title: ZNF597_p.L283V_N03_0E015_x2_D5


title: HCHF_2years_SAMPLE 56

status: Public on Jul 10 2022

type: RNA

city: Winston-Salem

first: Laura

middle: A

last: Cox

state: NC

address: Medical Center Boulevard

department: Internal medicine-Section of Molecular Medicine

country: USA

institute: Wake Forest School of Medicine

description: IL_BPP2yc_168_15292_HFHC_2yr_liv.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

data_processing:
data for all samples were pre-processed identically for background correction and normalization with Illumina
Data filtering: Only those transcripts whose detection levels equaled or exceeded 0.2 (of the detection p-value 0.95) in greater or equal to 50% of the total sample were filtered. The filtered transcript data were quantile normalized and log2 transformed.
normalized data file includes quantile normalized and log2 transformed with GUI R

label: biotin

molecule: total RNA

organism: Papio hamadryas

source_name: Baboon Frozen Liver

label_protocol: cRNA was synthesized and biotin labeled using Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted from the homogenate and impurities removed using the RNeasy MinElute Kit

treatment_protocol: Biotinylated cRNA were prepared with the Amp kit for Illumina arrays

tag: gender

value: Female

tag: timepoint

value: 2 years

tag: diet

value: HCHF diet

tag: tissue

value: liver

tag: sample number


title: ZNF597_p.V21L_J13_OE015_x6_S4

type: SRA

city: Seattle

first: Alice

last: Berger

state: Washington

address: 1100 Fairview Ave N, Mailstop C2-023

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

library_source: transcriptomic

data_processing:
Illumina HiSeq 4000 reads were aligned by STAR v2.5.3a to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts
EdgeR v.3.22.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Assembly: hg19/GRCh37
Supplementary files format and content: transcript_quants_log2TPM.csv is a comma-separated values file of the log2 of TPM values of all samples. Each row is a gene transcript and each column is a sample.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were cultured for one day before and 96 hours after treatment.

extract_protocol:
Cells were lysed and RNA extracted with TRIzol (Invitrogen)
Nextera XT Index Kit v2, 75bp paired-end pre-pooled libraries

treatment_protocol: Cells were transduced with the ORF construct (if applicable) one day after plating. Infection efficiency is assessed at 24 hours post-infection with antibody selection.

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: ectopic exression

value: ZNF597 p.V21L


title: ZBTB24_WT_O24_OE014_x8_S3

value: ZBTB24 WT


title: HCHF_2years_SAMPLE 54

description: IL_BPP2yc_162_15163_HFHC_2yr_liv.AVG_Signal

scan_protocol: Standard Illumina hybridization protocol


title: HCHF_2years_SAMPLE 52

description: IL_BPP2yc_156_15874_HFHC_2yr_liv.AVG_Signal

value: Male


title: HCHF_2years_SAMPLE 55

description: IL_BPP2yc_165_16829_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 53

description: IL_BPP2yc_159_16527_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_WT_O24_B6_S5


title: ZBTB24_WT_O24_OE014_x7_S3


title: ZBTB24_p.Q669R_D08_OE014_x7_S3

value: ZBTB24 p.Q669R


title: ZBTB24_p.Q669R_D08_C2_S5


title: ZNF597_p.V21L_J13_0E015_x2_C4


title: HCHF_2years_SAMPLE 49

description: IL_BPP2yc_147_16424_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 50

description: IL_BPP2yc_150_14350_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.M78I_K18_OE014_x7_S3

value: ZBTB24 p.M78I


title: ZBTB24_p.Q669R_D08_C8_S5


title: HCHF_2years_SAMPLE 51

description: IL_BPP2yc_153_15581_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.Q669R_D08_OE014_x8_S3


title: HCHF_2years_SAMPLE 47

description: IL_BPP2yc_141_12719_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 48

description: IL_BPP2yc_144_15571_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.M78I_K18_F4_S5


title: HCHF_2years_SAMPLE 44

description: IL_BPP2yc_132_14062_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 45

description: IL_BPP2yc_135_16436_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 46

description: IL_BPP2yc_138_16538_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 43

description: IL_BPP2yc_129_16383_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.M78I_K18_OE014_x8_S3


title: ZBTB24_p.K123M_C08_OE014_x7_S3

value: ZBTB24 p.K123M


title: ZBTB24_p.K123M_C08_G7_S5


title: ZBTB24_p.K123M_C08_OE014_x8_S3


title: HCHF_2years_SAMPLE 42

description: IL_BPP2yc_126_15575_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 40

description: IL_BPP2yc_120_12681_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.G693S_C22_OE014_x8_S3

value: ZBTB24 p.G693S


title: HCHF_2years_SAMPLE 39

description: IL_BPP2yc_117_12481_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.G693S_C22_OE014_x7_S3


title: ZBTB24_p.G693S_C22_B8_S5


title: HCHF_2years_SAMPLE 37

description: IL_BPP2yc_111_12717_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 36

description: IL_BPP2yc_108_15560_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.G568C_L24_OE014_x8_S3

value: ZBTB24 p.G568C


title: HCHF_2years_SAMPLE 35

description: IL_BPP2yc_123_14369_HFHC_2yr_liv.AVG_Signal


title: ZBTB24_p.G568C_L24_OE014_x7_S3


title: ZBTB24_p.G568C_L24_B11_S5


title: ZBTB24_p.G568C_L24_B5_S5


title: ZBTB24_p.K123M_C08_G1_S5


title: U2AF1_WT_C08_0E015_x3_G7

value: U2AF1 WT


title: U2AF1_WT_C08_OE015_x6_S4


title: HCHF_2years_SAMPLE 34


title: HCHF_2years_SAMPLE 32

description: IL_BPP2yc_114_12423_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 30

description: IL_BPP2yc_090_18938_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 28

description: IL_BPP2yc_084_16499_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 33


title: HCHF_2years_SAMPLE 31


title: HCHF_2years_SAMPLE 29

description: IL_BPP2yc_087_15178_HFHC_2yr_liv.AVG_Signal


title: TPK1_WT_E13_G8_S5

value: TPK1 WT


title: TPK1_WT_E13_OE014_x7_S3


title: HCHF_2years_SAMPLE 41


title: TPK1_WT_E13_G2_S5


title: HCHF_2years_SAMPLE 26

description: IL_BPP2yc_078_14916_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 38


title: HCHF_2years_SAMPLE 27

description: IL_BPP2yc_081_12152_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.T213S_M08_OE014_x8_S3

value: TPK1 p.T213S


title: TPK1_p.T213S_M08_OE014_x7_S3


title: ZBTB24_p.G693S_C22_B2_S5


title: HCHF_2years_SAMPLE 24

description: IL_BPP2yc_072_16879_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.T213S_M08_D5_S5


title: TPK1_p.T213S_M08_D11_S5


title: TPK1_p.T205S_G12_OE014_x8_S3

value: TPK1 p.T205S


title: U2AF1_WT_C08_0E015_x2_G1


title: HCHF_2years_SAMPLE 23

description: IL_BPP2yc_069_16548_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 22

description: IL_BPP2yc_066_16246_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.T205S_G12_OE014_x7_S3


title: TPK1_p.T205S_G12_B9_S5


title: TPK1_WT_E13_OE014_x8_S3


title: HCHF_2years_SAMPLE 21

description: IL_BPP2yc_063_18024_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 19

description: IL_BPP2yc_057_16019_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 17

description: IL_BPP2yc_051_14850_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.T205S_G12_B3_S5


title: TPK1_p.P152T_K15_OE014_x7_S3

value: TPK1 p.P152T


title: HCHF_2years_SAMPLE 20

description: IL_BPP2yc_060_16741_HFHC_2yr_liv.AVG_Signal

value: 2 years


title: HCHF_2years_SAMPLE 18

description: IL_BPP2yc_054_15232_HFHC_2yr_liv.AVG_Signal

value: HCHF diet


title: TPK1_p.P152T_K15_OE014_x8_S3


title: TPK1_p.L185I_C18_OE014_x7_S3

value: TPK1 p.L185I


title: HCHF_2years_SAMPLE 14

description: IL_BPP2yc_042_15475_HFHC_2yr_liv.AVG_Signal

value: liver


title: TPK1_p.P152T_K15_G4_S5

value: lung adenocarcinoma


title: HCHF_2years_SAMPLE 25

description: IL_BPP2yc_075_12282_HFHC_2yr_liv.AVG_Signal

value: Female


title: TPK1_p.K111M_K21_OE014_x8_S3

value: TPK1 p.K111M


title: TPK1_p.L185I_C18_A8_S5


title: TPK1_p.L185I_C18_A2_S5


title: HCHF_2years_SAMPLE 13

description: IL_BPP2yc_039_14867_HFHC_2yr_liv.AVG_Signal

value: Male


title: HCHF_2years_SAMPLE 12

description: IL_BPP2yc_036_15889_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 15

description: IL_BPP2yc_045_16748_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 11

description: IL_BPP2yc_033_15566_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.K111M_K21_OE014_x7_S3


title: TPK1_p.K111M_K21_H10_S5


title: TPK1_p.G48C_P08_OE014_x8_S3

value: TPK1 p.G48C


title: HCHF_2years_SAMPLE 9

description: IL_BPP2yc_027_14922_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 10

description: IL_BPP2yc_030_15870_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 7

description: IL_BPP2yc_021_13644_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 6

description: IL_BPP2yc_018_14181_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 8

description: IL_BPP2yc_024_14948_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.G48C_P08_OE014_x7_S3


title: HCHF_2years_SAMPLE 16

description: IL_BPP2yc_048_14290_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.E81Q_L17_OE014_x7_S3

value: TPK1 p.E81Q


title: TPK1_p.G48C_P08_C12_S5


title: TPK1_p.E81Q_L17_OE014_x8_S3


title: HCHF_2years_SAMPLE 2

description: IL_BPP2yc_006_14473_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.G48C_P08_C6_S5


title: TPK1_p.E81Q_L17_A5_S5


title: HCHF_2years_SAMPLE 5

description: IL_BPP2yc_015_14077_HFHC_2yr_liv.AVG_Signal


title: HCHF_2years_SAMPLE 3

description: IL_BPP2yc_009_14847_HFHC_2yr_liv.AVG_Signal


title: TPK1_p.E81Q_L17_A11_S5


title: HCHF_7week_SAMPLE 110

description: IL_BPP2yc_330_16517_HFHC_7wk_liv.AVG_Signal

value: 7 weeks

value: HCHF


title: TPK1_p.K111M_K21_H4_S5


title: STK11_WT_P04_D10

value: STK11 WT


title: HCHF_7week_SAMPLE 109

description: IL_BPP2yc_327_16289_HFHC_7wk_liv.AVG_Signal


title: STK11_WT_O03_A10


title: STK11_WT_O04_B10


title: STK11_WT_E16_OE015_x6_S4


title: HCHF_2years_SAMPLE 4

description: IL_BPP2yc_012_14642_HFHC_2yr_liv.AVG_Signal


title: HCHF_7week_SAMPLE 107

description: IL_BPP2yc_321_16000_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 106

description: IL_BPP2yc_318_15820_HFHC_7wk_liv.AVG_Signal


title: STK11_WT_E16_OE015_x5_S4


title: STK11_WT_E16_0E015_x2_C2


title: HCHF_7week_SAMPLE 104

description: IL_BPP2yc_312_17233_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 105

description: IL_BPP2yc_315_19165_HFHC_7wk_liv.AVG_Signal


title: STK11_WT_E16_0E015_x3_C8


title: HCHF_7week_SAMPLE 102

description: IL_BPP2yc_306_16363_HFHC_7wk_liv.AVG_Signal


title: HCHF_2years_SAMPLE 1

description: IL_BPP2yc_003_13597_HFHC_2yr_liv.AVG_Signal


title: STK11_p.D194Y_P09_G10

value: STK11 p.D194Y


title: STK11_p.D194Y_O10_F10


title: STK11_WT_P03_C10


title: STK11_p.D194Y_O09_E10


title: HCHF_7week_SAMPLE 108

description: IL_BPP2yc_324_16101_HFHC_7wk_liv.AVG_Signal


title: SOX2_WT_V5_G19_OE014_x7_S3

value: SOX2 WT


title: SOX2_WT_V5_G19_OE014_x8_S3


title: HCHF_7week_SAMPLE 100

description: IL_BPP2yc_300_15279_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 103

description: IL_BPP2yc_309_16761_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 98

description: IL_BPP2yc_294_16408_HFHC_7wk_liv.AVG_Signal


title: SOX2_WT_V5_G19_C3_S5


title: SMAD4_p.V492F_K24_OE015_x6_S4

value: SMAD4 p.V492F


title: HCHF_7week_SAMPLE 111

description: IL_BPP2yc_333_17268_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 95

description: IL_BPP2yc_285_15175_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 99

description: IL_BPP2yc_297_17776_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 96

description: IL_BPP2yc_288_16017_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.V492F_K24_OE015_x5_S4


title: HCHF_7week_SAMPLE 94

description: IL_BPP2yc_282_14944_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 93

description: IL_BPP2yc_279_17971_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.V492F_K24_0E015_x2_F4


title: SMAD4_p.V492F_K24_0E015_x3_F10


title: SMAD4_p.R361H_N01_OE015_x6_S4

value: SMAD4 p.R361H


title: HCHF_7week_SAMPLE 101

description: IL_BPP2yc_303_16329_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 91

description: IL_BPP2yc_273_17190_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 90

description: IL_BPP2yc_270_16787_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.R361H_N01_0E015_x3_C11


title: SMAD4_p.R361H_N01_OE015_x5_S4


title: HCHF_7week_SAMPLE 89

description: IL_BPP2yc_267_15545_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 97

description: IL_BPP2yc_291_18141_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.P356R_L02_OE015_x6_S4

value: SMAD4 p.P356R


title: SOX2_WT_V5_G19_C9_S5


title: SMAD4_p.R361H_N01_0E015_x2_C5


title: SMAD4_p.P356R_L02_OE015_x5_S4


title: HCHF_7week_SAMPLE 88

description: IL_BPP2yc_264_14852_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.P356R_L02_0E015_x2_H4


title: SMAD4_p.P356R_L02_0E015_x3_H10


title: HCHF_7week_SAMPLE 86

description: IL_BPP2yc_258_14172_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 85

description: IL_BPP2yc_255_17898_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 83

description: IL_BPP2yc_249_17981_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.P215S_L05_OE015_x6_S4

value: SMAD4 p.P215S


title: SMAD4_p.P215S_L05_OE015_x5_S4


title: HCHF_7week_SAMPLE 82

description: IL_BPP2yc_246_17141_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.P215S_L05_0E015_x3_A11


title: HCHF_7week_SAMPLE 84

description: IL_BPP2yc_252_17165_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.P215S_L05_0E015_x2_A5


title: HCHF_7week_SAMPLE 80

description: IL_BPP2yc_240_14058_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 81

description: IL_BPP2yc_243_14154_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.G386V_P09_OE015_x6_S4

value: SMAD4 p.G386V


title: HCHF_7week_SAMPLE 87

description: IL_BPP2yc_261_14355_HFHC_7wk_liv.AVG_Signal

value: liver


title: SMAD4_p.G386V_P09_OE015_x5_S4

value: lung adenocarcinoma


title: HCHF_7week_SAMPLE 78

description: IL_BPP2yc_234_17903_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 79

description: IL_BPP2yc_237_18015_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 74

description: IL_BPP2yc_222_16827_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 77

description: IL_BPP2yc_231_17871_HFHC_7wk_liv.AVG_Signal


title: SMAD4_p.G386V_P09_0E015_x3_G11


title: SMAD4_p.G386V_P09_0E015_x2_G5


title: SMAD4_p.D493N_H06_OE015_x5_S4

value: SMAD4 p.D493N


title: SMAD4_p.D493N_H06_OE015_x6_S4


title: SMAD4_p.D493N_H06_0E015_x3_F9


title: HCHF_7week_SAMPLE 76

description: IL_BPP2yc_228_17340_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 72

description: IL_BPP2yc_216_13694_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 75

description: IL_BPP2yc_225_17873_HFHC_7wk_liv.AVG_Signal

value: Female


title: SMAD4_p.D493N_H06_0E015_x2_F3


title: RIT1_WT_J01_C6

value: RIT1 WT


title: HCHF_7week_SAMPLE 71

description: IL_BPP2yc_213_17826_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 92

description: IL_BPP2yc_276_14924_HFHC_7wk_liv.AVG_Signal


title: RIT1_WT_I02_B6


title: RIT1_WT_J02_D6


title: HCHF_7week_SAMPLE 73

description: IL_BPP2yc_219_17325_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 68

description: IL_BPP2yc_204_14908_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 69

description: IL_BPP2yc_207_16708_HFHC_7wk_liv.AVG_Signal

value: Male


title: HCHF_7week_SAMPLE 70

description: IL_BPP2yc_210_17199_HFHC_7wk_liv.AVG_Signal


title: RIT1_p.T76insTDLT_H09_OE015_x5_S4

value: RIT1 p.T76insTDLT


title: RIT1_WT_I01_A6


title: RIT1_p.T76insTDLT_H09_0E015_x3_G9


title: RIT1_p.T76insTDLT_H09_OE015_x6_S4


title: HCHF_7week_SAMPLE 67

description: IL_BPP2yc_201_18395_HFHC_7wk_liv.AVG_Signal

value: 7 weeks


title: RIT1_p.T76insTDLT_H09_0E015_x2_G3


title: HCHF_7week_SAMPLE 66

description: IL_BPP2yc_198_12218_HFHC_7wk_liv.AVG_Signal

value: HCHF


title: HCHF_7week_SAMPLE 64

description: IL_BPP2yc_192_16371_HFHC_7wk_liv.AVG_Signal


title: RIT1_p.F82L_N07_OE015_x5_S4

value: RIT1 p.F82L


title: RIT1_p.F82L_N07_OE015_x6_S4


title: HCHF_7week_SAMPLE 63

description: IL_BPP2yc_189_17139_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 62

description: IL_BPP2yc_186_16338_HFHC_7wk_liv.AVG_Signal


title: RIT1_p.F82L_N07_0E015_x2_E5


title: RIT1_p.F82L_N07_0E015_x3_E11


title: RIT1_p.F82L_B16_D1


title: HCHF_7week_SAMPLE 65

description: IL_BPP2yc_195_16413_HFHC_7wk_liv.AVG_Signal


title: RIT1_p.F82L_B15_C1


title: RIT1_p.F82L_A16_B1


title: RIT1_p.F82L_A15_A1


title: RBM45_WT_E11_OE014_x8_S3

value: RBM45 WT


title: RBM45_WT_E11_F8_S5


title: RBM45_WT_E11_OE014_x7_S3


title: HCHF_7week_SAMPLE 56

description: IL_BPP2yc_168_15292_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 54

description: IL_BPP2yc_162_15163_HFHC_7wk_liv.AVG_Signal


title: RBM45_p.M126I_H13_OE014_x8_S3

value: RBM45 p.M126I


title: HCHF_7week_SAMPLE 58

description: IL_BPP2yc_174_17829_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 53

description: IL_BPP2yc_159_16527_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 52

description: IL_BPP2yc_156_15874_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 51

description: IL_BPP2yc_153_15581_HFHC_7wk_liv.AVG_Signal


title: RBM45_WT_E11_F2_S5


title: HCHF_7week_SAMPLE 50

description: IL_BPP2yc_150_14350_HFHC_7wk_liv.AVG_Signal


title: RBM45_p.M126I_H13_OE014_x7_S3


title: HCHF_7week_SAMPLE 60

description: IL_BPP2yc_180_16321_HFHC_7wk_liv.AVG_Signal


title: RBM45_p.D434Y_G02_A9_S5

value: RBM45 p.D434Y


title: HCHF_7week_SAMPLE 57

description: IL_BPP2yc_171_16880_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 49

description: IL_BPP2yc_147_16424_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 48

description: IL_BPP2yc_144_15571_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 47

description: IL_BPP2yc_141_12719_HFHC_7wk_liv.AVG_Signal


title: RBM45_p.D434Y_G02_A3_S5


title: HCHF_7week_SAMPLE 55

description: IL_BPP2yc_165_16829_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 46

description: IL_BPP2yc_138_16538_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 59

description: IL_BPP2yc_177_17916_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 61

description: IL_BPP2yc_183_16400_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 45

description: IL_BPP2yc_135_16436_HFHC_7wk_liv.AVG_Signal


title: RBM34_WT_P21_OE014_x8_S3

value: RBM34 WT


title: HCHF_7week_SAMPLE 44

description: IL_BPP2yc_132_14062_HFHC_7wk_liv.AVG_Signal


title: RBM34_WT_P21_F6_S5


title: RBM34_WT_P21_OE014_x7_S3


title: HCHF_7week_SAMPLE 41

description: IL_BPP2yc_123_14369_HFHC_7wk_liv.AVG_Signal


title: RBM45_p.M126I_H13_F3_S5


title: RBM45_p.M126I_H13_F9_S5


title: RBM10_p.W658Y_F09_OE014_x8_S3

value: RBM10 p.W658Y


title: RBM10_p.W658Y_F09_H8_S5


title: RBM45_p.D434Y_G02_OE014_x8_S3


title: HCHF_7week_SAMPLE 42

description: IL_BPP2yc_126_15575_HFHC_7wk_liv.AVG_Signal


title: RBM34_WT_P21_F12_S5


title: RBM10_p.W658Y_F09_OE014_x7_S3


title: RB1_WT_F07_OE015_x6_S4

value: RB1 WT


title: HCHF_7week_SAMPLE 38

description: IL_BPP2yc_114_12423_HFHC_7wk_liv.AVG_Signal


title: RB1_WT_F07_0E015_x2_H2


title: RB1_WT_F07_OE015_x5_S4


title: RB1_WT_D20_D3


title: HCHF_7week_SAMPLE 43

description: IL_BPP2yc_129_16383_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 37

description: IL_BPP2yc_111_12717_HFHC_7wk_liv.AVG_Signal


title: RB1_WT_D19_C3


title: HCHF_7week_SAMPLE 35


title: HCHF_7week_SAMPLE 33

description: IL_BPP2yc_117_12481_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 32


title: HCHF_7week_SAMPLE 39


title: HCHF_7week_SAMPLE 31


title: HCHF_7week_SAMPLE 28

description: IL_BPP2yc_083_16499_HFHC_7wk_liv.AVG_Signal


title: RB1_p.Y756C_O22_B12

value: RB1 p.Y756C


title: HCHF_7week_SAMPLE 26

description: IL_BPP2yc_077_14916_HFHC_7wk_liv.AVG_Signal

value: liver


title: HCHF_7week_SAMPLE 27

description: IL_BPP2yc_080_12152_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 36

description: IL_BPP2yc_108_15560_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 40

description: IL_BPP2yc_120_12681_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 30

description: IL_BPP2yc_090_18938_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 1, Cre+ side, Tx: Cold

city: La Jolla

first: Yu

last: Wang

state: CA

address: 10550 N. Torrey Pines Rd.

institute: Scripps Research

data_processing:
Raw sequencing data was checked by FastQC and aligned to the GRCm39 reference genome (Ensembl version 104), and gene counts were quantified using Salmon (v1.5.1)
Assembly: GRCm39 reference genome (Ensembl version 104)
Supplementary files format and content: plain-text, tab-separated quantification files

organism: Mus musculus

source_name: inguinal adipose tissue

extract_protocol:
Total RNA was extracted from frozen tissue using TRIzol (Invitrogen) and RNeasy Mini kits (Qiagen).
Total RNA samples were prepared into RNAseq libraries using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® following the manufacturer’s recommended protocol. Briefly, 1ug total RNA was polyA selected for each sample, converted to double-stranded cDNA followed by fragmentation and ligation of sequencing adapters. The library was then PCR amplified for 8 cycles using barcoded PCR primers, purified, and size selected using AMPure XP Beads before loading onto an Illumina NextSeq2000 for 100 base single read sequencing.

treatment_protocol: Mice receive unilateral sensory ablation. Basically, animals have AAV encoding Cre-dependent DTA injected bilaterally in to thoracic-lumbar dorsal root ganglia, have retrograde AAV expressing Cre delivered into one side of iWAT and retrograde AAV expressing YFP delivered into the other side of iWAT. 3-4 weeks after surgery, mice were exposed to room temperature (RT) or cold (4C) for 5 h. iWAT were extracted for transcriptional profiling. Mice ear tag #10 and #11 were excluded for analysis due to inefficient viral labeling assessed by histology.

value: inguinal adipose tissue

tag: treatment

value: unilateral sensory ablation

tag: ear tag

tag: associated unilateral_surgery

value: Cre+

tag: temperature challenge

value: Cold


title: RB1_p.Y756C_A10_OE015_x6_S4

value: lung adenocarcinoma


title: RB1_p.Y756C_A10_0E015_x3_B7


title: Ear Tag: 9, Cre+ side, Tx: RT

value: RT


title: HCHF_7week_SAMPLE 25

description: IL_BPP2yc_074_12282_HFHC_7wk_liv.AVG_Signal

value: Female

value: 7 weeks


title: HCHF_7week_SAMPLE 23

description: IL_BPP2yc_068_16548_HFHC_7wk_liv.AVG_Signal

value: Male

value: HCHF


title: RB1_p.Y756C_A10_0E015_x2_B1


title: RB1_WT_C19_A3


title: RB1_p.E398L_F08_OE015_x6_S4

value: RB1 p.E398L


title: HCHF_7week_SAMPLE 29

description: IL_BPP2yc_087_15178_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 24

description: IL_BPP2yc_071_16879_HFHC_7wk_liv.AVG_Signal


title: RB1_WT_C20_B3


title: Ear Tag: 9, Cre- side, Tx: RT

value: Cre-


title: HCHF_7week_SAMPLE 21

description: IL_BPP2yc_062_18024_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 8, Cre- side, Tx: Cold


title: HCHF_7week_SAMPLE 22

description: IL_BPP2yc_065_16246_HFHC_7wk_liv.AVG_Signal


title: RB1_p.Y756C_O21_A12


title: HCHF_7week_SAMPLE 19

description: IL_BPP2yc_056_16019_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 20

description: IL_BPP2yc_059_16741_HFHC_7wk_liv.AVG_Signal


title: RB1_p.E398L_F08_OE015_x5_S4


title: HCHF_7week_SAMPLE 18

description: IL_BPP2yc_053_15232_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 1, Cre- side, Tx: Cold


title: HCHF_7week_SAMPLE 34


title: HCHF_7week_SAMPLE 17

description: IL_BPP2yc_050_14850_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 12, Cre+ side, Tx: RT


title: RB1_p.E398L_F08_0E015_x3_A9


title: RB1_p.Y756C_P21_C12


title: Ear Tag: 12, Cre- side, Tx: RT


title: HCHF_7week_SAMPLE 16

description: IL_BPP2yc_047_14290_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 15

description: IL_BPP2yc_044_16748_HFHC_7wk_liv.AVG_Signal


title: RB1_p.E398L_F08_0E015_x2_A3


title: HCHF_7week_SAMPLE 14

description: IL_BPP2yc_041_15475_HFHC_7wk_liv.AVG_Signal


title: RB1_p.A772S_P02_OE015_x6_S4

value: RB1 p.A772S


title: RB1_p.A772S_P02_OE015_x5_S4


title: HCHF_7week_SAMPLE 13

description: IL_BPP2yc_038_14867_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 10

description: IL_BPP2yc_029_15870_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 12

description: IL_BPP2yc_035_15889_HFHC_7wk_liv.AVG_Signal


title: RB1_p.A772S_P02_0E015_x2_F5


title: Ear Tag: 7, Cre- side, Tx: Cold


title: HCHF_7week_SAMPLE 11

description: IL_BPP2yc_032_15566_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 8

description: IL_BPP2yc_023_14948_HFHC_7wk_liv.AVG_Signal


title: RB1_p.A772S_P02_0E015_x3_F11


title: HCHF_7week_SAMPLE 9

description: IL_BPP2yc_026_14922_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 6, Cre- side, Tx: RT


title: Ear Tag: 6, Cre+ side, Tx: RT


title: Ear Tag: 7, Cre+ side, Tx: Cold


title: RB1_p.A722S_N02_D8

value: RB1 p.A722S


title: Ear Tag: 8, Cre+ side, Tx: Cold


title: Ear Tag: 4, Cre+ side, Tx: RT


title: HCHF_7week_SAMPLE 4

description: IL_BPP2yc_011_14642_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 3

description: IL_BPP2yc_008_14847_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 4, Cre- side, Tx: RT


title: RB1_p.A722S_M02_B8


title: HCHF_7week_SAMPLE 2

description: IL_BPP2yc_005_14473_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 1

description: IL_BPP2yc_002_13597_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 5

description: IL_BPP2yc_014_14077_HFHC_7wk_liv.AVG_Signal


title: HCHF_7week_SAMPLE 6

description: IL_BPP2yc_017_14181_HFHC_7wk_liv.AVG_Signal


title: LCLF_SAMPLE 111

value: baseline

value: LCLF


title: Ear Tag: 3, Cre- side, Tx: Cold


title: LCLF_SAMPLE 110

value: liver


title: HCHF_7week_SAMPLE 7

description: IL_BPP2yc_020_13644_HFHC_7wk_liv.AVG_Signal


title: Ear Tag: 3, Cre+ side, Tx: Cold

value: inguinal adipose tissue


title: LCLF_SAMPLE 108


title: LCLF_SAMPLE 106


title: LCLF_SAMPLE 105


title: RALA_WT_V5_J16_OE015_x5_S4

value: RALA WT


title: LCLF_SAMPLE 103


title: LCLF_SAMPLE 107


title: RALA_WT_V5_J16_0E015_x3_D10


title: Ear Tag: 2, Cre- side, Tx: RT

value: unilateral sensory ablation


title: Ear Tag: 2, Cre+ side, Tx: RT

value: Cre+


title: LCLF_SAMPLE 101


title: LCLF_SAMPLE 102


title: DrosWingDisc_24REts2

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

address: Weill Hall

department: Molecular & Cell Biology

institute: University of California, Berkeley

description: Single-cell RNA sequencing data collected from wing discs 24 hours into regeneration.

library_source: transcriptomic single cell

data_processing:
Sequencing reads were aligned to the Drosophila genome using the CellRanger software (v6.1.0)
Assembly: Drosophila genome version 6.24 (Source: FlyBase)
Supplementary files format and content: *_filtered_matrix.mtx: Genes by cells UMI count matrix (filtered output from CellRanger)
Supplementary files format and content: *_filtered_barcodes.tsv: Cell barcodes for filtered_matrix.mtx (filtered output from CellRanger)
Supplementary files format and content: *_filtered_features.tsv: Gene names for filtered_matrix.mtx (filtered output from CellRanger)
Supplementary files format and content: *_raw_matrix.mtx: Genes by cells UMI count matrix (unfiltered output, including empty droplets, from CellRanger)
Supplementary files format and content: *_raw_barcodes.tsv: Cell barcodes for raw_matrix.mtx (unfiltered output, including empty droplets, from CellRanger)
Supplementary files format and content: *_raw_features.tsv: Gene names for raw_matrix.mtx (unfiltered output, including empty droplets, from CellRanger)

organism: Drosophila melanogaster

source_name: Drosophila wing-imaginal disc

growth_protocol: Ets21C mutant Drosophila were raised at 18 degrees Celsius for 7 days, then shifted up to 30 degrees Celsius for 40 hours, and then shifted back down to 18 degrees Celsius for 1 day before dissection.

extract_protocol:
Each sample was loaded onto and barcoded by the 10x Chromium Single Cell 3' platform (v3.1 chemistry).
Illumina sequencing adapters were ligated on to cDNA molecules.

treatment_protocol: Wing disc tissue was dissociated in a collagenase-TrypLE or 0.25% Trypsin-ETDA cocktail (first (24REts1) and second (24REts2) replicate, respectively) to generate a single-cell suspension. In both replicates, disc-associated myoblasts were identified via a myoblast-specific fluorescent marker (Him-GFP) and removed via FACS.

value: Drosophila wing-imaginal disc

tag: genotype

value: w ; Ets21C-/- ; rn-Gal4, tub-GAL80ts, UAS-egr / Him-GFP

tag: tissue ablation period

value: 40 hours, starting at 7 days after egg lay

tag: regeneration period

value: 24 hours after ablation period


title: NRAS_WT_H03_OE014_x8_S3

value: lung adenocarcinoma

value: NRAS WT


title: NRAS_WT_H03_OE014_x7_S3


title: RALA_WT_V5_J16_0E015_x2_D4


title: LCLF_SAMPLE 100

value: Female


title: RALA_WT_V5_J16_OE015_x6_S4


title: LCLF_SAMPLE 109


title: Dros24R2WingDisc scRNA-seq

description: Single-cell RNA sequencing data collected from wing discs 24 hours into regeneration. Myoblasts were removed via FACS using marker Him-GFP

data_processing:
Library strategy: scRNA-seq
Sequencing reads were aligned to the Drosophila genome using the CellRanger software (v2.2).
Genome_build: Drosophila genome version 6.24
Supplementary_files_format_and_content: *_matrix.mtx: Genes by cells UMI count matrix (filtered output from CellRanger)
Supplementary_files_format_and_content: *_barcodes.tsv: Cell barcodes for matrix.mtx (filtered output from CellRanger)
Supplementary_files_format_and_content: *_genes.tsv: Gene names for matrix.mtx (filtered output from CellRanger)
Supplementary_files_format_and_content: *_raw_gene_bc_matrices_h5.h5: Genes by cells UMI count matrix for all sequenced barcodes, including empty droplets, in h5 compressed format (unfiltered output from CellRanger)

growth_protocol: Drosophila were raised at 18 degrees Celsius for 7 days, then shifted up to 30 degrees Celsius for 40 hours, and then shifted back down to 18 degrees Celsius for 1 day before dissection.

extract_protocol:
Each sample was loaded onto and barcoded by the 10x Chromium Single Cell 3' platform (v2 chemistry).
Illumina sequencing adapters were ligated on to cDNA molecules.

treatment_protocol: Wing disc tissue was dissociated in a collagenase-TrypLE cocktail to generate a single-cell suspension. For the second replicate (24R2), disc-associated myoblasts were identified via a myoblast-specific fluorescent marker (Him-GFP) and removed via FACS.

value: w; + ; rn-GAL4, UAS-eiger, tub-GAL80ts / Him-GFP


title: LCLF_SAMPLE 98

value: Male


title: RB1_p.A722S_N01_C8

value: RB1 p.A722S


title: LCLF_SAMPLE 99

value: baseline


title: LCLF_SAMPLE 97

value: LCLF


title: LCLF_SAMPLE 96

value: liver


title: LCLF_SAMPLE 104


title: LCLF_SAMPLE 95


title: LCLF_SAMPLE 94


title: NRAS_p.Q61L_I23_OE014_x8_S3

value: NRAS p.Q61L


title: Patient4 adjacent normal esophageal tissue

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

country: China

institute: The Affiliated Cancer Hospital of Nanjing Medical University

data_processing:
Basecalls performed using Solexa pipeline v1.8
Sequencing quality are examined by FastQC and trimmed reads (pass Illumina quality filter, trimmed 5',3'-adaptor bases by cutadapt) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software.
The abundance of tRF & tiRNA are evaluated using their sequencing counts and is normalized as counts per million of total aligned reads (CPM).
Assembly: hg19
Supplementary files format and content: Normalized read counts using DESeq2 in the statistical program R after removing the tsRNAs that were expressed in low levels.
Supplementary files format and content: Expression profiles

source_name: esophagus

extract_protocol:
tRNA derived fragments (tRF & tiRNA) are heavily decorated by RNA modifications that interfere with small RNA-seq library construction. We do the following treatments before library preparation for total RNA samples: 3'-aminoacyl (charged) deacylation to 3'-OH for 3'adaptor ligation, 3'-cP (2',3'-cyclic phosphate) removal to 3'-OH for 3'adaptor ligation, 5'-OH (hydroxyl group) phosphorylation to 5'-P for 5'-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2101.
For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50bp singleread.

value: adjacent normal esophageal tissue

tag: age (years)

tag: Stage

value: III

value: male


title: LCLF_SAMPLE 92

tag: gender


title: Patient3 adjacent normal esophageal tissue

value: II


title: LCLF_SAMPLE 93

tag: timepoint


title: NRAS_p.Q61L_I23_OE014_x7_S3


title: Patient2 adjacent normal esophageal tissue


title: DrosWingDisc_24REts1

value: Drosophila wing-imaginal disc

value: w ; Ets21C-/- ; rn-Gal4, tub-GAL80ts, UAS-egr / Him-GFP


title: LCLF_SAMPLE 91

tag: diet


title: NRAS_p.Q61L_I23_H9_S5


title: NRAS_WT_H03_D9_S5


title: LCLF_SAMPLE 90

tag: tissue


title: Patient4 esophageal cancer tissue

value: esophageal cancer tissue


title: LCLF_SAMPLE 88

tag: sample number


title: NRAS_p.Q61L_I23_H3_S5

tag: cell line

value: lung adenocarcinoma


title: Patient1 adjacent normal esophageal tissue


title: Dros24R1WingDisc scRNA-seq

value: w/+ ; + ;  rn-GAL4, UAS-eiger, tub-GAL80ts / +

value: 40 hours, starting at 7 days after egg lay

value: 24 hours after ablation period


title: LCLF_SAMPLE 87

value: Female


title: Patient3 esophageal cancer tissue


title: NRAS_WT_H03_D3_S5

tag: cell type

value: NRAS WT


title: NFE2L2_WT_M23_E9

tag: ectopic exression

value: NFE2L2 WT


title: LCLF_SAMPLE 85

value: baseline

value: LCLF


title: LCLF_SAMPLE 86

value: liver


title: NFE2L2_WT_E19_OE015_x6_S4


title: LCLF_SAMPLE 83

value: Male


title: Patient2 esophageal cancer tissue


title: LCLF_SAMPLE 84


title: LCLF_SAMPLE 82


title: NFE2L2_WT_E19_OE015_x5_S4


title: Patient1 esophageal cancer tissue

value: III


title: LCLF_SAMPLE 81


title: LCLF_SAMPLE 80


title: NFE2L2_WT_E19_0E015_x3_E8


title: NFE2L2_WT_E19_0E015_x2_E2


title: LCLF_SAMPLE 79


title: Donor_2_FSL_1_12H_Rep3_S126

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

data_processing:
bcl2fastq software of Illumina was used to transform .bcl files to .fastq files, trim adaptor sequence, and mask low-complexity sequence.
FastQC(Andrews et al. 2010) and MultiQC(Ewels et al. 2016) were used to confirm the good quality of the .fastq data.
kallisto(Bray et al. 2016) was used with a GRCh38 reference to generate the counts of reads mapped to each gene.
-------------------------------
Alignment with Tophat+Bowtie
Counting of transcripts with htseq-count
QC with RSeqC
Differential expression with EdgeR
Assembly: GRCh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample.

source_name: PBMCs

growth_protocol: DMEM+10%FBS+1% P/S

extract_protocol: Lysed in 50uL lysis buffer

treatment_protocol: Cells were treated with 50ug/mL of different bacterial lipid fractions

value: 12H timepoint

value: Blood (buffy coat)

tag: age

value: not determined

tag: Sex

tag: fraction

value: Positive CTRL

tag: number of cells

tag: total volume

tag: collection buffer

value: Lysis/Binding buffer; Invitrogen, cat # A33562

tag: run date

tag: machine

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 78

tag: gender

tag: timepoint


title: LCLF_SAMPLE 76

tag: diet

tag: tissue


title: LCLF_SAMPLE 77

tag: sample number


title: NFE2L2_p.T80K_J02_OE015_x6_S4

tag: cell line

tag: cell type

value: lung adenocarcinoma

value: NFE2L2 p.T80K


title: Donor_2_FSL_1_12H_Rep1_S124

tag: age


title: LCLF_SAMPLE 74


title: LCLF_SAMPLE 72


title: Donor_2_FSL_1_12H_Rep2_S125

tag: Sex


title: LCLF_SAMPLE 73


title: Donor_2_Pam3CSK4_12H_Rep2_S122

tag: fraction


title: LCLF_SAMPLE 71


title: LCLF_SAMPLE 75


title: NFE2L2_p.T80K_J02_0E015_x3_A10

tag: ectopic exression


title: LCLF_SAMPLE 70


title: LCLF_SAMPLE 89


title: Donor_2_Pam3CSK4_12H_Rep1_S121

tag: number of cells

tag: total volume


title: LCLF_SAMPLE 69


title: LCLF_SAMPLE 68


title: Donor_2_Pam3CSK4_12H_Rep3_S123

tag: collection buffer

tag: run date


title: Donor_2_LPS_12H_Rep3_S120

tag: machine

tag: flowcell id


title: LCLF_SAMPLE 66

tag: gender


title: LCLF_SAMPLE 65

tag: timepoint


title: NFE2L2_p.T80K_E23_A5


title: Donor_2_LPS_12H_Rep2_S119

tag: data output


title: Donor_2_LPS_12H_Rep1_S118

tag: tissue


title: LCLF_SAMPLE 63

tag: diet

tag: sample number


title: LCLF_SAMPLE 67


title: LCLF_SAMPLE 64


title: NFE2L2_p.T80K_J02_OE015_x5_S4

tag: cell line

tag: cell type


title: MYC_WT_K13_OE014_x7_S3

value: MYC WT


title: LCLF_SAMPLE 62


title: MYC_WT_K13_E4_S5


title: LCLF_SAMPLE 61


title: Donor_2_DMSO_12H_Rep3_S117

tag: age

tag: Sex

value: Negative CTRL


title: NFE2L2_p.T80K_J02_0E015_x2_A4

tag: ectopic exression


title: LCLF_SAMPLE 59


title: LCLF_SAMPLE 60

value: Female


title: LCLF_SAMPLE 57


title: Donor_2_DMSO_12H_Rep2_S116

tag: fraction

tag: number of cells


title: LCLF_SAMPLE 58


title: NFE2L2_p.T80K_E24_B5


title: MYC_WT_K13_E10_S5


title: LCLF_SAMPLE 55


title: LCLF_SAMPLE 56


title: Donor_2_Stim_A3_12H_Rep3_S114

description: Stimulated by : Syn i15:0-a15:0 PE

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: total volume

tag: collection buffer


title: MYC_p.E366Q_O07_OE014_x8_S3

value: MYC p.E366Q


title: MYC_p.E366Q_O07_OE014_x7_S3


title: LCLF_SAMPLE 54

value: baseline


title: MYC_WT_K13_OE014_x8_S3


title: Donor_2_Stim_A3_12H_Rep2_S113

description: Stimulated by : Syn i15:0-a15:0 PE

tag: run date

tag: machine


title: MYC_p.E366Q_O07_H5_S5


title: LCLF_SAMPLE 51

tag: gender

value: LCLF


title: LCLF_SAMPLE 50

tag: timepoint

value: liver


title: LCLF_SAMPLE 49

value: Male


title: Donor_2_Stim_A3_12H_Rep1_S112

description: Stimulated by : Syn i15:0-a15:0 PE

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 48

tag: diet

tag: tissue


title: Donor_2_Stim_A2_12H_Rep3_S111

description: Stimulated by : Syn a15:0-i15:0 PE


title: MET_WT_B12_0E015_x2_F1

tag: cell line

value: MET WT


title: Donor_2_DMSO_12H_Rep1_S115

value: 12H timepoint


title: Donor_2_Stim_A2_12H_Rep2_S110

description: Stimulated by : Syn a15:0-i15:0 PE

value: Blood (buffy coat)


title: MAX_WT_I12_OE014_x8_S3

tag: cell type

value: MAX WT


title: MAX_WT_I12_OE014_x7_S3


title: Donor_2_Stim_A1_12H_Rep3_S108

description: Stimulated by : Nat a15:0-i15:0 PE

tag: age

value: not determined


title: LCLF_SAMPLE 45

tag: sample number


title: LCLF_SAMPLE 44


title: MAX_WT_I12_G3_S5

tag: ectopic exression


title: MAX_p.R60del_O13_OE014_x8_S3

value: MAX p.R60del


title: LCLF_SAMPLE 53


title: LCLF_SAMPLE 43


title: Donor_2_Stim_A1_12H_Rep2_S107

description: Stimulated by : Nat a15:0-i15:0 PE

tag: Sex

tag: fraction

value: Lysis/Binding buffer; Invitrogen, cat # A33562


title: LCLF_SAMPLE 52


title: Vangl1-2 knockout rep2

city: San Francisco

first: Pao-Tien

last: Chuang

address: 555 Mission Bay Blvd. South

institute: University of California, San Francisco

description:
Vangl1-2 knockout rep2
processed data file: Vangl1-2 knockout at E12.5dpc.csv

data_processing:
remove adaptor with 'trim_galore'
align the reading to genome with 'Hisat2'
sort the SAM file and convert it to BAM file
create table counts with 'featurecounts'
generate DEG table with DeSeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: csv file

source_name: Vangl1-2 knockout_lung

extract_protocol:
Embronic lungs were collected, snap freezed in liquid nitrogen, and RNAs were extracted with the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Vangl1-/-; Vangl2-/-

value: Mouse embryonic lung

tag: Stage


title: Vangl1-2 knockout rep1

description:
Vangl1-2 knockout rep1
processed data file: Vangl1-2 knockout at E12.5dpc.csv


title: Donor_2_Stim_A1_12H_Rep1_S106

description: Stimulated by : Nat a15:0-i15:0 PE

tag: number of cells

tag: total volume

tag: collection buffer

tag: run date


title: LCLF_SAMPLE 42

tag: gender

tag: timepoint


title: MYC_p.E366Q_O07_H11_S5

value: lung adenocarcinoma


title: MAX_p.R60del_O13_OE014_x7_S3


title: Donor_1_FSL_1_12H_Rep3_S105

value: Positive CTRL

tag: machine

tag: flowcell id

tag: data output


title: Vangl1-2 Control rep3

description:
Vangl1-2 Control rep3
processed data file: Vangl1-2 knockout at E12.5dpc.csv

source_name: Vangl1-2 Control_lung

tag: tissue


title: LCLF_SAMPLE 47

value: Female

tag: diet


title: MAX_p.R60del_O13_A6_S5

tag: cell line

tag: cell type


title: Donor_1_FSL_1_12H_Rep2_S104

tag: age

tag: Sex


title: LCLF_SAMPLE 40

tag: sample number


title: Vangl1-2 knockout rep3

description:
Vangl1-2 knockout rep3
processed data file: Vangl1-2 knockout at E12.5dpc.csv

tag: genotype

tag: Stage


title: MAX_p.R60del_O13_A12_S5

tag: ectopic exression


title: Vangl1-2 Control rep2

description:
Vangl1-2 Control rep2
processed data file: Vangl1-2 knockout at E12.5dpc.csv


title: LCLF_SAMPLE 39


title: LCLF_SAMPLE 41


title: Donor_2_Stim_A2_12H_Rep1_S109

description: Stimulated by : Syn a15:0-i15:0 PE

tag: fraction

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: number of cells

tag: total volume

tag: collection buffer


title: LCLF_SAMPLE 46

tag: gender

tag: timepoint

value: baseline


title: Donor_1_FSL_1_12H_Rep1_S103

tag: run date

tag: machine

tag: flowcell id

tag: data output


title: MAX_p.R60del_I22_F6

tag: cell line

tag: cell type


title: LCLF_SAMPLE 38

tag: diet

value: LCLF

tag: tissue


title: Wnt5a-Sox9-Cre Mutant rep3

description:
Wnt5a-Sox9-Cre Mutant rep3
processed data file: Wnt5a-Sox9-Cre at E13.5dpc.csv

source_name: Wnt5a-Sox9-Cre Mutant_lung

tag: genotype

value: Wnt5af/f; Sox9Cre


title: Donor_1_Pam3CSK4_12H_Rep3_S102

tag: age

tag: Sex


title: Vangl1-2 Control rep1

description:
Vangl1-2 Control rep1
processed data file: Vangl1-2 knockout at E12.5dpc.csv

tag: Stage


title: LCLF_SAMPLE 37

value: liver

tag: sample number


title: MAX_p.R60del_I21_E6

tag: ectopic exression


title: MAX_p.R35L_H09_G5

value: MAX p.R35L


title: Wnt5a-Sox9-Cre Mutant rep1

description:
Wnt5a-Sox9-Cre Mutant rep1
processed data file: Wnt5a-Sox9-Cre at E13.5dpc.csv


title: Wnt5a-Sox9-Cre Mutant rep2

description:
Wnt5a-Sox9-Cre Mutant rep2
processed data file: Wnt5a-Sox9-Cre at E13.5dpc.csv


title: Donor_1_Pam3CSK4_12H_Rep2_S101

value: 12H timepoint

tag: fraction

tag: number of cells

tag: total volume

tag: collection buffer


title: LCLF_SAMPLE 36

tag: gender

value: Male

tag: timepoint


title: Donor_1_Pam3CSK4_12H_Rep1_S100

value: Blood (buffy coat)

tag: run date

tag: machine

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 35

tag: diet

tag: tissue


title: MAX_p.R35L_G10_F5

tag: cell line

tag: cell type


title: Donor_1_LPS_12H_Rep3_S99

tag: age

value: not determined

tag: Sex


title: Wnt5a-Sox9-Cre Control rep3

description:
Wnt5a-Sox9-Cre Control rep3
processed data file: Wnt5a-Sox9-Cre at E13.5dpc.csv

source_name: Wnt5a-Sox9-Cre Control_lung

tag: genotype

value: Wnt5af/+; Sox9Cre

tag: Stage


title: Donor_1_LPS_12H_Rep2_S98

tag: fraction

tag: number of cells

value: Lysis/Binding buffer; Invitrogen, cat # A33562


title: LCLF_SAMPLE 33

tag: sample number


title: MAX_p.R35L_C13_OE014_x8_S3

tag: ectopic exression


title: MAX_p.R35L_G09_E5


title: Donor_1_LPS_12H_Rep1_S97

tag: timepoint

tag: total volume

tag: collection buffer


title: LCLF_SAMPLE 34

tag: gender


title: Wnt5a-Sox9-Cre Control rep1

description:
Wnt5a-Sox9-Cre Control rep1
processed data file: Wnt5a-Sox9-Cre at E13.5dpc.csv


title: Wnt5a-Sox9-Cre Control rep2

description:
Wnt5a-Sox9-Cre Control rep2
processed data file: Wnt5a-Sox9-Cre at E13.5dpc.csv


title: Wnt5a-Dermo1-Cre Mutant rep3

description:
Wnt5a-Dermo1-Cre Mutant rep3
processed data file: Wnt5a-Dermo1-Cre at E12.5dpc.csv

source_name: Wnt5a-Dermo1-Cre Mutant_lung

value: Wnt5af/f; Dermo1Cre


title: LCLF_SAMPLE 32


title: MAX_p.R35L_C13_OE014_x7_S3


title: Wnt5a-Dermo1-Cre Mutant rep2

description:
Wnt5a-Dermo1-Cre Mutant rep2
processed data file: Wnt5a-Dermo1-Cre at E12.5dpc.csv

value: Mouse embryonic lung


title: LCLF_SAMPLE 31


title: MAX_p.R35L_C13_H1_S5

value: lung adenocarcinoma


title: MAX_p.R35L_C13_H7_S5


title: Wnt5a-Dermo1-Cre Mutant rep1

description:
Wnt5a-Dermo1-Cre Mutant rep1
processed data file: Wnt5a-Dermo1-Cre at E12.5dpc.csv


title: Donor_1_DMSO_12H_Rep1_S94

value: Negative CTRL

tag: run date

tag: machine

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 29

value: Female

tag: diet

tag: tissue


title: LCLF_SAMPLE 30


title: Donor_1_DMSO_12H_Rep3_S96

tag: age

tag: Sex


title: Donor_1_DMSO_12H_Rep2_S95


title: Donor_1_Stim_A3_12H_Rep3_S93

description: Stimulated by : Syn i15:0-a15:0 PE

value: Bacterial Lipid fractions from Akkermansia muciniphila


title: LUCIFERASE_A05_OE015_x6_S4

tag: cell line

tag: cell type

value: LUCIFERASE


title: LUCIFERASE_A05_0E015_x3_A7


title: Donor_1_Stim_A3_12H_Rep2_S92

description: Stimulated by : Syn i15:0-a15:0 PE

tag: fraction

tag: number of cells


title: LCLF_SAMPLE 27

value: baseline

value: LCLF

tag: sample number


title: Donor_1_Stim_A3_12H_Rep1_S91

description: Stimulated by : Syn i15:0-a15:0 PE

tag: timepoint


title: KEAP1_WT_E20_OE015_x6_S4

tag: ectopic exression

value: KEAP1 WT


title: LCLF_SAMPLE 26

value: liver


title: LUCIFERASE_A05_0E015_x2_A1


title: LCLF_SAMPLE 25


title: Wnt5a-Dermo1-Cre Control rep3

description:
Wnt5a-Dermo1-Cre Control rep3
processed data file: Wnt5a-Dermo1-Cre at E12.5dpc.csv

source_name: Wnt5a-Dermo1-Cre Control_lung

tag: genotype

value: Wnt5af/+; Dermo1Cre

tag: Stage


title: KEAP1_p.G603W_K03_OE014_x8_S3

value: KEAP1 p.G603W


title: KEAP1_p.G603W_K03_OE014_x7_S3


title: Donor_1_Stim_A2_12H_Rep2_S89

description: Stimulated by : Syn a15:0-i15:0 PE

value: 12H timepoint

value: Blood (buffy coat)

tag: total volume

tag: collection buffer

tag: run date


title: LCLF_SAMPLE 24

tag: gender

value: Male


title: DAP-seq HALO-GST negative control

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

description: HALO-GST

library_source: genomic

data_processing:
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence, then mapped to the Osativa v.7 reference genome whole genome using bowtie2 v2.2.8 with default parameters. Reads were filtered to include only those that mapped to one genomic location.
Assembly: Osativa v.7 reference genome
Supplementary files format and content: NarrowPeak files were generated by GEM v2.5

molecule: genomic DNA

organism: Oryza sativa

source_name: leaf

growth_protocol: genomic DNA was extracted from rice nipponbare leaves

extract_protocol:
genomic DNA was purified using a standard phenol:chloroform extraction protocol. HALO-BZIP fusion proteins were expressed using Promega's TNT rabbit reticulocyte expression system.
sequencing libraries were constructed as described in Bartlett et al., 2017
DAP-seq

value: leaf

tag: strain

value: nipponbare


title: DAP-seq OsBZIP69

tag: tissue


title: DAP-seq OsBZIP77


title: DAP-seq OsBZIP42


title: LCLF_SAMPLE 23

tag: diet


title: Donor_1_Stim_A1_12H_Rep3_S87

description: Stimulated by : Nat a15:0-i15:0 PE

tag: age

value: not determined

tag: Sex

value: Lysis/Binding buffer; Invitrogen, cat # A33562

tag: machine

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 28

tag: sample number


title: KEAP1_p.G603W_K03_D4_S5

tag: cell line

tag: cell type

value: lung adenocarcinoma


title: Donor_1_Stim_A2_12H_Rep1_S88

description: Stimulated by : Syn a15:0-i15:0 PE

tag: timepoint

tag: fraction

tag: number of cells


title: KEAP1_p.G603W_K03_D10_S5

tag: ectopic exression


title: Medulloblastoma cell line H01_223100

type: genomic

city: San Diego

first: Jill

middle: P

last: Mesirov

address: 9500 Gilman Drive

department: Medicine

institute: University of California, San Diego

hyb_protocol: Genomic DNA was digested, adaptor ligated, and amplified by polymerase chain reaction to achieve fragments ranging from 200 base pairs to 1,100 base pairs. These fragments were pooled, concentrated, and additionally fragmented with DNaseI, which was followed by labeling, denaturing, and hybridization to arrays in batches of 96 samples

scan_protocol: Arrays were then scanned by using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Signal intensities were normalized against a reference set of normal genomic DNA data, as previously described.
The processed data was generated using archived module (SNPFileCreator_SNP6) on the GenePattern Server. That module is currently archived in GitHub: https://github.com/genepattern/SNPFileCreator_SNP6.
column header informaton:
1. Sample (sample name)
2. Chromosome (chromosome number)
3. Start Position (segment start position, in bases)
4. End Position (segment end position, in bases)
5. Num markers (number of markers in segment)
6. Seg.CN (log2() -1 of copy number)]

label: Biotin

source_name: Medulloblastoma cell line H01_223100

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was prepared by using the Puregene DNA Extraction Kit (Gentra Systems, Minneapolis, MN), and total RNA was extracted by using Trizol (Invitrogen, Carlsbad, CA), both per manufacturers' instructions.

treatment_protocol: Snap-frozen tumors were obtained from Children's Oncology Group (ACNS02B3; n = 89) and from Children's Hospital Boston (n = 55), University of Washington Medical Center (n = 27), Texas Children's Hospital (n = 24), and Johns Hopkins Medical Center (n = 10). Normal cerebellum (n = 11) was obtained from University of Washington Medical Center and NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland, Baltimore, MD. All samples were collected with approval from respective institutional review boards, and proper informed consent and/or assent was obtained from all patients or their parents.    Tumors were processed at Children's Hospital Boston except for samples from Texas Children's, where similar protocols were used

value: medulloblastoma


title: LCLF_SAMPLE 22


title: Wnt5a-Dermo1-Cre Control rep2

description:
Wnt5a-Dermo1-Cre Control rep2
processed data file: Wnt5a-Dermo1-Cre at E12.5dpc.csv

tag: genotype

value: Mouse embryonic lung

tag: Stage


title: Medulloblastoma cell line H02_223116

source_name: Medulloblastoma cell line H02_223116


title: HCRED_D22_H3

value: HCRED


title: LCLF_SAMPLE 21

tag: gender

value: baseline


title: Medulloblastoma cell line G12_223274

source_name: Medulloblastoma cell line G12_223274


title: HCRED_D21_G3


title: LCLF_SAMPLE 20

value: LCLF

tag: tissue


title: Medulloblastoma cell line H12_238544

source_name: Medulloblastoma cell line H12_238544


title: LCLF_SAMPLE 19

tag: diet


title: Donor_1_Stim_A1_12H_Rep2_S86

description: Stimulated by : Nat a15:0-i15:0 PE

tag: age

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: total volume

tag: collection buffer

tag: run date


title: Donor_2_FSL_1_6H_Rep2_S83

value: 6H timepoint

tag: Sex

value: Positive CTRL

tag: machine

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 18

tag: timepoint

value: liver

tag: sample number


title: HCRED_C22_F3

tag: cell line

tag: cell type


title: Medulloblastoma cell line H10_238540

source_name: Medulloblastoma cell line H10_238540


title: Donor_1_Stim_A1_12H_Rep1_S85

description: Stimulated by : Nat a15:0-i15:0 PE

value: 12H timepoint

tag: fraction

tag: number of cells


title: LCLF_SAMPLE 17

source_name: Baboon Frozen Liver

tag: gender


title: Donor_2_Pam3CSK4_6H_Rep3_S81

tag: tissue

value: Blood (buffy coat)


title: LCLF_SAMPLE 16

value: Male

tag: diet


title: HCRED_B05_OE015_x5_S4

tag: ectopic exression


title: Medulloblastoma cell line H09_238538

source_name: Medulloblastoma cell line H09_238538


title: Donor_2_Pam3CSK4_6H_Rep1_S79

tag: age

tag: total volume


title: HCRED_B05_0E015_x3_D7


title: HCRED_B05_OE015_x6_S4


title: LCLF_SAMPLE 15


title: HCRED_B05_0E015_x2_D1


title: Medulloblastoma cell line H08_238536

source_name: Medulloblastoma cell line H08_238536


title: Medulloblastoma cell line H07_238534

source_name: Medulloblastoma cell line H07_238534


title: Medulloblastoma cell line H06_238532

source_name: Medulloblastoma cell line H06_238532


title: Medulloblastoma cell line H11_238542

source_name: Medulloblastoma cell line H11_238542


title: Donor_2_FSL_1_6H_Rep1_S82

source_name: PBMCs

tag: collection buffer

tag: run date


title: HCRED_C21_E3


title: Wnt5a-Dermo1-Cre Control rep1

description:
Wnt5a-Dermo1-Cre Control rep1
processed data file: Wnt5a-Dermo1-Cre at E12.5dpc.csv

tag: genotype

value: Wnt5af/+; Dermo1Cre

tag: Stage


title: Donor_2_LPS_6H_Rep2_S77

tag: Sex

tag: machine

tag: flowcell id

tag: data output


title: Donor_2_Pam3CSK4_6H_Rep2_S80

tag: timepoint


title: Medulloblastoma cell line H04_238528

source_name: Medulloblastoma cell line H04_238528

tag: cell type

tag: cell line


title: Donor_2_LPS_6H_Rep1_S76

tag: fraction

tag: number of cells


title: LCLF_SAMPLE 13

tag: gender

tag: diet

tag: tissue

tag: sample number


title: Medulloblastoma cell line H01_238522

source_name: Medulloblastoma cell line H01_238522


title: HCRED_A06_A7_S5

tag: ectopic exression


title: Donor_2_DMSO_6H_Rep3_S75

tag: age

value: Negative CTRL

tag: total volume

tag: collection buffer

tag: run date


title: LCLF_SAMPLE 11


title: LCLF_SAMPLE 10


title: HCRED_A06_A1_S5


title: FBXW7_WT_N11_G8

value: FBXW7 WT


title: Medulloblastoma cell line G12_238520

source_name: Medulloblastoma cell line G12_238520


title: Donor_2_FSL_1_6H_Rep3_S84

value: not determined

tag: Sex

value: Lysis/Binding buffer; Invitrogen, cat # A33562

tag: machine


title: Medulloblastoma cell line H02_238524

source_name: Medulloblastoma cell line H02_238524

value: medulloblastoma


title: Donor_2_DMSO_6H_Rep2_S74

tag: flowcell id

tag: data output


title: LCLF_SAMPLE 9

tag: timepoint


title: Donor_2_DMSO_6H_Rep1_S73


title: FBXW7_WT_M12_F8

tag: cell line

tag: cell type

value: lung adenocarcinoma


title: HCRED_A06_OE014_x8_S3

value: HCRED


title: FBXW7_WT_M11_E8


title: Medulloblastoma cell line G08_238512

source_name: Medulloblastoma cell line G08_238512


title: LCLF_SAMPLE 14

value: baseline


title: Donor_2_Stim_A3_6H_Rep3_S72

description: Stimulated by : Syn i15:0-a15:0 PE

tag: fraction

tag: number of cells


title: LCLF_SAMPLE 12

tag: gender

tag: diet

value: LCLF


title: Medulloblastoma cell line G07_238510

source_name: Medulloblastoma cell line G07_238510


title: LCLF_SAMPLE 8

tag: tissue

tag: sample number


title: FBXW7_WT_J03_OE015_x6_S4

tag: ectopic exression


title: LCLF_SAMPLE 7


title: Donor_2_Stim_A3_6H_Rep2_S71

description: Stimulated by : Syn i15:0-a15:0 PE

tag: age

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: total volume


title: FBXW7_WT_J03_OE015_x5_S4


title: Medulloblastoma cell line G06_238508

source_name: Medulloblastoma cell line G06_238508


title: Donor_2_Stim_A3_6H_Rep1_S70

description: Stimulated by : Syn i15:0-a15:0 PE

value: 6H timepoint

tag: collection buffer

tag: run date


title: Medulloblastoma cell line G04_238504

source_name: Medulloblastoma cell line G04_238504


title: LCLF_SAMPLE 5


title: Donor_2_Stim_A2_6H_Rep3_S69

description: Stimulated by : Syn a15:0-i15:0 PE

tag: Sex

tag: machine


title: FBXW7_WT_J03_0E015_x3_B10


title: Donor_2_LPS_6H_Rep3_S78

value: Positive CTRL

tag: flowcell id

tag: data output


title: Medulloblastoma cell line G03_238502

source_name: Medulloblastoma cell line G03_238502

tag: cell line


title: LCLF_SAMPLE 6

tag: timepoint

value: liver


title: LCLF_SAMPLE 4


title: FBXW7_WT_J03_0E015_x2_B4

tag: cell type


title: Medulloblastoma cell line B02_238380

source_name: Medulloblastoma cell line B02_238380


title: LCLF_SAMPLE 3

source_name: Baboon Frozen Liver


title: FBXW7_p.V464E_P15_G11

value: FBXW7 p.V464E


title: Medulloblastoma cell line A12_238376

source_name: Medulloblastoma cell line A12_238376


title: LCLF_SAMPLE 2


title: Donor_2_Stim_A2_6H_Rep1_S67

description: Stimulated by : Syn a15:0-i15:0 PE

value: Blood (buffy coat)

tag: fraction

tag: number of cells


title: Donor_2_Stim_A1_6H_Rep3_S66

description: Stimulated by : Nat a15:0-i15:0 PE


title: Donor_2_Stim_A2_6H_Rep2_S68

description: Stimulated by : Syn a15:0-i15:0 PE


title: FBXW7_p.V464E_O16_F11


title: Medulloblastoma cell line A10_238372

source_name: Medulloblastoma cell line A10_238372


title: Medulloblastoma cell line A07_238366

source_name: Medulloblastoma cell line A07_238366


title: LCLF_SAMPLE 1

tag: gender

value: Male

tag: diet


title: FBXW7_p.V464E_O15_E11


title: Donor_2_Stim_A1_6H_Rep2_S65

description: Stimulated by : Nat a15:0-i15:0 PE

tag: tissue


title: Donor_2_Stim_A1_6H_Rep1_S64

description: Stimulated by : Nat a15:0-i15:0 PE


title: Medulloblastoma cell line A05_238362

source_name: Medulloblastoma cell line A05_238362


title: Donor_1_FSL_1_6H_Rep3_S63


title: FBXW7_p.V464E_P16_H11

tag: ectopic exression


title: Medulloblastoma cell line H11_228672

source_name: Medulloblastoma cell line H11_228672


title: FBXW7_p.V464E_F01_0E015_x3_G8


title: Medulloblastoma cell line A04_238360

source_name: Medulloblastoma cell line A04_238360


title: FBXW7_p.V464E_F01_OE015_x6_S4


title: Donor_1_FSL_1_6H_Rep2_S62

source_name: PBMCs

tag: age


title: Donor_1_FSL_1_6H_Rep1_S61

tag: total volume


title: Medulloblastoma cell line H10_228656

source_name: Medulloblastoma cell line H10_228656


title: FBXW7_p.V464E_F01_OE015_x5_S4


title: morula RNA siMLL34 rep2

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road

department: School of life science and technology

institute: Tongji University

data_processing:
Sequenced reads were mapped to mm10 genome with hisat2 and only reads with MAPQ>30 were considered in following analysis. Expression index (RPKM) is generated by Stringtie. Reads count matrix for genes is generated by htseq. Differential expression analysis were performed by DESeq2 with adjusted p.value < 0.1, fold change >=1.5 and RPKM in higher expression condition >=1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files (generated by HT-seq) include raw reads count of genes in each Sample

source_name: mouse embryo

extract_protocol:
Harvested cells were washed three times in 0.5% BSA-PBS solution and transferred into the lysis buffer. cDNA were synthesized using primers with 24-nt poly(dT),then a universal tail was added to the second strand cDNAs. After 18-20 cyclesof PCR, the PCR product is purified by QIAquick PCR purification kit(28104).
The prepared cDNA are sheared using Covaris S220. Fragment ends are repaired using NEBNext End Repair Module(E6050), then a NEBNext dA-Tailing Module(E6053) was used to yield a protruding 3- 'A' base for ligation of Illumina's adapters.After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles. library fragments of 200-500bp were band isolated from an agarose gel.

treatment_protocol: For gene knockdown，small interference RNAs (siRNAs) against mouse Ash2l and Mll3，Mll4 were diluted in nuclease-free water to 20 μM. The siRNAs for a given gene were mixed for knock-down, with a working concentration of 5 μM. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. Allow oocytes to recover for at least 1 h in the incubator prior to in-vitro fertilization. The fertilized injected embryos were observed and summarized from the 2-cell stage to and 4.5 days post-activation (dpa).

tag: development stage

value: morula embryo

tag: transfection

tag: strain


title: FBXW7_p.V464E_F01_0E015_x2_G2


title: morula RNA siMLL34 rep1


title: morula RNA siMLL34 rep3


title: morula RNA siASH2L rep4


title: morula RNA siMLL34 rep5


title: Donor_1_Pam3CSK4_6H_Rep3_S60

tag: Sex

tag: collection buffer

tag: run date

tag: machine


title: ETV1_WT_V5_G24_OE015_x5_S4

tag: cell line

value: ETV1 WT


title: Medulloblastoma cell line H05_228576

source_name: Medulloblastoma cell line H05_228576

tag: cell type


title: Medulloblastoma cell line H08_228624

source_name: Medulloblastoma cell line H08_228624


title: morula RNA siMLL34 rep4


title: Donor_1_LPS_6H_Rep3_S57

tag: timepoint

tag: fraction

tag: flowcell id

tag: data output


title: morula RNA siASH2L rep3


title: Donor_1_Pam3CSK4_6H_Rep1_S58

tag: tissue

tag: number of cells


title: ETV1_WT_V5_G24_0E015_x3_E9

tag: ectopic exression


title: Medulloblastoma cell line H06_228592

source_name: Medulloblastoma cell line H06_228592


title: Medulloblastoma cell line H03_228544

source_name: Medulloblastoma cell line H03_228544


title: Medulloblastoma cell line H02_228528

source_name: Medulloblastoma cell line H02_228528


title: ETV1_WT_V5_G24_0E015_x2_E3


title: morula RNA siASH2L rep1


title: Donor_1_DMSO_6H_Rep3_S54

tag: age

value: Negative CTRL

tag: total volume


title: Donor_1_LPS_6H_Rep2_S56

value: not determined


title: Medulloblastoma cell line G07_228606

source_name: Medulloblastoma cell line G07_228606


title: Donor_1_LPS_6H_Rep1_S55

value: Lysis/Binding buffer; Invitrogen, cat # A33562


title: Donor_1_Pam3CSK4_6H_Rep2_S59


title: EGFR_WT_F16_OE015_x5_S4

value: EGFR WT


title: morula RNA siCtrl rep2

tag: development stage

tag: transfection

value: siCtrl


title: Medulloblastoma cell line G06_228590

source_name: Medulloblastoma cell line G06_228590

value: medulloblastoma


title: ETV1_WT_V5_G24_OE015_x6_S4

value: lung adenocarcinoma


title: morula RNA siCtrl rep3

tag: strain


title: EGFR_WT_F16_0E015_x3_B9


title: morula RNA siCtrl rep1


title: EGFR_WT_F16_0E015_x2_B3


title: Donor_1_DMSO_6H_Rep1_S52

tag: Sex

tag: collection buffer


title: Donor_1_DMSO_6H_Rep2_S53

tag: run date

tag: machine


title: Medulloblastoma cell line G05_228574

source_name: Medulloblastoma cell line G05_228574

tag: cell type

tag: cell line


title: morula RNA siASH2L rep2


title: EGFR_WT_F01_C4


title: EGFR_WT_F16_OE015_x6_S4


title: morula H3K4me1 siMLL34 rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm10 reference genome using bowtie2, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were detected (with Q30 unique reads) using macs14 (with -p 1e-6, --nomodel and --shiftize 73 parameters) relative to input samples. Peaks with fold enrichment < 10 were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files are generated using macs2 and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

extract_protocol:
500cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

treatment_protocol: For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For gene knockdown，small interference RNAs (siRNAs) against mouse Ash2l and Mll3，Mll4 were diluted in nuclease-free water to 20 μM. The siRNAs for a given gene were mixed for knock-down, with a working concentration of 5 μM. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. Allow oocytes to recover for at least 1 h in the incubator prior to in-vitro fertilization. The fertilized injected embryos were observed and summarized from the 2-cell stage to and 4.5 days post-activation (dpa).

tag: chip antibody


title: Medulloblastoma cell line G02_228526

source_name: Medulloblastoma cell line G02_228526


title: Medulloblastoma cell line G04_228558

source_name: Medulloblastoma cell line G04_228558


title: Donor_1_Stim_A3_6H_Rep3_S51

description: Stimulated by : Syn i15:0-a15:0 PE

tag: timepoint

tag: fraction

tag: flowcell id


title: morula H3K4me1 siMLL34 rep1


title: EGFR_WT_E02_B4


title: Medulloblastoma cell line G01_228510

source_name: Medulloblastoma cell line G01_228510


title: morula H3K4me3 siASH2L rep2


title: Donor_1_Stim_A3_6H_Rep2_S50

description: Stimulated by : Syn i15:0-a15:0 PE

tag: tissue

tag: number of cells

tag: data output


title: EGFR_p.T790M_p.L858R_P11_C11

tag: ectopic exression

value: EGFR p.T790M p.L858R


title: EGFR_WT_E01_A4


title: Donor_1_Stim_A3_6H_Rep1_S49

description: Stimulated by : Syn i15:0-a15:0 PE

tag: age

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: total volume


title: Medulloblastoma cell line F10_228652

source_name: Medulloblastoma cell line F10_228652


title: EGFR_p.T790M_p.L858R_O12_B11


title: Donor_1_Stim_A2_6H_Rep3_S48

description: Stimulated by : Syn a15:0-i15:0 PE

value: 6H timepoint


title: morula H3K4me1 siASH2L rep2

tag: development stage

tag: transfection

tag: strain


title: Donor_1_Stim_A2_6H_Rep2_S47

description: Stimulated by : Syn a15:0-i15:0 PE

tag: Sex

tag: collection buffer

tag: run date


title: morula H3K4me3 siASH2L rep1


title: EGFR_p.T790M_p.L858R_O11_A11

tag: cell line

tag: cell type


title: Donor_1_Stim_A2_12H_Rep3_S90

description: Stimulated by : Syn a15:0-i15:0 PE

tag: timepoint

value: 12H timepoint

tag: machine


title: Donor_1_Stim_A2_6H_Rep1_S46

description: Stimulated by : Syn a15:0-i15:0 PE

tag: fraction

tag: flowcell id


title: Medulloblastoma cell line F06_228588

source_name: Medulloblastoma cell line F06_228588


title: morula input siMLL34

tag: chip antibody


title: EGFR_p.T790M_p.L858R_E17_OE015_x6_S4


title: Medulloblastoma cell line F03_228540

source_name: Medulloblastoma cell line F03_228540


title: Donor_1_Stim_A1_6H_Rep3_S45

description: Stimulated by : Nat a15:0-i15:0 PE

source_name: PBMCs

tag: tissue

tag: number of cells

tag: data output


title: EGFR_p.T790M_p.L858R_E17_OE015_x5_S4

tag: ectopic exression


title: Medulloblastoma cell line F01_228508

source_name: Medulloblastoma cell line F01_228508


title: Medulloblastoma cell line E11_228666

source_name: Medulloblastoma cell line E11_228666


title: Donor_1_Stim_A1_6H_Rep2_S44

description: Stimulated by : Nat a15:0-i15:0 PE

tag: age

tag: total volume


title: morula H3K4me1 siASH2L rep1

source_name: mouse embryo

tag: development stage

tag: transfection

tag: strain


title: morula input siASH2L


title: EGFR_p.T790M_p.L858R_E17_0E015_x3_D8


title: Medulloblastoma cell line F07_228604

source_name: Medulloblastoma cell line F07_228604


title: Donor_1_Stim_A1_6H_Rep1_S43

description: Stimulated by : Nat a15:0-i15:0 PE

tag: Sex

tag: collection buffer

tag: run date


title: morula H3K4me3 siCtrl rep1


title: morula H3K4me3 siCtrl rep2


title: Medulloblastoma cell line E06_228586

source_name: Medulloblastoma cell line E06_228586

tag: cell type

tag: cell line


title: Donor_2_FSL_1_2H_Rep2_S41

tag: timepoint

value: 2H timepoint

tag: fraction

value: Positive CTRL

tag: machine


title: Medulloblastoma cell line E04_228554

source_name: Medulloblastoma cell line E04_228554


title: EGFR_p.S645C_B08_OE014_x8_S3

value: EGFR p.S645C


title: morula H3K4me1 siCtrl rep1

tag: chip antibody


title: Medulloblastoma cell line E03_228538

source_name: Medulloblastoma cell line E03_228538


title: EGFR_p.S645C_B08_OE014_x7_S3


title: morula input siCtrl


title: Donor_2_Pam3CSK4_2H_Rep3_S39

tag: tissue

value: Blood (buffy coat)

tag: number of cells

tag: flowcell id


title: EGFR_p.S645C_B08_E7_S5

tag: ectopic exression


title: Medulloblastoma cell line E02_228522

source_name: Medulloblastoma cell line E02_228522


title: EGFR_p.S645C_B08_E1_S5


title: Medulloblastoma cell line D09_228632

source_name: Medulloblastoma cell line D09_228632


title: CTNNB1_WT_H05_E9_S5

value: CTNNB1 WT


title: Donor_2_Pam3CSK4_2H_Rep2_S38

tag: age

tag: total volume

tag: data output


title: Donor_2_FSL_1_2H_Rep1_S40


title: ESC input

source_name: mouse embryonic stem cells

tag: development stage

value: mouse embryonic stem cells

tag: transfection

value: wild type

tag: strain

value: mouse ES cell R1


title: morula H3K4me1 rep2

value: morula embryo


title: Medulloblastoma cell line D05_228568

source_name: Medulloblastoma cell line D05_228568


title: Donor_2_FSL_1_2H_Rep3_S42

value: not determined

tag: Sex

tag: collection buffer

value: Lysis/Binding buffer; Invitrogen, cat # A33562

tag: run date


title: Donor_2_Pam3CSK4_2H_Rep1_S37

tag: timepoint


title: Medulloblastoma cell line D07_228600

source_name: Medulloblastoma cell line D07_228600

tag: cell type

value: medulloblastoma

tag: cell line


title: ESC H3K4me1 rep1

tag: chip antibody


title: CTNNB1_p.S37C_J06_OE014_x8_S3

value: lung adenocarcinoma

value: CTNNB1 p.S37C


title: EGFR_p.T790M_p.L858R_E17_0E015_x2_D2

value: EGFR p.T790M p.L858R


title: Medulloblastoma cell line D10_228648

source_name: Medulloblastoma cell line D10_228648


title: Donor_2_LPS_2H_Rep2_S35

tag: tissue

tag: fraction

tag: machine


title: morula H3K4me1 rep1


title: CTNNB1_WT_H05_E3_S5

tag: ectopic exression


title: Medulloblastoma cell line D01_228504

source_name: Medulloblastoma cell line D01_228504


title: CTNNB1_p.S37C_J06_B10_S5


title: Donor_2_LPS_2H_Rep3_S36

tag: age

tag: number of cells

tag: flowcell id


title: ESC H3K4me1 rep2

tag: development stage


title: morula input

tag: transfection


title: Donor_2_LPS_2H_Rep1_S34

tag: total volume

tag: data output


title: Medulloblastoma cell line C09_228630

source_name: Medulloblastoma cell line C09_228630


title: morula H3K4me1 siCtrl rep2

value: siCtrl

tag: strain


title: CTNNB1_p.S33N_B07_D7_S5

value: CTNNB1 p.S33N


title: Medulloblastoma cell line C07_228598

source_name: Medulloblastoma cell line C07_228598


title: Donor_2_DMSO_2H_Rep3_S33

source_name: PBMCs

value: 2H timepoint

tag: Sex

value: Negative CTRL

tag: collection buffer

tag: run date


title: 8 cell H3K4me1 rep2

value: 8-cell embryo


title: Donor_2_DMSO_2H_Rep2_S32

tag: timepoint

value: Blood (buffy coat)


title: Donor_2_DMSO_2H_Rep1_S31


title: CASP8_WT_V5_P19_OE015_x6_S4

tag: cell line

tag: cell type

value: CASP8 WT


title: Medulloblastoma cell line C01_228502

source_name: Medulloblastoma cell line C01_228502


title: CASP8_WT_V5_P19_OE015_x5_S4


title: 4 cell H3K4me1 rep2

value: 4-cell embryo

tag: chip antibody


title: 8 cell input

value: wild type


title: Donor_2_Stim_A3_2H_Rep2_S29

description: Stimulated by : Syn i15:0-a15:0 PE

tag: tissue

tag: fraction

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: machine


title: CASP8_WT_V5_P19_0E015_x2_H5

tag: ectopic exression


title: CASP8_WT_V5_P19_0E015_x3_H11


title: Medulloblastoma cell line B09_228628

source_name: Medulloblastoma cell line B09_228628


title: Medulloblastoma cell line C02_228518

source_name: Medulloblastoma cell line C02_228518


title: Medulloblastoma cell line B11_228660

source_name: Medulloblastoma cell line B11_228660


title: 4 cell H3K4me1 rep1

source_name: mouse embryo


title: CTNNB1_p.S33N_B07_OE014_x7_S3


title: Donor_2_Stim_A3_2H_Rep3_S30

description: Stimulated by : Syn i15:0-a15:0 PE

tag: age

tag: number of cells

tag: flowcell id


title: Donor_2_Stim_A3_2H_Rep1_S28

description: Stimulated by : Syn i15:0-a15:0 PE

tag: total volume


title: Donor_2_Stim_A2_2H_Rep3_S27

description: Stimulated by : Syn a15:0-i15:0 PE

tag: data output


title: 4 cell input

tag: development stage

tag: transfection

tag: strain


title: CASP8_WT_N15_C9


title: Medulloblastoma cell line B07_228596

source_name: Medulloblastoma cell line B07_228596


title: 2 cell H3K4me1 rep2

value: 2-cell embryo


title: 8 cell H3K4me1 rep1


title: Medulloblastoma cell line A12_228674

source_name: Medulloblastoma cell line A12_228674


title: Medulloblastoma cell line C05_228566

source_name: Medulloblastoma cell line C05_228566


title: Donor_2_Stim_A2_2H_Rep1_S25

description: Stimulated by : Syn a15:0-i15:0 PE

value: not determined

tag: Sex

tag: collection buffer

tag: run date


title: 2 cell input


title: Medulloblastoma cell line A08_228610

source_name: Medulloblastoma cell line A08_228610

tag: cell type

tag: cell line


title: CASP8_WT_M15_A9


title: Donor_2_Stim_A2_2H_Rep2_S26

description: Stimulated by : Syn a15:0-i15:0 PE

tag: timepoint

tag: tissue

value: Lysis/Binding buffer; Invitrogen, cat # A33562


title: CASP8_WT_N16_D9


title: AURKB_WT_V5_A17_OE014_x8_S3

value: AURKB WT


title: Medulloblastoma cell line A07_228594

source_name: Medulloblastoma cell line A07_228594

value: medulloblastoma


title: Donor_2_Stim_A1_2H_Rep3_S24

description: Stimulated by : Nat a15:0-i15:0 PE

tag: fraction

tag: machine


title: Donor_2_Stim_A1_2H_Rep2_S23

description: Stimulated by : Nat a15:0-i15:0 PE

tag: age


title: Medulloblastoma cell line A06_228578

source_name: Medulloblastoma cell line A06_228578


title: C2-DJH-9-4

first: Hongmeng

last: Yu

address: No.83, Fenyang Road

department: Department of Otolaryngology

institute: Eye & ENT Hospital, Fudan University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Assembly: hg19

organism: Rattus norvegicus

source_name: DMSO-treated BMSC

extract_protocol: RNA extraction

tag: gender

value: female

value: Bone marrow-derived stem cell

tag: treatment

value: DMSO


title: C3-DJH-9-4


title: R3-DJH-9-4

source_name: Ginsenoside Rb1-treated BMSC

value: Ginsenoside Rb1


title: AURKB_WT_V5_A17_OE014_x7_S3

value: lung adenocarcinoma

tag: ectopic exression


title: CASP8_WT_M16_B9


title: Donor_2_Stim_A1_2H_Rep1_S22

description: Stimulated by : Nat a15:0-i15:0 PE

value: 2H timepoint

tag: number of cells

tag: total volume

tag: flowcell id

tag: data output


title: 2 cell H3K4me1 rep1

tag: development stage

tag: chip antibody

tag: transfection

tag: strain


title: C1-DJH-9-4

tag: cell type


title: AURKB_WT_V5_A17_C7_S5

tag: cell line


title: Donor_1_FSL_1_2H_Rep2_S20

tag: timepoint

tag: tissue

tag: Sex

value: Positive CTRL

tag: collection buffer

tag: run date


title: Donor_1_FSL_1_2H_Rep3_S21

value: Blood (buffy coat)

tag: age

tag: fraction

tag: machine


title: AURKB_WT_V5_A17_C1_S5

tag: ectopic exression


title: R1-DJH-9-4

tag: gender

tag: treatment


title: 2326409_MPLW515L_IL13_rep3

city: Memphis

first: Shibiao

last: Wan

state: Tennessee

address: 262 DANNY THOMAS PLACE

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (GRCh38) (STAR v2.7) and then the gene level values were quantified (RSEM v1.31) based on GENCODE annotation (v31) .
Assembly: mm10
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Primary cells

growth_protocol: cKIT+ cells were cultured in StemSpan media for 4 days

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: In the presence or absence of murine IL-13

value: Megakaryocytes


title: 2326407_MPLW515L_IL13_rep1


title: Donor_1_Pam3CSK4_2H_Rep3_S18

tag: number of cells

tag: total volume

tag: flowcell id

tag: data output


title: ARAF_WT_N09_F5_S5

tag: cell type

value: ARAF WT


title: ARAF_WT_OE014_x8_S3

tag: cell line


title: Donor_1_FSL_1_2H_Rep1_S19

tag: timepoint


title: R2-DJH-9-4


title: 2326406_MPLW515L_Ctrl_rep3

value: Ctrl


title: 2326408_MPLW515L_IL13_rep2


title: EPC non-infected 3

city: Helsinki

first: Krista

last: Tuohinto

address: Haartmaninkatu 8

department: Research Program Unit, CAN-PRO

country: Finland

institute: University of Helsinki

data_processing:
Data was processed by Novogene (Cambridge, UK):
Original image data was transformed to sequenced reads by CASAVA base recognition (base calling).
Raw data were cleaned from low quality reads and reads containing adapter and poly-N-sequences in FASTP.
Clean reads were mapped to the human genome (GRCh38.p12) using HISAT2 with parameters—dta—phred33.
Read counts were generated by FeatureCounts.
Differentially expressed genes were determined using the R package DESeq2. The resulting P values were adjusted using Benjamini and Hochberg’s approach for controlling FDR. Genes with adjusted P value <0.05 were assigned as differentially expressed.
Assembly: GRCh38.p12
Supplementary files format and content: Samples combined as matrix both as tab-delimited text file and as tab-separated values in Excel spreadsheet.

source_name: EPC

growth_protocol: EPCs were maintained in EBM-2 media supplemented with 10% fetal bovine serum (FBS) and microvascular supplement bullet kit (EGM-2, Lonza) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol: Total RNA was isolated from three independent experiments using the NucleoSpin RNA extraction kit (Macherey-Nagel), after which purity and concentration was determined with NanoDrop spectrophotometer (Thermo Scientific).

treatment_protocol: EPCs were mock (no virus) or KSHV-infected for 7 days at MOI 1-2 in the presence of polybrene 8 ug/ml by spinoculation at 450g 30min RT.

value: EPC

value: primary endothelial cells

tag: source

value: whole peripheral blood

tag: developmental stage

value: progenitor

value: non-infected

tag: time

value: Day 7


title: Donor_1_LPS_2H_Rep3_S15

tag: tissue

value: not determined

tag: Sex

tag: collection buffer

value: Lysis/Binding buffer; Invitrogen, cat # A33562

tag: run date


title: ARAF_WT_OE014_x7_S3

tag: ectopic exression


title: EPC non-infected 2


title: Donor_1_LPS_2H_Rep1_S13

tag: age

tag: fraction

tag: machine


title: B15_blood_CTLA4_late_rep5

first: Robert

last: Saddawi-Konefka

address: 3855 Health Sciences Dr

institute: UC San Diego

data_processing:
reads were aligned to the mm10 GRCm39 genome using STAR v2.7.9 with default options
resulting BAM files were sorted by name using samtools v1.7
reads per transcript were quantified using HTSeq-count v0.13.5
transcript ensembl IDs were translated to MGI IDs using biomaRt, in the case that multiple transcripts corresponded to a single MGI ID the reads were summed
Genome_build: mm10 GRCm39
Supplementary_files_format_and_content: HTSeq-count .counts files

source_name: Peripheral blood

growth_protocol: Orthotopic transplantation of 10^6 4MOSC1 tumor cells into the tongues of WT C57Bl/6 animals; grown for 10 days in vivo.

extract_protocol:
Blood was collected with cheek bleeds into BD Microtainer capillary blood collection tubes (365974) to a volume of at least 100μL per animal. Care was taken to remove clots from samples and 100μL of each sample was transferred into microcentrifuge tubes containing 1mL TRIzol. RNA was then isolated using Qiagen RNeasy® Mini Columns (74004; Qiagen, Germantown MD) according to manufacturers recommendations and including an on-column DNase I digestion. Yield and integrity of RNA was confirmed by reading absorbance at 260, 280 and 230 nm using a NanoDrop ND-1000 (NanoDrop Technologies; Thermo Fisher Scientific, Inc., Wilmington, DE, USA) and with the Agilent 2200 Tapestation (Agilent Technologies, Inc.). Library preparation and paired-end 150bp (PE150, Illumina) RNA sequencing was performed by Novogene (Novogene Corporation, Sacramento, USA).
Paired end reads were aligned using STAR v2.7.9 using default options. STAR index was created using the GRCm39 primary genome FASTA and annotation files.
Resulting BAM files were sorted by name using samtools v1.7 then gene counts were quantified using HTSeq-count v0.13.5. Pairwise differential expression was calculated and PCA plots were created using DESeq2 v1.32.0.

treatment_protocol: Treatment in vivo with two doses of ⍺CTLA-4 followed by either an early or late neck dissection.

tag: strain

tag: treatment

tag: surgery

value: Late


title: EPC non-infected 1

tag: cell type


title: 2326405_MPLW515L_Ctrl_rep2


title: B12_blood_CTLA4_late_rep2


title: Donor_1_Pam3CSK4_2H_Rep2_S17

source_name: PBMCs

tag: number of cells

tag: total volume

tag: flowcell id

tag: data output


title: 2326404_MPLW515L_Ctrl_rep1


title: Donor_1_Pam3CSK4_2H_Rep1_S16

tag: timepoint


title: ARAF_p.V145L_M02_OE014_x8_S3

tag: cell line

value: ARAF p.V145L


title: ARAF_p.V145L_M02_OE014_x7_S3

value: lung adenocarcinoma


title: EPC KSHV-infected 3

tag: source

tag: developmental stage

value: KSHV-infection

tag: time


title: B13_blood_CTLA4_late_rep3


title: ARAF_p.V145L_M02_C11_S5

tag: ectopic exression


title: ARAF_p.V145L_M02_C5_S5


title: Donor_1_DMSO_2H_Rep3_S12

value: 2H timepoint

tag: tissue

tag: age

tag: Sex

value: Negative CTRL

tag: collection buffer

tag: run date


title: EPC KSHV-infected 1

tag: treatment


title: Donor_1_LPS_2H_Rep2_S14

value: Blood (buffy coat)

tag: fraction

value: Positive CTRL

tag: machine


title: ARAF_p.S214F_P10_OE014_x8_S3

tag: cell type

value: ARAF p.S214F


title: B11_blood_CTLA4_late_rep1

tag: strain

tag: surgery


title: ARAF_WT_N09_F11_S5

value: ARAF WT


title: EPC KSHV-infected 2

value: EPC

value: primary endothelial cells


title: Donor_1_DMSO_2H_Rep2_S11

tag: timepoint

tag: number of cells

tag: total volume

tag: flowcell id

tag: data output


title: B14_blood_CTLA4_late_rep4


title: Donor_1_Stim_A3_2H_Rep3_S9

description: Stimulated by : Syn i15:0-a15:0 PE

value: Bacterial Lipid fractions from Akkermansia muciniphila


title: ARAF_p.S214F_P10_OE014_x7_S3

tag: cell line

tag: ectopic exression


title: B10_blood_CTLA4_early_rep5

value: Early


title: ARAF_p.S214F_P10_D6_S5


title: Donor_1_DMSO_2H_Rep1_S10

tag: tissue

tag: age


title: ARAF_p.S214F_P10_D12_S5


title: Donor_1_Stim_A3_2H_Rep2_S8

description: Stimulated by : Syn i15:0-a15:0 PE

tag: Sex

tag: collection buffer


title: B8_blood_CTLA4_early_rep3

tag: treatment


title: S04 - KO HDM-02

city: Xi'an

first: Ying

last: Chang

address: Xianning West Road

institute: Xi'an Jiaotong University

description: 04_M19_130155-130327-Chang-KO_HDM-465_Data

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.

source_name: asthmatic mouse model

label_protocol: Microarray assay was performed using a service provider (LC Sciences). A strand-labeling reaction was carried out with total RNA (0.5 ug), control oligo-nucleotides, App-Cap3(5’-adenylated and 3’-dideoxy oligo-adaptor) and T4 RNA ligase (Rnl2tr-K227Q, New England BioLabs) in T4 RNA ligase buffer with PEG 8000 and RNase inhibitor (Promega).  The reaction mixture was incubated at 16ºC for 16 hours and stopped by adding equal volume of hybridization buffer.  The adapter sequence contains a tag segment for capturing fluorescent dye during a later dye staining process.

growth_protocol: C57BL/6 female mice (6-8 wk) were purchased from Charles River (Montreal, Canada). All animals were treated and maintained under a protocol approved by the Animal Care Committee of McGill University, in accordance with guidelines set by the Canadian Council on Animal Use and Care.

extract_protocol: Total miRNA were extracted from mouse lung tissue by miRNA extracting kit (Qiagen, Germany). Equal amount of RNA sample from each mice of different groups was pooled respectively for miRNA profiling assay using µParaflo®Microfluidic Biochip miRNA microarray (LC Sciences, Houston, USA).

treatment_protocol: Wild type and IL-17KO mice were exposed to purified HDM extract (Greer Laboratories, Lenoir, NC) intranasally (25 ug of protein in 10 ul of saline) for 5 days/week for five consecutive weeks. The equivalent volume of saline was used as the control. Each group contained 10 mice. The mice were killed at 24 h after the last exposure.

value: lung tissue

tag: genotype

value: HDM extract


title: S03 - KO Saline-03

description: 03_M19_130152-130327-Chang-KO_Saline-455_Data

value: saline


title: S04 - KO HDM-03


title: ARAF_p.S214F_p.D429A_C05_OE014_x8_S3

value: ARAF p.S214F p.D429A


title: S04 - KO HDM-01


title: ARAF_p.S214F_p.D429A_C05_OE014_x7_S3


title: B6_blood_CTLA4_early_rep1


title: S03 - KO Saline-02


title: B9_blood_CTLA4_early_rep4


title: ARAF_p.S214F_p.D429A_C05_F1_S5


title: B5_blood_unt_none_rep5

value: Untreated


title: Donor_1_Stim_A2_2H_Rep1_S4

description: Stimulated by : Syn a15:0-i15:0 PE

value: not determined

tag: fraction

value: Lysis/Binding buffer; Invitrogen, cat # A33562

tag: run date

tag: machine


title: ARAF_p.S214C_p.D429A_N08_OE014_x8_S3

tag: cell type

value: lung adenocarcinoma

value: ARAF p.S214C p.D429A


title: Donor_1_Stim_A3_2H_Rep1_S7

description: Stimulated by : Syn i15:0-a15:0 PE

tag: timepoint

value: 2H timepoint

value: Blood (buffy coat)


title: B7_blood_CTLA4_early_rep2

tag: strain

tag: surgery


title: Donor_1_Stim_A1_2H_Rep3_S3

description: Stimulated by : Nat a15:0-i15:0 PE

tag: number of cells

tag: total volume

tag: flowcell id


title: B2_blood_unt_none_rep2


title: B1_blood_unt_none_rep1


title: Donor_1_Stim_A1_2H_Rep1_S1

description: Stimulated by : Nat a15:0-i15:0 PE

tag: data output


title: S02 - WT HDM-01

description: 02_M19_130151-130327-Chang-WT_HDM-450_Data

tag: tissue

value: WT


title: HCT116_OTS964_P-Ser7_ChIP_seq_rep2

status: Public on Jul 09 2022

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA.
Sequence reads with an alignment score <20 reads were discarded.
Resulting bam files were converted into bedgraph format using the genomecov command of bedtools.
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph

source_name: HCT116 cells in culture, 4h after treatment

growth_protocol: Human colorectal HCT116 cell line was maintained in DMEM/high glucose media supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2.

extract_protocol:
Protein G Dynabeads (Thermo Fisher Scientific, 10009D) were pre-blocked with BSA for 4 h, washed 3 times with RIPA buffer (50 mM Tris-Cl, pH 8, 150 mM NaCl, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1x protease inhibitors, Sigma, P8340), followed by the incubation with specific antibody for 4 h at 4°C. Cells were crosslinked with 1% formaldehyde for 10 min, reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed twice with ice-cold PBS, scraped, and pelleted. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20 x 7s (amp 0.85) using 5/64 probe (QSonica Q55A). Clarified extracts (13,000g for 10 min) were precleared with protein G Dynabeads rotating for 2-4 h at 4°C and then incubated overnight with antibody pre-bound to protein G Dynabeads. For each ChIP-seq experiment we performed 2 technical replicates and pooled them together.
ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2, NEB E7335S, E7500S).

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. HCT116 cells were plated onto 150 cm2 plates to reach 75 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO) or 30 nM OTS964 for 4 h.

value: HCT116 (wild type)

tag: time point

value: OTS964 30nM

tag: chip antibody

value: RNA pol II CTD phospho Ser7 antibody (Active Motif #61087)


title: Donor_1_Stim_A1_2H_Rep2_S2

description: Stimulated by : Nat a15:0-i15:0 PE

tag: age

tag: Sex

value: Bacterial Lipid fractions from Akkermansia muciniphila

tag: collection buffer


title: S01 - WT Saline-01

description: 01_M19_130150-130327-Chang-WT_Saline-450_Data

tag: genotype

tag: treatment


title: S03 - KO Saline-01


title: Donor_1_Stim_A2_2H_Rep3_S6

description: Stimulated by : Syn a15:0-i15:0 PE

tag: fraction

tag: run date

tag: machine


title: ARAF_p.S214F_p.D429A_C05_F7_S5

data_processing:
Illumina HiSeq 4000 reads were aligned by STAR v2.5.3a to BAM files.
Picard tools v.1.114 used mark duplicate reads, add read group info, and reorder BAMs.
BAMs are indexed using samtools v.0.1.19
FeatureCounts from Subread v.1.5.3 was used to quantify gene transcripts
EdgeR v.3.22.3 was used to normalize read counts and obtain CPM and RPKM values.
CPM values were used to filter the gene list  down to the 12,887 genes with average log2CPM >0.1 across all samples. RPKM values were converted into TPM values.
Assembly: hg19/GRCh37
Supplementary files format and content: transcript_quants_log2TPM.csv is a comma-separated values file of the log2 of TPM values of all samples. Each row is a gene transcript and each column is a sample.

extract_protocol:
Cells were lysed and RNA extracted with TRIzol (Invitrogen)
Nextera XT Index Kit v2, 75bp paired-end pre-pooled libraries

tag: cell line

tag: cell type

tag: ectopic exression


title: Donor_1_Stim_A2_2H_Rep2_S5

description: Stimulated by : Syn a15:0-i15:0 PE

tag: timepoint

tag: number of cells

tag: total volume


title: ARAF_p.S214C_p.D429A_N08_OE014_x7_S3


title: S02 - WT HDM-03

tag: tissue


title: HCT116_OTS964_RNAPII_ChIP_seq_rep2

tag: time point

value: Rpb1 NTD (D8L4Y) Rabbit mA (Cell Signaling, #14958)


title: HCT116_OTS964_P-Ser2_ChIP_seq_rep1

tag: chip antibody

value: RNA pol II CTD phospho Ser2 antibody (Active Motif #61083)


title: B4_blood_unt_none_rep4

tag: strain

tag: surgery


title: S01 - WT Saline-03

value: lung tissue


title: B3_blood_unt_none_rep3


title: S02 - WT HDM-02

value: HDM extract


title: HCT116_DMSO_P-Ser7_ChIP_seq_rep2

value: DMSO (solvent)


title: ARAF_p.S214C_p.D429A_N08_E5_S5


title: HCT116_DMSO_P-Ser7_ChIP_seq_rep1


title: HCT116_DMSO_P-Ser2_ChIP_seq_rep1


title: HCT116_DMSO_P-Ser5_ChIP_seq_rep1

value: RNA pol II CTD phospho Ser5 antibody (Active Motif #61085)


title: HCT116_DMSO_P-Ser2_ChIP_seq_rep2


title: HCT116_OTS964_P-Ser2_ChIP_seq_rep2


title: HCT116_OTS964_P-Ser5_ChIP_seq_rep1


title: HCT116_OTS964_P-Ser5_ChIP_seq_rep2


title: HCT116_DMSO_RNAPII_ChIP_seq_rep1


title: HCT116_OTS964_RNAPII_ChIP_seq_rep1


title: S01 - WT Saline-02

value: saline


title: HCT116_OTS964_P-Ser7_ChIP_seq_rep1


title: db21-aqr-ots964-rep2

data_processing:
library strategy: iCLIP
iCLIP sequencing reads were processed on the iMaps server using the iCount software (https://github.com/tomazc/iCount).
Experimental barcodes were removed and sequencing reads aligned with STAR (Dobin et al., 2013) to hg38 human reference genome (build GRCh38 primary assembly GENCODE version 27), allowing two mismatches and ten secondary alignments.
Unique Molecular Identifiers (UMIs), were used to distinguish and remove PCR duplicates. To determine protein-RNA contact sites, the uniquely mapped sequencing read preceding nucleotide was assigned as the crosslink site event.
Summary of cDNA counts within genes and genic regions was generated with iCount summary function after normalising the counts by the length of corresponding regions.
Significant contact sites were identified as iCLIP peaks, using the iCount peak function, based on false discovery rate (FDR) < 0.05 comparing specific sites within a window of three nucleotides with randomised data (100 permutations) and within co-transcribed regions (https://github.com/tomazc/iCount/blob/master/iCount/analysis/peaks.py).
The significant crosslink signal was normalised by sequencing deep and million of tags (CPM). Combined genome-wide BigWig coverage tracks of U2AF65, SF3B1 and AQR iCLIP were generated using deepTools (Ramirez et al., 2014) normalised by sequencing deep and million of tags (CPM) and binned per nucleotide.
Genome_build: GRCh38 GENCODE version 27 annotation
Supplementary_files_format_and_content: Individual cross-link bed files, individual cross-link peaks bedgraphs,  grouped cross-link bed files  and CPM normalised bigwigs

extract_protocol:
Described in detail in library construction protocol
iCLIP was performed as previously described (Huppertz et al., 2014) with only minor modifications described below. Each cell pellet (originally from one 150 cm2 plate) was lysed in 1 ml of lysis buffer and the lysate was homogenized by passing three-times through an insulin syringe. Lysate was treated with 4 U/ml Turbo DNase (Thermo Fisher, AM2238), 12 U/ml RNase I (Thermo Fisher, AM2295) shaking at 1100 rpm and 37°C for 3 min. Clarified extracts (21000g for 30 min) were incubated for 2 h with appropriate antibody pre-bound to 50 µl of protein G Dynabeads. After series of stringent washes, adenylated L3 RNA adapter was ligated to the 3’end of crosslinked RNAs. Proteins and crosslinked RNAs were resolved by SDS-PAGE (NuPAGE 4-12% Bis-Tris Protein Gel, Thermo Fisher Scientific, NP0322) and transferred to nitrocellulose membrane. The region of the membrane containing the radioactively labeled crosslinked protein–RNA complexes was excised, RNA was isolated and reverse transcribed to cDNA. cDNA was fractionated using urea denaturing gel electrophoresis and three fractions running between 70-85 nt (L-low), 85-120 nt (M-medium) and 120-200 nt (H-high) were isolated. Each fraction was independently circularized by single-stranded DNA ligase, annealed to an oligonucleotide complementary to the restriction site and cut between the two adapter regions by BamHI. After final PCR amplification using P3 and P5 Solexa primers all three fractions were pooled together in ratio 1:5:5 (L:M:H). Multiplexed libraries were sequenced as 50bp single-end reads on Illumina sequencer (EMBL, Heidelberg).

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. The Pladienolide B inhibitor was purchased from Cayman Chemical (#16538) and diluted in DMSO. HCT116 cells were plated onto 150 cm2 plates to reach 75 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO), 50 nM OTS964, 186nM Pladienolide B for 1 h. The cells were than crosslinked by UV-C (254 nm, 200 mJ/cm2).

tag: cell line background

tag: group


title: db21-sf3b1-dmso-rep1

tag: treatment

value: DMSO


title: db21-sf3b1-plad-rep2

value: PLAD


title: db21-sf3b1-ots964-rep1


title: db21-sf3b1-dmso-rep2