title: Primary intestinal epithelial cells from wild type mice Run1_S54_WT_M1_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S59_WT_M1_TA

status: Public on Jul 13 2019

type: SRA

city: Boston

first: Adam

last: Haber

state: Massachusetts

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

country: USA

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

library_source: transcriptomic

data_processing:
Read alignment to genome and transcriptome (bowtie, tophat)
Gene expression estimation (RSEM)
PCA (prcomp in R)
kNN-based graph clustering (R code)
Supplementary_files_format_and_content: TPM expression values for each gene (rows) in each cell (columns)

molecule: total RNA

organism: Mus musculus

source_name: WT mouse intestinal epithelial cells

extract_protocol:
SMART-Seq2
10X Genomics Chromium Prep

tag: strain

tag: genotype

value: WT


title: Primary intestinal epithelial cells from wild type mice Run1_S55_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S53_WT_M1_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S52_WT_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S50_WT_M1_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S51_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S4_WT_M1_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S49_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S46_WT_M1_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S62_WT_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S44_WT_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S380_KO_M1_Enterocyte.prog.early

source_name: ATG16L2 KO mouse intestinal epithelial cells


title: Primary intestinal epithelial cells from wild type mice Run1_S42_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S41_WT_M1_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S37_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S40_WT_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S39_WT_M1_Paneth


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S376_KO_M1_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S374_KO_M1_Tuft


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S375_KO_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S373_KO_M1_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S377_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S378_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S371_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S382_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S370_KO_M1_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S43_WT_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S379_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S368_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S36_WT_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S369_KO_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S38_WT_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S366_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S367_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S364_KO_M1_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S363_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S381_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S362_KO_M1_TA


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title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S352_KO_M1_Paneth


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S354_KO_M1_Stem


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title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S355_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S346_KO_M1_TA


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title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S345_KO_M1_Stem


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title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S343_KO_M1_Stem


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title: Primary intestinal epithelial cells from wild type mice Run1_S33_WT_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S340_KO_M1_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S338_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S339_KO_M1_Enteroendocrine


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title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S337_KO_M1_Enterocyte.prog.early


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title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S358_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S333_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S353_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S351_KO_M1_Tuft


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S332_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S348_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S32_WT_M1_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S329_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S334_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S34_WT_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S324_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S331_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S325_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S330_KO_M1_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S327_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S342_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S323_KO_M1_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S322_KO_M1_Paneth


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S313_KO_M1_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S317_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S314_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S312_KO_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S31_WT_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S316_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S320_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S315_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S311_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S310_KO_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S30_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S319_KO_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S307_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S309_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S308_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S303_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S300_KO_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S2_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S29_WT_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S305_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S318_KO_M1_Paneth


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S302_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S293_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S299_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S304_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S301_KO_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S290_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S297_KO_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S296_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S294_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S284_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S282_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S286_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S279_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S278_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S28_WT_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S291_KO_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S292_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S283_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S277_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S285_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S275_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S289_KO_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S281_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S273_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S280_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S269_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S267_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S265_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S271_KO_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S27_WT_M1_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S276_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S298_KO_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S272_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S268_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S270_KO_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S26_WT_M1_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S266_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S262_KO_M2_Paneth


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S258_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S274_KO_M2_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S252_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S251_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S256_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S255_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S249_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S248_KO_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S24_WT_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S254_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S259_KO_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S25_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S264_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S245_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S263_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S260_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S244_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S246_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S242_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S247_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S243_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S240_KO_M2_Enterocyte


title: Primary intestinal epithelial cells from wild type mice Run1_S23_WT_M1_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S250_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S239_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S241_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S234_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S233_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S236_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S232_KO_M2_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S231_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S230_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S229_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S228_KO_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S22_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S227_KO_M2_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S226_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S224_KO_M2_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S223_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S222_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S221_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S220_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S21_WT_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S217_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S216_KO_M2_Paneth


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S214_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S213_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S215_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S210_KO_M2_Enterocyte


title: Primary intestinal epithelial cells from wild type mice Run1_S20_WT_M1_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S237_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S212_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S225_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S211_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S208_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S206_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S204_KO_M2_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S207_KO_M2_Goblet


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S205_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S203_KO_M2_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S197_KO_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S18_WT_M1_Enteroendocrine


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S200_KO_M2_TA


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S202_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S201_KO_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S19_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S199_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S198_KO_M2_Stem


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S218_KO_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S185_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S183_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S189_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S179_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S187_WT_M2_Enterocyte


title: Primary intestinal epithelial cells from wild type mice Run1_S184_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S176_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S174_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S177_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S190_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S172_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S186_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S209_KO_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S171_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S170_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S167_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S17_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S182_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S175_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S178_WT_M2_Stem


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title: Primary intestinal epithelial cells from wild type mice Run1_S173_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S152_WT_M2_Enterocyte


title: Primary intestinal epithelial cells from ATG16L2 KO mice Run1_S257_KO_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S16_WT_M1_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S14_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S146_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S169_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S166_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S168_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S165_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S143_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S140_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S13_WT_M1_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S163_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S162_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S139_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S160_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S138_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S136_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S15_WT_M1_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S133_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S159_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S134_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S158_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S154_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S128_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S127_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S126_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S153_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S129_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S148_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S135_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S147_WT_M2_Enterocyte


title: Primary intestinal epithelial cells from wild type mice Run1_S145_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S151_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S118_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S119_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S122_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S116_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S144_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S130_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S156_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S142_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S141_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S111_WT_M2_Enterocyte


title: Primary intestinal epithelial cells from wild type mice Run1_S114_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S120_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S10_WT_M1_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S150_WT_M2_Paneth


title: Primary intestinal epithelial cells from wild type mice Run1_S112_WT_M2_TA


title: Primary intestinal epithelial cells from wild type mice Run1_S137_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S109_WT_M2_Enterocyte.prog.early


title: MEC1_RNU1_3_WT_B

city: Toronto

first: Shimin

last: Shuai

state: ON

address: MaRS Centre, 661 University Avenue Suite 510

country: Canada

institute: ONTARIO INSTITUTE FOR CANCER RESEARCH

data_processing:
Reads aligned with STAR-2.5.4b
Splice junctions quantified with STAR-2.5.4b during the mapping
Gene-level read counts generated by htseq-count (v0.9.1)
Raw splice junctions were clustered by leafCutter (v0.2.8)
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each sample
Supplementary_files_format_and_content: CLL_cell_line.htseq-count.collapsed.tab.gz: Gene-level read counts
Supplementary_files_format_and_content: CLL_cell_line_splice_junction_read_counts.txt.gz: splice junction read counts

organism: Homo sapiens

source_name: MEC1 cell line

extract_protocol:
total RNA from cell lines was extracted with the Trizol method
stranded total RNA-Seq libraries with ribodepletion were prepared for all samples

tag: cell line

tag: cell type

value: chronic lymphocytic leukemia


title: MEC1_RNU1_3_WT_A


title: Primary intestinal epithelial cells from wild type mice Run1_S125_WT_M2_Enterocyte.prog.late


title: Primary intestinal epithelial cells from wild type mice Run1_S131_WT_M2_Enterocyte


title: HG3_RNU1_3_WT_B

source_name: HG3 cell line


title: Primary intestinal epithelial cells from wild type mice Run1_S124_WT_M2_Stem


title: HG3_RNU1_3_WT_A


title: Primary intestinal epithelial cells from wild type mice Run1_S105_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S132_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S121_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S123_WT_M2_Stem


title: Primary intestinal epithelial cells from wild type mice Run1_S117_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S115_WT_M2_TA


title: JVM3_RNU1_3_AC_A

source_name: JVM3 cell line

value: MUT


title: Primary intestinal epithelial cells from wild type mice Run1_S113_WT_M2_Enterocyte.prog.early


title: CBX4+/+ hMSC, sample incubated with H3K4me3 antibody during ChIP assay [H3K4me3-ChIP-WT-1]

city: Beijing

first: Boqiang

middle: John

last: Hu

address: 5th Yiheyuan Road

department: bio-dynamic imaging center

country: China

institute: Peking university

description:
H3K4me3-ChIP-WT-1
processed data file: H3K4me3_WT.bw

library_source: genomic

data_processing:
For RNA-Seq, the whole pipeline were available in https://github.com/huboqiang/RNA_v2 for details.
QC
Tophat (v2.0.9) mapping.
Cufflinks (v2.2.11) quantification.
For ChIP-Seq, the whole pipeline were available in https://github.com/huboqiang/ChIP .
QC
bwa mapping (0.7.5a).
macs2 (v2.1.0.20150731) calling peaks with IDR pipeline.
DNA-Seq CNV
QC
bwa mapping (0.7.5a).
samtools view depth and bedtools genomecov.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed data of RNA-seq were FPKM values in csv format.
Supplementary_files_format_and_content: ChIP-Seq data were bigwig results of MACSs2.
Supplementary_files_format_and_content: DNA-Seq were average depth information with 1Mbp intervals.

molecule: genomic DNA

growth_protocol: hESCs were maintained on Matrigel-coated plates with mTeSR medium. hMSCs were cultured in MEM-a medium supplemented with 10% fetal bovine serum, 1% Penicillin-Streptomycin, 1% non-essential amino acids, 1% GlutaMAX and 1 ng/ml bFGF.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen). To obtain the genomic DNA fragments of interest for ChIP-seq, the cells were crosslinked and lysed, and then the chromatin was sheared into fragments using sonication. Then samples were incubated with anti-H3K4me3 antibody (Abcam, ab8050, lot#GR3190162-1) or anti-FLAG antibody overnight. The DNA was de-crosslinked and extracted on the next day.
1.5 μg of total RNA was used to construct RNA sequencing libraries by NEB Next Ultra RNA Library Prep Kit (NEB) for Illumina following the manufacturer’s recommended protocol. The ChIP-sequencing library and copy number variation analysis sequencing library were constructed by NEB Next Ultra DNA Library Prep Kit (NEB) for Illumina according to the manufacturer’s instructions.

treatment_protocol: CBX4-/- hMSCs were infected with lentiviruses expressing CBX4 or Luc.

value: MSC

tag: passages

tag: chip antibody


title: Primary intestinal epithelial cells from wild type mice Run1_S104_WT_M2_Enterocyte


title: Primary intestinal epithelial cells from wild type mice Run1_S107_WT_M2_Goblet


title: Primary intestinal epithelial cells from wild type mice Run1_S106_WT_M2_TA


title: MEC1_RNU1_3_AC_A


title: Primary intestinal epithelial cells from wild type mice Run1_S110_WT_M2_Goblet


title: PLAC-seq-NALM6-H3K27ac-2

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

data_processing:
Library strategy: PLAC-seq
PLAC-Sequencing and data analysis: One repplicate per experiment were sequenced approximately 3 times deeper but  to optimize interaction calling fastq-files containing both read 1 and read 2 with their counter parts from the two replicates were combined for a total of 200-250M paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (v0.5.0) (--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.9.0), using Bowtie2 13, 14 for alignment against hg19 (GRCh37) reference genome, assigning mapped reads to a hg19 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.18.23)(https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs.
Single-end sequenced fastq files from the NALM6 H3K4me3 or H3K27ac ChIP-seq were used as inputs for the generation of interaction anchor points. Reads were trimmed using Trim Galore in single-end mode (--gzip --fastqc --clip_R1 10 --three_prime_clip_R1 3), and trimmed reads were aligned with Bowtie2 to the hg19 reference genome and Homer tag directories were created from the aligned reads (in bam format (converted from sam using samtools 15)) with the makeTagDirectory command from the HOMER platform 9. Prior to peak calling replicate tag directories were merged using makeTagDirectory and regions were identified using findPeaks (-style histone). Identified regions were migrated to the bed-format using pos2bed.pl and these regions were used as anchor points in the PLAC-seq interaction identification.  Bias corrected significant interactions (FDR <= 0.05) between anchor points and other anchor points/non-anchor-points  (peak-to-all) were identified with the FitHiChIP pipeline (https://www.biorxiv.org/content/early/2018/09/10/412833) using the HiC-Pro valid pairs and identified ChIP-anchors as input files with following settings: GCSize (size of the window upstream and downstream the restriction site used to calculate the GC content)=200, MappSize (size of the window upstream and downstream the restriction site used to calculate the mappability)=500, BINSIZE (Size of the bins in bases, for detecting the interactions.)=5000, LowDistThr (Lower distance threshold of interaction between two segments)=10000, UppDistThr (Upper distance threshold of interaction between two segments)=3000000, BiasCorrection with Coverage specific bias.
Interactions shared between samples within 1 bin size (5kb) were merged with a custom adaption of the merge2Dbed.pl from the HOMER platform9 (https://github.com/stela2502/LoopBed). Interaction anchor points were annotated against hg19 with a custom bash script utilizing the HOMER (v4.10) annotation database (annotatePeaks.pl).
A custom bash script utilizing Bedtools intersect 22was used to derive interactions overlapping transcription factor ChIP-seq peaks in either or both end-points.
Code is available at  https://github.com/stela2502/LoopBed and https://github.com/jonasungerback/sigvardsson_lab_plac_tools.
Genome_build: hg19
Supplementary_files_format_and_content: All genomic coordinates are relative to hg19 assembly.

source_name: NALM6 B-ALL cells

extract_protocol: PLAC-sequencing: 10M NALM6 cells that had been cross-linked with 1% formaldehyde for 10 minutes (see Chromatin immunoprecipitation section) were thawed on ice for 5 minutes, re-suspended in ice cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1X Roche protease inhibitors – 11697498001 (PIC)) and incubated on ice for 15 min. Samples were spun for 5 min @ 4C at 2,500g and cell pellet was washed in ice-cold lysis buffer + PIC. The pellet was resuspended in 0.5% SDS and incubated @ 62C for 10 min. The SDS reaction was quenched by addition of water and 10% Triton X-100 followed by 15min incubation @ 37C. The sample was digested with 40U MboI restriction enzyme with addition of 25 µl NEBuffer2 followed by 2h incubation @ 37C with shaking (900 RPM). After restriction enzyme digestion the samples were incubated for 20min @ 62C to inactivate MboI followed by a cool-down to RT. A fill in reaction was conducted using 0.3 mM Biotin-14-dATP (ThermoFisher, 19524016), 0.3 mM dCTP, 0.3 mM dTTP, 0.3 mM dGTP and 40U Klenow (NEB, M0210) @ 37C for 1.5h with shaking (900 RPM). Next a Ligation master mix (1X T4 ligation buffer (NEB, B0202), 1% Triton-X 100, 120 ug BSA (NEB, B9000), 4000 U T4 DNA ligase (NEB, M0202)) was added and samples were incubated @ RT with rotation for 2h. The samples were centrifugated 2,500g 5min @ 4C, supernatant was removed and cell pellet was resuspended in 250 µl ChIP SDS-lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC followed by 18 rounds of sonication (30s max intensity followed by 30s rest) with a Bioruptor (Diagenode). Sheared chromatin was centrifuged for 10 min @ 4C, 13000 rpm and supernatants were transferred to new tubes and diluted in 750 µl 1xHBSS + 1 ml 2X RIPA (20 mM Tris–HCl, pH 7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% sodium deoxycholate, 200 mM NaCl) + PIC. 1% input was removed from supernatant, and 10 µg H3K4me3 (Millipore, 07-473) or 10 µg H3K27ac (Abcam, ab4729) antibody adsorbed to 60 µl ProteinG dynabeads (ab adsorbation to beads as in ChIP-seq protocol) were added to the remaining supernatant and incubated @ 4C over night with rotation. Samples were washed as follows: 2 times with 1 ml Low Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton X-100, 2 mM EDTA, 50 mM Tris-HCl pH8, 150 mM NaCl), 2 times with 1 ml High Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton X-100, 2 mM EDTA, 50 mM Tris-HCl pH8, 500 mM NaCl), 1 time with 1 ml LiCl Immune Complex Wash Buffer (0.25 M LiCl, 1% Igepal-CA630, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH8), 2 times with 1 ml TE buffer (10 mM Tris–HCl, pH 8.0, 10 mM EDTA) followed by elution of chromatin from magnetic beads with two rounds of 100 µl elution buffer (1%SDS, 100 mM NaHCO3) with shaking (1500 RPM) @ RT. Supernatants were transferred to new tubes and chromatin complexes were reverse cross-linked over night @ 65C with the addition of 250 mM NaCl, 100 μg RNase A (ThermoFisher, EN0531) and 50 μg proteinase K (ThermoFisher, AM2546) followed by Zymo Research ChIP DNA Clean & Concentrator (BIOSITE-D5205) clean up. 25 μL of Streptavidin T1 beads (Thermo Fisher, 65601) were washed with Tween Wash Buffer (5 mM Tris-HCl pH 8, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) then resuspended in 50 μL of 2X Biotin Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2M NaCl). Beads were added to the samples and incubated at room temperature for 15 minutes with shaking. After capture, beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 μl 1X T4 DNA ligation buffer. Beads were collected on a magnet and resuspended on 100 µl end-repair mastermix (0.5 mM dNTPs(VWR, E636-40UMOLE), 12U T4 DNA Polymerase (NEB, M0203), 50U T4 Polynucleotide Kinase (NEB, M0201), 5U Klenow (NEB, M0210), 1X NEB T4 DNA ligase buffer) followed by incubation @ RT for 30 min with shaking (900 RPM). 300 μl Tween Wash Buffer was added and beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 1X NEB2 buffer. Beads were collected on a magnet and resuspended on 100 µl A-tailing mastermix (0.5 mM dATP (ThermoFisher), 25U Klenow Exo- (NEB, M0212), 1X NEB2 buffer) and incubated @ 37°C for 30 min with shaking (900 RPM). 300 µl Tween Wash Buffer was added and beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 1X Fast-Link ligation buffer (Epicenter, LK0750H ) followed by NEXTflex DNA barcode ligation  (BIOO scientific) using the Fast-link ligation kit (Epicenter, LK0750H). 300 µl Tween Wash Buffer was added and beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 10mM Tris-HCl pH 8.0, resuspended in 45 µl and a 1:1000 dilution was made for qPCR determination of number cycles needed for final PCR amplification. After final PCR, T1 streptavidin beads were collected on a magnet, supernatant transferred to new tubes and Ampure XP beads (x0.8 sample volume) were used to clean up libraries. PLAC-seq libraries were subject to 2X 75 cycles of paired end sequencing on a NextSeq500.

treatment_protocol: NALM6 were cultured in RPMI-1640 with UltraGlutamine (Lonza, Basel, Swiss) supplemented with 10% heat-inactivated FCS, 20mM HEPES, 50mg/ml Gentamicin and 50mM β-ME.

tag: tissue

value: Human B-ALL cell line

tag: chip (antibody)

value: Rabbit polyclonal anti-H3K27Ac IgG [ab4729, Abcam]


title: HG3_RNU1_3_AC_B


title: ATAC-seq-NALM6-2

data_processing:
ATAC-Sequencing and data analysis: NALM6 ATAC-seq analysis were  single-end processed with the ENCODE ATAC-Seq/DNase-Seq Pipeline (https://github.com/kundajelab/atac_dnase_pipelines) with the following settings: -species hg19 -no_xcor -enable_idr -auto_detect_adapter -out_dir out_NALM6_standard_se -rm_chr_from_tag mito -no_random_source -multimapping 4 -nth 8 -se.
Genome_build: hg19
Supplementary_files_format_and_content: All genomic coordinates are relative to hg19 assembly.

extract_protocol: ATAC-sequencing: ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers Libraries were run single read on the Illumina NexSeq500.


title: CBX4+/+ hMSC differentiated from hESC, early passage for RNA-seq [RNA-MSC-WT1]

description:
RNA-MSC-WT1
processed data file: FPKM.csv


title: Primary intestinal epithelial cells from wild type mice Run1_S103_WT_M2_Enterocyte.prog.late


title: HG3_RNU1_3_AC_A


title: MEC1_RNU1_3_AC_B


title: JVM3_RNU1_3_WT_B


title: Primary intestinal epithelial cells from wild type mice Run1_S102_WT_M2_TA


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-Luc, incubated with Flag Ab during ChIP [Flag-ChIP-Flag-Luc-2]

description:
Flag-ChIP-Flag-Luc-2
processed data file: PC2_WT2.bw

source_name: CBX4-/- hMSC induced with lentiviruses expressing Flag-Luc, sample incubated with Flag antibody

value: Flag


title: ChIP-seq-NALM6-a-H3K4me3-1

data_processing:
ChIP-Sequencing and data analysis:  For the human NALM6 cell line ChIP-seq analysis, reads were aligned to the human reference genome hg19 using Bowtie2 (v2.3.4.3), transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor. Transcription factor peak reproducibility was determined by a HOMER (v4.10) adaptation of the IDR (Irreproducibility Discovery Rate) package 16 (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high-quality peaks, defined by normalized scores of at least 10 tags/10 million and an acceptable IDR score, were submitted to further analysis.
NALM6 cell line H3K4Me3 and H3K27Ac ChIP-seq analysis: Single-end sequenced fastq files from the NALM6 H3K4me3 or H3K27ac ChIP-seq were used as inputs for the generation of interaction anchor points. Reads were trimmed using Trim Galore (0.5.0) in single-end mode (--gzip --fastqc --clip_R1 10 --three_prime_clip_R1 3), and trimmed reads were aligned with Bowtie2 to the hg19 reference genome and Homer tag directories were created from the aligned reads (in bam format (converted from sam using samtools 15)) with the makeTagDirectory command from the HOMER platform 9. Prior to peak calling replicate tag directories were merged using makeTagDirectory and regions were identified using findPeaks (-style histone). Identified regions were migrated to the bed-format using pos2bed.pl and these regions were used as anchor points in the PLAC-seq interaction identification.
Genome_build: hg19
Supplementary_files_format_and_content: All genomic coordinates are relative to hg19 assembly.

extract_protocol: ChIP-Seq:  10M cells for transcriptions factor ChIP were fixed at RT in 1 mg/ml DSG (ThermoFisher Scientific) in PBS for 30 min followed by an additional 10 min after addition of formaldehyde up to 1%. Cells (10M) for Histone modification ChIP were fixed in 1% formaldehyde for 10 min. The reactions were quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed in PBS. Nuclei were isolated by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (1X Roche protease inhibitors – 11697498001) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC and sonicated on a Bioruptor (Diagenode). Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC) for transcription factor ChIP and in HBSS (Lonza, Verviersa, Belgium) +PIC and 2X RIPA buffer (20 mM Tris–HCl, pH 7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% Sodiumdeoxycholate, 200 mM NaCl) + PIC for histone modification ChIPs. Ten μg per 10M cells of antibody Rabbit anti-Ikzf1 polyclonal IgG [ab26083, Abcam], Rabbit polyclonal anti-Ebf1 [ABE1294, Millipore], Rabbit polyclonal anti-Pax5 [ab183575, Abcam], Rabbit polyclonal anti-RUNX1 [ab23980, Abcam] or 10μl of H3K4Me3 polyclonal IgG [07-473 Millipore], or 10μg of Rabbit anti H3K27Ac IgG [ab4729, Abcam] was hybridized to 70μl Protein-G or A Dynabeads (Life Technologies). ChIP was performed over night at 4°C, and subsequently washed (1 time with 500 μl Low Salt Immune Complex Wash Buffer, 1 time with 200 μl High Salt Immune Complex Wash Buffer, 1 time with 200 μl LiCl Immune Complex Wash Buffer, 2 times with 200 μl TE buffer) and eluted for 6 h at 65°C (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, 100 μg RNase A and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator before ChIP-qPCR or ChIP-seq library preparation using NEXTflex DNA barcodes (BIOO scientific). 76 bp single read sequencing was performed on an Illumina NextSeq500.


title: Primary intestinal epithelial cells from wild type mice Run1_S157_WT_M2_Enterocyte.prog.early


title: Primary intestinal epithelial cells from wild type mice Run1_S101_WT_M2_Enterocyte.prog.late


title: JVM3_RNU1_3_WT_A


title: JVM3_RNU1_3_AC_B


title: Primary intestinal epithelial cells from wild type mice Run1_S100_WT_M2_Stem


title: CBX4-/- hMSC, sample incubated with H3K4me3 antibody during ChIP assay [H3K4me3-ChIP-KO-1]

description:
H3K4me3-ChIP-KO-1
processed data file: H3K4me3_KO.bw


title: ChIP-seq-NALM6-a-H3K27ac-2


title: CBX4-/- hMSC, sample as input for H3K4me3 ChIP assay [Input-KO-1]

description:
Input-KO-1
processed data file: H3K4me3_KO.bw

source_name: CBX4-/- hMSC


title: PLAC-seq-NALM6-H3K4me3-2

value: H3K4Me3 polyclonal IgG [07-473 Millipore]


title: CBX4-/- hMSC differentiated from hESC, early passage for RNA-seq [RNA-MSC-KO2]

description:
RNA-MSC-KO2
processed data file: FPKM.csv


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-CBX4, input for Flag during ChIP assay [Input-Flag-CBX4-2]

description:
Input-Flag-CBX4-2
processed data file: PC2_WT2.bw


title: PLAC-seq-NALM6-H3K4me3-1


title: PLAC-seq-NALM6-H3K27ac-1


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-CBX4, incubated with Flag Ab during ChIP [Flag-ChIP-Flag-CBX4-1]

description:
Flag-ChIP-Flag-CBX4-1
processed data file: PC2_KO1.bw

source_name: CBX4-/- hMSC induced with lentiviruses expressing Flag-CBX4, sample incubated with Flag antibody


title: CBX4+/+ hMSC, sample as input for H3K4me3 ChIP assay [Input-WT-1]

description:
Input-WT-1
processed data file: H3K4me3_WT.bw

source_name: CBX4+/+ hMSC


title: ATAC-seq-NALM6-3


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-CBX4, incubated with Flag Ab during ChIP [Flag-ChIP-Flag-CBX4-2]

description:
Flag-ChIP-Flag-CBX4-2
processed data file: PC2_KO2.bw


title: CBX4+/+ hMSC differentiated from hESC, early passage for RNA-seq [RNA-MSC-WT2]

description:
RNA-MSC-WT2
processed data file: FPKM.csv


title: ATAC-seq-NALM6-1


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-Luc, input for Flag during ChIP assay [Input-Flag-Luc-2]

description:
Input-Flag-Luc-2
processed data file: PC2_KO2.bw


title: ChIP-seq-NALM6-input-for-histone-samples


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-Luc, input for Flag during ChIP assay [Input-Flag-Luc-1]

description:
Input-Flag-Luc-1
processed data file: PC2_KO1.bw


title: CBX4+/+ hMSC differentiated from hESC, early passage for copy number variation [CNV-WT-1]

description:
CNV-WT-1
processed data file: CNV-WT-1.intervals.bed

data_processing:
Library strategy: DNA-Seq
For RNA-Seq, the whole pipeline were available in https://github.com/huboqiang/RNA_v2 for details.
QC
Tophat (v2.0.9) mapping.
Cufflinks (v2.2.11) quantification.
For ChIP-Seq, the whole pipeline were available in https://github.com/huboqiang/ChIP .
QC
bwa mapping (0.7.5a).
macs2 (v2.1.0.20150731) calling peaks with IDR pipeline.
DNA-Seq CNV
QC
bwa mapping (0.7.5a).
samtools view depth and bedtools genomecov.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed data of RNA-seq were FPKM values in csv format.
Supplementary_files_format_and_content: ChIP-Seq data were bigwig results of MACSs2.
Supplementary_files_format_and_content: DNA-Seq were average depth information with 1Mbp intervals.


title: CBX4-/- hMSC differentiated from hESC, early passage for RNA-seq [RNA-MSC-KO1]

description:
RNA-MSC-KO1
processed data file: FPKM.csv


title: ChIP-seq-NALM6-a-RUNX1-2

value: Rabbit polyclonal anti-RUNX1 [ab23980, Abcam]


title: ChIP-seq-NALM6-a-IKZF1-1

value: Rabbit anti-Ikzf1 polyclonal IgG [ab26083, Abcam]


title: ChIP-seq-NALM6-a-H3K4me3-2


title: ChIP-seq-NALM6-a-H3K27ac-1


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-Luc, incubated with Flag Ab during ChIP [Flag-ChIP-Flag-Luc-1]

description:
Flag-ChIP-Flag-Luc-1
processed data file: PC2_WT1.bw


title: REC8

city: jinan

first: yundong

last: sun

address: wenhua west road 44

institute: shanda university

description: processed data file: otu_table_tax.txt

data_processing:
Library strategy: 16s rDNA-sequencing
Basecalls and quality filtering on Illumina MiSeq sequencer.
Samples were separated by barcode.
After adaptor-trimming and low quality reads removing by Trimmomatic software, and paired-end merging by flash software, optimized reads were used for OTU clustering, and the OTU matrix of all samples were generated. The most abundant sequence in each OTU was selected as the representative sequence of that OTU.
Then these OTU representative sequences were aligned to Greengenes database, and generated the sample and taxonomy abundance matrix. mothur software and R environment were used to perform alpha diversity, beta diversity, statistics analysis and plotting.
Picrust software was used to perform function prediction.
Genome_build: Greengenes database
Supplementary_files_format_and_content: otu_table_tax.txt: Tab-delimited text file

organism: mouse gut metagenome

source_name: Gastric flora

growth_protocol: Fed mice with sterile feed.

extract_protocol:
Extracting DNA from mouse gastric flora.
The 16S rRNA gene comprising V3 and V4 regions was amplified by PCR, and the resulting amplicons were cleaned, quantified, and sequenced on the Illumina MiSeq platform.

treatment_protocol: There are 10 mice in the experiment, named REC. The mice were fed with high salt diets (5% NaCl) for 4 weeks and then fed with normal salt diets for 4 weeks.

tag: mouse age

value: 6-8 weeks

tag: mouse strain

tag: mouse sex

value: Male

tag: mouse diet

value: High-salt diet for 4 wk, then normal-salt diet for 4 wk

value: Gastric flora


title: REC7

description: processed data file: otu_table_tax.txt


title: ChIP-seq-NALM6-Input-2


title: REC6

description: processed data file: otu_table_tax.txt


title: REC9

description: processed data file: otu_table_tax.txt


title: ChIP-seq-NALM6-Input-1


title: CBX4-/- hMSC induced with lentiviruses expressing Flag-CBX4, input for Flag during ChIP assay [Input-Flag-CBX4-1]

description:
Input-Flag-CBX4-1
processed data file: PC2_WT1.bw


title: Qb0.2: WTCHG_337410_243130

city: Oxford

first: Ariane

middle: Cruz

last: Gomes

address: Roosevelt drive

country: United Kingdom

institute: University of Oxford

data_processing:
Trimmomatic 0.35
For read mapping, Star aligner v2.5.2b [15] was used on the Gencode M12 transcriptome (mm10) with settings "--outSAMmultNmax 20".  Reads were assigned to genes using featureCounts v1.5.1 [16] with settings "-C -B -M -s 2 -p".
To calculate log2 fold change estimates between groups, a negative binomial general linear model was fit using DESeq2 [17]  and only genes with a Benjamini-Hochberg [18]  corrected Wald test FDR of less than 5% were labelled significant.

source_name: spleen

growth_protocol: Sorting of splenic DCs was performed with immunomagnetic positive selection of mouse CD11c+ cells (EasySep Mouse CD11c, StemCell Tech) according to the manufacture’s instruction.

extract_protocol:
Total RNA was extracted from sorted splenic DCs from immunised mice following the manufacturer’s protocol (RNeasy Midi Kit, Qiagen), using an on-column DNase-I digest step
TruSeq Stranded Total RNA kit (Illumina)
Libraries were amplified on a Tetrad (Bio-Rad) using in-house unique dual indexing primers [13]. Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly

tag: Sex

value: female

tag: time-point

value: 24h post immunisation

value: CD11c+ splenocytes

value: dendritic cells (DCs)


title: Qb0.3: WTCHG_337410_244142


title: ChIP-seq-NALM6-a-IKZF1-2


title: Qb0.1: WTCHG_337410_242118


title: ChIP-seq-NALM6-a-RUNX1-1


title: E14_NS_FBS, biological rep2

type: RNA

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: For hybridization to a GeneChip Mouse Genome 430 2.0 Array (Affymetrix), 15 mg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA and 1x manufacturer-recommended hybridization buffer in a 45°C rotisserie oven for 16 h.

scan_protocol: Stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing: Data were normalized using Percellome methods.

label: Biotin

source_name: NS/PCs isolated from E14.5 mouse brain

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

growth_protocol: NS/PCs were prepared from telencephalons of E14.5 mice and cultured in N2-supplemented Dulbecco's Modified Eagle's Medium with F12 (GIBCO) containing 10 ng/ml basic FGF (Peproteck).

extract_protocol: Total RNAs were purified using an RNeasy Mini kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: NS/PCs were cultured for five days with different conditions (bFGF + EGF or LIF or BMP4 or LIF + BMP4 or FBS).

value: Neural stem/progenitor cells (NS/PCs)

tag: developmental stage

tag: treatment

value: FBS


title: CBX4-/- hMSC differentiated from hESC, early passage for copy number variation [CNV-KO-1]

description:
CNV-KO-1
processed data file: CNV-KO-1.intervals.bed

value: MSC


title: ChIP-seq-NALM6-a-Pax5-2

value: Human B-ALL cell line

value: Rabbit polyclonal anti-Pax5 [ab183575, Abcam]


title: E14_NS_FBS, biological rep3


title: E14_NS_LIFBMP4, biological rep2

value: LIF + BMP4


title: CBX4+/+ hESC for RNA-seq [RNA-ESC-WT-2]

description:
RNA-ESC-WT-2
processed data file: FPKM.csv

source_name: CBX4+/+ hESC

value: ESC


title: E14_NS_FBS, biological rep1


title: REC4

description: processed data file: otu_table_tax.txt


title: REC3

description: processed data file: otu_table_tax.txt


title: REC5

description: processed data file: otu_table_tax.txt


title: ChIP-seq-NALM6-a-Pax5-1


title: CBX4+/+ hESC for RNA-seq [RNA-ESC-WT-1]

description:
RNA-ESC-WT-1
processed data file: FPKM.csv


title: ChIP-seq-NALM6-a-Ebf1-2

value: Rabbit polyclonal anti-Ebf1 [ABE1294, Millipore]


title: ChIP-seq-NALM6-a-Ebf1-1


title: REC10

description: processed data file: otu_table_tax.txt


title: CBX4-/- hESC for RNA-seq [RNA-ESC-KO-1]

description:
RNA-ESC-KO-1
processed data file: FPKM.csv

source_name: CBX4-/- hESC


title: QbB3: WTCHG_337410_235129


title: Qb2: WTCHG_337410_240189


title: CBX4-/- hESC for RNA-seq [RNA-ESC-KO-2]

description:
RNA-ESC-KO-2
processed data file: FPKM.csv


title: Brassica napus [P]

city: Vancouver

first: David

middle: Christopher

last: Tack

state: B. C.

address: 3529-6720 University Boulevard

department: Botany

institute: Universtiy of British Columbia

description:
Natural
P
PQR_raw.tsv

data_processing:
FastQC
GSNAP
Python
R
Genome_build:JJMF00000000.1, AENI01000000, CCCW010000001 to CCCW010044187
Genome_build:B. rapa (sourced from Wang X, et al. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nature genetics, 43(10), 1035-1039)
Genome_build:B. oleracea (sourced from Parkin, I. A., Koh, C., Tang, H., Robinson, S. J., Kagale, S., Clarke, W. E., ... & Denoeud, F. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome biology, 15(6), R77.)
Genome_build:B. napus (sourced from Chalhoub B, et al. 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science. 345: 950   953.)
Gene_ids: the identifiers used by the B. oleracea genome assembly. They are identical to the identifiers used in the B. napus paper when the B. napus genome was compared to it.
Supplementary_files_format_and_content: Raw counts of reads aligned to genes, and raw counts of alternative splicing events, tab delimited.

organism: Brassica napus

source_name: Brassica napus

growth_protocol: 20°C and 50% humidity under 16h/8h light dark cycles in a growth chamber.

extract_protocol:
RNAqueous Kit w/ Liquid Nitrogen
Ilumina Kit (Performed by Genome Quebec)

value: First True Leaf


title: Qb3: WTCHG_337410_241106


title: P5. Dimerizer (4 h)

city: San Francisco

first: Shaun

last: Cullen

state: CA

address: 1435 16th Avenue

institute: Genentech

data_processing:
FASTQ files were aligned to the mouse reference genome (mm9) using the GSNAP alignment tool
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: mouse reference genome (mm9)
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: NIH 3T3 Fibroblasts

growth_protocol: 1x106 cells/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: Cells were either left unstimulated, or stimulated with dimerizer (10 uM) or TNF (20 ng/ml) for the indicated times

tag: background strain

value: NIH/Swiss

value: wild-type

value: dimerizer for 4 h

tag: molecule

value: polysome RNA


title: P4. TNFa (4 h)

tag: genotype

value: TNF for 4 h


title: Qb1: WTCHG_337410_239177

tag: strain

value: female

value: 24h post immunisation


title: QbxB3: WTCHG_337410_238165

tag: cell type

value: CD11c+ splenocytes

value: dendritic cells (DCs)


title: QbxB2: WTCHG_337410_237153


title: REC2

description: processed data file: otu_table_tax.txt

value: 6-8 weeks

value: Male

value: High-salt diet for 4 wk, then normal-salt diet for 4 wk

value: Gastric flora


title: E14_NS_LIF, biological rep2

value: Neural stem/progenitor cells (NS/PCs)

value: LIF


title: QbxB1: WTCHG_337410_236141


title: E14_NS_bFE, biological rep2

value: bFGF + EGF


title: E14_NS_LIFBMP4, biological rep1

value: LIF + BMP4


title: REC1

description: processed data file: otu_table_tax.txt


title: E14_NS_BMP4, biological rep1


title: serum_Pre_whole_virion_vaccine 170_Pre

first: ruth

middle: Elizabeth

last: Drury

state: Oxforshire

address: Centre for Tropical Medicine and Vaccinology, Churchill Drive

department: Paediatrics

description:
serum_Pre_whole_virion_vaccine
Pre vaccination miRNA expression in serum

hyb_protocol: Samples were hybridised for 40 hours to increase specific signal against background.

scan_protocol: Serum miRNA levels were assessed using the Human miRNA Microarray 60k (Agilentà Technologies). Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C US84300231 using one color scan setting for 1x44k array slides.

data_processing:
The scanned images were analyzed using protocol  miRNA_107_Sep09 and Grid: 031181_D_F_20110707).  Processed normalised data was obtained by filtering out miRNAs detected in less than 50% of sample. Where a miRNA was not detected in a sample, its fluorescence value was set to half the value of the minimum detected fluorescence value across all samples for that miRNA. Data were then normalised in R using variance stabilised normalisation (from the R package vsn version 3.40).
vsn normalized signal intensity

source_name: serum, baseline, participant 170

label_protocol: The concentration of the RNA was measured using a NanoDropà ND-8000 UV-Vis spec- trophotometer (Thermo Scientific, Massachusetts, USA). For each sample 100ng total RNA (at 50 ng/μl) was taken and used in the miRNA microarray labelling procedure (Agilent Tech- nologies, Santa Clara, USA; Cat: 5190-0456). This procedure followed the Agilent miRNA pro- tocol (Version 2.4 September 2011, http://www.chem.agilent.com/library/usermanuals/ public/g4170-90011_mirna_complete_2.4.pdf); with the exception that after the labelling with Cy3-pCp molecule samples were dried and ‘Step 2’ was omitted.

extract_protocol: Total RNA was extracted from 200 microlitres of previously frozen sera using the Total RNA Extraction Kit (Norgen cat# 17200) as specified by the protocol.

treatment_protocol: Serum samples were collected immediately before vaccination and 21 days (minus 7 days to plus 14 days) after second vaccination with either a

value: serum

tag: gender

value: male

tag: age

tag: vaccination group

value: whole virion non-adjuvanted H1N1 vaccine


title: NA Pos_Ctrl_4

description:
NA
NA

tag: tissue


title: E14_NS_bFE, biological rep1


title: QbB2: WTCHG_337410_234117


title: E14_NS_LIF, biological rep1


title: P2. NT (no treatment)

value: NIH/Swiss

value: wild-type

value: untreated

value: polysome RNA


title: E14_NS_LIF, biological rep3


title: QbB1: WTCHG_337410_233105

value: female

value: 24h post immunisation

value: CD11c+ splenocytes


title: P6. Dimerizer (4 h)

value: dimerizer for 4 h


title: colonic epithelial cells KO-2 (827)

city: Dallas

first: Luis

last: Sifuentes-Dominguez

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatrics

institute: University of Texas Southwestern Medical Center

data_processing:
After adapter trimming, sequences were aligned to reference genome, GRCm38, using Hisat2.
Duplicate reads are marked and removed using SAMBAMBA.
Features are then counted using featurecounts.
Differential expression analysis was performed using edgeR with cutoffs of 2 and 0.05 for FC and FDR respectively
Genome_build: GRCm38
Supplementary_files_format_and_content: countTable.fpkm (abundance), edgeR.results.txt (DEA)

source_name: colonic epithelium

extract_protocol:
RNA was purified from epithelial cell preparations using Rneasy columns as per the manufacturer's instructions
Librarues were prepared using standard Illumina protocols

value: colonic epithelium

value: 12-13 week old

value: CDX2 Cre Ngn3 f/f


title: Brassica napus [R]

description:
Natural
R
PQR_raw.tsv

value: First True Leaf


title: Brassica napus [Q]

description:
Natural
Q
PQR_raw.tsv


title: P1. NT (no treatment)


title: colonic epithelial cells KO-3 (864)


title: P3. TNFa (4 h)

value: TNF for 4 h


title: S6. Dimerizer (4 h)

value: total RNA


title: colonic epithelial cells KO-1 (826)


title: colonic epithelial cells WT-3 (863)

value: Ngn3 f/f


title: colonic epithelial cells WT-2 (829)


title: E14_NS_bFE, biological rep3

value: Neural stem/progenitor cells (NS/PCs)

value: bFGF + EGF


title: Sox11_ChIP-seq_2

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie2 with default single-end settings (Langmead et al., 2009). Next, all non-nuclear, non-mapping, and low-quality reads were discarded. Duplicated reads were then removed with picard MarkDuplicates. Peak calling was carried out with Homer (findPeaks  -style factor) (Heinz et al., 2010). Blacklisted regions from mm9 were also removed from the individual and comprehensive peak files (bedtools –subtract). Motif enrichment analysis was conducted with Homer (findMotifsGenome.pl).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated from merged tag directories output from HOMER; peak files are the result of peak calling in HOMER in bed format

source_name: keratinocytes transduced with Sox11-Flag lentivirus

extract_protocol:
Nuclei were prepared from approximately 100 million cells and lysed in the sonication buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS). Chromatin was sheered by sonication in iced water (Bioruptur XL, Diagenode), 30 sec on/30 sec off, for 35 min, to achieve 100–500-bp DNA fragments. After dialysis against the low SDS buffer (20 mM Tris-HCl pH 8, 10 mM EDTA, and 0.01% SDS) overnight, the sonicated samples were centrifuged at 20,000 g for 10 min. The soluble whole-cell extracts were added with Triton X-100 (final 1%) and NaCl (final 150 mM), and incubated with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 10-µg mouse anti-FLAG antibody (Sigma) or mouse IgG. Beads were washed 1´ with low-salt immune complex wash buffer (0.1% SDS, 1% TritonX-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH8.1), 1´ with high-salt immune complex wash buffer(0.1% SDS, 1% TritonX-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-HCl, pH8.1), 1´ with LiCl immune complex wash buffer (250 mM LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1), and 1´ with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65oC for 30 min (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA, and 1% SDS) in a Thermomix. IgG ChIPs were performed under the same conditions as the experimental ChIPs. Crosslinking was reversed by incubating samples at 65oC for 6 hr. Whole-cell extract DNA reserved from the sonication step was treated in parallel to reverse crosslinking. After crosslink reversal, samples were treated with RNase and proteinase K prior to DNA extraction.
Rubicon ThruPlex DNA-Seq library preparation system

tag: strain background

value: mixed 129SvEx:C57BL/6

value: primary keratinocytes

tag: genotype/variation

tag: chip antibody

value: mouse anti-FLAG antibody (Sigma)


title: serum, post split virion vaccine, paticipant 124_Post

description:
serum, post split virion vaccine, paticipant
miRNA expression in serum 3 weeks after receiving 2 doses of a ASO3B adjuvanted split virion H1N1 vaccine

source_name: serum, post split virion vaccine, participant 124

value: serum


title: serum_Pre_split_virion_vaccine 840_Pre

description:
serum_Pre_split_virion_vaccine
Pre vaccination miRNA expression in serum

source_name: serum, baseline, participant 840

value: female

value: ASO3B adjuvanted split virion H1N1 vaccine


title: serum, post split virion vaccine, paticipant 596_Post

source_name: serum, post split virion vaccine, participant 596

value: male


title: serum_Pre_split_virion_vaccine 238_Pre

source_name: serum, baseline, participant 238


title: NA Pos_Ctrl_3

description:
NA
NA


title: serum_Post_whole_virion_vaccine 795_Post

description:
serum_Post_whole_virion_vaccine
miRNA expression in serum 3 weeks after receiving 2 doses of a whole virion non-adjuvanted H1N1 vaccine

source_name: serum, post whole virion vaccine, participant 795


title: S5. Dimerizer (4 h)

value: NIH/Swiss

value: wild-type

value: dimerizer for 4 h


title: S4. TNFa (4 h)


title: serum, post split virion vaccine, paticipant 662_Post

source_name: serum, post split virion vaccine, participant 662


title: serum_Pre_whole_virion_vaccine 365_Pre

source_name: serum, baseline, participant 365

value: whole virion non-adjuvanted H1N1 vaccine


title: serum_Pre_whole_virion_vaccine 763_Pre

source_name: serum, baseline, participant 763


title: serum, post split virion vaccine, paticipant 238_Post

source_name: serum, post split virion vaccine, participant 238


title: serum_Post_whole_virion_vaccine 763_Post

source_name: serum, post whole virion vaccine, participant 763


title: E14_NS_BMP4, biological rep2

source_name: NS/PCs isolated from E14.5 mouse brain


title: Sox4_ChIP-seq_2

source_name: keratinocytes transduced with Sox4-Flag lentivirus


title: Sox11_ChIP-seq_1


title: S2. NT (no treatment)

value: untreated


title: colonic epithelial cells WT-1 (828)

value: colonic epithelium

value: 12-13 week old


title: S1. NT (no treatment)

value: total RNA


title: Input_ChIP-seq

source_name: keratinocytes

value: IgG


title: T12. T4 h dimerizer

source_name: NIH 3T3 Fibroblasts


title: serum_Pre_whole_virion_vaccine 226_Pre

source_name: serum, baseline, participant 226


title: T11. T4 h dimerizer


title: serum_Post_whole_virion_vaccine 178_Post

source_name: serum, post whole virion vaccine, participant 178


title: serum_Pre_whole_virion_vaccine 57_Pre

source_name: serum, baseline, participant 57


title: EG19732 replicate 2

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Salmonella enterica serivar Typhimurium 14028s whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
The mapped reads were counted by featureCounts (http://bioinf.wehi.edu.au/featureCounts/) and normalized by using DESeq2.
Genome_build: NCBI accession - PRJNA33067, assembly ID - GCA_000022165.1
Supplementary_files_format_and_content: Tab-delimited text files including log2 fold change values calculated by DeSeq2 and locus_tags for genes of Salmonella enterica serovar Typhimurium 14028s

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: S. Typhimurium 14028s_vector control

growth_protocol: The strains were grown in N-minimal media to exponential phase, and harvested after IPTG treatment.

extract_protocol:
After cell harvest, RNA samples were prepared using RNeasy kit. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Bacteria) (MRZMB126, Illumina, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 0.25 mM IPTG was added to the media for 60 min.

value: harboring pUH21, the empty vector

tag: growth media

value: N-minimal media

tag: growth phase

value: exponential phase

tag: induced with

value: 0.25 mM IPTG for 60min


title: EG19733 replicate 2

source_name: S. Typhimurium 14028s_mgtC overexpression

value: harboring pUH-mgtC which contains the mgtC gene


title: T10. T3 h dimerizer

value: dimerizer for 3 h


title: EG19733 replicate 1


title: serum, post split virion vaccine, paticipant 792_Post

source_name: serum, post split virion vaccine, participant 792

value: serum

value: female

value: ASO3B adjuvanted split virion H1N1 vaccine


title: S3. TNFa (4 h)

value: NIH/Swiss

value: wild-type

value: TNF for 4 h


title: Sox4_ChIP-seq_1

value: mixed 129SvEx:C57BL/6

value: primary keratinocytes

value: mouse anti-FLAG antibody (Sigma)


title: EG19732 replicate 1


title: T8. T2 h dimerizer

value: dimerizer for 2 h

value: total RNA


title: T9. T3 h dimerizer


title: serum_Pre_split_virion_vaccine 662_Pre

source_name: serum, baseline, participant 662


title: T4. T0.5 h dimerizer

value: dimerizer for 0.5 h


title: serum_Pre_whole_virion_vaccine 55_Pre

source_name: serum, baseline, participant 55

value: whole virion non-adjuvanted H1N1 vaccine


title: T7. T2 h dimerizer


title: serum_Post_whole_virion_vaccine 226_Post

source_name: serum, post whole virion vaccine, participant 226

value: male


title: T6. T1 h dimerizer

value: dimerizer for 1 h


title: serum_Pre_split_virion_vaccine 549_Pre

source_name: serum, baseline, participant 549


title: NA Pos_Ctrl_1

description:
NA
NA


title: serum_Post_whole_virion_vaccine 519_Post

source_name: serum, post whole virion vaccine, participant 519


title: T5. T1 h dimerizer


title: serum, post split virion vaccine, paticipant 549_Post

source_name: serum, post split virion vaccine, participant 549


title: serum_Pre_whole_virion_vaccine 519_Pre

source_name: serum, baseline, participant 519


title: serum_Pre_split_virion_vaccine 792_Pre

source_name: serum, baseline, participant 792


title: serum, post split virion vaccine, paticipant 840_Post

source_name: serum, post split virion vaccine, participant 840


title: serum, post split virion vaccine, paticipant 639_Post

source_name: serum, post split virion vaccine, participant 639


title: T3. T0.5 h dimerizer

source_name: NIH 3T3 Fibroblasts


title: serum_Post_whole_virion_vaccine 170_Post

source_name: serum, post whole virion vaccine, participant 170


title: serum, post split virion vaccine, paticipant 652_Post

source_name: serum, post split virion vaccine, participant 652


title: serum_Post_whole_virion_vaccine 55_Post

source_name: serum, post whole virion vaccine, participant 55


title: serum_Pre_split_virion_vaccine 596_Pre

source_name: serum, baseline, participant 596


title: serum_Post_whole_virion_vaccine 57_Post

source_name: serum, post whole virion vaccine, participant 57


title: T2. NT (no treatment)

value: untreated


title: serum_Post_whole_virion_vaccine 0_Post

source_name: serum, post whole virion vaccine, participant 0


title: serum_Post_whole_virion_vaccine 577_Post

source_name: serum, post whole virion vaccine, participant 577


title: serum_Pre_split_virion_vaccine 124_Pre

source_name: serum, baseline, participant 124


title: T1. NT (no treatment)


title: Synthetic Mix (rapa and oleracea mid) [S]

description:
Synthetic Mix (rapa and oleracea mid)
S
ABCDEFGHIJKLMNOS_raw.tsv

organism: synthetic construct

source_name: Synthetic Mix (rapa and oleracea mid)

value: First True Leaf


title: Resynthesized Brassica napus P3 [M]

description:
P3
M
ABCDEFGHIJKLMNOS_raw.tsv

organism: Brassica rapa


title: Resynthesized Brassica napus P3 [N]

description:
P3
N
ABCDEFGHIJKLMNOS_raw.tsv


title: serum_Post_whole_virion_vaccine 365_Post

source_name: serum, post whole virion vaccine, participant 365

value: serum


title: Resynthesized Brassica napus P3 [O]

description:
P3
O
ABCDEFGHIJKLMNOS_raw.tsv


title: serum_Pre_whole_virion_vaccine 577_Pre

source_name: serum, baseline, participant 577

value: female


title: Resynthesized Brassica napus P2 [J]

description:
P2
J
ABCDEFGHIJKLMNOS_raw.tsv


title: Resynthesized Brassica napus P2 [L]

description:
P2
L
ABCDEFGHIJKLMNOS_raw.tsv


title: Resynthesized Brassica napus P1 [I]

description:
P1
I
ABCDEFGHIJKLMNOS_raw.tsv


title: Resynthesized Brassica napus P2 [K]

description:
P2
K
ABCDEFGHIJKLMNOS_raw.tsv


title: Ci2YB

first: Luming

last: Zou

state: PR

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

description: sample of Vitis cinera which was harvested during YB

data_processing:
The reads were trimmed using FASTX-Toolkit (version 0.11.5)
The clean reads were mapped to the grape genome by using tophat (version 2.0.14) with default parameters.
Ragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks (version 2.2.1).
Genome_build: 12X grape genome of IGGP
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample ...

organism: Vitis cinerea

source_name: berries

growth_protocol: All the vines received standard fertilization, irrigation, pruning and pests and diseases control.

extract_protocol:
We isolated total RNA from above ground samples (100mg per sample) using Sigma RNA Mini-Prep following the manufacturer's instructions (Zymo Research Corporation, Irvine, CA, USA) and the extracted RNA were treated with DNAse (Applied Biosystems/Ambion, Austin, TX, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Special boxes (measuring 40 cm×25 cm×25cm) were covered with aluminum foil were used for sunlight exclusion. The grape clusters were either exposed to sunlight throughout their development (CK) or put in the boxes to exclude sunlight during specific stages of berry development.

tag: cultivar

value: American native grape species

tag: developmental stage

value: young berry

tag: anthocyanins concentration

value: berries


title: Ci2VC

description: sample of Vitis cinera which was harvested during veraison and which was exposure to sunlight (CK)

value: veraison

tag: treatment

value: exposure to sunlight (CK)


title: Ci2V2R

description: sample of Vitis cinera which was harvested during veraison and which was treated with exclusion of sunlight before veraison

value: exclusion of sunlight before veraison


title: Ci2MC

description: sample of Vitis cinera which was harvested during mature and which was treated exposure to sunlight (CK)

value: mature


title: serum_Pre_whole_virion_vaccine 0_Pre

source_name: serum, baseline, participant 0


title: serum_Pre_split_virion_vaccine 639_Pre

source_name: serum, baseline, participant 639

value: ASO3B adjuvanted split virion H1N1 vaccine


title: serum_Pre_split_virion_vaccine 652_Pre

source_name: serum, baseline, participant 652


title: serum_Post_whole_virion_vaccine 545_Post

source_name: serum, post whole virion vaccine, participant 545


title: Brassica rapa [B]

description:
rapa
B
ABCDEFGHIJKLMNOS_raw.tsv

source_name: Brassica rapa


title: NA Pos Ctrl 2

description:
NA
NA


title: serum_Pre_whole_virion_vaccine 545_Pre

source_name: serum, baseline, participant 545


title: Resynthesized Brassica napus P1 [H]

description:
P1
H
ABCDEFGHIJKLMNOS_raw.tsv


title: Resynthesized Brassica napus P1 [G]

description:
P1
G
ABCDEFGHIJKLMNOS_raw.tsv


title: Ci2PV1R

description: sample of Vitis cinera which was harvested during PV and which was treated with exclusion of sunlight before pre-veraison

value: 2 weeks before veraison (pre-veraison)


title: La2YB

organism: Vitis labrusca

value: hybrid of Vitis vinerfera and Vitis labrusca


title: Brassica rapa [A]

description:
rapa
A
ABCDEFGHIJKLMNOS_raw.tsv


title: serum_Pre_whole_virion_vaccine 892_Pre

source_name: serum, baseline, participant 892

value: whole virion non-adjuvanted H1N1 vaccine


title: serum_Pre_whole_virion_vaccine 795_Pre

source_name: serum, baseline, participant 795


title: Ci2M3R

description: sample of Vitis cinera which was harvested during mature and which was treated with exclusion of sunlight during the whole developmental stages


title: serum_Post_whole_virion_vaccine 892_Post

source_name: serum, post whole virion vaccine, participant 892


title: La2PVC

description: sample of Vitis cinera which was harvested during PV and which was exposure to sunlight (CK)


title: Ci2M2R

description: sample of Vitis cinera which was harvested during mature and which was treated with exclusion of sunlight before veraison


title: La2MC


title: La2M3R

value: exclusion of sunlight during the whole developmental stages


title: Brassica rapa [C]

description:
rapa
C
ABCDEFGHIJKLMNOS_raw.tsv


title: Ci2V1R

description: sample of Vitis cinera which was harvested during veraison and which was treated with exclusion of sunlight before pre-veraison


title: Ci2M1R

description: sample of Vitis cinera which was harvested during mature and which was treated with exclusion of sunlight before pre-veraison


title: La2V2R

value: 2 weeks after veraison


title: La2PV1R

value: exclusion of sunlight before pre-veraison


title: La2VC


title: Ci22VC

description: sample of Vitis cinera which was harvested during 2V and which was exposure to sunlight (CK)


title: Ci1YB


title: Ci22V2R

description: sample of Vitis cinera which was harvested during 2V and which was treated with exclusion of sunlight before veraison


title: La22V2R


title: La22V1R

description: sample of Vitis cinera which was harvested during 2V and which was treated with exclusion of sunlight before pre-veraison


title: La22VC


title: La2M2R


title: Ci1VC


title: La1PVC


title: La1PV1R


title: La1VC


title: La2M1R


title: La1YB


title: La1V2R


title: Ci22V1R


title: La1MC


title: Ci1V1R


title: Ci1PVC


title: Ci1PV1R


title: Ci1MC


title: La1M1R


title: La1M3R


title: La12VC


title: Ci1M2R


title: AcV2R

description: sample of Vitis acerifolia which was harvested during veraison and which was treated with exclusion of sunlight before veraison

organism: Vitis acerifolia

value: wild species


title: AcVC

description: sample of Vitis acerifolia which was harvested during veraison and which was exposure to sunlight (CK)


title: La1M2R


title: La12V2R


title: Ci12VC


title: Ci1M3R


title: La12V1R


title: AcV1R

description: sample of Vitis acerifolia which was harvested during veraison and which was treated with exclusion of sunlight before pre-veraison


title: Brassica oleracea [F]

description:
oleracea
F
ABCDEFGHIJKLMNOS_raw.tsv

organism: Brassica oleracea

source_name: Brassica oleracea

value: First True Leaf


title: Brassica oleracea [D]

description:
oleracea
D
ABCDEFGHIJKLMNOS_raw.tsv


title: Ci12V1R


title: Brassica oleracea [E]

description:
oleracea
E
ABCDEFGHIJKLMNOS_raw.tsv


title: control-rep2

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: control_colon tissue

extract_protocol:
Total RNA was extracted by TRIZOL reagent according to the manufacturer’s instructions (Invitrogen, USA). The quality and quantity of total RNA were assesses using 2% agarose gels and Qubit® 3.0 fluurometer (Life Technologies, CA, USA). The concentration and integrity of RNA were assessed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 7 week older

tag: mouse group

value: control

value: colon tissue


title: AcPVC

description: sample of Vitis acerifolia which was harvested during PV and which was exposure to sunlight (CK)

value: berries


title: AcMC

description: sample of Vitis acerifolia which was harvested during mature and which was exposure to sunlight (CK)


title: control-rep3

tag: strain


title: AcPV1R

description: sample of Vitis acerifolia which was harvested during PV and which was treated with exclusion of sunlight before pre-veraison


title: TBLV-splice donor #9 tumor (9T)

city: Austin

first: Dennis

middle: Cates

last: Wylie

address: 102 East 24th Street

department: Center for Biomedical Research Support

institute: University of Texas at Austin

description:
exogenous retrovirus
PCR product sizes were 2.2 kb (Env-LTR), 1.6 kb (pol), and 0.56 (Gapdh)
s5

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were aligned to fasta file containing TBLV genome and mouse GAPDH sequence using BWA-MEM (version 0.7.12) in paired end mode using default settings
Likely PCR and optical duplicates were marked using Picard MarkDuplicates (version 2.19.1) using default settings and removed using samtools (version 0.1.19)
Number of reads aligned with each reference base at each position quantified using bam-readcount (version 0.8.0)
Genome_build: tblv_plusminus_rem_reference.fasta
Supplementary_files_format_and_content: tblv_plusminus_rem_processed_readcounts.tsv.gz contains aligned read counts for each position in reference.fasta in (gzipped) tab-separated values (tsv) text format

organism: Viruses

source_name: TBLV-SD-induced T-cell tumor

extract_protocol: PCR products were fragmented by sonication (200 bp target size) and used to make standard Illumina gDNA libraries by the the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF)

value: T-cell tumor-inducing MMTV-related strain TBLV with a mutation in 3' splice donor site (SD)

tag: amplicon

value: Two different portions of the wild-type TBLV genome plus Gapdh

tag: pcr product

value: Each sample had three PCR products:one from the TBLV pol region primers, one from the TBLV primers for the env-3'LTR junction, and one from cellular Gapdh primers as a control


title: TBLV-splice donor #10 tumor (10T)

description:
exogenous retrovirus
PCR product sizes were 2.2 kb (Env-LTR), 1.6 kb (pol), and 0.56 (Gapdh)
s6


title: TBLV-wild type #9 tumor (9T)

description:
exogenous retrovirus
PCR product sizes were 2.2 kb (Env-LTR), 1.6 kb (pol), and 0.56 (Gapdh)
s2

source_name: TBLV-WT-induced T-cell tumor

value: T-cell tumor-inducing MMTV-related strain TBLV


title: control-rep1

tag: age


title: TBLV-splice donor #7 tumor (7T)

description:
exogenous retrovirus
PCR product sizes were 2.2 kb (Env-LTR), 1.6 kb (pol), and 0.56 (Gapdh)
s4


title: TBLV-wild type #10 tumor (10T)

description:
exogenous retrovirus
PCR product sizes were 2.2 kb (Env-LTR), 1.6 kb (pol), and 0.56 (Gapdh)
s3


title: AcM3R

description: sample of Vitis acerifolia which was harvested during mature and which was treated with exclusion of sunlight during the whole developmental stages

value: mature


title: DSS-rep2

source_name: DSS_colon tissue

value: dextran sulfate sodium (DSS)-induced chronic colitis


title: AcM2R

description: sample of Vitis acerifolia which was harvested during mature and which was treated with exclusion of sunlight before veraison

value: exclusion of sunlight before veraison


title: DSS-rep3


title: AcM1R

description: sample of Vitis acerifolia which was harvested during mature and which was treated with exclusion of sunlight before pre-veraison


title: Ac2V2R

description: sample of Vitis acerifolia which was harvested during 2V and which was treated with exclusion of sunlight before veraison


title: TBLV-wild type #6 tumor (6T)

description:
exogenous retrovirus
PCR product sizes were 2.2 kb (Env-LTR), 1.6 kb (pol), and 0.56 (Gapdh)
s1


title: DSS-rep1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep3

status: Public on Jul 12 2019

city: Lakewood

first: Will

middle: E

last: Hinckley

address: 4440 Gondar Ave

department: Biology

institute: CSULB

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2A4R1

data_processing:
Rsubread aligned reads to the TAIR10 Genome
Rsubread converted aligned reads to count data
Noiseq normalized count data to read length to generate an FPKM dataset
Noiseq normalized to library size
HTSfilter removed genes with consistently low expression (zero at every time-point)
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKMafterfilter contains the FPKM values for every detectable transcipt in each of 36 libraries. The first part of the library name is the sample ,(W=WT, T1=TM1, T2=TM2), The letter refers to the replicate (A,B, or C), and the number at the end refers to the time-point (0 ,2, 4, or 6). If you average WA0, WB0, and WC0 you will have the average expression value for a given transcript in WT tissue at timepoint zero.
Supplementary_files_format_and_content: The other three files contain the averaged values of the 3 replicates for each detectable transcript. The 4 columns are the 4 time-points, in order.

organism: Arabidopsis thaliana

source_name: 6th true leaf

growth_protocol: All plants were grown in Sunshine® Mix #1 Fafard®-1P RSi (Sungro Horticulture). The soil was treated with Gnatrol WDG (Valent Professional Products) (0.3 g/500 ml H2O) to inhibit the growth of fungus gnat larvae, and plants were sub-irrigated with Gro-Power 4-8-2 (Gro-Power, Inc.) (10 ml per gallon). Plants were grown at 24°C in Percival AR66L2X growth chambers under a 20:4 light:dark diurnal cycle with a light intensity of 26-28 umoles photons m-2 sec-1. The low light intensity prevents light stress in older leaves, which was evident as anthocyanin accumulation at higher light intensities. To compensate for the reduced light intensity, the day length was extended. The 6th leaf to emerge was marked by tying threads around the petioles soon after emergence from the meristem. Plants were rotated daily and randomized in the chamber to prevent chamber position affects.

extract_protocol:
(n=54 per genotype) WT, atx Triple Mutant 1 (TM1), and atx Triple Mutant 2 (TM2) were grown simultaneously. Bolting (1 cm inflorescence) was measured and plants that bolted at the peak of TM bolting (days 24 and 25) were recorded and added to a list. At each time-point, 10 TM1 and 10 TM2 plants were randomly selected from this list and harvested. This strategy was used to ensure that harvested TM plants were developmentally similar. 10 random vegetative WT plants (same age) were selected for harvesting at the each time-point. Harvesting began at the peak of triple mutant bolting and continued three more times in two day increments. Leaf 6 was harvested (N=10 per line, per time point), ground, and homogenized in liquid nitrogen via mortar and pestle, and stored at -80C. The ground powder was divided into three for the production of three RNA-seq libraries (A-C) for each genotype.
BrAD-seq, (Townsley et. al.) https://doi.org/10.3389/fpls.2015.00366

treatment_protocol: no treatments

tag: development

value: bolting at T0, leaf senescence detected via separate phenotype analysis 2 days after T6


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep10

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2C2R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep12

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2C6R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep11

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2C4R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep5

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2B0R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep8

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2B6R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep6

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2B2R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep1

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2A0R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep2

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2A2R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep12

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1C6R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep11

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1C4R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep10

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1C2R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep7

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2B4R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 2 (TM2) rep4

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM2 FPKM
FPKMafterfilter
T2A6R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep3

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1A4R1


title: Homozygous atx1/atx3/atx4 Triple Mutant 1 (TM1) rep7

description:
ATX1=AT2G31650/SDG27            atx1  =SALK_149002                                    ATX3=AT3G61740/SDG14                         atx3  =GABI_128H01                                             ATX4=AT4G27910/SDG16                   atx4  =SALK_060156
190627 TM1 FPKM
FPKMafterfilter
T1B4R1


title: Wildtype Columbia-0 Ecotype rep11

description:
Wildtype Columbia Type 0
190627 WT FPKM
FPKMafterfilter
WC4R1

value: vegetative throughout timecourse