: Sample 355_E7.5_Plate1_G1


title: Sample 359_E7.5_Plate1_G6


title: Sample 360_E7.5_Plate1_G7


title: Sample 356_E7.5_Plate1_G3


title: Sample 354_E7.5_Plate1_G12


title: Sample 353_E7.5_Plate1_G11


title: Sample 352_E7.5_Plate1_G10


title: Sample 345_E7.5_Plate1_F2


title: Sample 347_E7.5_Plate1_F4


title: Sample 351_E7.5_Plate1_F9


title: Sample 348_E7.5_Plate1_F6


title: Sample 349_E7.5_Plate1_F7


title: Sample 350_E7.5_Plate1_F8


title: Sample 346_E7.5_Plate1_F3


title: Sample 343_E7.5_Plate1_F12


title: Sample 341_E7.5_Plate1_F10


title: Sample 340_E7.5_Plate1_E9


title: Sample 339_E7.5_Plate1_E8


title: Sample 338_E7.5_Plate1_E7


title: Sample 337_E7.5_Plate1_E6


title: Sample 332_E7.5_Plate1_E1


title: Sample 333_E7.5_Plate1_E2


title: Sample 335_E7.5_Plate1_E4


title: Sample 334_E7.5_Plate1_E3


title: Sample 330_E7.5_Plate1_E11


title: Sample 329_E7.5_Plate1_E10


title: Sample 336_E7.5_Plate1_E5


title: Sample 324_E7.5_Plate1_D4


title: Sample 331_E7.5_Plate1_E12


title: Sample 326_E7.5_Plate1_D6


title: Sample 344_E7.5_Plate1_F1


title: Sample 323_E7.5_Plate1_D3


title: Sample 342_E7.5_Plate1_F11


title: Sample 322_E7.5_Plate1_D1


title: Sample 321_E7.5_Plate1_D12


title: Sample 316_E7.5_Plate1_C7


title: Sample 317_E7.5_Plate1_C8


title: Sample 319_E7.5_Plate1_D10


title: Sample 320_E7.5_Plate1_D11


title: Sample 318_E7.5_Plate1_C9


title: Sample 310_E7.5_Plate1_C1


title: Sample 314_E7.5_Plate1_C5


title: Sample 308_E7.5_Plate1_C11


title: Sample 327_E7.5_Plate1_D8


title: Sample 307_E7.5_Plate1_C10


title: Sample 313_E7.5_Plate1_C4


title: Sample 303_E7.5_Plate1_B6


title: Sample 312_E7.5_Plate1_C3


title: Sample 305_E7.5_Plate1_B8


title: Sample 306_E7.5_Plate1_B9


title: Sample 304_E7.5_Plate1_B7


title: Sample 325_E7.5_Plate1_D5


title: Sample 302_E7.5_Plate1_B5


title: Sample 301_E7.5_Plate1_B4


title: Sample 299_E7.5_Plate1_B2


title: Sample 328_E7.5_Plate1_D9


title: Sample 300_E7.5_Plate1_B3


title: Sample 298_E7.5_Plate1_B1


title: Sample 295_E7.5_Plate1_A9


title: Sample 294_E7.5_Plate1_A8


title: Sample 290_E7.5_Plate1_A2


title: Sample 311_E7.5_Plate1_C2


title: Sample 291_E7.5_Plate1_A4


title: Sample 292_E7.5_Plate1_A6


title: Sample 296_E7.5_Plate1_B11


title: Sample 315_E7.5_Plate1_C6


title: Sample 297_E7.5_Plate1_B12


title: Sample 293_E7.5_Plate1_A7


title: Sample 286_E7.5_Plate1_A10


title: Sample 282_E6.75_Plate1_H6


title: Sample 283_E6.75_Plate1_H7


title: Sample 288_E7.5_Plate1_A12


title: Sample 309_E7.5_Plate1_C12


title: Sample 280_E6.75_Plate1_H4


title: Sample 284_E6.75_Plate1_H8


title: Sample 277_E6.75_Plate1_H1


title: Sample 285_E6.75_Plate1_H9


title: Sample 287_E7.5_Plate1_A11


title: Sample 279_E6.75_Plate1_H3


title: Sample 276_E6.75_Plate1_H12


title: Sample 278_E6.75_Plate1_H2


title: Sample 275_E6.75_Plate1_H11


title: Sample 281_E6.75_Plate1_H5


title: Sample 273_E6.75_Plate1_G9


title: Sample 272_E6.75_Plate1_G8


title: Sample 274_E6.75_Plate1_H10


title: Sample 289_E7.5_Plate1_A1


title: Sample 267_E6.75_Plate1_G3


title: Sample 268_E6.75_Plate1_G4


title: Sample 265_E6.75_Plate1_G1


title: Sample 270_E6.75_Plate1_G6


title: Sample 271_E6.75_Plate1_G7


title: Sample 263_E6.75_Plate1_G11


title: Sample 264_E6.75_Plate1_G12


title: Sample 269_E6.75_Plate1_G5


title: Sample 262_E6.75_Plate1_G10


title: Sample 261_E6.75_Plate1_F9


title: Sample 260_E6.75_Plate1_F8


title: Sample 252_E6.75_Plate1_F12


title: Sample 253_E6.75_Plate1_F1


title: Sample 251_E6.75_Plate1_F11


title: Sample 250_E6.75_Plate1_F10


title: Sample 256_E6.75_Plate1_F4


title: Sample 258_E6.75_Plate1_F6


title: Sample 254_E6.75_Plate1_F2


title: Sample 249_E6.75_Plate1_E9


title: Sample 259_E6.75_Plate1_F7


title: Sample 245_E6.75_Plate1_E5


title: Sample 246_E6.75_Plate1_E6


title: Sample 257_E6.75_Plate1_F5


title: Sample 247_E6.75_Plate1_E7


title: Sample 255_E6.75_Plate1_F3


title: Sample 244_E6.75_Plate1_E4


title: Sample 242_E6.75_Plate1_E2


title: Sample 266_E6.75_Plate1_G2


title: Sample 248_E6.75_Plate1_E8


title: Sample 241_E6.75_Plate1_E1


title: Sample 243_E6.75_Plate1_E3


title: Sample 238_E6.75_Plate1_E10


title: Sample 240_E6.75_Plate1_E12


title: Sample 236_E6.75_Plate1_D8


title: Sample 237_E6.75_Plate1_D9


title: Sample 235_E6.75_Plate1_D7


title: Sample 239_E6.75_Plate1_E11


title: Sample 231_E6.75_Plate1_D3


title: Sample 232_E6.75_Plate1_D4


title: Sample 230_E6.75_Plate1_D2


title: Sample 228_E6.75_Plate1_D12


title: Sample 227_E6.75_Plate1_D11


title: Sample 226_E6.75_Plate1_D10


title: Sample 225_E6.75_Plate1_C9


title: Sample 223_E6.75_Plate1_C7


title: Sample 229_E6.75_Plate1_D1


title: Sample 220_E6.75_Plate1_C4


title: Sample 222_E6.75_Plate1_C6


title: Sample 221_E6.75_Plate1_C5


title: Sample 216_E6.75_Plate1_C12


title: Sample 224_E6.75_Plate1_C8


title: Sample 217_E6.75_Plate1_C1


title: Sample 215_E6.75_Plate1_C11


title: Sample 218_E6.75_Plate1_C2


title: Sample 219_E6.75_Plate1_C3


title: Sample 211_E6.75_Plate1_B7


title: Sample 214_E6.75_Plate1_C10


title: Sample 234_E6.75_Plate1_D6


title: Sample 212_E6.75_Plate1_B8


title: Sample 210_E6.75_Plate1_B5


title: Sample 209_E6.75_Plate1_B4


title: Sample 208_E6.75_Plate1_B3


title: Sample 233_E6.75_Plate1_D5


title: Sample 207_E6.75_Plate1_B2


title: Sample 206_E6.75_Plate1_B1


title: Sample 205_E6.75_Plate1_B12


title: Sample 204_E6.75_Plate1_B11


title: Sample 203_E6.75_Plate1_B10


title: Sample 201_E6.75_Plate1_A8


title: Sample 202_E6.75_Plate1_A9


title: Sample 199_E6.75_Plate1_A6


title: Sample 197_E6.75_Plate1_A4


title: Sample 195_E6.75_Plate1_A2


title: Sample 196_E6.75_Plate1_A3


title: Sample 193_E6.75_Plate1_A12


title: Sample 194_E6.75_Plate1_A1


title: Sample 213_E6.75_Plate1_B9


title: Sample 190_E6.5_Plate2_H9


title: Sample 185_E6.5_Plate2_H4


title: Sample 184_E6.5_Plate2_H2


title: Sample 189_E6.5_Plate2_H8


title: Sample 187_E6.5_Plate2_H6


title: Sample 183_E6.5_Plate2_H1


title: Sample 188_E6.5_Plate2_H7


title: Sample 192_E6.75_Plate1_A11


title: Sample 186_E6.5_Plate2_H5


title: Sample 179_E6.5_Plate2_G9


title: Sample 180_E6.5_Plate2_H10


title: Sample 178_E6.5_Plate2_G8


title: Sample 182_E6.5_Plate2_H12


title: Sample 177_E6.5_Plate2_G7


title: Sample 176_E6.5_Plate2_G5


title: Sample 200_E6.75_Plate1_A7


title: Sample 198_E6.75_Plate1_A5


title: Sample 173_E6.5_Plate2_G2


title: Sample 174_E6.5_Plate2_G3


title: Sample 172_E6.5_Plate2_G1


title: Sample 171_E6.5_Plate2_G12


title: Sample 191_E6.75_Plate1_A10


title: Sample 168_E6.5_Plate2_F9


title: Sample 169_E6.5_Plate2_G10


title: Sample 166_E6.5_Plate2_F7


title: Sample 167_E6.5_Plate2_F8


title: Sample 165_E6.5_Plate2_F6


title: Sample 164_E6.5_Plate2_F5


title: Sample 181_E6.5_Plate2_H11


title: Sample 162_E6.5_Plate2_F3


title: Sample 161_E6.5_Plate2_F2


title: Sample 163_E6.5_Plate2_F4


title: Sample 175_E6.5_Plate2_G4


title: Sample 156_E6.5_Plate2_E9


title: Sample 155_E6.5_Plate2_E8


title: Sample 158_E6.5_Plate2_F11


title: Sample 159_E6.5_Plate2_F12


title: Sample 153_E6.5_Plate2_E6


title: Sample 160_E6.5_Plate2_F1


title: Sample 151_E6.5_Plate2_E4


title: Sample 154_E6.5_Plate2_E7


title: Sample 152_E6.5_Plate2_E5


title: Sample 150_E6.5_Plate2_E3


title: Sample 149_E6.5_Plate2_E2


title: Sample 148_E6.5_Plate2_E1


title: Sample 170_E6.5_Plate2_G11


title: Sample 145_E6.5_Plate2_E10


title: Sample 146_E6.5_Plate2_E11


title: Sample 147_E6.5_Plate2_E12


title: Sample 140_E6.5_Plate2_D5


title: Sample 144_E6.5_Plate2_D9


title: Sample 141_E6.5_Plate2_D6


title: Sample 143_E6.5_Plate2_D8


title: Sample 142_E6.5_Plate2_D7


title: Sample 139_E6.5_Plate2_D4


title: Sample 138_E6.5_Plate2_D3


title: Sample 137_E6.5_Plate2_D2


title: Sample 136_E6.5_Plate2_D1


title: Sample 134_E6.5_Plate2_D11


title: Sample 133_E6.5_Plate2_D10


title: Sample 135_E6.5_Plate2_D12


title: Sample 157_E6.5_Plate2_F10


title: Sample 132_E6.5_Plate2_C9


title: Sample 131_E6.5_Plate2_C8


title: Sample 127_E6.5_Plate2_C4


title: Sample 130_E6.5_Plate2_C7


title: Sample 123_E6.5_Plate2_C12


title: Sample 125_E6.5_Plate2_C2


title: Sample 128_E6.5_Plate2_C5


title: Sample 121_E6.5_Plate2_C10


title: Sample 119_E6.5_Plate2_B8


title: Sample 122_E6.5_Plate2_C11


title: Sample 117_E6.5_Plate2_B6


title: Sample 126_E6.5_Plate2_C3


title: Sample 124_E6.5_Plate2_C1


title: Sample 118_E6.5_Plate2_B7


title: Sample 114_E6.5_Plate2_B3


title: Sample 112_E6.5_Plate2_B1


title: Sample 111_E6.5_Plate2_B12


title: Sample 116_E6.5_Plate2_B5


title: Sample 120_E6.5_Plate2_B9


title: Sample 113_E6.5_Plate2_B2


title: Sample 110_E6.5_Plate2_B11


title: Sample 109_E6.5_Plate2_B10


title: Sample 108_E6.5_Plate2_A9


title: Sample 129_E6.5_Plate2_C6


title: Sample 107_E6.5_Plate2_A8


title: Sample 106_E6.5_Plate2_A7


title: Sample 103_E6.5_Plate2_A4


title: Sample 104_E6.5_Plate2_A5


title: Sample 102_E6.5_Plate2_A3


title: Sample 105_E6.5_Plate2_A6


title: Sample 100_E6.5_Plate2_A1


title: Sample 99_E6.5_Plate2_A12


title: Sample 97_E6.5_Plate2_A10


title: Sample 96_E6.5_Plate1_H9


title: Sample 94_E6.5_Plate1_H7


title: Sample 95_E6.5_Plate1_H8


title: Sample 93_E6.5_Plate1_H6


title: Sample 91_E6.5_Plate1_H4


title: Sample 92_E6.5_Plate1_H5


title: Sample 89_E6.5_Plate1_H2


title: Sample 90_E6.5_Plate1_H3


title: Sample 115_E6.5_Plate2_B4


title: Sample 81_E6.5_Plate1_G6


title: Sample 84_E6.5_Plate1_G9


title: Sample 85_E6.5_Plate1_H10


title: Sample 86_E6.5_Plate1_H11


title: Sample 83_E6.5_Plate1_G8


title: Sample 82_E6.5_Plate1_G7


title: Sample 88_E6.5_Plate1_H1


title: Sample 87_E6.5_Plate1_H12


title: Sample 98_E6.5_Plate2_A11


title: Sample 77_E6.5_Plate1_G2


title: Sample 79_E6.5_Plate1_G4


title: Sample 78_E6.5_Plate1_G3


title: Sample 101_E6.5_Plate2_A2


title: Sample 73_E6.5_Plate1_G10


title: Sample 76_E6.5_Plate1_G1


title: Sample 75_E6.5_Plate1_G12


title: Sample 74_E6.5_Plate1_G11


title: Sample 71_E6.5_Plate1_F8


title: Sample 69_E6.5_Plate1_F6


title: Sample 68_E6.5_Plate1_F5


title: Sample 72_E6.5_Plate1_F9


title: Sample 70_E6.5_Plate1_F7


title: Sample 67_E6.5_Plate1_F4


title: Sample 65_E6.5_Plate1_F2


title: Sample 63_E6.5_Plate1_F12


title: Sample 62_E6.5_Plate1_F11


title: Sample 61_E6.5_Plate1_F10


title: Sample 80_E6.5_Plate1_G5


title: Sample 59_E6.5_Plate1_E8


title: Sample 60_E6.5_Plate1_E9


title: Sample 57_E6.5_Plate1_E6


title: Sample 53_E6.5_Plate1_E2


title: Sample 55_E6.5_Plate1_E4


title: Sample 51_E6.5_Plate1_E12


title: Sample 49_E6.5_Plate1_E10


title: Sample 54_E6.5_Plate1_E3


title: Sample 46_E6.5_Plate1_D7


title: Sample 52_E6.5_Plate1_E1


title: Sample 44_E6.5_Plate1_D5


title: Sample 48_E6.5_Plate1_D9


title: Sample 45_E6.5_Plate1_D6


title: Sample 50_E6.5_Plate1_E11


title: Sample 66_E6.5_Plate1_F3


title: Sample 43_E6.5_Plate1_D4


title: Sample 41_E6.5_Plate1_D2


title: Sample 42_E6.5_Plate1_D3


title: Sample 64_E6.5_Plate1_F1


title: Sample 39_E6.5_Plate1_D12


title: Sample 38_E6.5_Plate1_D11


title: Sample 40_E6.5_Plate1_D1


title: Sample 58_E6.5_Plate1_E7


title: Sample 36_E6.5_Plate1_C9


title: Sample 34_E6.5_Plate1_C7


title: Sample 56_E6.5_Plate1_E5


title: Sample 32_E6.5_Plate1_C5


title: Sample 30_E6.5_Plate1_C3


title: Sample 31_E6.5_Plate1_C4


title: Sample 35_E6.5_Plate1_C8


title: Sample 33_E6.5_Plate1_C6


title: Sample 28_E6.5_Plate1_C1


title: Sample 29_E6.5_Plate1_C2


title: Sample 27_E6.5_Plate1_C12


title: Sample 25_E6.5_Plate1_C10


title: Sample 26_E6.5_Plate1_C11


title: Sample 23_E6.5_Plate1_B8


title: Sample 21_E6.5_Plate1_B6


title: Sample 19_E6.5_Plate1_B4


title: Sample 24_E6.5_Plate1_B9


title: Sample 22_E6.5_Plate1_B7


title: Sample 18_E6.5_Plate1_B3


title: Sample 37_E6.5_Plate1_D10


title: Sample 20_E6.5_Plate1_B5


title: Sample 17_E6.5_Plate1_B2


title: Sample 12_E6.5_Plate1_A9


title: Sample 14_E6.5_Plate1_B11


title: Sample 15_E6.5_Plate1_B12


title: Sample 10_E6.5_Plate1_A7


title: Sample 8_E6.5_Plate1_A5


title: Sample 16_E6.5_Plate1_B1


title: Sample 7_E6.5_Plate1_A4


title: Sample 4_E6.5_Plate1_A1


title: Sample 6_E6.5_Plate1_A3


title: Sample 3_E6.5_Plate1_A12


title: Sample 2_E6.5_Plate1_A11


title: Sample 960_EB_repeat_Plate9_H12

growth_protocol: Tet[1-/- ,2 -/- ,3 -/-] (C57BL6/129/FVB) and matching wild-type mouse ES cells75 were cultured in 2i+LIF media (serum-free N2B27 (N2 & B27; Gibco)  supplemented with LIF, MEK inhibitor PD0325901 (1 µM) and GSK3 inhibitor CHIR99021 (3 µM), (all Department of Biochemistry, University of Cambridge). ES cells were cultured on tissue culture plastic pre-coated with 0.1% gelatine in H2O and were passaged when approaching confluence (2-3d). For the embryoid body (EB) differentiation assay, 2x104  ES cells were collected in serum media consisting of DMEM (Life Technologies, 10566-016), 15% Fetal Bovine Serum (FBS) (Gibco, 10270106), 1x non-essential amino acids (NEAA) (Life Technologies, 11140050), 0.1 mM 2-mercaptoethanol (Life Technologies, 31350-010), 2 mM L-Glutamine (Life Technologies, 25030-024) in ultra-low attachment 96-well plates (Sigma-Aldrich, CLS7007). All cells were cultured in a humidified incubator at 37°C in 5% CO2 and 20% O2. EBs were collected 3 and 7 days after induction of differentiation and dissociated into single cells using accutase.

value: embryonic stem cell

tag: genotype/variation

tag: time point


title: Sample 957_EB_repeat_Plate9_H09


title: Sample 954_EB_repeat_Plate9_H06

value: WT


title: Sample 13_E6.5_Plate1_B10


title: Sample 953_EB_repeat_Plate9_H05


title: Sample 956_EB_repeat_Plate9_H08


title: Sample 952_EB_repeat_Plate9_H04


title: Sample 949_EB_repeat_Plate9_H01


title: Sample 958_EB_repeat_Plate9_H10


title: Sample 955_EB_repeat_Plate9_H07


title: Sample 959_EB_repeat_Plate9_H11


title: Sample 950_EB_repeat_Plate9_H02


title: Sample 11_E6.5_Plate1_A8


title: Sample 951_EB_repeat_Plate9_H03


title: Sample 9_E6.5_Plate1_A6


title: Sample 946_EB_repeat_Plate9_G10


title: Sample 947_EB_repeat_Plate9_G11


title: Sample 948_EB_repeat_Plate9_G12


title: Sample 944_EB_repeat_Plate9_G08


title: Sample 942_EB_repeat_Plate9_G06


title: Sample 1_E6.5_Plate1_A10


title: Sample 5_E6.5_Plate1_A2


title: Sample 943_EB_repeat_Plate9_G07


title: Sample 941_EB_repeat_Plate9_G05


title: Sample 940_EB_repeat_Plate9_G04


title: Sample 937_EB_repeat_Plate9_G01


title: Sample 939_EB_repeat_Plate9_G03


title: Sample 936_EB_repeat_Plate9_F12


title: Sample 934_EB_repeat_Plate9_F10


title: Sample 933_EB_repeat_Plate9_F09


title: Sample 945_EB_repeat_Plate9_G09


title: Sample 930_EB_repeat_Plate9_F06


title: Sample 932_EB_repeat_Plate9_F08


title: Sample 927_EB_repeat_Plate9_F03


title: Sample 925_EB_repeat_Plate9_F01


title: Sample 935_EB_repeat_Plate9_F11


title: Sample 931_EB_repeat_Plate9_F07


title: Sample 924_EB_repeat_Plate9_E12


title: Sample 920_EB_repeat_Plate9_E08


title: Sample 923_EB_repeat_Plate9_E11


title: Sample 922_EB_repeat_Plate9_E10


title: Sample 929_EB_repeat_Plate9_F05


title: Sample 921_EB_repeat_Plate9_E09


title: Sample 919_EB_repeat_Plate9_E07


title: Sample 918_EB_repeat_Plate9_E06


title: Sample 915_EB_repeat_Plate9_E03


title: Sample 914_EB_repeat_Plate9_E02


title: Sample 916_EB_repeat_Plate9_E04


title: Sample 938_EB_repeat_Plate9_G02


title: Sample 917_EB_repeat_Plate9_E05


title: Sample 913_EB_repeat_Plate9_E01


title: Sample 912_EB_repeat_Plate9_D12


title: Sample 911_EB_repeat_Plate9_D11


title: Sample 910_EB_repeat_Plate9_D10


title: Sample 928_EB_repeat_Plate9_F04


title: Sample 926_EB_repeat_Plate9_F02


title: Sample 909_EB_repeat_Plate9_D09


title: Sample 908_EB_repeat_Plate9_D08


title: Sample 907_EB_repeat_Plate9_D07


title: Sample 904_EB_repeat_Plate9_D04


title: Sample 905_EB_repeat_Plate9_D05


title: Sample 900_EB_repeat_Plate9_C12


title: Sample 899_EB_repeat_Plate9_C11


title: Sample 903_EB_repeat_Plate9_D03


title: Sample 902_EB_repeat_Plate9_D02


title: Sample 897_EB_repeat_Plate9_C09


title: Sample 906_EB_repeat_Plate9_D06


title: Sample 901_EB_repeat_Plate9_D01


title: Sample 896_EB_repeat_Plate9_C08


title: Sample 893_EB_repeat_Plate9_C05


title: Sample 890_EB_repeat_Plate9_C02


title: Sample 894_EB_repeat_Plate9_C06


title: Sample 889_EB_repeat_Plate9_C01


title: Sample 895_EB_repeat_Plate9_C07


title: Sample 898_EB_repeat_Plate9_C10


title: Sample 888_EB_repeat_Plate9_B12


title: Sample 47_E6.5_Plate1_D8


title: Sample 891_EB_repeat_Plate9_C03


title: Sample 892_EB_repeat_Plate9_C04


title: Sample 887_EB_repeat_Plate9_B11


title: Sample 886_EB_repeat_Plate9_B10


title: Sample 885_EB_repeat_Plate9_B09


title: Sample 883_EB_repeat_Plate9_B07


title: Sample 882_EB_repeat_Plate9_B06


title: Sample 884_EB_repeat_Plate9_B08


title: Sample 881_EB_repeat_Plate9_B05


title: Sample 880_EB_repeat_Plate9_B04


title: Sample 879_EB_repeat_Plate9_B03


title: Sample 876_EB_repeat_Plate9_A12


title: Sample 877_EB_repeat_Plate9_B01


title: Sample 873_EB_repeat_Plate9_A09


title: Sample 874_EB_repeat_Plate9_A10


title: Sample 871_EB_repeat_Plate9_A07


title: Sample 878_EB_repeat_Plate9_B02


title: Sample 875_EB_repeat_Plate9_A11


title: Sample 870_EB_repeat_Plate9_A06


title: Sample 872_EB_repeat_Plate9_A08


title: Sample 869_EB_repeat_Plate9_A05


title: Sample 865_EB_repeat_Plate9_A01


title: Sample 861_EB_repeat_Plate8_H09


title: Sample 866_EB_repeat_Plate9_A02


title: Sample 864_EB_repeat_Plate8_H12


title: Sample 868_EB_repeat_Plate9_A04


title: Sample 862_EB_repeat_Plate8_H10


title: Sample 858_EB_repeat_Plate8_H06


title: Sample 860_EB_repeat_Plate8_H08


title: Sample 856_EB_repeat_Plate8_H04


title: Sample 859_EB_repeat_Plate8_H07


title: Sample 857_EB_repeat_Plate8_H05


title: Sample 854_EB_repeat_Plate8_H02


title: Sample 852_EB_repeat_Plate8_G12


title: Sample 851_EB_repeat_Plate8_G11


title: Sample 853_EB_repeat_Plate8_H01


title: Sample 848_EB_repeat_Plate8_G08


title: Sample 849_EB_repeat_Plate8_G09


title: Sample 846_EB_repeat_Plate8_G06


title: Sample 867_EB_repeat_Plate9_A03


title: Sample 863_EB_repeat_Plate8_H11


title: Sample 847_EB_repeat_Plate8_G07


title: Sample 850_EB_repeat_Plate8_G10


title: Sample 831_EB_repeat_Plate8_F03


title: Sample 841_EB_repeat_Plate8_G01


title: Sample 838_EB_repeat_Plate8_F10


title: Sample 842_EB_repeat_Plate8_G02


title: Sample 832_EB_repeat_Plate8_F04


title: Sample 834_EB_repeat_Plate8_F06


title: Sample 844_EB_repeat_Plate8_G04


title: Sample 837_EB_repeat_Plate8_F09


title: Sample 843_EB_repeat_Plate8_G03


title: Sample 845_EB_repeat_Plate8_G05


title: Sample 839_EB_repeat_Plate8_F11


title: Sample 840_EB_repeat_Plate8_F12


title: Sample 829_EB_repeat_Plate8_F01


title: Sample 836_EB_repeat_Plate8_F08


title: Sample 855_EB_repeat_Plate8_H03


title: Sample 830_EB_repeat_Plate8_F02


title: Sample 835_EB_repeat_Plate8_F07


title: Sample 824_EB_repeat_Plate8_E08


title: Sample 825_EB_repeat_Plate8_E09


title: Sample 828_EB_repeat_Plate8_E12


title: Sample 822_EB_repeat_Plate8_E06


title: Sample 826_EB_repeat_Plate8_E10


title: Sample 821_EB_repeat_Plate8_E05


title: Sample 820_EB_repeat_Plate8_E04


title: Sample 818_EB_repeat_Plate8_E02


title: Sample 819_EB_repeat_Plate8_E03


title: Sample 833_EB_repeat_Plate8_F05


title: Sample 827_EB_repeat_Plate8_E11


title: Sample 814_EB_repeat_Plate8_D10


title: Sample 813_EB_repeat_Plate8_D09


title: Sample 807_EB_repeat_Plate8_D03


title: Sample 811_EB_repeat_Plate8_D07


title: Sample 810_EB_repeat_Plate8_D06


title: Sample 808_EB_repeat_Plate8_D04


title: Sample 816_EB_repeat_Plate8_D12


title: Sample 809_EB_repeat_Plate8_D05


title: Sample 815_EB_repeat_Plate8_D11


title: Sample 812_EB_repeat_Plate8_D08


title: Sample 803_EB_repeat_Plate8_C11


title: Sample 804_EB_repeat_Plate8_C12


title: Sample 805_EB_repeat_Plate8_D01


title: Sample 802_EB_repeat_Plate8_C10


title: Sample 823_EB_repeat_Plate8_E07


title: Sample 798_EB_repeat_Plate8_C06


title: Sample 799_EB_repeat_Plate8_C07


title: Sample 817_EB_repeat_Plate8_E01


title: Sample 801_EB_repeat_Plate8_C09


title: Sample 800_EB_repeat_Plate8_C08


title: Sample 806_EB_repeat_Plate8_D02


title: Sample 796_EB_repeat_Plate8_C04


title: Sample 795_EB_repeat_Plate8_C03


title: Sample 790_EB_repeat_Plate8_B10


title: Sample 793_EB_repeat_Plate8_C01


title: Sample 791_EB_repeat_Plate8_B11


title: Sample 794_EB_repeat_Plate8_C02


title: Sample 789_EB_repeat_Plate8_B09


title: Sample 788_EB_repeat_Plate8_B08


title: Sample 786_EB_repeat_Plate8_B06


title: Sample 784_EB_repeat_Plate8_B04


title: Sample 785_EB_repeat_Plate8_B05


title: Sample 783_EB_repeat_Plate8_B03


title: Sample 780_EB_repeat_Plate8_A12


title: Sample 779_EB_repeat_Plate8_A11


title: Sample 778_EB_repeat_Plate8_A10


title: Sample 777_EB_repeat_Plate8_A09


title: Sample 776_EB_repeat_Plate8_A08


title: Sample 775_EB_repeat_Plate8_A07


title: Sample 787_EB_repeat_Plate8_B07


title: Sample 781_EB_repeat_Plate8_B01


title: Sample 797_EB_repeat_Plate8_C05


title: Sample 774_EB_repeat_Plate8_A06


title: Sample 792_EB_repeat_Plate8_B12


title: Sample 773_EB_repeat_Plate8_A05


title: Sample 771_EB_repeat_Plate8_A03


title: Sample 772_EB_repeat_Plate8_A04


title: Sample 769_EB_repeat_Plate8_A01


title: Sample 770_EB_repeat_Plate8_A02


title: Sample 768_EB_repeat_Plate7_H12


title: Sample 765_EB_repeat_Plate7_H09


title: Sample 763_EB_repeat_Plate7_H07


title: Sample 764_EB_repeat_Plate7_H08


title: Sample 766_EB_repeat_Plate7_H10


title: Sample 782_EB_repeat_Plate8_B02


title: Sample 762_EB_repeat_Plate7_H06


title: Sample 758_EB_repeat_Plate7_H02


title: Sample 756_EB_repeat_Plate7_G12


title: Sample 754_EB_repeat_Plate7_G10


title: Sample 757_EB_repeat_Plate7_H01


title: Sample 751_EB_repeat_Plate7_G07


title: Sample 752_EB_repeat_Plate7_G08


title: Sample 749_EB_repeat_Plate7_G05


title: Sample 760_EB_repeat_Plate7_H04


title: Sample 747_EB_repeat_Plate7_G03


title: Sample 750_EB_repeat_Plate7_G06


title: Sample 759_EB_repeat_Plate7_H03


title: Sample 755_EB_repeat_Plate7_G11


title: Sample 746_EB_repeat_Plate7_G02


title: Sample 748_EB_repeat_Plate7_G04


title: Sample 745_EB_repeat_Plate7_G01


title: Sample 744_EB_repeat_Plate7_F12


title: Sample 743_EB_repeat_Plate7_F11


title: Sample 742_EB_repeat_Plate7_F10


title: Sample 767_EB_repeat_Plate7_H11


title: Sample 741_EB_repeat_Plate7_F09


title: Sample 740_EB_repeat_Plate7_F08


title: Sample 761_EB_repeat_Plate7_H05


title: Sample 739_EB_repeat_Plate7_F07


title: Sample 738_EB_repeat_Plate7_F06


title: Sample 736_EB_repeat_Plate7_F04


title: Sample 737_EB_repeat_Plate7_F05


title: Sample 734_EB_repeat_Plate7_F02


title: Sample 735_EB_repeat_Plate7_F03


title: Sample 753_EB_repeat_Plate7_G09


title: Sample 732_EB_repeat_Plate7_E12


title: Sample 731_EB_repeat_Plate7_E11


title: Sample 729_EB_repeat_Plate7_E09


title: Sample 730_EB_repeat_Plate7_E10


title: Sample 727_EB_repeat_Plate7_E07


title: Sample 728_EB_repeat_Plate7_E08


title: Sample 720_EB_repeat_Plate7_D12


title: Sample 719_EB_repeat_Plate7_D11


title: Sample 717_EB_repeat_Plate7_D09


title: Sample 724_EB_repeat_Plate7_E04


title: Sample 723_EB_repeat_Plate7_E03


title: Sample 722_EB_repeat_Plate7_E02


title: Sample 725_EB_repeat_Plate7_E05


title: Sample 716_EB_repeat_Plate7_D08


title: Sample 718_EB_repeat_Plate7_D10


title: Sample 715_EB_repeat_Plate7_D07


title: Sample 721_EB_repeat_Plate7_E01


title: Sample 714_EB_repeat_Plate7_D06


title: Sample 733_EB_repeat_Plate7_F01


title: Sample 712_EB_repeat_Plate7_D04


title: Sample 711_EB_repeat_Plate7_D03


title: Sample 713_EB_repeat_Plate7_D05


title: Sample 710_EB_repeat_Plate7_D02


title: Sample 709_EB_repeat_Plate7_D01


title: Sample 707_EB_repeat_Plate7_C11


title: Sample 706_EB_repeat_Plate7_C10


title: Sample 708_EB_repeat_Plate7_C12


title: Sample 726_EB_repeat_Plate7_E06


title: Sample 704_EB_repeat_Plate7_C08


title: Sample 701_EB_repeat_Plate7_C05


title: Sample 702_EB_repeat_Plate7_C06


title: Sample 698_EB_repeat_Plate7_C02


title: Sample 697_EB_repeat_Plate7_C01


title: Sample 695_EB_repeat_Plate7_B11


title: Sample 692_EB_repeat_Plate7_B08


title: Sample 693_EB_repeat_Plate7_B09


title: Sample 696_EB_repeat_Plate7_B12


title: Sample 694_EB_repeat_Plate7_B10


title: Sample 690_EB_repeat_Plate7_B06


title: Sample 689_EB_repeat_Plate7_B05


title: Sample 686_EB_repeat_Plate7_B02


title: Sample 687_EB_repeat_Plate7_B03


title: Sample 705_EB_repeat_Plate7_C09


title: Sample 685_EB_repeat_Plate7_B01


title: Sample 683_EB_repeat_Plate7_A11


title: Sample 682_EB_repeat_Plate7_A10


title: Sample 688_EB_repeat_Plate7_B04


title: Sample 679_EB_repeat_Plate7_A07


title: Sample 700_EB_repeat_Plate7_C04


title: Sample 678_EB_repeat_Plate7_A06


title: Sample 677_EB_repeat_Plate7_A05


title: Sample 676_EB_repeat_Plate7_A04


title: Sample 680_EB_repeat_Plate7_A08


title: Sample 674_EB_repeat_Plate7_A02


title: Sample 675_EB_repeat_Plate7_A03


title: Sample 703_EB_repeat_Plate7_C07


title: Sample 673_EB_repeat_Plate7_A01


title: Sample 681_EB_repeat_Plate7_A09


title: Sample 691_EB_repeat_Plate7_B07


title: Sample 669_EB_repeat_Plate10_H09


title: Sample 699_EB_repeat_Plate7_C03


title: Sample 668_EB_repeat_Plate10_H08


title: Sample 666_EB_repeat_Plate10_H06


title: Sample 670_EB_repeat_Plate10_H10


title: Sample 671_EB_repeat_Plate10_H11


title: Sample 667_EB_repeat_Plate10_H07


title: Sample 684_EB_repeat_Plate7_A12


title: Sample 664_EB_repeat_Plate10_H04


title: Sample 663_EB_repeat_Plate10_H03


title: Sample 665_EB_repeat_Plate10_H05


title: Sample 661_EB_repeat_Plate10_H01


title: Sample 660_EB_repeat_Plate10_G12


title: Sample 662_EB_repeat_Plate10_H02


title: Sample 657_EB_repeat_Plate10_G09


title: Sample 658_EB_repeat_Plate10_G10


title: Sample 659_EB_repeat_Plate10_G11


title: Sample 655_EB_repeat_Plate10_G07


title: Sample 654_EB_repeat_Plate10_G06


title: Sample 656_EB_repeat_Plate10_G08


title: Sample 652_EB_repeat_Plate10_G04


title: Sample 651_EB_repeat_Plate10_G03


title: Sample 648_EB_repeat_Plate10_F12


title: Sample 649_EB_repeat_Plate10_G01


title: Sample 672_EB_repeat_Plate10_H12


title: Sample 646_EB_repeat_Plate10_F10


title: Sample 653_EB_repeat_Plate10_G05


title: Sample 642_EB_repeat_Plate10_F06


title: Sample 643_EB_repeat_Plate10_F07


title: Sample 640_EB_repeat_Plate10_F04


title: Sample 638_EB_repeat_Plate10_F02


title: Sample 639_EB_repeat_Plate10_F03


title: Sample 645_EB_repeat_Plate10_F09


title: Sample 641_EB_repeat_Plate10_F05


title: Sample 637_EB_repeat_Plate10_F01


title: Sample 634_EB_repeat_Plate10_E10


title: Sample 635_EB_repeat_Plate10_E11


title: Sample 636_EB_repeat_Plate10_E12


title: Sample 632_EB_repeat_Plate10_E08


title: Sample 633_EB_repeat_Plate10_E09


title: Sample 631_EB_repeat_Plate10_E07


title: Sample 630_EB_repeat_Plate10_E06


title: Sample 628_EB_repeat_Plate10_E04


title: Sample 647_EB_repeat_Plate10_F11


title: Sample 625_EB_repeat_Plate10_E01


title: Sample 650_EB_repeat_Plate10_G02


title: Sample 624_EB_repeat_Plate10_D12


title: Sample 626_EB_repeat_Plate10_E02


title: Sample 627_EB_repeat_Plate10_E03


title: Sample 621_EB_repeat_Plate10_D09


title: Sample 622_EB_repeat_Plate10_D10


title: Sample 618_EB_repeat_Plate10_D06


title: Sample 623_EB_repeat_Plate10_D11


title: Sample 644_EB_repeat_Plate10_F08


title: Sample 620_EB_repeat_Plate10_D08


title: Sample 619_EB_repeat_Plate10_D07


title: Sample 613_EB_repeat_Plate10_D01


title: Sample 617_EB_repeat_Plate10_D05


title: Sample 611_EB_repeat_Plate10_C11


title: Sample 629_EB_repeat_Plate10_E05


title: Sample 610_EB_repeat_Plate10_C10


title: Sample 607_EB_repeat_Plate10_C07


title: Sample 608_EB_repeat_Plate10_C08


title: Sample 612_EB_repeat_Plate10_C12


title: Sample 606_EB_repeat_Plate10_C06


title: Sample 605_EB_repeat_Plate10_C05


title: Sample 609_EB_repeat_Plate10_C09


title: Sample 602_EB_repeat_Plate10_C02


title: Sample 601_EB_repeat_Plate10_C01


title: Sample 599_EB_repeat_Plate10_B11


title: Sample 600_EB_repeat_Plate10_B12


title: Sample 598_EB_repeat_Plate10_B10


title: Sample 596_EB_repeat_Plate10_B08


title: Sample 594_EB_repeat_Plate10_B06


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title: Sample 597_EB_repeat_Plate10_B09


title: Sample 591_EB_repeat_Plate10_B03


title: Sample 592_EB_repeat_Plate10_B04


title: Sample 590_EB_repeat_Plate10_B02


title: Sample 589_EB_repeat_Plate10_B01


title: Sample 614_EB_repeat_Plate10_D02


title: Sample 616_EB_repeat_Plate10_D04


title: Sample 615_EB_repeat_Plate10_D03


title: Sample 588_EB_repeat_Plate10_A12


title: Sample 604_EB_repeat_Plate10_C04


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title: Sample 584_EB_repeat_Plate10_A08


title: Sample 583_EB_repeat_Plate10_A07


title: Sample 603_EB_repeat_Plate10_C03


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title: Sample 581_EB_repeat_Plate10_A05


title: Sample 586_EB_repeat_Plate10_A10


title: Sample 580_EB_repeat_Plate10_A04


title: Sample 579_EB_repeat_Plate10_A03


title: Sample 577_EB_repeat_Plate10_A01


title: Sample 574_EB_Plate6_H10


title: Sample 573_EB_Plate6_H09


title: Sample 576_EB_Plate6_H12


title: Sample 575_EB_Plate6_H11


title: Sample 571_EB_Plate6_H07


title: Sample 569_EB_Plate6_H05


title: Sample 570_EB_Plate6_H06


title: Sample 572_EB_Plate6_H08


title: Sample 568_EB_Plate6_H04


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title: Sample 566_EB_Plate6_H02


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title: Sample 562_EB_Plate6_G10


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title: Sample 560_EB_Plate6_G08


title: Sample 559_EB_Plate6_G07


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title: Sample 557_EB_Plate6_G05


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title: Sample 555_EB_Plate6_G03


title: Sample 558_EB_Plate6_G06


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title: Sample 536_EB_Plate6_E08


title: Sample 530_EB_Plate6_E02


title: Sample 528_EB_Plate6_D12


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title: Sample 520_EB_Plate6_D04


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title: Sample 542_EB_Plate6_F02


title: Sample 515_EB_Plate6_C11


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title: Sample 512_EB_Plate6_C08


title: Sample 508_EB_Plate6_C04


title: Sample 507_EB_Plate6_C03


title: Sample 506_EB_Plate6_C02


title: Sample 524_EB_Plate6_D08


title: Sample 503_EB_Plate6_B11


title: Sample 505_EB_Plate6_C01


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title: Sample 504_EB_Plate6_B12


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title: Sample 496_EB_Plate6_B04


title: Sample 493_EB_Plate6_B01


title: Sample 499_EB_Plate6_B07


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title: Sample 497_EB_Plate6_B05


title: Sample 529_EB_Plate6_E01


title: Sample 509_EB_Plate6_C05


title: Sample 487_EB_Plate6_A07


title: Sample 485_EB_Plate6_A05


title: Sample 490_EB_Plate6_A10


title: Sample 486_EB_Plate6_A06


title: Sample 491_EB_Plate6_A11


title: Sample 482_EB_Plate6_A02


title: Sample 483_EB_Plate6_A03


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title: Sample 484_EB_Plate6_A04


title: Sample 501_EB_Plate6_B09


title: Sample 488_EB_Plate6_A08


title: Sample 480_EB_Plate3_H12


title: Sample 477_EB_Plate3_H09


title: Sample 479_EB_Plate3_H11


title: Sample 481_EB_Plate6_A01


title: Sample 476_EB_Plate3_H08


title: Sample 478_EB_Plate3_H10


title: Sample 475_EB_Plate3_H07


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title: Sample 473_EB_Plate3_H05


title: Sample 472_EB_Plate3_H04


title: Sample 471_EB_Plate3_H03


title: Sample 466_EB_Plate3_G10


title: Sample 469_EB_Plate3_H01


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title: Sample 465_EB_Plate3_G09


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title: Sample 464_EB_Plate3_G08


title: Sample 458_EB_Plate3_G02


title: Sample 463_EB_Plate3_G07


title: Sample 456_EB_Plate3_F12


title: Sample 455_EB_Plate3_F11


title: Sample 461_EB_Plate3_G05


title: Sample 452_EB_Plate3_F08


title: Sample 454_EB_Plate3_F10


title: Sample 453_EB_Plate3_F09


title: Sample 460_EB_Plate3_G04


title: Sample 474_EB_Plate3_H06


title: Sample 448_EB_Plate3_F04


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title: Sample 450_EB_Plate3_F06


title: Sample 451_EB_Plate3_F07


title: Sample 470_EB_Plate3_H02


title: Sample 467_EB_Plate3_G11


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title: Sample 437_EB_Plate3_E05


title: Sample 435_EB_Plate3_E03


title: Sample 434_EB_Plate3_E02


title: Sample 436_EB_Plate3_E04


title: Sample 430_EB_Plate3_D10


title: Sample 429_EB_Plate3_D09


title: Sample 428_EB_Plate3_D08


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title: Sample 432_EB_Plate3_D12


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title: Sample 421_EB_Plate3_D01


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title: Sample 431_EB_Plate3_D11


title: Sample 420_EB_Plate3_C12


title: Sample 422_EB_Plate3_D02


title: Sample 441_EB_Plate3_E09


title: Sample 419_EB_Plate3_C11


title: Sample 418_EB_Plate3_C10


title: Sample 438_EB_Plate3_E06


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title: Sample 417_EB_Plate3_C09


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title: Sample 414_EB_Plate3_C06


title: Sample 411_EB_Plate3_C03


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title: Sample 410_EB_Plate3_C02


title: Sample 409_EB_Plate3_C01


title: Sample 408_EB_Plate3_B12


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title: Sample 400_EB_Plate3_B04


title: Sample 399_EB_Plate3_B03


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title: Sample 398_EB_Plate3_B02


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title: Sample 396_EB_Plate3_A12


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title: Sample 413_EB_Plate3_C05


title: Sample 389_EB_Plate3_A05


title: Sample 386_EB_Plate3_A02


title: Sample 388_EB_Plate3_A04


title: Sample 385_EB_Plate3_A01


title: Sample 380_EB_Plate2_H10


title: Sample 383_EB_plate2_H12


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title: Sample 106_EB_Plate1_E05


title: Sample 104_EB_Plate1_E04


title: Sample 128_EB_Plate1_F04


title: Sample 103_EB_plate1_E04


title: Sample 102_EB_Plate1_E03


title: Sample 101_EB_plate1_E03


title: Sample 99_EB_plate1_E02


title: Sample 125_EB_plate1_F03


title: Sample 107_EB_plate1_E06


title: Sample 96_EB_Plate1_D12


title: Sample 98_EB_Plate1_E01


title: Sample 97_EB_plate1_E01


title: Sample 100_EB_Plate1_E02


title: Sample 94_EB_Plate1_D11


title: Sample 93_EB_plate1_D11


title: Sample 92_EB_Plate1_D10


title: Sample 91_EB_plate1_D10


title: Sample 90_EB_Plate1_D09


title: Sample 110_EB_Plate1_E07


title: Sample 89_EB_plate1_D09


title: Sample 87_EB_plate1_D08


title: Sample 84_EB_Plate1_D06


title: Sample 78_EB_Plate1_D03


title: Sample 80_EB_Plate1_D04


title: Sample 82_EB_Plate1_D05


title: Sample 86_EB_Plate1_D07


title: Sample 85_EB_plate1_D07


title: Sample 77_EB_plate1_D03


title: Sample 76_EB_Plate1_D02


title: Sample 79_EB_plate1_D04


title: Sample 81_EB_plate1_D05


title: Sample 83_EB_plate1_D06


title: Sample 74_EB_Plate1_D01


title: Sample 95_EB_plate1_D12


title: Sample 72_EB_Plate1_C12


title: Sample 71_EB_plate1_C12


title: Sample 75_EB_plate1_D02


title: Sample 73_EB_plate1_D01


title: Sample 70_EB_Plate1_C11


title: Sample 66_EB_Plate1_C09


title: Sample 65_EB_plate1_C09


title: Sample 64_EB_Plate1_C08


title: Sample 88_EB_Plate1_D08


title: Sample 67_EB_plate1_C10


title: Sample 62_EB_Plate1_C07


title: Sample 61_EB_plate1_C07


title: Sample 69_EB_plate1_C11


title: Sample 57_EB_plate1_C05


title: Sample 56_EB_Plate1_C04


title: Sample 58_EB_Plate1_C05


title: Sample 68_EB_Plate1_C10


title: Sample 52_EB_Plate1_C02


title: Sample 50_EB_Plate1_C01


title: Sample 55_EB_plate1_C04


title: Sample 51_EB_plate1_C02


title: Sample 42_EB_Plate1_B09


title: Sample 47_EB_plate1_B12


title: Sample 49_EB_plate1_C01


title: Sample 45_EB_plate1_B11


title: Sample 46_EB_Plate1_B11


title: Sample 43_EB_plate1_B10


title: Sample 40_EB_Plate1_B08


title: Sample 54_EB_Plate1_C03


title: Sample 41_EB_plate1_B09


title: Sample 44_EB_Plate1_B10


title: Sample 53_EB_plate1_C03


title: Sample 38_EB_Plate1_B07


title: Sample 63_EB_plate1_C08


title: Sample 39_EB_plate1_B08


title: Sample 60_EB_Plate1_C06


title: Sample 59_EB_plate1_C06


title: Sample 37_EB_plate1_B07


title: Sample 48_EB_Plate1_B12


title: Sample 32_EB_Plate1_B04


title: Sample 34_EB_Plate1_B05


title: Sample 36_EB_Plate1_B06


title: Sample 30_EB_Plate1_B03


title: Sample 31_EB_plate1_B04


title: Sample 28_EB_Plate1_B02


title: Sample 29_EB_plate1_B03


title: Sample 23_EB_plate1_A12


title: Sample 24_EB_Plate1_A12


title: Sample 18_EB_Plate1_A09


title: Sample 20_EB_Plate1_A10


title: Sample 27_EB_plate1_B02


title: Sample 22_EB_Plate1_A11


title: Sample 25_EB_plate1_B01


title: Sample 16_EB_Plate1_A08


title: Sample 19_EB_plate1_A10


title: Sample 21_EB_plate1_A11


title: Sample 13_EB_plate1_A07


title: Sample 26_EB_Plate1_B01


title: Sample 9_EB_plate1_A05


title: Sample 12_EB_Plate1_A06


title: Sample 6_EB_Plate1_A03


title: Sample 10_EB_Plate1_A05


title: Sample 5_EB_plate1_A03


title: Sample 3_EB_plate1_A02


title: Sample 4_EB_Plate1_A02


title: Sample 7_EB_plate1_A04


title: Sample 8_EB_Plate1_A04


title: Sample 2_EB_Plate1_A01


title: Sample 15_EB_plate1_A08


title: Sample 17_EB_plate1_A09


title: Sample 1_EB_plate1_A01


title: Sample 33_EB_plate1_B05


title: Sample 14_EB_Plate1_A07


title: PS_VE_Plate9_H09

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina Nextseq500 platform using the default RTA analysis software.
BS-seq libraries were aligned to the bisuflite converted GRCm38 mouse genome using Bismark (v0.22.1) in single-end nondirectional mode. Following the removal of PCR duplicates, we retained a mean of 1.6 million reads per cell. Methylation calling and separation of endogenous methylation (from A-C-G and T-C-G trinucleotides) and chromatin accessibility (G-C-A, G-C-C and G-C-T trinucleotides) was performed with Bismark using the --NOMe option of the coverage2cytosine script.
Following our previous approach, individual CpG or GpC sites in each cell were modelled using a binomial distribution where the number of successes is the number of reads that support methylation and the number of trials is the total number of reads. A CpG methylation or GpC accessibility rate for each site and cell was calculated by maximum likelihood. The rates were subsequently rounded to the nearest integer (0 or 1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Accessibiliy and methylation table: A table of format  <chromosome><position><methylated_reads><nonmethylated_reads><binary_accessibility_status>

molecule: genomic DNA

extract_protocol: Single-cells were sorted either manually (E4.5, E5.5) or using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

tag: tissue

value: E7.5 embryo

tag: molecule subtype

value: bisulfite converted genomic DNA


title: PS_VE_Plate9_H11


title: PS_VE_Plate9_H08


title: PS_VE_Plate9_H12


title: PS_VE_Plate9_H10


title: Sample 11_EB_plate1_A06


title: PS_VE_Plate9_H07


title: PS_VE_Plate9_H06


title: PS_VE_Plate9_H05


title: PS_VE_Plate9_H02


title: PS_VE_Plate9_H01


title: PS_VE_Plate9_G12


title: PS_VE_Plate9_G11


title: PS_VE_Plate9_G10


title: PS_VE_Plate9_G08


title: PS_VE_Plate9_G07


title: PS_VE_Plate9_G02


title: PS_VE_Plate9_G04


title: PS_VE_Plate9_G03


title: PS_VE_Plate9_G09


title: PS_VE_Plate9_F12


title: PS_VE_Plate9_G05


title: PS_VE_Plate9_F11


title: PS_VE_Plate9_H04


title: PS_VE_Plate9_H03


title: PS_VE_Plate9_G01


title: PS_VE_Plate9_F10


title: PS_VE_Plate9_F09


title: PS_VE_Plate9_F07


title: PS_VE_Plate9_F06


title: PS_VE_Plate9_F05


title: PS_VE_Plate9_F08


title: PS_VE_Plate9_F02


title: PS_VE_Plate9_F03


title: PS_VE_Plate9_E11


title: PS_VE_Plate9_E12


title: PS_VE_Plate9_E09


title: PS_VE_Plate9_E07


title: PS_VE_Plate9_G06


title: PS_VE_Plate9_E06


title: PS_VE_Plate9_E04


title: PS_VE_Plate9_E02


title: PS_VE_Plate9_E05


title: PS_VE_Plate9_E03


title: PS_VE_Plate9_E08


title: PS_VE_Plate9_E01


title: PS_VE_Plate9_D11


title: PS_VE_Plate9_D07


title: PS_VE_Plate9_D08


title: PS_VE_Plate9_D09


title: PS_VE_Plate9_D10


title: PS_VE_Plate9_D12


title: PS_VE_Plate9_F04


title: PS_VE_Plate9_F01


title: PS_VE_Plate9_D03


title: PS_VE_Plate9_D01


title: PS_VE_Plate9_C11


title: PS_VE_Plate9_D06


title: PS_VE_Plate9_D04


title: PS_VE_Plate9_E10


title: PS_VE_Plate9_D05


title: PS_VE_Plate9_C10


title: PS_VE_Plate9_C12


title: PS_VE_Plate9_D02


title: PS_VE_Plate9_C09


title: PS_VE_Plate9_C07


title: PS_VE_Plate9_C05


title: PS_VE_Plate9_B12


title: PS_VE_Plate9_C03


title: PS_VE_Plate9_C02


title: PS_VE_Plate9_B11


title: PS_VE_Plate9_C01


title: PS_VE_Plate9_B10


title: PS_VE_Plate9_B07


title: PS_VE_Plate9_B04


title: PS_VE_Plate9_B08


title: PS_VE_Plate9_B03


title: PS_VE_Plate9_B09


title: PS_VE_Plate9_B06


title: PS_VE_Plate9_C08


title: PS_VE_Plate9_B05


title: PS_VE_Plate9_C06


title: PS_VE_Plate9_B02


title: Sample 35_EB_plate1_B06


title: PS_VE_Plate9_A10


title: PS_VE_Plate9_A12


title: PS_VE_Plate9_A07


title: PS_VE_Plate9_A04


title: PS_VE_Plate9_A11


title: PS_VE_Plate9_A05


title: PS_VE_Plate9_A06


title: PS_VE_Plate9_A03


title: PS_VE_Plate9_B01


title: PS_VE_Plate9_A08


title: PS_VE_Plate9_A02


title: PS_VE_Plate9_A09


title: PS_VE_Plate5_H12


title: PS_VE_Plate9_C04


title: PS_VE_Plate5_H11


title: PS_VE_Plate5_H09


title: PS_VE_Plate9_A01


title: PS_VE_Plate5_H10


title: PS_VE_Plate5_H08


title: PS_VE_Plate5_H06


title: PS_VE_Plate5_H07


title: PS_VE_Plate5_H05


title: PS_VE_Plate5_H04


title: PS_VE_Plate5_G11


title: PS_VE_Plate5_H01


title: PS_VE_Plate5_H03


title: PS_VE_Plate5_H02


title: PS_VE_Plate5_G12


title: PS_VE_Plate5_G07


title: PS_VE_Plate5_G08


title: PS_VE_Plate5_G04


title: PS_VE_Plate5_G10


title: PS_VE_Plate5_G06


title: PS_VE_Plate5_G03


title: PS_VE_Plate5_F11


title: PS_VE_Plate5_F10


title: PS_VE_Plate5_G01


title: PS_VE_Plate5_F09


title: PS_VE_Plate5_F08


title: PS_VE_Plate5_F06


title: PS_VE_Plate5_F07


title: PS_VE_Plate5_F04


title: PS_VE_Plate5_F05


title: PS_VE_Plate5_F02


title: PS_VE_Plate5_F01


title: PS_VE_Plate5_E12


title: PS_VE_Plate5_G05


title: PS_VE_Plate5_G02


title: PS_VE_Plate5_E11


title: PS_VE_Plate5_G09


title: PS_VE_Plate5_E07


title: PS_VE_Plate5_E10


title: PS_VE_Plate5_E08


title: PS_VE_Plate5_E05


title: PS_VE_Plate5_E09


title: PS_VE_Plate5_E06


title: PS_VE_Plate5_E04


title: PS_VE_Plate5_E03


title: PS_VE_Plate5_E02


title: PS_VE_Plate5_E01


title: PS_VE_Plate5_F12


title: PS_VE_Plate5_D12


title: PS_VE_Plate5_D11


title: PS_VE_Plate5_F03


title: PS_VE_Plate5_D08


title: PS_VE_Plate5_D07


title: PS_VE_Plate5_D06


title: PS_VE_Plate5_D05


title: PS_VE_Plate5_D04


title: PS_VE_Plate5_D03


title: PS_VE_Plate5_D02


title: PS_VE_Plate5_D09


title: PS_VE_Plate5_D01


title: PS_VE_Plate5_C12


title: PS_VE_Plate5_C11


title: PS_VE_Plate5_C10


title: PS_VE_Plate5_C09


title: PS_VE_Plate5_D10


title: PS_VE_Plate5_C05


title: PS_VE_Plate5_C08


title: PS_VE_Plate5_B12


title: PS_VE_Plate5_C04


title: PS_VE_Plate5_B10


title: PS_VE_Plate5_C07


title: PS_VE_Plate5_C03


title: PS_VE_Plate5_C01


title: PS_VE_Plate5_B09


title: PS_VE_Plate5_C06


title: PS_VE_Plate5_B08


title: PS_VE_Plate5_B05


title: PS_VE_Plate5_B06


title: PS_VE_Plate5_B07


title: PS_VE_Plate5_B04


title: PS_VE_Plate5_B01


title: PS_VE_Plate5_C02


title: PS_VE_Plate5_B02


title: PS_VE_Plate5_A12


title: PS_VE_Plate5_A11


title: PS_VE_Plate5_A09


title: PS_VE_Plate5_A10


title: PS_VE_Plate5_B03


title: PS_VE_Plate5_B11


title: PS_VE_Plate5_A07


title: PS_VE_Plate5_A05


title: PS_VE_Plate5_A06


title: PS_VE_Plate5_A04


title: PS_VE_Plate1_H10


title: PS_VE_Plate5_A02


title: PS_VE_Plate5_A03


title: PS_VE_Plate1_H12


title: PS_VE_Plate5_A01


title: PS_VE_Plate1_H08


title: PS_VE_Plate1_H09


title: PS_VE_Plate1_H06


title: PS_VE_Plate1_H04


title: PS_VE_Plate1_H05


title: PS_VE_Plate1_H11


title: PS_VE_Plate1_H02


title: PS_VE_Plate1_H03


title: PS_VE_Plate5_A08


title: PS_VE_Plate1_G12


title: PS_VE_Plate1_G09


title: PS_VE_Plate1_G05


title: PS_VE_Plate1_G08


title: PS_VE_Plate1_G06


title: PS_VE_Plate1_G10


title: PS_VE_Plate1_G07


title: PS_VE_Plate1_G04


title: PS_VE_Plate1_H07


title: PS_VE_Plate1_G03


title: PS_VE_Plate1_F11


title: PS_VE_Plate1_G01


title: PS_VE_Plate1_H01


title: PS_VE_Plate1_G02


title: PS_VE_Plate1_F06


title: PS_VE_Plate1_F08


title: PS_VE_Plate1_G11


title: PS_VE_Plate1_F04


title: PS_VE_Plate1_F09


title: PS_VE_Plate1_F05


title: PS_VE_Plate1_F07


title: PS_VE_Plate1_F02


title: PS_VE_Plate1_E12


title: PS_VE_Plate1_E10


title: PS_VE_Plate1_E09


title: PS_VE_Plate1_F01


title: PS_VE_Plate1_F12


title: PS_VE_Plate1_E11


title: PS_VE_Plate1_E08


title: PS_VE_Plate1_E05


title: PS_VE_Plate1_E02


title: PS_VE_Plate1_E06


title: PS_VE_Plate1_E04


title: PS_VE_Plate1_E03


title: PS_VE_Plate1_E01


title: PS_VE_Plate1_F10


title: PS_VE_Plate1_F03


title: PS_VE_Plate1_D12


title: PS_VE_Plate1_D10


title: PS_VE_Plate1_D11


title: PS_VE_Plate1_E07


title: PS_VE_Plate1_C09


title: PS_VE_Plate1_D03


title: PS_VE_Plate1_D09


title: PS_VE_Plate1_D08


title: PS_VE_Plate1_C10


title: PS_VE_Plate1_D06


title: PS_VE_Plate1_C12


title: PS_VE_Plate1_C07


title: PS_VE_Plate1_C06


title: PS_VE_Plate1_D01


title: PS_VE_Plate1_D02


title: PS_VE_Plate1_B11


title: PS_VE_Plate1_D04


title: PS_VE_Plate1_C11


title: PS_VE_Plate1_D07


title: PS_VE_Plate1_D05


title: PS_VE_Plate1_B10


title: PS_VE_Plate1_B08


title: PS_VE_Plate1_C03


title: PS_VE_Plate1_C08


title: PS_VE_Plate1_B07


title: PS_VE_Plate1_B05


title: PS_VE_Plate1_B06


title: PS_VE_Plate1_B09


title: PS_VE_Plate1_C02


title: PS_VE_Plate1_C04


title: PS_VE_Plate1_C01


title: PS_VE_Plate1_B12


title: PS_VE_Plate1_C05


title: PS_VE_Plate1_B01


title: PS_VE_Plate1_A12


title: PS_VE_Plate1_B02


title: PS_VE_Plate1_A11


title: PS_VE_Plate1_B04


title: PS_VE_Plate1_A10


title: PS_VE_Plate1_A09


title: PS_VE_Plate1_A04


title: E7.5_Plate16_H09


title: PS_VE_Plate1_A02


title: PS_VE_Plate1_A07


title: PS_VE_Plate1_A03


title: PS_VE_Plate1_A05


title: E7.5_Plate16_F09


title: PS_VE_Plate1_A06


title: E7.5_Plate16_G02


title: E7.5_Plate16_G03


title: E7.5_Plate16_F08


title: PS_VE_Plate1_B03


title: E7.5_Plate16_G04


title: PS_VE_Plate1_A01


title: PS_VE_Plate1_A08


title: E7.5_Plate16_G12


title: E7.5_Plate16_G06


title: E7.5_Plate16_G01


title: E7.5_Plate16_E08


title: E7.5_Plate16_E01


title: E7.5_Plate16_D01


title: E7.5_Plate16_E06


title: E7.5_Plate16_F01


title: E7.5_Plate16_C09


title: E7.5_Plate16_C08


title: E7.5_Plate16_A08


title: E7.5_Plate16_A01


title: E7.5_Plate16_B07


title: E7.5_Plate15_H09


title: E7.5_Plate16_C01


title: E7.5_Plate16_A06


title: E7.5_Plate15_G08


title: E7.5_Plate15_G12


title: E7.5_Plate15_G07


title: E7.5_Plate15_G03


title: E7.5_Plate15_G09


title: E7.5_Plate15_D09


title: E7.5_Plate15_E03


title: E7.5_Plate15_C09


title: E7.5_Plate15_E09


title: E7.5_Plate15_E06


title: E7.5_Plate15_B12


title: E7.5_Plate15_B09


title: E7.5_Plate15_C12


title: E7.5_Plate15_A12


title: E7.5_Plate15_A04


title: E7.5_Plate15_B03


title: E7.5_Plate15_A09


title: E7.5_Plate16_A02


title: E7.5_Plate15_B07


title: E7.5_Plate14_G08


title: E7.5_Plate14_E06


title: E7.5_Plate15_F09


title: E7.5_Plate14_F04


title: E7.5_Plate14_F01


title: E7.5_Plate14_E01


title: E7.5_Plate14_D06


title: E7.5_Plate14_F11


title: E7.5_Plate14_D01


title: E7.5_Plate15_C03


title: E7.5_Plate14_C08


title: E7.5_Plate14_C04


title: E7.5_Plate14_G01


title: E7.5_Plate14_C01


title: E7.5_Plate14_C02


title: E7.5_Plate14_A10


title: E7.5_Plate14_A01


title: E7.5_Plate14_A12


title: E7.5_Plate14_F06


title: E7.5_Plate14_B06


title: E7.5_Plate13_G12


title: E7.5_Plate14_B01


title: E7.5_Plate14_B03


title: E7.5_Plate13_F10


title: E7.5_Plate13_H09


title: E7.5_Plate13_F09


title: E7.5_Plate13_F04


title: E7.5_Plate13_G09


title: E7.5_Plate14_D09


title: E7.5_Plate13_D09


title: E7.5_Plate13_D12


title: E7.5_Plate13_E09


title: E7.5_Plate13_D07


title: E7.5_Plate13_B10


title: E7.5_Plate13_B12


title: E7.5_Plate14_C03


title: E7.5_Plate13_C03


title: E7.5_Plate13_C09


title: E7.5_Plate13_C11


title: E7.5_Plate13_A09


title: E7.5_Plate13_B04


title: E7.5_Plate12_G11


title: E7.5_Plate12_H02


title: E7.5_Plate12_E12


title: E7.5_Plate11_B04


title: E7.5_Plate11_E10


title: E7.5_Plate11_B01


title: E7.5_Plate11_G09


title: TET_EB_repeat_Plate9_H09

extract_protocol:
Single-cells were sorted  using flow cytometry into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing.
Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

tag: cell type

tag: developmental stage/timepoint


title: TET_EB_repeat_Plate9_H08


title: TET_EB_repeat_Plate9_H10


title: E7.5_Plate11_A03


title: TET_EB_repeat_Plate9_H11


title: E7.5_Plate13_D08


title: TET_EB_repeat_Plate9_H12


title: TET_EB_repeat_Plate9_H06


title: TET_EB_repeat_Plate9_H07


title: E7.5_Plate13_B09


title: TET_EB_repeat_Plate9_H04


title: TET_EB_repeat_Plate9_H02


title: TET_EB_repeat_Plate9_H05


title: TET_EB_repeat_Plate9_G10


title: TET_EB_repeat_Plate9_G12


title: TET_EB_repeat_Plate9_H01


title: TET_EB_repeat_Plate9_G08


title: TET_EB_repeat_Plate9_G09


title: E7.5_Plate11_F03


title: E7.5_Plate11_E06


title: TET_EB_repeat_Plate9_G06


title: TET_EB_repeat_Plate9_G05


title: TET_EB_repeat_Plate9_G11


title: TET_EB_repeat_Plate9_G04


title: TET_EB_repeat_Plate9_G07


title: TET_EB_repeat_Plate9_G01


title: TET_EB_repeat_Plate9_G03


title: TET_EB_repeat_Plate9_F11


title: TET_EB_repeat_Plate9_F05


title: TET_EB_repeat_Plate9_F06


title: TET_EB_repeat_Plate9_F08


title: TET_EB_repeat_Plate9_F10


title: TET_EB_repeat_Plate9_F07


title: TET_EB_repeat_Plate9_F09


title: TET_EB_repeat_Plate9_F02


title: TET_EB_repeat_Plate9_F03


title: TET_EB_repeat_Plate9_H03


title: TET_EB_repeat_Plate9_F04


title: TET_EB_repeat_Plate9_E12


title: TET_EB_repeat_Plate9_E11


title: TET_EB_repeat_Plate9_F01


title: TET_EB_repeat_Plate9_E10


title: TET_EB_repeat_Plate9_E09


title: TET_EB_repeat_Plate9_E08


title: TET_EB_repeat_Plate9_E05


title: TET_EB_repeat_Plate9_E02


title: TET_EB_repeat_Plate9_E03


title: TET_EB_repeat_Plate9_E04


title: TET_EB_repeat_Plate9_E07


title: TET_EB_repeat_Plate9_D12


title: TET_EB_repeat_Plate9_E06


title: TET_EB_repeat_Plate9_G02


title: TET_EB_repeat_Plate9_F12


title: TET_EB_repeat_Plate9_E01


title: TET_EB_repeat_Plate9_D09


title: TET_EB_repeat_Plate9_D08


title: TET_EB_repeat_Plate9_D06


title: TET_EB_repeat_Plate9_D07


title: TET_EB_repeat_Plate9_D10


title: TET_EB_repeat_Plate9_C11


title: TET_EB_repeat_Plate9_D01


title: TET_EB_repeat_Plate9_D02


title: TET_EB_repeat_Plate9_C12


title: TET_EB_repeat_Plate9_D04


title: TET_EB_repeat_Plate9_D05


title: TET_EB_repeat_Plate9_C10


title: TET_EB_repeat_Plate9_C09


title: TET_EB_repeat_Plate9_C08


title: TET_EB_repeat_Plate9_D03


title: TET_EB_repeat_Plate9_C06


title: TET_EB_repeat_Plate9_C07


title: TET_EB_repeat_Plate9_D11


title: TET_EB_repeat_Plate9_C03


title: TET_EB_repeat_Plate9_C02


title: TET_EB_repeat_Plate9_C05


title: TET_EB_repeat_Plate9_B12


title: TET_EB_repeat_Plate9_B08


title: TET_EB_repeat_Plate9_B07


title: TET_EB_repeat_Plate9_B10


title: TET_EB_repeat_Plate9_B06


title: TET_EB_repeat_Plate9_B05


title: TET_EB_repeat_Plate9_B04


title: TET_EB_repeat_Plate9_B03


title: TET_EB_repeat_Plate9_B01


title: TET_EB_repeat_Plate9_A11


title: TET_EB_repeat_Plate9_A10


title: TET_EB_repeat_Plate9_A09


title: TET_EB_repeat_Plate9_A12


title: TET_EB_repeat_Plate9_A07


title: TET_EB_repeat_Plate9_A06


title: TET_EB_repeat_Plate9_A08


title: TET_EB_repeat_Plate9_B02


title: TET_EB_repeat_Plate9_C04


title: TET_EB_repeat_Plate9_A03


title: TET_EB_repeat_Plate9_A02


title: TET_EB_repeat_Plate9_A01


title: TET_EB_repeat_Plate9_C01


title: TET_EB_repeat_Plate9_B09


title: TET_EB_repeat_Plate9_A05


title: TET_EB_repeat_Plate2_H12


title: TET_EB_repeat_Plate9_B11


title: TET_EB_repeat_Plate2_H11


title: TET_EB_repeat_Plate2_H08


title: TET_EB_repeat_Plate2_H09


title: TET_EB_repeat_Plate2_H06


title: TET_EB_repeat_Plate2_H05


title: TET_EB_repeat_Plate2_H10


title: TET_EB_repeat_Plate2_H03


title: TET_EB_repeat_Plate2_H04


title: TET_EB_repeat_Plate2_H07


title: TET_EB_repeat_Plate9_A04


title: TET_EB_repeat_Plate2_H01


title: TET_EB_repeat_Plate2_G11


title: TET_EB_repeat_Plate2_G10


title: TET_EB_repeat_Plate2_G12


title: TET_EB_repeat_Plate2_G07


title: TET_EB_repeat_Plate2_G03


title: TET_EB_repeat_Plate2_G09


title: TET_EB_repeat_Plate2_G05


title: TET_EB_repeat_Plate2_G02


title: TET_EB_repeat_Plate2_G06


title: TET_EB_repeat_Plate2_G01


title: TET_EB_repeat_Plate2_F10


title: TET_EB_repeat_Plate2_F11


title: TET_EB_repeat_Plate2_F12


title: TET_EB_repeat_Plate2_G04


title: TET_EB_repeat_Plate2_F09


title: TET_EB_repeat_Plate2_F07


title: TET_EB_repeat_Plate2_F06


title: TET_EB_repeat_Plate2_G08


title: TET_EB_repeat_Plate2_F08


title: TET_EB_repeat_Plate2_F05


title: TET_EB_repeat_Plate2_F02


title: TET_EB_repeat_Plate2_F04


title: TET_EB_repeat_Plate2_F03


title: TET_EB_repeat_Plate2_H02


title: TET_EB_repeat_Plate2_F01


title: TET_EB_repeat_Plate2_E11


title: TET_EB_repeat_Plate2_E10


title: TET_EB_repeat_Plate2_E09


title: TET_EB_repeat_Plate2_E12


title: TET_EB_repeat_Plate2_E07


title: TET_EB_repeat_Plate2_E08


title: TET_EB_repeat_Plate2_E06


title: TET_EB_repeat_Plate2_E01


title: TET_EB_repeat_Plate2_E02


title: TET_EB_repeat_Plate2_D12


title: TET_EB_repeat_Plate2_D11


title: TET_EB_repeat_Plate2_E03


title: TET_EB_repeat_Plate2_D06


title: TET_EB_repeat_Plate2_D07


title: TET_EB_repeat_Plate2_D05


title: TET_EB_repeat_Plate2_D09


title: TET_EB_repeat_Plate2_D04


title: TET_EB_repeat_Plate2_D02


title: TET_EB_repeat_Plate2_D03


title: TET_EB_repeat_Plate2_D01


title: TET_EB_repeat_Plate2_D08


title: TET_EB_repeat_Plate2_C12


title: TET_EB_repeat_Plate2_C08


title: TET_EB_repeat_Plate2_C10


title: TET_EB_repeat_Plate2_E05


title: TET_EB_repeat_Plate2_C05


title: TET_EB_repeat_Plate2_E04


title: TET_EB_repeat_Plate2_C03


title: TET_EB_repeat_Plate2_C04


title: TET_EB_repeat_Plate2_C02


title: TET_EB_repeat_Plate2_D10


title: TET_EB_repeat_Plate2_B12


title: TET_EB_repeat_Plate2_C01


title: TET_EB_repeat_Plate2_B11


title: TET_EB_repeat_Plate2_B10


title: TET_EB_repeat_Plate2_B09


title: TET_EB_repeat_Plate2_C09


title: TET_EB_repeat_Plate2_B08


title: TET_EB_repeat_Plate2_B05


title: TET_EB_repeat_Plate2_B06


title: TET_EB_repeat_Plate2_C11


title: TET_EB_repeat_Plate2_B07


title: TET_EB_repeat_Plate2_B04


title: TET_EB_repeat_Plate2_B03


title: TET_EB_repeat_Plate2_C07


title: TET_EB_repeat_Plate2_C06


title: TET_EB_repeat_Plate2_B01


title: TET_EB_repeat_Plate2_A12


title: TET_EB_repeat_Plate2_A11


title: TET_EB_repeat_Plate2_A08


title: TET_EB_repeat_Plate2_A10


title: TET_EB_repeat_Plate2_A06


title: TET_EB_repeat_Plate2_A07


title: TET_EB_repeat_Plate2_A02


title: TET_EB_repeat_Plate2_A05


title: TET_EB_repeat_Plate2_A01


title: pGHR10-1

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

country: USA

institute: Massachusetts General Hospital

description: Tumor microglia EV-GFP negative

data_processing:
Total RNA was isolated and sequencing libraries were made using SMARTer Ultra Low Input RNA Kit. Sequencing was done using an Illumina NextSeq and bioinformatic analysis was performed using DESeq2 in R
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and removed.
The uniquely aligned reads were then counted against Gencode’s GRCm38.p3 GTF annotations using htseq-count in the intersection-strict mode
Data analysis of mapped counts was performed in R 3.2.3 using the DESeq2 package
Samples with less than 6000 genes with at least 5 mapped reads were excluded from analysis
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Mouse brain

extract_protocol:
Microglia are isolated from mouse brain following manufacturings protocol of Neural P kit (Miltenyi Biotec). Total RNA was isolated using RNeasy Plus Micro kit (Qiagen) using the total RNA isolation protocol.
Total RNA was isolated and sequencing libraries following SMARTer Ultra Low Input RNA Kit. Sequencing was done using an Illumina NextSeq

value: miR-21 null

tag: age

value: 12 -18 weeks

value: microglia


title: pGHR9-2

description: Tumor microglia EV-GFP postive


title: pGHR8-2

description: Tumor microglia EV-GFP postive


title: pGHR10-2

description: Tumor microglia EV-GFP postive


title: TET_EB_repeat_Plate2_A04


title: mock7

description: Control microglia


title: TET_EB_repeat_Plate2_A09


title: HOM3_0.5ng

city: Lexington

first: Hualin

last: Xi

address: 34 webb st

institute: AbbVie

description: the indicated amound of RNA (_ng) was added to the Reverse Transcription reaction.

data_processing:
aligned to hg19 reference genome using STAR v2.4
count uniquely aligned reads per gene using FeatureCount from Subread package and gencode v19 as the gene model annotation

source_name: Frontal Cortex

extract_protocol:
3-month-old GFAP-IL6 homozygous or wild-type mice were euthanized by cervical dislocation followed by decapitation. Frontal cortex was dissected and snap-frozen in RNAse-free tubes on dry ice. Total RNA was isolated by Trizol-chloroform extraction, followed by RNeasy clean-up.
3'Pool-seq

value: Frontal Cortex

value: 3 month post-natal

tag: genotype


title: WT2_0.5ng


title: WT3_0.5ng


title: HOM2_0.5ng


title: HOM1_0.5ng


title: WT4_0.5ng


title: HOM4_1ng


title: HOM3_1ng


title: HOM2_1ng


title: HOM1_1ng


title: TET_EB_repeat_Plate2_A03


title: WT1_0.5ng


title: HOM4_10ng


title: WT4_1ng


title: WT3_1ng


title: WT2_1ng


title: HOM3_10ng


title: pGHR9-1

description: Tumor microglia EV-GFP negative


title: HOM4_0.5ng


title: mock6

description: Control microglia


title: HOM1_10ng


title: pGHR8-1

description: Tumor microglia EV-GFP negative


title: WT1_10ng


title: TET_EB_repeat_Plate2_B02


title: HOM2_10ng


title: WT2_10ng


title: WT4_10ng


title: WT3_10ng


title: HOM1_50ng


title: HOM2_50ng


title: WT3_1ngB

description: the indicated amound of cDNA (_ng) was added to the tagmentation reaction.


title: WT3_50ng


title: HOM3_1ngB


title: HOM3_50ng


title: WT4_50ng


title: WT1_1ng


title: HOM2_1ngB


title: WT2_50ng


title: HOM4_50ng


title: WT1_50ng


title: WT2_1ngB


title: HOM1_1ngB


title: WT1_1ngB


title: mock8

description: Control microglia


title: HOM3_2ngB


title: HOM2_2ngB


title: WT3_2ngB


title: HOM3_1ngA


title: WT1_2ngB


title: WT2_2ngB


title: HOM2_1ngA


title: WT3_1ngA


title: HOM1_1ngA


title: HOM2_2ngA


title: WT2_1ngA


title: HOM3_2ngA


title: HOM1_2ngA


title: WT3_2ngA


title: HOM-ctx-1

extract_protocol:
3-month-old GFAP-IL6 homozygous or wild-type mice were euthanized by cervical dislocation followed by decapitation. Frontal cortex was dissected and snap-frozen in RNAse-free tubes on dry ice. Total RNA was isolated by Trizol-chloroform extraction, followed by RNeasy clean-up.
Illumina TruSeq mRNA library preparation


title: WT-ctx-2


title: HOM-ctx-2


title: WT-ctx-3


title: HOM-ctx-3


title: WT1_2ngA


title: WT2_2ngA


title: E7.5_Plate4_H5 (scBS-Seq)

data_processing:
Libraries were sequenced on the Illumina Nextseq 500 platform using the default RTA analysis software.
BS-seq libraries were aligned to the bisuflite converted GRCm38 mouse genome using Bismark (v0.19.1) in single-end nondirectional mode. Following the removal of PCR duplicates, we retained a mean of 1.6 million reads per cell. Methylation calling and separation of endogenous methylation (from A-C-G and T-C-G trinucleotides) and chromatin accessibility (G-C-A, G-C-C and G-C-T trinucleotides) was performed with Bismark using the --NOMe option of the coverage2cytosine script.
Following our previous approach, individual CpG or GpC sites in each cell were modelled using a binomial distribution where the number of successes is the number of reads that support methylation and the number of trials is the total number of reads. A CpG methylation or GpC accessibility rate for each site and cell was calculated by maximum likelihood. The rates were subsequently rounded to the nearest integer (0 or 1).
Genome_build: GRCm38
Supplementary_files_format_and_content: [Accessibility file]  A table of format  <chromosome><position><methylated_reads><nonmethylated_reads><binary_accessibility_status>
Supplementary_files_format_and_content: [Methylation file]  A table of format  <chromosome><position><methylated_reads><nonmethylated_reads><binary_methylation_status>

tag: sample type

value: single cell


title: HOM1_2ngB


title: E7.5_Plate4_H6 (scBS-Seq)


title: E7.5_Plate4_H9 (scBS-Seq)


title: E7.5_Plate4_H7 (scBS-Seq)


title: E7.5_Plate4_H4 (scBS-Seq)


title: E7.5_Plate4_H8 (scBS-Seq)


title: E7.5_Plate4_H1 (scBS-Seq)


title: E7.5_Plate4_H2 (scBS-Seq)


title: E7.5_Plate4_H3 (scBS-Seq)


title: E7.5_Plate4_H11 (scBS-Seq)


title: E7.5_Plate4_H10 (scBS-Seq)


title: E7.5_Plate4_G9 (scBS-Seq)


title: E7.5_Plate4_G8 (scBS-Seq)


title: E7.5_Plate4_G7 (scBS-Seq)


title: E7.5_Plate4_G5 (scBS-Seq)


title: E7.5_Plate4_G6 (scBS-Seq)


title: E7.5_Plate4_G4 (scBS-Seq)


title: WT1_1ngA


title: E7.5_Plate4_F8 (scBS-Seq)


title: E7.5_Plate4_G2 (scBS-Seq)


title: E7.5_Plate4_F9 (scBS-Seq)


title: E7.5_Plate4_G3 (scBS-Seq)


title: E7.5_Plate4_F6 (scBS-Seq)


title: E7.5_Plate4_G11 (scBS-Seq)


title: E7.5_Plate4_H12 (scBS-Seq)


title: E7.5_Plate4_G10 (scBS-Seq)


title: E7.5_Plate4_G1 (scBS-Seq)


title: E7.5_Plate4_G12 (scBS-Seq)


title: E7.5_Plate4_F1 (scBS-Seq)


title: E7.5_Plate4_F3 (scBS-Seq)


title: E7.5_Plate4_F12 (scBS-Seq)


title: E7.5_Plate4_F10 (scBS-Seq)


title: E7.5_Plate4_F11 (scBS-Seq)


title: E7.5_Plate4_E8 (scBS-Seq)


title: E7.5_Plate4_E7 (scBS-Seq)


title: E7.5_Plate4_F5 (scBS-Seq)


title: E7.5_Plate4_E5 (scBS-Seq)


title: E7.5_Plate4_E6 (scBS-Seq)


title: E7.5_Plate4_E4 (scBS-Seq)