title: RPI46_31_eGFP++


title: RPI46_30_eGFP++

status: Public on Feb 15 2017

type: SRA

city: Philadelphia

first: Pablo

middle: G

last: Camara

state: PA

address: 3700 Hamilton Walk

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Sequenced reads were de-multiplexed, trimmed, and mapped to the UCSC mouse reference (mm10) using tophat v2.1.1 with parameter –no-novel-juncs
Gene expression was quantified using htseq-count v0.6.1 with parameters -s no
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: In vitro differentiation of mESCs into motor neurons, main experiment

growth_protocol: mESC based differentiations into motor neurons were performed using the method of Wichterle at al. (Cell 110, 385-397, (2010))

extract_protocol:
Embryoid bodies were dissociated into single cells using the Worthington Biochemical Papain Dissociation System (LK003178). Single cell deposition was accomplished using a Beckman Coulter MoFlo Astrios EQ cell sorter into 96 well plates. Cells were then snap-frozen and subsequently lysed.
Single-cell RNA-seq libraries were prepared using a modified CEL-seq protocol (Hashimshony et al., Cell Reports 2, 666-673 (2012)). Briefly, the mRNA in each cell lysate was reverse transcribed with barcoded primers, the single cell samples were pooled, second strand cDNA was synthesized, and then linearly amplified by in vitro transcription with T7 RNA polymerase. The amplified RNA (aRNA) was chemically fragmented and T4 RNA ligase was used to ligate Illumina 3’-RNA adapters. The aRNA was then run on an Agilent Bioanalyzer to assess proper fragmentation and then reverse transcribed to generate cDNA and subjected to PCR enrichment.

tag: sampling day

value: Day 6


title: RPI46_25_eGFP++


title: RPI46_26_eGFP++


title: RPI46_24_eGFP++


title: RPI46_23_eGFP++


title: RPI46_22_eGFP++


title: RPI46_27_eGFP++


title: RPI46_19_eGFP++


title: RPI46_20_eGFP++


title: RPI46_21_eGFP++


title: RPI46_18_eGFP++


title: RPI46_17_eGFP++


title: RPI46_16_eGFP++


title: RPI46_13_eGFP++


title: RPI46_35_eGFP++


title: RPI46_11_eGFP++


title: RPI46_14_eGFP++


title: RPI46_9_eGFP++


title: RPI46_10_eGFP++


title: RPI46_5_eGFP++


title: RPI46_8_eGFP++


title: RPI46_29_eGFP++


title: RPI46_6_eGFP++


title: RPI46_41_eGFP++


title: RPI46_28_eGFP++


title: RPI46_3_eGFP++


title: RPI39_95


title: RPI39_94


title: RPI46_0_eGFP++


title: RPI46_1_eGFP++


title: RPI46_2_eGFP++


title: RPI39_90


title: RPI39_91


title: RPI39_93


title: RPI39_89


title: RPI46_12_eGFP++


title: RPI39_87


title: RPI39_86


title: RPI39_85


title: RPI39_83


title: RPI39_84


title: RPI46_7_eGFP++


title: RPI46_4_eGFP++


title: RPI39_92


title: RPI39_82


title: RPI39_78


title: RPI39_77


title: RPI39_80


title: RPI39_75


title: RPI39_76


title: RPI39_79


title: RPI39_74


title: RPI39_73


title: RPI39_72


title: RPI39_71


title: RPI39_70


title: RPI39_88


title: RPI39_68


title: RPI39_81


title: RPI39_67


title: RPI39_64


title: RPI39_66


title: RPI39_65


title: RPI39_69


title: RPI39_62


title: RPI39_61


title: RPI39_60


title: RPI39_63


title: RPI39_59


title: RPI39_55


title: RPI39_56


title: RPI39_53


title: RPI39_58


title: RPI39_54


title: RPI39_57


title: RPI39_46


title: RPI39_49


title: RPI39_47


title: RPI39_50


title: RPI39_52


title: RPI39_51


title: RPI39_43


title: RPI39_36


title: RPI39_42


title: RPI39_44


title: RPI39_33


title: RPI39_34


title: RPI39_32


title: RPI39_30


title: RPI39_40


title: RPI39_29


title: RPI39_26


title: RPI39_39


title: RPI39_27


title: RPI39_25


title: RPI39_31


title: RPI39_37


title: RPI39_38


title: RPI39_28


title: RPI39_45


title: RPI39_48


title: RPI39_20


title: RPI39_35


title: RPI39_17


title: RPI39_24


title: RPI39_18


title: RPI39_23


title: RPI39_15


title: RPI39_8


title: RPI39_12


title: RPI39_13


title: RPI39_10


title: RPI39_7


title: RPI39_6


title: RPI39_9


title: RPI39_21


title: RPI39_11


title: RPI39_1


title: RPI39_4


title: RPI39_2


title: RPI39_22


title: RPI39_41


title: RPI39_0


title: RPI39_3


title: RPI39_5


title: RPI39_19


title: RPI33_93

value: Day 3


title: RPI33_92


title: RPI39_16


title: RPI33_89


title: RPI33_94


title: RPI33_95


title: RPI33_91


title: RPI39_14


title: RPI33_83


title: RPI33_81


title: RPI33_87


title: RPI33_82


title: RPI33_80


title: RPI33_76


title: RPI33_85


title: RPI33_78


title: RPI33_75


title: RPI33_84


title: RPI33_73


title: RPI33_77


title: RPI33_72


title: RPI33_79


title: RPI33_70


title: RPI33_69


title: RPI33_68


title: RPI33_67


title: RPI33_71


title: RPI33_88


title: RPI33_65


title: RPI33_62


title: RPI33_64


title: RPI33_60


title: RPI33_58


title: RPI33_74


title: RPI33_66


title: RPI33_57


title: RPI33_61


title: RPI33_55


title: RPI33_59


title: RPI33_51


title: RPI33_53


title: RPI33_54


title: RPI33_46


title: RPI33_47


title: RPI33_48


title: RPI33_49


title: RPI46_15_eGFP++


title: RPI33_90


title: RPI33_40


title: RPI33_39


title: RPI33_44


title: RPI33_63


title: RPI33_43


title: RPI33_42


title: RPI33_56


title: RPI40_65


title: RPI33_41


title: RPI33_52


title: RPI33_37


title: RPI33_36


title: RPI33_38


title: RPI33_45


title: RPI33_50


title: RPI33_34


title: RPI33_86


title: RPI33_28


title: RPI33_29


title: RPI33_23


title: RPI33_26


title: RPI33_31


title: RPI33_32


title: RPI33_33


title: RPI33_20


title: RPI33_19


title: RPI33_22


title: RPI33_30


title: RPI33_18


title: RPI33_35


title: RPI33_14


title: RPI33_15


title: RPI33_12


title: RPI33_16


title: RPI33_7


title: RPI33_13


title: RPI33_6


title: RPI33_25


title: RPI33_17


title: RPI33_24


title: RPI33_10


title: RPI33_11


title: RPI33_27


title: RPI33_5


title: RPI27_95

value: Day 5


title: RPI33_2


title: RPI33_0


title: RPI27_94


title: RPI33_1


title: RPI27_93


title: RPI33_3


title: RPI33_21


title: RPI33_9


title: RPI27_90


title: RPI27_89


title: RPI33_8


title: RPI27_91


title: RPI27_88


title: RPI27_87


title: RPI27_85


title: RPI27_92


title: RPI27_83


title: RPI27_86


title: RPI27_84


title: RPI27_81


title: RPI27_80


title: RPI27_77


title: RPI33_4


title: RPI27_79


title: RPI27_75


title: RPI27_76


title: RPI27_74


title: RPI27_78


title: RPI27_72


title: RPI27_71


title: RPI27_68


title: RPI27_67


title: RPI27_69


title: RPI27_70


title: RPI27_66


title: RPI27_65


title: RPI27_60


title: RPI27_63


title: RPI27_82


title: RPI27_62


title: RPI27_59


title: RPI27_64


title: RPI27_56


title: RPI27_55


title: RPI27_58


title: RPI27_54


title: RPI27_50


title: RPI27_53


title: RPI27_49


title: RPI27_52


title: RPI27_57


title: RPI27_48


title: RPI27_47


title: RPI27_51


title: RPI27_45


title: RPI27_46


title: RPI27_42


title: RPI27_40


title: RPI27_61


title: RPI27_38


title: RPI27_39


title: RPI27_44


title: RPI27_37


title: RPI27_43


title: RPI27_34


title: RPI27_73


title: RPI27_36


title: RPI27_33


title: RPI27_41


title: RPI27_32


title: RPI27_35


title: RPI27_31


title: RPI27_30


title: RPI27_29


title: RPI27_26


title: RPI27_28


title: RPI27_27


title: RPI27_25


title: RPI27_24


title: RPI27_19


title: RPI27_22


title: RPI27_23


title: RPI27_18


title: RPI27_21


title: RPI27_16


title: RPI27_17


title: RPI27_14


title: RPI27_13


title: RPI27_15


title: RPI27_7


title: RPI27_8


title: RPI27_10


title: RPI27_6


title: RPI27_3


title: RPI27_4


title: RPI27_11


title: RPI27_2


title: RPI27_12


title: RPI27_5


title: RPI27_1


title: RPI27_0


title: RPI41_94

value: Day 2


title: RPI41_93


title: RPI41_92


title: RPI41_95


title: RPI41_89


title: RPI27_20


title: RPI41_87


title: RPI41_91


title: RPI41_86


title: RPI41_88


title: RPI41_85


title: RPI41_90


title: RPI27_9


title: RPI41_84


title: RPI41_81


title: RPI41_82


title: RPI41_78


title: RPI41_74


title: RPI41_80


title: RPI41_75


title: RPI41_76


title: RPI41_73


title: RPI41_77


title: RPI41_69


title: RPI41_68


title: RPI41_67


title: RPI41_72


title: RPI41_64


title: RPI41_65


title: RPI41_66


title: RPI41_62


title: RPI41_63


title: RPI41_60


title: RPI41_70


title: RPI41_61


title: RPI41_59


title: RPI41_58


title: RPI41_55


title: RPI41_83


title: RPI41_54


title: RPI41_79


title: RPI41_57


title: RPI41_71


title: RPI41_53


title: RPI41_52


title: RPI41_51


title: RPI41_48


title: RPI41_47


title: RPI41_50


title: RPI41_49


title: RPI41_45


title: RPI41_43


title: RPI41_44


title: RPI41_42


title: RPI41_41


title: RPI41_39


title: RPI41_36


title: RPI41_38


title: RPI41_34


title: RPI41_56


title: RPI41_40


title: RPI41_37


title: RPI41_32


title: RPI41_33


title: RPI41_35


title: RPI41_29


title: RPI41_31


title: RPI41_30


title: RPI41_27


title: RPI41_26


title: RPI41_25


title: RPI41_46


title: RPI41_24


title: RPI41_23


title: RPI41_22


title: RPI41_20


title: RPI41_18


title: RPI41_19


title: RPI41_17


title: RPI41_16


title: RPI41_14


title: RPI41_13


title: RPI41_28


title: RPI41_8


title: RPI41_10


title: RPI41_12


title: RPI41_11


title: RPI41_7


title: RPI41_4


title: RPI41_6


title: RPI41_5


title: RPI41_9


title: RPI29_95

value: Day 4


title: RPI41_1


title: RPI41_0


title: RPI41_2


title: RPI29_90


title: RPI29_92


title: RPI29_91


title: RPI29_89


title: RPI29_88


title: RPI41_21


title: RPI41_15


title: RPI29_85


title: RPI29_84


title: RPI41_3


title: RPI29_82


title: RPI29_81


title: RPI29_83


title: RPI29_80


title: RPI29_75


title: RPI29_76


title: RPI29_74


title: RPI29_79


title: RPI29_77


title: RPI29_71


title: RPI29_94


title: RPI29_73


title: RPI29_72


title: RPI29_69


title: RPI29_87


title: RPI29_68


title: RPI29_66


title: RPI29_64


title: RPI29_63


title: RPI29_67


title: RPI29_62


title: RPI29_86


title: RPI29_61


title: RPI29_60


title: RPI29_59


title: RPI29_55


title: RPI29_70


title: RPI29_54


title: RPI29_53


title: RPI29_52


title: RPI29_51


title: RPI29_57


title: RPI29_50


title: RPI29_48


title: RPI29_56


title: RPI29_47


title: RPI29_65


title: RPI29_44


title: RPI29_45


title: RPI29_46


title: RPI29_58


title: RPI29_42


title: RPI29_41


title: RPI29_43


title: RPI29_39


title: RPI29_40


title: RPI29_38


title: RPI29_37


title: RPI29_36


title: RPI29_35


title: RPI29_34


title: RPI29_32


title: RPI29_49


title: RPI29_31


title: RPI29_78


title: RPI29_29


title: RPI29_30


title: RPI29_27


title: RPI29_23


title: RPI29_24


title: RPI29_22


title: RPI29_20


title: RPI29_21


title: RPI29_19


title: RPI29_17


title: RPI29_18


title: RPI29_16


title: RPI29_15


title: RPI29_11


title: RPI29_14


title: RPI29_12


title: RPI29_33


title: RPI29_9


title: RPI29_8


title: RPI29_7


title: RPI29_5


title: RPI29_28


title: RPI29_6


title: RPI29_25


title: RPI29_26


title: RPI29_4


title: RPI29_0


title: RPI29_1


title: RPI29_13


title: RPI2_93


title: RPI2_92


title: RPI2_95


title: RPI2_94


title: RPI29_10


title: RPI2_90


title: RPI2_89


title: RPI2_91


title: RPI2_84


title: RPI2_82


title: RPI2_86


title: RPI2_80


title: RPI2_83


title: RPI2_85


title: RPI2_81


title: RPI2_78


title: RPI2_77


title: RPI29_2


title: RPI2_74


title: RPI2_75


title: RPI29_3


title: RPI2_73


title: RPI2_88


title: RPI2_72


title: RPI2_69


title: RPI2_71


title: RPI2_66


title: RPI2_63


title: RPI2_67


title: RPI2_70


title: RPI2_65


title: RPI29_93


title: RPI2_68


title: RPI2_62


title: RPI2_79


title: RPI2_61


title: RPI2_58


title: RPI2_59


title: RPI2_60


title: RPI2_56


title: RPI2_76


title: RPI2_55


title: RPI2_54


title: RPI2_53


title: RPI2_51


title: RPI2_49


title: RPI2_50


title: RPI2_48


title: RPI2_64


title: RPI2_87


title: RPI2_40


title: RPI2_45


title: RPI2_37


title: RPI2_41


title: RPI2_47


title: RPI2_39


title: RPI2_44


title: RPI2_42


title: RPI2_52


title: RPI2_36


title: RPI2_57


title: RPI2_34


title: RPI2_33


title: RPI2_46


title: RPI2_31


title: RPI2_35


title: RPI2_29


title: RPI2_28


title: RPI2_27


title: RPI2_23


title: RPI2_25


title: RPI2_43


title: RPI2_26


title: RPI2_21


title: RPI2_22


title: RPI2_20


title: RPI2_32


title: RPI2_24


title: RPI2_18


title: RPI2_19


title: RPI2_14


title: RPI2_13


title: RPI2_11


title: RPI2_12


title: RPI2_17


title: RPI2_16


title: RPI2_15


title: RPI2_9


title: RPI2_7


title: RPI2_8


title: RPI2_10


title: RPI2_4


title: RPI2_30


title: RPI2_5


title: RPI2_6


title: RPI2_3


title: RPI2_2


title: RPI9_94_eGFP++


title: RPI9_92_eGFP++


title: RPI2_1


title: RPI9_95_eGFP++


title: RPI2_0


title: RPI9_93_eGFP++


title: RPI9_91_eGFP++


title: RPI9_89_eGFP++


title: RPI9_88_eGFP++


title: RPI9_86_eGFP++


title: RPI9_90_eGFP++


title: RPI9_87_eGFP++


title: RPI9_83_eGFP++


title: RPI9_85_eGFP++


title: RPI9_79_eGFP++


title: RPI9_78_eGFP++


title: RPI9_82_eGFP++


title: RPI9_80_eGFP++


title: RPI9_84_eGFP++


title: RPI9_75_eGFP++


title: RPI9_76_eGFP++


title: RPI9_73_eGFP++


title: RPI9_77_eGFP++


title: RPI9_74_eGFP++


title: RPI9_72_eGFP++


title: RPI9_70_eGFP++


title: RPI9_69_eGFP++


title: RPI9_65_eGFP++


title: RPI9_68_eGFP++


title: RPI9_67_eGFP++


title: RPI9_64_eGFP++


title: RPI9_66_eGFP++


title: RPI9_63_eGFP++


title: RPI9_62_eGFP++


title: RPI9_81_eGFP++


title: RPI9_61_eGFP++


title: RPI9_57_eGFP++


title: RPI9_60_eGFP++


title: RPI9_54_eGFP++


title: RPI9_55_eGFP++


title: RPI9_59_eGFP++


title: RPI9_53_eGFP++


title: RPI9_49_eGFP++


title: RPI9_52_eGFP++


title: RPI9_71_eGFP++


title: RPI9_56_eGFP++


title: RPI9_51_eGFP++


title: RPI9_45_eGFP++


title: RPI9_48_eGFP++


title: RPI9_47_eGFP++


title: RPI9_50_eGFP++


title: RPI9_43_eGFP++


title: RPI9_46_eGFP++


title: RPI9_41_eGFP++


title: RPI9_38_eGFP++


title: RPI9_35_eGFP++


title: RPI9_42_eGFP++


title: RPI9_39_eGFP++


title: RPI9_34_eGFP++


title: RPI9_58_eGFP++


title: RPI9_31_eGFP++


title: RPI9_37_eGFP++


title: RPI9_32_eGFP++


title: RPI9_33_eGFP++


title: RPI9_36_eGFP++


title: RPI9_28_eGFP++


title: RPI9_40_eGFP++


title: RPI9_27_eGFP++


title: RPI9_26_eGFP++


title: RPI9_25_eGFP++


title: RPI9_30_eGFP++


title: RPI9_24_eGFP++


title: RPI9_19_eGFP++


title: RPI9_22_eGFP++


title: RPI9_23_eGFP++


title: RPI9_20_eGFP++


title: RPI9_21_eGFP++


title: RPI9_14_eGFP++


title: RPI9_13_eGFP++


title: RPI9_17_eGFP++


title: RPI9_16_eGFP++


title: RPI9_11_eGFP++


title: RPI9_10_eGFP++


title: RPI9_15_eGFP++


title: RPI9_12_eGFP++


title: RPI9_6_eGFP++


title: RPI9_7_eGFP++


title: RPI9_18_eGFP++


title: RPI9_0_eGFP++


title: RPI9_9_eGFP++


title: RPI9_1_eGFP++


title: RPI47_93_eGFP++


title: RPI47_94_eGFP++


title: RPI9_8_eGFP++


title: RPI47_90_eGFP++


title: RPI47_88_eGFP++


title: RPI47_89_eGFP++


title: RPI47_87_eGFP++


title: RPI9_3_eGFP++


title: RPI47_85_eGFP++


title: RPI9_4_eGFP++


title: RPI47_83_eGFP++


title: RPI47_82_eGFP++


title: RPI9_29_eGFP++


title: RPI47_95_eGFP++


title: RPI9_2_eGFP++


title: RPI47_81_eGFP++


title: RPI47_80_eGFP++


title: RPI47_92_eGFP++


title: RPI47_86_eGFP++


title: RPI47_78_eGFP++


title: RPI9_5_eGFP++


title: RPI47_91_eGFP++


title: RPI47_74_eGFP++


title: RPI47_76_eGFP++


title: RPI47_77_eGFP++


title: RPI47_73_eGFP++


title: RPI47_72_eGFP++


title: RPI47_84_eGFP++


title: RPI47_69_eGFP++


title: RPI47_71_eGFP++


title: RPI47_70_eGFP++


title: RPI47_63_eGFP++


title: RPI47_62_eGFP++


title: RPI47_61_eGFP++


title: RPI47_64_eGFP++


title: RPI47_59_eGFP++


title: RPI47_67_eGFP++


title: RPI47_66_eGFP++


title: RPI47_65_eGFP++


title: RPI47_79_eGFP++


title: RPI2_38


title: RPI47_54_eGFP++


title: RPI47_58_eGFP++


title: RPI47_56_eGFP++


title: RPI47_53_eGFP++


title: RPI9_44_eGFP++


title: RPI47_75_eGFP++


title: RPI47_48_eGFP++


title: RPI47_52_eGFP++


title: RPI47_51_eGFP++


title: RPI47_68_eGFP++


title: RPI47_49_eGFP++


title: RPI47_46_eGFP++


title: RPI47_44_eGFP++


title: RPI47_45_eGFP++


title: RPI47_43_eGFP++


title: RPI47_60_eGFP++


title: RPI47_41_eGFP++


title: RPI47_55_eGFP++


title: RPI47_39_eGFP++


title: RPI47_42_eGFP++


title: RPI47_34_eGFP++


title: RPI47_40_eGFP++


title: RPI47_57_eGFP++


title: RPI47_38_eGFP++


title: RPI47_30_eGFP++


title: RPI47_37_eGFP++


title: RPI47_36_eGFP++


title: RPI47_33_eGFP++


title: RPI47_47_eGFP++


title: RPI47_31_eGFP++


title: RPI47_28_eGFP++


title: RPI47_27_eGFP++


title: RPI47_25_eGFP++


title: RPI47_21_eGFP++


title: RPI47_29_eGFP++


title: RPI47_35_eGFP++


title: RPI47_24_eGFP++


title: RPI47_20_eGFP++


title: RPI47_26_eGFP++


title: RPI47_19_eGFP++


title: RPI47_18_eGFP++


title: RPI47_23_eGFP++


title: RPI47_22_eGFP++


title: RPI47_32_eGFP++


title: RPI47_15_eGFP++


title: RPI47_14_eGFP++


title: RPI47_13_eGFP++


title: RPI47_17_eGFP++


title: RPI47_12_eGFP++


title: RPI47_9_eGFP++


title: RPI47_10_eGFP++


title: RPI47_4_eGFP++


title: RPI47_16_eGFP++


title: RPI47_8_eGFP++


title: RPI47_6_eGFP++


title: RPI47_2_eGFP++


title: RPI47_11_eGFP++


title: RPI47_5_eGFP++


title: RPI47_1_eGFP++


title: RPI47_50_eGFP++


title: RPI47_0_eGFP++


title: RPI35_94


title: RPI35_91


title: RPI35_89


title: RPI35_92


title: RPI35_88


title: RPI35_95


title: RPI35_93


title: RPI35_87


title: RPI35_90


title: RPI35_82


title: RPI35_81


title: RPI47_7_eGFP++


title: RPI47_3_eGFP++


title: RPI35_84


title: RPI35_80


title: RPI35_77


title: RPI35_76


title: RPI35_79


title: RPI35_75


title: RPI35_78


title: RPI35_73


title: RPI35_85


title: RPI35_71


title: RPI35_69


title: RPI35_70


title: RPI35_72


title: RPI35_68


title: RPI35_67


title: RPI35_64


title: RPI35_86


title: RPI35_83


title: RPI35_59


title: RPI35_60


title: RPI35_62


title: RPI35_61


title: RPI35_53


title: RPI35_54


title: RPI35_74


title: RPI35_51


title: RPI35_55


title: RPI35_49


title: RPI35_46


title: RPI35_56


title: RPI35_47


title: RPI35_45


title: RPI35_50


title: RPI35_43


title: RPI35_48


title: RPI35_44


title: RPI35_66


title: RPI35_41


title: RPI35_65


title: RPI35_63


title: RPI35_38


title: RPI35_35


title: RPI35_58


title: RPI35_34


title: RPI35_36


title: RPI35_52


title: RPI35_37


title: RPI35_30


title: RPI35_32


title: RPI35_27


title: RPI35_28


title: RPI35_42


title: RPI35_40


title: RPI35_23


title: RPI35_26


title: RPI35_25


title: RPI35_29


title: RPI35_21


title: RPI35_22


title: RPI35_19


title: RPI35_18


title: RPI35_31


title: RPI35_57


title: RPI35_39


title: RPI35_20


title: RPI35_17


title: RPI35_33


title: RPI35_15


title: RPI35_13


title: RPI35_16


title: RPI35_12


title: RPI35_9


title: RPI35_11


title: RPI35_14


title: RPI35_8


title: RPI35_7


title: RPI35_6


title: RPI35_24


title: RPI35_4


title: RPI35_10


title: RPI35_0


title: RPI35_2


title: RPI35_3


title: RPI35_1


title: RPI25_95


title: RPI25_92


title: RPI25_93


title: RPI25_94


title: RPI25_91


title: RPI25_89


title: RPI25_90


title: RPI25_88


title: RPI25_86


title: RPI25_84


title: RPI25_87


title: RPI25_85


title: RPI25_83


title: RPI25_81


title: RPI25_79


title: RPI25_78


title: RPI25_80


title: RPI25_77


title: RPI25_76


title: RPI25_82


title: RPI35_5


title: RPI25_72


title: RPI25_73


title: RPI25_71


title: RPI25_74


title: RPI25_68


title: RPI25_69


title: RPI25_75


title: RPI25_70


title: RPI25_65


title: RPI25_64


title: RPI25_61


title: RPI25_62


title: RPI25_59


title: RPI25_67


title: RPI25_60


title: RPI25_57


title: RPI25_56


title: RPI25_66


title: RPI25_55


title: RPI25_53


title: RPI25_54


title: RPI25_51


title: RPI25_48


title: RPI25_49


title: RPI25_52


title: RPI25_50


title: RPI25_46


title: RPI25_47


title: RPI25_42


title: RPI25_44


title: RPI25_63


title: RPI25_39


title: RPI25_41


title: RPI25_36


title: RPI25_40


title: RPI25_34


title: RPI25_35


title: RPI25_33


title: RPI25_31


title: RPI25_38


title: RPI25_30


title: RPI25_45


title: RPI25_58


title: RPI25_37


title: RPI25_29


title: RPI25_27


title: RPI25_26


title: RPI25_24


title: RPI25_25


title: RPI25_28


title: RPI25_23


title: RPI25_22


title: RPI25_43


title: RPI25_21


title: RPI25_18


title: RPI25_19


title: RPI25_20


title: RPI25_17


title: RPI25_16


title: RPI25_14


title: RPI25_32


title: RPI25_11


title: RPI25_12


title: RPI25_13


title: RPI25_8


title: RPI25_9


title: RPI25_7


title: RPI25_6


title: RPI25_3


title: RPI25_5


title: RPI25_1


title: RPI25_15


title: RPI25_10


title: RPI25_0


title: NA_39

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
Illumina's CASAVA 1.8.2 was used for basecalling.
Illumina sequence quality will be surveyed with FastQC. Adaptor and lower-quality bases will be trimmed with Trim-galore. Trimmed reads will be aliged to the Gencode mouse genome(GRCm38) with STAR-2.4.1d. The readcount of each sample was obtained using HTSeq-0.6.1 (htseq-count).
STAR aligner 2.4.1d
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

molecule: total RNA

extract_protocol:
Kidneys were harvested from mice and immediately frozen using liquid nitrogen and stored in (-80) until all samples were collected and processed together to extract RNA
Total RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNase1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilent 2100 Bioanalyzer.  Briefly, total RNA was converted to cDNA using oligodT, which was then used for Illumina sequencing library preparation. Single end 100 bp RNA-seq was carried on an Illumina HiSeq2500.

tag: genotype

value: Control

tag: tissue

value: kidney


title: NA_30


title: G1NF_42

source_name: Kidney_G1-APOL1_risk allele


title: GINF_44


title: NAP_3


title: G1NF_28

value: wild type (single mutant)


title: NA_27


title: 300 min LPS (10-1)

city: Stanford

first: David

middle: Ashley

last: Van Valen

state: CA

address: 443 Via Ortega, Shriram Center Rm 62

department: Bioengineering

institute: Stanford

description: cell_ids.csv, fpms.csv, single_cell_dynamics.csv

data_processing:
Alignment to mouse genome (mm10) using Kallisto
Quality control of sequencing reads with BBTools
Quantification via Bayesian inference with SCDE (Kharchenko et al 2014) – counts placed in fpms.csv. Unstimulated cells at 150 minutes were not quantified with SCDE.
Manual segmentation of nuclei and extraction of the median nuclear fluorescence over time to produce a time series of NF-kB activity for each cell. This data is stored in single_cell_dynamics.csv. A list of conditions and id’s for each cell is stored in cell_ids.csv.
Genome_build: mm10
Supplementary_files_format_and_content: csv - contains estimated counts for gene expression as determined by SCDE
Supplementary_files_format_and_content: fpms.csv contains single cell RNA seq counts after reads were aligned to the transcriptome. single_cell_dynamics.csv contains time series of NF-kB activity for each cell. cell_ids.csv contains the condition and id of each cell in our study.

source_name: RAW 264.7 cells

extract_protocol:
Lysis was performed inside a microfluidic chip
Libraries were prepared according to protocols for Clontech's SMARTer library preparation kit for the fluidigm C1
SMARTer single cell RNA-seq kit for the Fluidigm C1

treatment_protocol: Cells were stimulated with LPS (100 ng/ml) and imaged inside a Fluidigm C1 chip

tag: cell line

tag: time point

value: 300 min

tag: condition

value: LPS


title: RPI25_4


title: 300 min LPS (10-4)


title: GNA1_18


title: GNA_73

source_name: Kidney_G2-APOL1_risk allele


title: 300 min LPS (10-10)


title: GNA_78M


title: 300 min LPS (10-2)


title: 300 min LPS (10-12)


title: RPI25_2


title: 300 min LPS (10-9)


title: 300 min LPS (9-50)


title: 300 min LPS (10-11)


title: 300 min LPS (10-3)


title: 300 min LPS (10-7)


title: 300 min LPS (9-94)


title: 300 min LPS (9-34)


title: 300 min LPS (9-67)


title: 300 min LPS (9-56)


title: 300 min LPS (9-47)


title: 300 min LPS (9-46)


title: 300 min LPS (9-25)


title: 300 min LPS (9-53)


title: 300 min LPS (9-62)


title: 300 min LPS (9-93)


title: 300 min LPS (9-87)


title: 300 min LPS (9-42)


title: 300 min LPS (9-45)


title: 300 min LPS (9-91)


title: 300 min LPS (9-65)


title: 300 min LPS (9-40)


title: 300 min LPS (9-96)


title: 300 min LPS (9-39)


title: 300 min LPS (9-29)


title: 300 min LPS (9-49)


title: 300 min LPS (9-41)


title: 300 min LPS (9-88)


title: 300 min LPS (9-28)


title: 300 min LPS (9-89)


title: 300 min LPS (9-60)


title: 300 min LPS (9-54)


title: 300 min LPS (9-85)


title: 300 min LPS (9-59)


title: 300 min LPS (9-52)


title: 300 min LPS (9-21)


title: 300 min LPS (9-33)


title: 300 min LPS (9-43)


title: 300 min LPS (9-27)


title: 300 min LPS (9-23)


title: 300 min LPS (9-55)


title: 300 min LPS (9-22)


title: 300 min LPS (9-90)


title: 300 min LPS (9-35)


title: 300 min LPS (9-58)


title: 300 min LPS (9-38)


title: 300 min LPS (9-24)


title: 300 min LPS (9-61)


title: 300 min LPS (9-32)


title: 300 min LPS (9-92)


title: 300 min LPS (9-86)


title: 300 min LPS (9-31)


title: 300 min LPS (9-36)


title: 300 min LPS (9-30)


title: 300 min LPS (9-57)


title: 300 min LPS (9-64)


title: 300 min LPS (2-42)


title: 300 min LPS (9-51)


title: 300 min LPS (9-84)


title: 300 min LPS (9-63)


title: 300 min LPS (9-44)


title: 300 min LPS (9-37)


title: 300 min LPS (9-26)


title: 300 min LPS (2-81)


title: 300 min LPS (2-77)


title: 300 min LPS (2-40)


title: 300 min LPS (9-48)


title: 300 min LPS (2-74)


title: 300 min LPS (2-63)


title: 300 min LPS (2-80)


title: 300 min LPS (2-58)


title: 300 min LPS (2-94)


title: 300 min LPS (2-73)


title: 300 min LPS (2-59)


title: 300 min LPS (2-66)


title: 300 min LPS (2-93)


title: 300 min LPS (2-60)


title: 300 min LPS (9-66)


title: 300 min LPS (2-95)


title: 300 min LPS (2-55)


title: 300 min LPS (2-83)


title: 300 min LPS (2-45)


title: 300 min LPS (2-76)


title: 300 min LPS (2-56)


title: 300 min LPS (2-44)


title: 300 min LPS (2-96)


title: 300 min LPS (2-71)


title: 300 min LPS (2-52)


title: 300 min LPS (2-65)


title: 300 min LPS (2-64)


title: 300 min LPS (2-89)


title: 300 min LPS (2-69)


title: 300 min LPS (2-85)


title: 300 min LPS (2-72)


title: 300 min LPS (2-61)


title: 300 min LPS (2-41)


title: 300 min LPS (2-49)


title: 300 min LPS (2-91)


title: 300 min LPS (2-47)


title: 300 min LPS (2-86)


title: 300 min LPS (2-78)


title: 300 min LPS (2-67)


title: 300 min LPS (2-70)


title: 300 min LPS (2-53)


title: 300 min LPS (2-50)


title: 300 min LPS (2-54)


title: 300 min LPS (2-68)


title: 300 min LPS (2-75)


title: 300 min LPS (2-43)


title: 300 min LPS (2-48)


title: 300 min LPS (2-79)


title: 300 min LPS (2-46)


title: 300 min LPS (2-88)


title: 300 min LPS (2-87)


title: 300 min LPS (2-57)


title: 300 min LPS (2-82)


title: 300 min LPS (2-84)


title: 300 min LPS (2-90)


title: 300 min LPS (2-92)


title: 150 min LPS (10-24)

value: 150 min


title: 300 min LPS (2-62)


title: 150 min LPS (10-17)


title: 150 min LPS (10-18)


title: 150 min LPS (10-28)


title: 150 min LPS (10-31)


title: 150 min LPS (10-33)


title: 150 min LPS (10-15)


title: 150 min LPS (10-20)


title: 150 min LPS (10-13)


title: 150 min LPS (10-27)


title: 150 min LPS (10-16)


title: 150 min LPS (10-21)


title: 150 min LPS (10-25)


title: 150 min LPS (8-52)


title: 150 min LPS (8-53)


title: 150 min LPS (8-49)


title: 150 min LPS (10-14)


title: 150 min LPS (8-68)


title: 150 min LPS (8-38)


title: 150 min LPS (8-47)


title: 150 min LPS (10-29)


title: 150 min LPS (8-64)


title: 150 min LPS (8-46)


title: 150 min LPS (10-22)


title: 150 min LPS (8-45)


title: 150 min LPS (8-51)


title: 150 min LPS (8-70)


title: 150 min LPS (8-55)


title: 150 min LPS (8-77)


title: 150 min LPS (8-54)


title: 150 min LPS (8-65)


title: 150 min LPS (8-75)


title: 150 min LPS (8-57)


title: 150 min LPS (8-42)


title: 150 min LPS (8-71)


title: 150 min LPS (8-79)


title: 150 min LPS (8-33)


title: 150 min LPS (8-59)


title: 150 min LPS (8-60)


title: 150 min LPS (8-32)


title: 150 min LPS (8-40)


title: 150 min LPS (8-35)


title: 150 min LPS (8-44)


title: 150 min LPS (8-67)


title: 150 min LPS (8-48)


title: 150 min LPS (8-39)


title: 150 min LPS (8-58)


title: 150 min LPS (8-76)


title: 150 min LPS (8-72)


title: 150 min LPS (8-63)


title: 150 min LPS (8-43)


title: 150 min LPS (8-74)


title: 150 min LPS (8-73)


title: 150 min LPS (8-31)


title: 150 min LPS (8-62)


title: 150 min LPS (8-56)


title: 150 min LPS (8-36)


title: 150 min LPS (8-61)


title: 150 min LPS (6-39)


title: 150 min LPS (6-59)


title: 150 min LPS (6-41)


title: 150 min LPS (8-78)


title: 150 min LPS (6-30)


title: 150 min LPS (6-21)


title: 150 min LPS (6-75)


title: 150 min LPS (8-66)


title: 150 min LPS (6-34)


title: 150 min LPS (6-45)


title: 150 min LPS (6-27)


title: 150 min LPS (6-74)


title: 150 min LPS (8-69)


title: 150 min LPS (8-50)


title: 150 min LPS (6-52)


title: 150 min LPS (6-61)


title: 150 min LPS (6-80)


title: 150 min LPS (6-49)


title: 150 min LPS (6-67)


title: 150 min LPS (8-34)


title: 150 min LPS (6-65)


title: 150 min LPS (6-64)


title: 150 min LPS (6-19)


title: 150 min LPS (6-77)


title: 150 min LPS (6-26)


title: 150 min LPS (6-68)


title: 150 min LPS (6-24)


title: 150 min LPS (6-73)


title: 150 min LPS (6-47)


title: 150 min LPS (6-44)


title: 150 min LPS (6-32)


title: 150 min LPS (6-72)


title: 150 min LPS (6-25)


title: 150 min LPS (6-76)


title: 150 min LPS (6-31)


title: 150 min LPS (6-71)


title: 150 min LPS (6-58)


title: 150 min LPS (6-33)


title: 150 min LPS (6-51)


title: 150 min LPS (6-18)


title: 150 min LPS (6-70)


title: 150 min LPS (6-20)


title: 150 min LPS (6-54)


title: 150 min LPS (6-48)


title: 150 min LPS (6-78)


title: 150 min LPS (6-16)


title: 150 min LPS (6-28)


title: 150 min LPS (6-29)


title: 150 min LPS (6-55)


title: 150 min LPS (6-37)


title: 150 min LPS (6-66)


title: 150 min LPS (6-23)


title: 150 min LPS (6-38)


title: 150 min LPS (6-63)


title: 150 min LPS (6-53)


title: 150 min LPS (6-36)


title: 150 min LPS (8-41)


title: 150 min LPS (6-40)


title: 150 min LPS (6-22)


title: 150 min LPS (6-50)


title: 150 min LPS (6-42)


title: 150 min LPS (6-57)


title: 150 min LPS (6-35)


title: 150 min LPS (6-60)


title: 150 min LPS (6-46)


title: 150 min LPS (6-17)


title: 150 min LPS (6-56)


title: 150 min LPS (6-69)


title: 150 min LPS (5-21)


title: 150 min LPS (5-30)


title: 150 min LPS (5-8)


title: 150 min LPS (5-38)


title: 150 min LPS (5-14)


title: 150 min LPS (5-40)


title: 150 min LPS (5-20)


title: 150 min LPS (5-43)


title: 150 min LPS (5-39)


title: 150 min LPS (5-34)


title: 150 min LPS (5-13)


title: 150 min LPS (5-36)


title: 150 min LPS (5-26)


title: 150 min LPS (5-23)


title: 150 min LPS (5-33)


title: 150 min LPS (5-28)


title: 150 min LPS (5-15)


title: 150 min LPS (5-41)


title: 150 min LPS (5-5)


title: 150 min LPS (5-2)


title: 150 min LPS (5-6)


title: 150 min LPS (5-45)


title: 150 min LPS (5-12)


title: 150 min LPS (5-18)


title: 150 min LPS (5-29)


title: 150 min LPS (5-17)


title: 150 min LPS (5-4)


title: 150 min LPS (5-11)


title: 150 min LPS (5-42)


title: 150 min LPS (5-10)


title: 150 min LPS (5-37)


title: 150 min LPS (5-22)


title: 150 min LPS (5-35)


title: 150 min LPS (5-44)


title: 150 min LPS (5-19)


title: 150 min LPS (5-9)


title: 150 min LPS (5-3)


title: 150 min LPS (5-7)


title: 150 min LPS (5-1)


title: 150 min LPS (5-46)


title: 150 min LPS (5-32)


title: 150 min LPS (4-87)


title: 150 min LPS (4-85)


title: 150 min LPS (5-27)


title: 150 min LPS (5-24)


title: 150 min LPS (4-96)


title: 150 min LPS (4-83)


title: 150 min LPS (4-93)


title: 150 min LPS (4-82)


title: 150 min LPS (4-89)


title: 150 min LPS (4-74)


title: 150 min LPS (4-90)


title: 150 min LPS (4-91)


title: 150 min LPS (4-86)


title: 150 min LPS (5-16)


title: 150 min LPS (4-77)


title: 150 min LPS (4-92)


title: 150 min LPS (4-95)


title: 150 min LPS (4-75)


title: 150 min LPS (4-81)


title: 150 min LPS (4-80)


title: 150 min LPS (4-76)


title: 150 min LPS (4-84)


title: 150 min LPS (4-94)


title: 150 min LPS (4-79)


title: 150 min LPS (4-73)


title: 150 min LPS (3-13)


title: 150 min LPS (3-3)


title: 150 min LPS (3-17)


title: 150 min LPS (3-2)


title: 150 min LPS (3-62)


title: 150 min LPS (3-14)


title: 150 min LPS (3-27)


title: 150 min LPS (3-5)


title: 150 min LPS (3-52)


title: 150 min LPS (3-51)


title: 150 min LPS (3-9)


title: 150 min LPS (3-16)


title: 150 min LPS (3-61)


title: 150 min LPS (3-54)


title: 150 min LPS (3-4)


title: 150 min LPS (4-88)


title: 150 min LPS (3-47)


title: 150 min LPS (3-53)


title: 150 min LPS (3-34)


title: 150 min LPS (3-29)


title: 150 min LPS (3-49)


title: 150 min LPS (3-15)


title: 150 min LPS (3-35)


title: 150 min LPS (3-10)


title: 150 min LPS (3-19)


title: 150 min LPS (3-38)


title: 150 min LPS (3-11)


title: small RNA-seq ctrl_before MDP, replicate1

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

description:
smallrna_ctrl_ustim_r1
Small RNA-seq

data_processing:
RNA-seq: Basecalling by CASAVA version 1.8. All the reads are then filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50, trimmed from 3' ends using fastq_quality_trimmer (fastx_toolkit) -t 20 -l 50 and mapped to hg19 by Tophat version 2.0.6, using --segment-length 25.
Small RNA-seq: Basecalling by CASAVA version 1.8. All the reads are filtered by fastq_quality_filter (fastx_toolkit) using -q 30 -p 50 and are trimmed for adaptor sequences (TGGAATTCTCGGGTGCCAAGGAACTCCAGTC) using fastx_clipper -l 18. Finally, the reads are then mapped to hg19 by Bowtie version 0.12.7 using --strata --best -k 10.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig files are TPM-normalized signals of mapped RNA-seq/smallRNA-seq reads using above mapping steps.

organism: Homo sapiens

source_name: Monocytes, healthy, WT, unstimulated

extract_protocol:
Total RNA from unstimulated and MDP-stimulated monocytes was prepared using NucleoSpin RNA II isolation kit (Macherey-Nagel).
TruSeq Small RNA Library Preparation Kit from Illumina.

tag: cell type

value: monocytes

tag: disease status

value: healthy

value: WT NOD2 + WT ATG16L1

tag: treatment

value: unstimulated


title: small RNA-seq ctrl_after MDP, replicate2

description:
smallrna_ctrl_mdp_r2
Small RNA-seq

source_name: Monocytes, healthy, WT, stimulated with MDP

value: stimulated with muramyl dipeptide (MDP)


title: small RNA-seq ctrl_after MDP, replicate1

description:
smallrna_ctrl_mdp_r1
Small RNA-seq


title: 150 min LPS (3-41)


title: 150 min LPS (3-65)


title: 150 min LPS (3-33)


title: small RNA-seq CD WT before MDP, replicate2

description:
smallrna_crohn_wt_ustim_r2
Small RNA-seq

source_name: Monocytes, CD, WT, unstimulated

value: Crohn's disease


title: 150 min LPS (3-12)


title: 150 min LPS (3-40)


title: small RNA-seq CD WT before MDP, replicate1

description:
smallrna_crohn_wt_ustim_r1
Small RNA-seq


title: small RNA-seq CD WT after MDP, replicate1

description:
smallrna_crohn_wt_mdp_r1
Small RNA-seq

source_name: Monocytes, CD, WT, stimulated with MDP


title: 150 min LPS (3-44)


title: 150 min LPS (3-39)


title: small RNA-seq CD NOD2 before MDP, replicate3

description:
smallrna_crohn_snp_ustim_r3
Small RNA-seq

source_name: Monocytes, CD, NOD2 SNP, unstimulated

value: HET SNP13/HET SNP8 + WT ATG16L1


title: 150 min LPS (3-59)


title: small RNA-seq ctrl_before MDP, replicate2

description:
smallrna_ctrl_ustim_r2
Small RNA-seq


title: 150 min LPS (3-36)


title: small RNA-seq CD NOD2 before MDP, replicate2

description:
smallrna_crohn_snp_ustim_r2
Small RNA-seq

value: HET SNP13/HET SNP12 + WT ATG16L1


title: 150 min LPS (3-22)


title: small RNA-seq CD WT after MDP, replicate2

description:
smallrna_crohn_wt_mdp_r2
Small RNA-seq


title: small RNA-seq CD NOD2 after MDP, replicate3

description:
smallrna_crohn_snp_mdp_r3
Small RNA-seq

source_name: Monocytes, CD, NOD2 SNP, stimulated with MDP


title: small RNA-seq CD NOD2 after MDP, replicate2

description:
smallrna_crohn_snp_mdp_r2
Small RNA-seq


title: RNA-seq healthy control before MDP, replicate1

extract_protocol:
Total RNA from unstimulated and MDP-stimulated monocytes was prepared using NucleoSpin RNA II isolation kit (Macherey-Nagel).
Illumina TruSeq Standard RNA Sample Prep was used with 1.5 ug of total RNA for the construction of sequencing libraries.


title: RNA-seq healthy control after MDP, replicate2


title: small RNA-seq CD NOD2 after MDP, replicate1

description:
smallrna_crohn_snp_mdp_r1
Small RNA-seq

value: HOM SNP13 + WT ATG16L1


title: RNA-seq healthy control after MDP, replicate1


title: small RNA-seq CD NOD2 before MDP, replicate1

description:
smallrna_crohn_snp_ustim_r1
Small RNA-seq


title: RNA-seq CD WT before MDP, replicate1


title: RNA-seq CD WT after MDP, replicate2


title: RNA-seq CD WT after MDP, replicate1


title: 150 min LPS (3-42)


title: 150 min LPS (2-5)


title: 150 min LPS (2-30)


title: 150 min LPS (3-50)


title: 150 min LPS (2-25)


title: 150 min LPS (3-7)


title: 150 min LPS (3-6)


title: 150 min LPS (3-37)


title: 150 min LPS (2-11)


title: 150 min LPS (3-1)


title: RNA-seq CD WT before MDP, replicate2


title: 150 min LPS (2-6)


title: 150 min LPS (3-24)


title: 150 min LPS (2-31)


title: 150 min LPS (3-43)


title: 150 min LPS (3-45)


title: 150 min LPS (2-8)


title: RNA-seq CD NOD2 before MDP, replicate3


title: RNA-seq healthy control before MDP, replicate2


title: 150 min LPS (2-39)


title: RNA-seq CD NOD2 before MDP, replicate2


title: RNA-seq CD NOD2 after MDP, replicate3


title: 150 min LPS (2-18)


title: 150 min LPS (2-20)


title: 150 min LPS (6-43)


title: RNA-seq CD NOD2 after MDP, replicate2


title: 150 min LPS (2-21)


title: RNA-seq CD NOD2 after MDP, replicate1


title: 150 min LPS (2-15)


title: 150 min LPS (2-24)


title: 150 min LPS (2-4)


title: 150 min LPS (2-26)


title: 150 min LPS (2-17)


title: 559-T

city: Baltimore

first: Zhixiong

last: Wang

state: Maryland

address: 1503 E. Jefferson St., Rm. 112.

department: gastroenterology

institute: Johns Hopkins University

data_processing:
The processing data were obtained by using BaseSpace® RNA-Seq Alignment v1.0 App（illumina). The APP can run STAR and tools from the Tuxedo Suite (Bowtie, TopHat,Cufflinks) to produce aligned reads, variant calls, and FPKM abundance estimates of reference genes and transcripts
Pre-sample reads using FASTQ
Filtering—Bowtie(Only sequences that do not align against abundant sequences are passed through  to the next phase of the analysis. Bowtie filters read pairs when at least 1 read  aligns to an abundant sequence. Also, Bowtie trims off 2 bases from the 5’ end of  the read because of a high mismatch rate from these 2 bases in the RNA-Seq  libraries)
Alignment to ERCC—STAR
Alignment—The STAR or TopHat2 aligner performs a spliced alignment of the  filtered reads against the genome
Fusion Calling— Manta-fusion and the TopHat
Variant Calling—The Isaac Variant Caller
The Cufflinks Assembly & DE v2.0 App uses the analysis results from the RNA-Seq Alignment App to perform novel transcript merging and differential expression.
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: fpkm

source_name: esophageal epithelium

growth_protocol: Frozen tissues

extract_protocol:
Illumina's instructions of TruSight RNA Pan-Cancer Panel kit
Libraries were prepared according to Illumina's instructions of TruSight RNA Pan-Cancer Panel kit

value: esophageal adenocarcinoma


title: 943-T


title: 1180-T


title: 150 min LPS (2-36)


title: 150 min LPS (2-3)


title: 150 min LPS (2-16)


title: 150 min LPS (2-34)


title: 150 min LPS (2-23)


title: 150 min LPS (2-14)


title: 559-N

value: matched non-malignant esophageal epithelial tissue


title: 150 min LPS (2-33)


title: 150 min LPS (2-7)


title: RNA-seq CD NOD2 before MDP, replicate1


title: 150 min LPS (2-28)


title: 150 min LPS (2-1)


title: 150 min LPS (2-19)


title: 1180-N


title: 150 min LPS (2-38)


title: 150 min LPS (2-35)


title: 943-N


title: 1330-T


title: 150 min LPS (2-32)


title: 150 min LPS (2-10)


title: 1330-N


title: 150 min LPS (2-2)


title: 150 min LPS (2-22)


title: 150 min LPS (2-12)


title: 511-N


title: 150 min LPS (2-37)


title: 1424-T


title: 150 min LPS (1-29)


title: 5061-T


title: 4083-T


title: 150 min LPS (2-27)


title: 150 min LPS (2-29)


title: 1424-N


title: 3434-T


title: 511-T


title: 4083-N


title: 150 min LPS (1-28)


title: 150 min LPS (1-36)


title: 150 min LPS (1-77)


title: 150 min LPS (1-15)


title: 150 min LPS (1-35)


title: 150 min LPS (1-33)


title: 4045-T


title: 3434-N


title: 150 min LPS (1-53)


title: 523-T


title: 4033-T


title: 5061-N


title: 150 min LPS (1-65)


title: 150 min LPS (1-47)


title: 523-N


title: 150 min LPS (1-63)


title: 4045-N


title: 1173-N


title: 623-T


title: 150 min LPS (1-76)


title: 1111-T


title: 150 min LPS (1-16)


title: 150 min LPS (1-22)


title: 150 min LPS (1-56)


title: 150 min LPS (1-74)


title: 150 min LPS (1-60)


title: 1181-T


title: 1181-N


title: 150 min LPS (1-72)


title: 150 min LPS (1-12)


title: 2116-T


title: 150 min LPS (1-69)


title: 2116-N


title: 150 min LPS (1-75)


title: 4039-T


title: 150 min LPS (1-95)


title: 1173-T


title: 1990-T


title: 150 min LPS (1-4)


title: 1111-N


title: 150 min LPS (1-3)


title: 4039-N


title: 150 min LPS (1-10)


title: 623-N


title: 2136-T


title: 2136-N


title: 150 min LPS (1-91)


title: 150 min LPS (1-87)


title: 150 min LPS (1-57)


title: 1337-N


title: 4033-N


title: 150 min LPS (1-82)


title: 1337-T


title: 150 min LPS (1-5)


title: 4013-N


title: 150 min LPS (1-96)


title: 4013-T


title: 4006-N


title: 2129-N


title: 150 min LPS (1-38)


title: 4006-T


title: 150 min LPS (1-70)


title: 150 min LPS (1-11)


title: 3869-T


title: 150 min LPS (1-37)


title: 150 min LPS (1-19)


title: 150 min LPS (1-79)


title: 3869-N


title: 150 min LPS (1-62)


title: 2129-T


title: 3555-T


title: 1990-N


title: 150 min LPS (1-58)


title: 1184-T


title: 1184-N


title: 150 min LPS (1-84)


title: 4091-T


title: 3838-N


title: 4091-N


title: 150 min LPS (1-67)


title: 150 min LPS (1-93)


title: 3542-T


title: 3542-N


title: 150 min LPS (1-83)


title: 4065-T


title: 150 min LPS (1-8)


title: 150 min LPS (1-66)


title: 4065-N


title: 2036-T


title: 3555-N


title: 1342-T


title: 150 min LPS (1-39)


title: 150 min LPS (1-59)


title: 1342-N


title: 150 min LPS (1-94)


title: 3838-T


title: 150 min LPS (1-13)


title: 150 min LPS (1-18)


title: 2036-N


title: 150 min LPS (1-81)


title: 150 min LPS (1-73)


title: 150 min LPS (1-46)


title: 150 min LPS (1-24)


title: 3381-T


title: 3480-T


title: 3480-N


title: 150 min LPS (1-2)


title: 150 min LPS (1-85)


title: 3340-T


title: 150 min LPS (1-51)


title: 3381-N


title: 150 min LPS (1-80)


title: 150 min LPS (1-21)


title: 3340-N


title: 150 min LPS (1-30)


title: 3325-T


title: 3274-T


title: 3325-N


title: 3253-T


title: 150 min LPS (1-23)


title: 3274-N


title: 150 min LPS (1-32)


title: 2629-N


title: 3253-N


title: 150 min LPS (1-61)


title: 150 min LPS (1-1)


title: 150 min LPS (1-48)


title: 150 min LPS (1-92)


title: 150 min LPS (1-40)


title: 150 min LPS (1-88)


title: 150 min LPS (1-68)


title: 2629-T


title: 150 min LPS (1-7)


title: 150 min LPS (1-90)


title: 150 min LPS (1-43)


title: 150 min LPS (1-86)


title: 150 min LPS (1-27)


title: 150 min LPS (1-20)


title: 150 min LPS (1-52)


title: 150 min LPS (1-6)


title: 150 min LPS (1-78)


title: 150 min LPS (1-71)


title: 150 min LPS (1-55)


title: 150 min LPS (1-42)


title: 150 min LPS (1-14)


title: 150 min LPS (1-50)


title: 150 min LPS (1-54)


title: 150 min LPS (1-45)


title: 150 min LPS (1-26)


title: 150 min No stimulation (9-75)

value: No stimulation


title: 150 min LPS (1-17)


title: 150 min LPS (1-89)


title: 150 min LPS (1-64)


title: 150 min LPS (1-44)


title: 150 min LPS (1-34)


title: 150 min LPS (1-49)


title: 150 min No stimulation (9-74)


title: 150 min No stimulation (9-82)


title: 150 min No stimulation (9-76)


title: 150 min No stimulation (9-70)


title: 150 min No stimulation (9-81)


title: 150 min No stimulation (9-68)


title: 150 min No stimulation (9-78)


title: 150 min No stimulation (9-69)


title: 150 min No stimulation (9-71)


title: 150 min No stimulation (9-77)


title: 150 min No stimulation (9-80)


title: 150 min No stimulation (9-79)


title: 150 min No stimulation (9-83)


title: 150 min No stimulation (9-72)


title: 75 min LPS (8-10)

value: 75 min


title: 75 min LPS (8-25)


title: 75 min LPS (8-28)


title: 75 min LPS (8-14)


title: 75 min LPS (8-3)


title: 150 min No stimulation (9-73)


title: 75 min LPS (8-17)


title: 75 min LPS (8-5)


title: 75 min LPS (8-2)


title: 75 min LPS (8-12)


title: 75 min LPS (8-19)


title: 75 min LPS (8-27)


title: 75 min LPS (8-7)


title: 75 min LPS (8-21)


title: 75 min LPS (8-16)


title: 75 min LPS (8-18)


title: 75 min LPS (8-15)


title: 75 min LPS (8-26)


title: 75 min LPS (8-1)


title: 75 min LPS (8-8)


title: 75 min LPS (8-20)


title: 75 min LPS (8-29)


title: 75 min LPS (8-11)


title: 75 min LPS (8-9)


title: 75 min LPS (7-28)


title: 75 min LPS (7-11)


title: 75 min LPS (7-23)


title: 75 min LPS (7-1)


title: 75 min LPS (7-14)


title: 75 min LPS (7-34)


title: 75 min LPS (7-17)


title: 75 min LPS (8-23)


title: 75 min LPS (7-92)


title: 75 min LPS (7-25)


title: 75 min LPS (7-9)


title: 75 min LPS (8-24)


title: 75 min LPS (7-20)


title: 75 min LPS (8-30)


title: 75 min LPS (8-6)


title: 75 min LPS (7-24)


title: 75 min LPS (7-87)


title: 75 min LPS (7-19)


title: 75 min LPS (7-93)


title: 75 min LPS (7-26)


title: 75 min LPS (7-10)


title: 75 min LPS (7-33)


title: 75 min LPS (7-22)


title: 75 min LPS (7-7)


title: 75 min LPS (7-27)


title: 75 min LPS (7-3)


title: 75 min LPS (7-35)


title: 75 min LPS (7-12)


title: 75 min LPS (7-38)


title: 75 min LPS (7-18)


title: 75 min LPS (7-4)


title: 75 min LPS (7-96)


title: 75 min LPS (7-6)


title: 75 min LPS (7-37)


title: 75 min LPS (7-21)


title: 75 min LPS (7-30)


title: 75 min LPS (7-8)


title: 75 min LPS (7-90)


title: 75 min LPS (7-2)


title: 75 min LPS (7-94)


title: 75 min LPS (7-5)


title: 75 min LPS (6-85)


title: 75 min LPS (7-15)


title: 75 min LPS (7-91)


title: 75 min LPS (7-95)


title: 75 min LPS (7-36)


title: 75 min LPS (7-88)


title: 75 min LPS (7-89)


title: 75 min LPS (6-88)


title: 75 min LPS (7-31)


title: 75 min LPS (6-92)


title: 75 min LPS (6-82)


title: 75 min LPS (7-32)


title: 75 min LPS (7-16)


title: 75 min LPS (6-94)


title: 75 min LPS (6-89)


title: 75 min LPS (7-86)


title: 75 min LPS (6-83)


title: 75 min LPS (6-81)


title: 75 min LPS (6-96)


title: 75 min LPS (6-90)


title: 75 min LPS (6-93)


title: 75 min LPS (6-84)


title: 75 min LPS (6-95)


title: 75 min LPS (4-22)


title: 75 min LPS (6-86)


title: 75 min LPS (4-21)


title: 75 min LPS (4-17)


title: 75 min LPS (6-91)


title: 75 min LPS (6-87)


title: 75 min LPS (4-3)


title: 75 min LPS (4-18)


title: 75 min LPS (4-5)


title: 75 min LPS (4-19)


title: 75 min LPS (4-14)


title: 75 min LPS (4-15)


title: 75 min LPS (4-23)


title: 75 min LPS (4-24)


title: 75 min LPS (4-11)


title: 75 min LPS (4-9)


title: 75 min LPS (4-8)


title: 75 min LPS (4-6)


title: 75 min LPS (4-25)


title: 75 min LPS (4-12)


title: 75 min LPS (4-1)


title: 75 min LPS (4-16)


title: 75 min LPS (4-13)


title: 75 min LPS (4-7)


title: 75 min LPS (4-20)


title: 75 min LPS (3-93)


title: 75 min LPS (3-78)


title: 75 min LPS (3-73)


title: 75 min LPS (3-68)


title: 75 min LPS (3-85)


title: 75 min LPS (3-90)


title: 75 min LPS (3-96)


title: 75 min LPS (3-76)


title: 75 min LPS (3-77)


title: 75 min LPS (4-2)


title: 75 min LPS (3-82)


title: 75 min LPS (3-69)


title: 75 min LPS (3-87)


title: 75 min LPS (3-70)


title: 75 min LPS (3-79)


title: 75 min LPS (3-81)


title: 75 min LPS (3-72)


title: 75 min LPS (3-89)


title: 75 min LPS (4-4)


title: 75 min LPS (4-10)


title: 75 min LPS (3-83)


title: 75 min LPS (3-95)


title: 75 min LPS (3-86)


title: 75 min LPS (3-91)


title: 75 min LPS (3-84)


title: 75 min LPS (3-71)


title: 75 min LPS (3-88)


title: 75 min LPS (3-92)


title: 75 min LPS (3-80)


title: 75 min LPS (3-67)


title: 75 min LPS (3-75)


title: 0 min No stimulation (9-5)

value: 0 min


title: 75 min LPS (3-94)


title: 75 min LPS (3-74)


title: 0 min No stimulation (9-4)


title: 0 min No stimulation (9-3)


title: 0 min No stimulation (9-1)


title: 0 min No stimulation (9-7)


title: 0 min No stimulation (9-12)


title: 0 min No stimulation (9-10)


title: 0 min No stimulation (9-20)


title: 0 min No stimulation (9-2)


title: 0 min No stimulation (9-6)


title: 0 min No stimulation (9-13)


title: 0 min No stimulation (9-19)


title: 0 min No stimulation (9-16)


title: 0 min No stimulation (9-8)


title: 0 min No stimulation (9-18)


title: 0 min No stimulation (9-17)


title: 0 min No stimulation (9-14)


title: 0 min No stimulation (9-9)


title: 0 min No stimulation (8-85)


title: 0 min No stimulation (8-91)


title: 0 min No stimulation (8-92)


title: 0 min No stimulation (8-88)


title: 0 min No stimulation (8-87)


title: 0 min No stimulation (8-82)


title: 0 min No stimulation (8-81)


title: 0 min No stimulation (8-96)


title: 0 min No stimulation (8-86)


title: 0 min No stimulation (8-84)


title: 0 min No stimulation (8-80)


title: 0 min No stimulation (8-89)


title: 0 min No stimulation (8-94)


title: 0 min No stimulation (9-15)


title: 0 min No stimulation (9-11)


title: 0 min No stimulation (7-54)


title: 0 min No stimulation (8-90)


title: 0 min No stimulation (8-83)


title: 0 min No stimulation (7-55)


title: 0 min No stimulation (8-93)


title: 0 min No stimulation (7-42)


title: 0 min No stimulation (7-56)


title: 0 min No stimulation (7-68)


title: 0 min No stimulation (7-44)


title: 0 min No stimulation (7-60)


title: 0 min No stimulation (7-73)


title: 0 min No stimulation (7-39)


title: 0 min No stimulation (7-67)


title: 0 min No stimulation (7-51)


title: 0 min No stimulation (8-95)


title: 0 min No stimulation (7-72)


title: 0 min No stimulation (7-53)


title: 0 min No stimulation (7-80)


title: 0 min No stimulation (7-71)


title: 0 min No stimulation (7-84)


title: 0 min No stimulation (7-43)


title: 0 min No stimulation (7-63)


title: 0 min No stimulation (7-64)


title: 0 min No stimulation (7-47)


title: 0 min No stimulation (7-50)


title: 0 min No stimulation (7-79)


title: 0 min No stimulation (7-83)


title: 0 min No stimulation (7-49)


title: 0 min No stimulation (7-82)


title: 0 min No stimulation (7-57)


title: 0 min No stimulation (7-76)


title: 0 min No stimulation (7-52)


title: 0 min No stimulation (7-61)


title: 0 min No stimulation (7-48)


title: 0 min No stimulation (7-62)


title: 0 min No stimulation (7-70)


title: 0 min No stimulation (7-65)


title: 0 min No stimulation (7-77)


title: 0 min No stimulation (7-45)


title: 0 min No stimulation (7-66)


title: 0 min No stimulation (7-40)


title: 0 min No stimulation (7-78)


title: 0 min No stimulation (6-1)


title: 0 min No stimulation (6-10)


title: 0 min No stimulation (7-81)


title: 0 min No stimulation (6-12)


title: 0 min No stimulation (7-58)


title: 0 min No stimulation (6-6)


title: 0 min No stimulation (6-14)


title: 0 min No stimulation (7-69)


title: 0 min No stimulation (7-46)


title: 0 min No stimulation (6-13)


title: 0 min No stimulation (7-59)


title: 0 min No stimulation (6-9)


title: 0 min No stimulation (7-75)


title: 0 min No stimulation (6-3)


title: 0 min No stimulation (6-8)


title: 0 min No stimulation (5-57)


title: 0 min No stimulation (5-54)


title: 0 min No stimulation (5-62)


title: 0 min No stimulation (6-4)


title: 0 min No stimulation (5-48)


title: 0 min No stimulation (5-72)


title: 0 min No stimulation (5-84)


title: 0 min No stimulation (5-95)


title: 0 min No stimulation (6-5)


title: 0 min No stimulation (6-11)


title: 0 min No stimulation (5-50)


title: 0 min No stimulation (5-94)


title: 0 min No stimulation (5-49)


title: 0 min No stimulation (5-61)


title: 0 min No stimulation (5-71)


title: 0 min No stimulation (5-67)


title: 0 min No stimulation (5-55)


title: 0 min No stimulation (5-92)


title: 0 min No stimulation (5-81)


title: 0 min No stimulation (5-76)


title: 0 min No stimulation (6-7)


title: 0 min No stimulation (6-2)


title: 0 min No stimulation (5-83)


title: 0 min No stimulation (5-68)


title: 0 min No stimulation (5-75)


title: 0 min No stimulation (5-79)


title: 0 min No stimulation (5-63)


title: 0 min No stimulation (5-64)


title: 0 min No stimulation (5-65)


title: 0 min No stimulation (5-51)


title: 0 min No stimulation (5-59)


title: 0 min No stimulation (5-87)


title: 0 min No stimulation (5-78)


title: 0 min No stimulation (5-60)


title: 0 min No stimulation (5-66)


title: 0 min No stimulation (5-69)


title: 0 min No stimulation (5-80)


title: 0 min No stimulation (5-96)


title: 0 min No stimulation (5-88)


title: 0 min No stimulation (5-73)


title: 0 min No stimulation (5-56)


title: 0 min No stimulation (5-93)


title: 0 min No stimulation (5-77)


title: 0 min No stimulation (5-52)


title: 0 min No stimulation (5-85)


title: 0 min No stimulation (5-91)


title: 0 min No stimulation (5-70)


title: 0 min No stimulation (5-53)


title: 0 min No stimulation (5-86)


title: 0 min No stimulation (4-40)


title: 0 min No stimulation (5-82)


title: 0 min No stimulation (4-43)


title: 0 min No stimulation (4-72)


title: 0 min No stimulation (4-61)


title: 0 min No stimulation (4-26)


title: 0 min No stimulation (4-48)


title: 0 min No stimulation (4-50)


title: 0 min No stimulation (4-59)


title: 0 min No stimulation (4-34)


title: 0 min No stimulation (4-71)


title: 0 min No stimulation (4-65)


title: 0 min No stimulation (4-35)


title: 0 min No stimulation (4-45)


title: 0 min No stimulation (4-67)


title: 0 min No stimulation (4-63)


title: 0 min No stimulation (4-60)


title: 0 min No stimulation (4-47)


title: 0 min No stimulation (4-51)


title: 0 min No stimulation (5-58)


title: 0 min No stimulation (4-52)


title: 0 min No stimulation (4-28)


title: 0 min No stimulation (4-56)


title: 0 min No stimulation (4-39)


title: 0 min No stimulation (4-42)


title: 0 min No stimulation (4-53)


title: 0 min No stimulation (4-69)


title: 0 min No stimulation (4-44)


title: 0 min No stimulation (4-36)


title: 0 min No stimulation (4-57)


title: 0 min No stimulation (4-32)


title: 0 min No stimulation (4-64)


title: 0 min No stimulation (4-33)


title: 0 min No stimulation (4-58)


title: 0 min No stimulation (4-29)


title: 0 min No stimulation (4-68)


title: 0 min No stimulation (4-41)


title: 0 min No stimulation (4-54)


title: 0 min No stimulation (5-90)


title: 0 min No stimulation (4-38)


title: 0 min No stimulation (4-27)


title: 0 min No stimulation (4-49)


title: 0 min No stimulation (4-37)


title: TM014_38_eGFP++

source_name: In vitro differentiation of mESCs into motor neurons, pilot experiment

value: Day 6


title: TM014_37_eGFP++


title: 0 min No stimulation (4-31)


title: TM014_36_eGFP++


title: 0 min No stimulation (4-46)


title: TM014_32_eGFP++


title: TM014_39_eGFP++


title: TM014_35_eGFP++


title: TM014_31_eGFP++


title: TM014_30_eGFP++


title: TM014_33_eGFP++


title: TM014_34_eGFP++


title: 0 min No stimulation (4-30)


title: TM014_28_eGFP++


title: 0 min No stimulation (4-66)


title: TM014_25_eGFP++


title: TM014_29_eGFP++


title: TM014_26_eGFP++


title: TM014_24_eGFP++


title: TM014_23_eGFP++


title: TM014_22_eGFP++


title: TM014_27_eGFP++


title: TM014_21_eGFP++


title: TM014_19_eGFP++


title: TM014_17_eGFP++


title: TM014_18_eGFP++


title: TM014_15_eGFP++


title: TM014_12_eGFP++


title: TM014_13_eGFP++


title: TM014_11_eGFP++


title: TM014_9_eGFP++


title: TM014_8_eGFP++


title: TM014_7_eGFP++


title: TM014_5_eGFP++


title: TM014_10_eGFP++


title: TM014_3_eGFP++


title: TM014_4_eGFP++


title: TM014_2_eGFP++


title: TM018_36


title: TM018_37


title: TM018_39


title: TM018_34


title: TM018_35


title: TM018_33


title: TM018_38


title: TM014_20_eGFP++


title: TM014_0_eGFP++


title: TM014_16_eGFP++


title: TM014_14_eGFP++


title: TM018_29


title: TM018_30


title: TM018_31


title: TM018_32


title: TM014_6_eGFP++


title: TM018_26


title: TM018_25


title: TM018_24


title: TM014_1_eGFP++


title: TM018_23


title: TM018_20


title: TM018_28


title: TM018_22


title: TM018_19


title: TM018_16


title: TM018_17


title: TM018_14


title: TM018_21


title: TM018_15


title: TM018_11


title: TM018_10


title: TM018_9


title: TM018_27


title: TM018_4


title: TM018_8


title: TM018_1


title: TM018_6


title: TM018_12


title: TM018_0


title: TM017_38


title: TM017_35


title: TM017_36


title: TM018_2


title: TM017_37


title: TM017_39


title: TM018_5


title: TM017_34


title: TM017_33


title: TM018_18


title: TM018_3


title: TM017_32


title: TM017_31


title: TM017_30


title: TM017_29


title: TM017_24


title: TM017_22


title: TM018_13


title: TM017_28


title: TM017_27


title: TM018_7


title: TM017_25


title: TM017_19


title: TM017_21


title: TM017_20


title: TM017_26


title: TM017_18


title: TM017_16


title: TM017_9


title: TM017_10


title: TM017_11


title: TM017_13


title: TM017_12


title: TM017_14


title: TM017_15


title: TM017_8


title: TM017_5


title: TM017_4


title: TM017_6


title: TM017_3


title: TM017_23


title: TM017_1


title: TM017_2


title: TM017_0


title: TM019_34

value: Day 5


title: TM019_36


title: TM019_38


title: TM019_39


title: TM017_17


title: TM019_33


title: TM019_35


title: TM019_32


title: TM017_7


title: TM019_30


title: TM019_31


title: TM019_28


title: TM019_29


title: TM019_26


title: TM019_25


title: TM019_22


title: TM019_21


title: TM019_24


title: TM019_27


title: TM019_23


title: TM019_20


title: TM019_19


title: TM019_16


title: TM019_37


title: TM019_18


title: TM019_17


title: TM019_15


title: TM019_14


title: TM019_13


title: TM019_9


title: TM019_10


title: TM019_11


title: TM019_7


title: TM019_8


title: TM019_6


title: TM019_5


title: TM019_2


title: TM019_3


title: TM019_4


title: TM019_1


title: TM016_39


title: TM019_0


title: TM016_38


title: TM016_33


title: TM016_34


title: TM016_37


title: TM016_32


title: TM016_36


title: TM016_30


title: TM019_12


title: TM016_25


title: TM016_26


title: TM016_27


title: TM016_24


title: TM016_28


title: TM016_29


title: TM016_23


title: TM016_20


title: TM016_19


title: TM016_17


title: TM016_16


title: TM016_18


title: TM016_22


title: TM016_31


title: TM016_35


title: TM016_11


title: TM016_14


title: TM016_15


title: TM016_9


title: TM016_10


title: TM016_12


title: TM016_7


title: TM016_6


title: TM016_8


title: TM016_3


title: TM016_4


title: TM016_0


title: TM016_2


title: TM016_1


title: TM016_21


title: TM015_39

value: Day 4


title: TM015_38


title: TM015_37


title: TM015_34


title: TM015_33


title: TM016_13


title: TM015_31


title: TM015_30


title: TM015_29


title: TM015_28


title: TM015_25


title: TM016_5


title: TM015_26


title: TM015_23


title: TM015_22


title: TM015_18


title: TM015_21


title: TM015_20


title: TM015_27


title: TM015_35


title: TM015_15


title: TM015_14


title: TM015_36


title: TM015_12


title: TM015_9


title: TM015_13


title: TM015_32


title: TM015_7


title: TM015_6


title: TM015_24


title: TM015_5


title: TM015_3


title: TM015_1


title: TM015_0


title: TM015_2


title: TM013_38


title: TM013_39


title: TM015_16


title: TM013_35


title: TM013_37


title: TM015_17


title: TM015_10


title: TM013_33


title: TM013_31


title: TM015_8


title: TM013_34


title: TM013_27


title: TM013_36


title: TM013_32


title: TM013_28


title: TM013_26


title: TM013_30


title: TM015_11


title: TM013_29


title: TM013_24


title: TM015_19


title: TM013_25


title: TM013_23


title: TM013_22


title: TM013_21


title: TM013_20


title: TM013_19


title: TM013_18


title: TM013_14


title: TM013_17


title: TM013_12


title: TM013_15


title: TM013_11


title: TM013_13


title: TM013_9


title: TM013_10


title: TM013_6


title: TM013_3


title: TM013_8


title: TM013_2


title: TM015_4


title: TM013_1


title: TM013_5


title: TM012_39

value: Day 3


title: TM013_4


title: TM013_0


title: TM012_38


title: wild-type zebrafish treated with naphthol biological replicate 2

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence quality was accessed via FastQC, and low-quality bases and adapter sequences were removed using Trimmomatic.
Processed paired-reads were mapped to zebrafish genome (danRer7) using Tophat 2.0.13 with iGenome zebrafish (danRer7 UCSC) reference and following parameters: -p 8 -r 0 --no-novel-juncs.
Raw counts of reads mapped per gene were calculated using subread:featureCounts function
Sample outlier (wt_20_6) was excluded from the downstream voom+limma analysis that identified differentially expressed genes.
Genome_build: danRer7
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads mapped per gene for each Sample ...

organism: Danio rerio

source_name: Zebrafish embroys

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild type control

value: treated with 20 ug/5 mL 1-naphthol


title: wild-type zebrafish treated with naphthol biological replicate 3


title: TM012_37


title: wild-type zebrafish treated with naphthol biological replicate 4


title: wild-type zebrafish treated with naphthol biological replicate 5


title: TM013_16


title: wild-type zebrafish treated with naphthol biological replicate 1


title: TM012_36


title: TM012_35


title: TM012_34


title: TM012_32


title: wild-type zebrafish no naphthol treatment biological replicate 5

value: no 1-naphthol treatment


title: TM012_33


title: wild-type zebrafish no naphthol treatment biological replicate 3


title: wild-type zebrafish no naphthol treatment biological replicate 4


title: wild-type zebrafish no naphthol treatment biological replicate 2


title: wild-type zebrafish no naphthol treatment biological replicate 1


title: p53 knock out Zebrafish treated with naphthol biological replicate 4

value: p53 mutant


title: p53 knock out Zebrafish treated with naphthol biological replicate 3


title: p53 knock out Zebrafish treated with naphthol biological replicate 5


title: p53 knock out Zebrafish treated with naphthol biological replicate 2


title: p53 knock out Zebrafish treated with naphthol biological replicate 1


title: p53 knock out Zebrafish no naphthol treatment biological replicate 5


title: p53 knock out Zebrafish no naphthol treatment biological replicate 4


title: p53 knock out Zebrafish no naphthol treatment biological replicate 3


title: p53 knock out Zebrafish no naphthol treatment biological replicate 2


title: T6

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
Two independent RNA isolations were combined for library preparation.
rRNA depleted RNA

data_processing:
Adaptor trimming with Cutadapt v. 1.8.1
Sequence alignment with Tophat v 2.0.13
Normalized FPKM calculation with Cufflinks v 2.2.1
Genome_build: Ensembl GRCz10
Supplementary_files_format_and_content: FPKM

source_name: Cd41 antibody positive cells from peripheral blood

extract_protocol:
RNA was isolated using Trizol LS.
Total RNA was depleted of ribosomal RNA using Ribogone (Takara 634846). Library preparation was then performed with SMARTer® Universal Low Input RNA Kit for Sequencing (Takara 634938). The samples were sequenced on a HiSeq Illumina sequencer.

tag: strain

tag: developmental stage

value: Adult

value: thrombocyte


title: Eco_TolC_30min_Carolacton_B

city: Braunschweig

first: Jannik

last: Donner

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz-Center for Infection Research

data_processing:
Sequenced reads were trimmed for adaptor sequences using FastQC v0.11.2.
Raw read counts of transcripts were obtained by aligning samples 1-14 to the reference genome and counting mapped reads per feature using Rockhopper v2.0.3.
Genome_build: CP018801 (https://www.ncbi.nlm.nih.gov/nuccore/CP018801)
Supplementary_files_format_and_content: The tab-delimited text files include raw read values for each time-point for both biol. replicates of control and Carolacton-treated samples as obtained from Rockhopper. A FASTA file on the series record contains the transcript sequences.

organism: Escherichia coli

source_name: planktonic cells

growth_protocol: E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm.

extract_protocol:
Total cellular RNAs were extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturers protocol. Residual DNA in the fractions was digested by addition of 27 Kunitz units Dnase I (Qiagen), and absence of DNA verified by Polymerase chain reaction (PCR). mRNA enrichment was conducted using the Ribo-Zero kit for Gram-negative bacteria (epicentre). RNA quality control of the RNA extracts, as well as the successful mRNA enrichment, was conducted by using an Agilent 2100 Bioanalyzer.
Libraries of RNA fractions were constructed with the ScriptSeq V2 RNA-Seq Library Prep Kit (Illumina) according to the manufacturers guidelines.

treatment_protocol: An o/n culture of E. coli TolC was diluted to an OD600 of 0.1 and supplied with a final concentration of 0.5 µg/ml Carolacton in MeOH. Controls received the same volume MeOH. Three early time-points (t) were chosen to be analyzed by RNA-seq. Prior to addition of Carolacton (t0), t5, t15 and t30 min after addition of Carolacton. At each point, 5 ml of culture were mixed with an equal volume RNAprotect (Qiagen), incubated at room temperature (RT) for 5 min, the cells harvested by centrifugation, and the pellet frozen and stored at -80°C.

value: 0.5 µg/ml Carolacton

value: TolC defective (TolC-)

tag: time point (minutes)


title: p53 knock out Zebrafish no naphthol treatment biological replicate 1


title: Eco_TolC_30min_control_B


title: Eco_TolC_30min_Carolacton_A


title: TM013_7


title: Eco_TolC_30min_control_A


title: Eco_TolC_15min_control_A


title: Eco_TolC_15min_Carolacton_A


title: Eco_TolC_15min_Carolacton_B


title: Eco_TolC_5min_Carolacton_A


title: Eco_TolC_5min_Carolacton_B


title: Eco_TolC_15min_control_B


title: Eco_TolC_0min_B


title: Eco_TolC_5min_control_B


title: Eco_TolC_5min_control_A


title: Eco_TolC_0min_A


title: neuron_d12_1

city: Beijing

first: Xiaopeng

last: Ma

state: Outside US and Canada

address: HaiDian district

department: Biology

country: China

institute: Tsinghua Univeristy

description:
rep1
trans-spliced RNA with tag-SL1

data_processing:
Firstly, we filtered the reads that did not start with SL1(G16C), then trimmed adapter sequence with the program trimmomatic. We trimmed 22-bp SL1(G16C) sequence from each clean reads and aligned them to the C. elegans genome WS249 with tophat2 using WS249 gene model annotations, allowing 2 mismatches. A Python script was used to annotate the location of TSASs for both modENCODE data and our data
Trans-splicing accept sites(TSASs) on exact or 100 bp upstream or downstream of the 5΄-start site of an annotated exon were considered as annotated TSASs. Others were non-annotated, and were further classified into 3 categories: those in the intergenic region that were more than 1 kb upstream of known genes (‘intergenic’); those on the antisense strand of known genes (‘antisense’); and others (‘undetermined’). In the calculations of gene expression, we considered only the reads on the first exon of a gene's transcripts (i.e. ‘trans-splicing site’) and ignored these on the ‘cis-splicing site’, similar to a previous study
Read counts of each profile were normalized by reads per million mapped reads (RPM), then further normalized by upper-quantile normalization as previously described. DEGs were detected with the R package DESeq using a negative binomial test, with the parameters of method = ‘pooled’ and sharingMode = ‘fit-only’. Benjamini–Hochberg adjusted P-values were used.
Genome_build: WS249
Supplementary_files_format_and_content: the excel file containing the expression reads count of every TSAS and related gene

organism: Caenorhabditis elegans

source_name: pan-neuron

growth_protocol: Worms were grown on NGM plates seeded with OP50 bacteria at 20°C using the standard culture method.

extract_protocol:
Total RNA was extracted with the Trizol/phenol/isopropanol method as described (Invitrogen)
A total of 300–600 μg RNA was pulled-down with a biotin-labelled probe (antisense to tag, biotin-AGATCGGAAGAGCGTCGTGT) with a PolyATract mRNA kit according to the manufacturer's instruction (Promega, #Z5310) except that the polyT probe in the kit was replaced by the anti-tag probe. All of the pulled-down RNA was then reverse-transcribed with pRT(ATTTAGGTGACACTATAGAAGCAGAAGACGGCATACGAT(20)V) with PrimeScriptTM II Reverse Transcriptase (Takara, #2690A) at 42°C for 90 min to get full length cDNA. Then the cDNAs were PCR amplified for 10 cycles (98°C 10 s, 58°C 30 s, 72°C 1.5 min) with primer pF1 (ACACGACGCTCTTCCGATC) and pR1 (ATTTAGGTGACACTATAGAAGCAGAA) with Ex-Taq HS (takara, #RR006). To get higher specificity, nested PCR was performed (98°C 10 s, 58°C 30 s, 72°C 1.5 min) with pF2 (GACGCTCTTCCGATCTGGTT) and pR2 (CAAGCAGAAGACGGCATACGA) for another 10 cycles. The resulting cDNAs were fragmented and tagged with adapters with Tn5 transposase (Vazyme) at 55°C for 10 min, then amplified with pFY(AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGGTT) and pN7(CAAGCAGAAGACGGCATACGAGATIIIIIIIIGTCTCGTGGGCTCGG, ‘I’ represents index) with Q5 polymerase (NEB, #M0494) for 12–15 cycles (pre-PCR: 72°C 3min, PCR-cycle: 98°C 10 s, 66°C 30 s, 72°C 50 s) and purified with Ampure XP beads. PCR product was then sequenced on an Illumina HiSeq2000 using 2 × 100 bp or 2 × 125 bp mode.

treatment_protocol: Synchronized worms were obtained by treating with sodium hypochlorite, followed by embryo hatching on NGM plates without food. After overnight hatching, synchronized worms were considered as L1 larvae. About 12 h after feeding, worms were considered L2 larvae. About 2 days after feeding, most worms had a couple of eggs in their gonads and were considered as young adults. Synchronized L1, L2 and young adult worms were harvested to store in Trizol for RNA extraction. Aging worms were obtained by growing on Fluorodeoxyuridine containing NGM plates (400 μM) until the 12th day (young adult as day 1) as described previously.The dauer worms were grown and purified according to the previous method. Briefly, transgenic worms were cultured in liquid at 20°C with vigorous shaking for 3–4 days. Then they were treated with 1% SDS for 15 min to kill non-dauers, followed by sucrose floatation and Ficoll precipitation to separate live worms from debris. The purity of dauer status was examined under stereo-microscope to make sure that more than 90% of worms were live dauers. The harvested dauers recovered overnight in 0.1 M NaCl at 20°C to eliminate stressful stimuli to worms during the tough treatment.

value: pan-neuron

value: old stage, day-12

tag: transgenic strain


title: neuron_YA_1

description:
rep1
trans-spliced RNA with tag-SL1

value: young adult stage


title: neuron_d12_2

description:
rep2
trans-spliced RNA with tag-SL1


title: muscle_SL2

description:
rep1
trans-spliced RNA with tag-SL1

source_name: muscle

value: muscle

value: mixed stage


title: HBS1LV3 rescue with HBS1LV3 KD replicate B

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

data_processing:
base caling CASAVA v1.8.2
aligmnent STAR v2.4.0 with default settings
further processing, filtering, counting, QC  - custom scripts emploing samtools v1.2-10, HTSeq v0.6.1, RSeQ v2.6.1, FastQC v0.11.3
differential expression analysis DESeq2 v1.8.2

source_name: HEK293 Flp-In T-REx

growth_protocol: HEK293 Flp-In T-REx and derived stable cell lines were grown in cell culture dishes in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (FBS; Gibco) at 37°C in a 5% CO2 humidified atmosphere.

extract_protocol:
RNA was isolated from HEK293 Flp-In T-REx cell lines using TRI Reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
Total RNA was treated with Turbo-DNase (Life Technologies). Then, rRNA was removed from samples using a Ribo-Zero Kit (Epicentre), according to the manufacturer’s protocols with minor modifications. To control for experimental performance, external RNA (ERCC RNA Spike-In Mix; Life Technologies) was added to the samples. RNA libraries were prepared using a TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s manual, with the following changes: i) the RNA sequencing sample was obtained from total RNA, ii) SuperScript III Reverse Transcriptase was used instead of SuperScript II Reverse Transcriptase (Life Technologies) for first strand cDNA synthesis, iii) an alternative master mix that contained dUTP was added to the sample to synthesize the second strand, and dUTPs were incorporated into the emerging second strand to allow for the subsequent digestion of this strand and to obtain strand-specific libraries, iv) before PCR amplification of double stranded cDNA, the second strand was digested with 0.04 U/μl USER enzyme (Uracil-Specific Excision Reagent; BioLabs) for 30 min at 37°C; and v) a PCR amplification alternative mix was used.

treatment_protocol: siRNA-mediated knockdown was performed using siRNA (Eurogentec) and Lipofectamine RNAiMAX Reagent (Invitrogen) according to the manufacturer’s instructions. siRNA molecules as well as a negative control were used at a final concentration of 25 nM. To induce production of exogenous protein variants, cells were grown in the presence of doxycycline for an additional 48 hours before harvesting.

tag: overexpressed protein

value: siRNA insensitive protein HBS1LV3

tag: sirna

value: HEK 293


title: HBS1LV1 rescue with HBS1LV1 KD replicate B

value: siRNA insensitive protein HBS1LV1


title: Rrp44-endo-HTP_miniseq

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

country: United Kingdom

institute: University of Edinburgh - WTCCB

description: barcode NNNGTGAGC

data_processing:
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign version 2.07.00 and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gtf format

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: sample type

value: HISx6-TEV protease cleavage site-protA


title: HBS1LV3 rescue with HBS1LV3 KD replicate A


title: HBS1LV1 rescue with HBS1LV1 KD replicate C


title: muscle_YA_2

description:
rep2
trans-spliced RNA with tag-SL1


title: muscle_d12_1

description:
rep1
trans-spliced RNA with tag-SL1


title: T-REx cells with HBS1LV3 KD replicate C


title: neuron_YA_2

description:
rep2
trans-spliced RNA with tag-SL1


title: muscle_dauer_2

description:
rep2
trans-spliced RNA with tag-SL1

value: dauer larvae


title: Repo/TDP43:S22_small RNA

city: Cold Spring Harbor

first: Wen-Wei

last: Liao

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: processed data file: small_RNA_count.txt

data_processing:
Reads were mapped to the Drosophila dm3 genome with Bowtie allowing up to 2 mismatches and a maximum of 100 multiple alignments.
Feature abundances were obtained by annotating reads based on genomic locations against ribosomal RNAs, microRNAs (miRBase), exons (RefSeq), transposable elements (FlyBase), introns (RefSeq), and piRNA clusters (proTRAC) using intersectBed from BedTools.
For the multiple mapped reads, the read counts were evenly distributed between all equivalently aligned matches.
Genome_build: dm3
Supplementary_files_format_and_content: raw counts of sequencing reads for the genomic features

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
All small RNA libraries were constructed from 15-20 ug of TRIzol isolated total RNA.
18-29 nucleotide long small RNAs were size selected on 15% PAGE-UREA gel. After 3’- and 5’-adapter ligation, subsequent gel purification steps and reverse transcription cDNAs were PCR amplified with barcoded primers. PCR products were size selected on 6% PAGE gel, and quantified on Bioanalyzer. Loading concentrations were determined using the NEBNext Library Quant kit for Illumina (NEB). The libraries were sequenced on illumina NextSeq 500 platform.

value: head

tag: genotype/variation


title: Repo/TDP43:S23_small RNA


title: T-REx cells with HBS1LV3 KD replicate B


title: Repo/TDP43:S24_small RNA


title: muscle_YA_1

description:
rep1
trans-spliced RNA with tag-SL1


title: Repo/2U:S21_small RNA


title: muscle_dauer_1

description:
rep1
trans-spliced RNA with tag-SL1


title: T-REx cells with HBS1LV3 KD replicate A


title: muscle_L2

description:
rep1
trans-spliced RNA with tag-SL1

value: L2 larvae


title: Repo/2U:S20_small RNA


title: muscle_L1

description:
rep1
trans-spliced RNA with tag-SL1

value: L1 larvae


title: T-REx cells with HBS1LV1 KD replicate B


title: T-REx cells with HBS1LV1 KD replicate A


title: U2-3_1

description:
rep1
trans-spliced RNA with tag-SL1

source_name: multiple tissues

value: multiple tissues


title: HBS1LV1 rescue with HBS1LV1 KD replicate A


title: TDP43/2U:S15

data_processing:
Reads were mapped to the Drosophila dm3 genome with STAR allowing up to 4 mismatches and a maximum of 100 multiple alignments.
Reads were annotated based on genomic locations against ribosomal RNAs, transposable elements (FlyBase), and RefSeq genes (UCSC genome database RefSeq track).
Reads mapped to ribosomal RNAs were removed from each library. For the remaining reads, expression abundance estimation and differential expression analysis were performed using the TEtranscripts package.
Genome_build: dm3
Supplementary_files_format_and_content: raw counts of sequencing reads for the genes/TEs

extract_protocol:
Fly heads were collected for each genotype and total RNA was purified with Trizol (Invitrogen).
RNA-Seq libraries were constructed using the NuGEN Ovation Drosophila RNA-Seq kit including DNase treatmen with HL-dsDNase (ArcticZymes Cat. # 70800-201) and cDNA fragmenation using the Covaris E220 system according to manufacturer recommendations.  After amplification library quality was measured using the Agilent Bioanalyzer system and quantity was determined using Life Technologies Qubit dsDNA HS Assay kit (for use with the Qubit 2.0 Fluorometer).  Prior to sequencing pooled libraries were quantified using the Illumina Library Quantification kit (with Universal qPCR mix) from Kapa Biosystems and a 1.2 pM loading concentration was used for PE101 on the Illumina NextSeq500 platform.


title: HBS1LV3 rescue with HBS1LV3 KD replicate C


title: T-REx cells with SKIV2L KD replicate B


title: TDP43/2U:S14


title: deltaR_dawn_15min

city: Cambridge

first: Anna

middle: M

last: Puszynska

address: 455 Main street

institute: Whitehead Institute for Biomedical Research

description: Expression_timecoursexls, column Y

data_processing:
Read alignment: Bowtie, v 0.12.7, -v 3 -m 1 --best –-un –-max
Gene expression quantification: the alignment output from Bowtie was analyzed in Matlab using custom code as described in Markson et al., 2013. To obtain gene expression values, we counted the number of coding-strand sequencing reads that had 5’ ends between the start and stop positions of the coding region of each gene (Markson et al., 2013).
Gene expression normalization: We performed RPKM normalization using a custom Matlab script.
Genome_build: Main chromosome: NC_007604.1; plasmid pANL (plasmid 1), NC_004073.2; plasmid pANS (plasmid 2), NC_004990.1
Supplementary_files_format_and_content: xls file with RPKM normalized gene expression values

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: cells

growth_protocol: Cell cultures were grown in tissue culture flasks under illumination with cool fluorescent light at 40 μE m-2 s-1 (μmoles photons m-2 s-1) in BG11 medium at 30 °C. Cells were initially inoculated in the presence of antibiotics (7.5 ug/mL kanamycin (“clock rescue” strain) or 2 ug/mL gentamycin and 7.5 ug/mL kanamycin (the rpaA- “clock rescue” strain)), and subsequently diluted with BG-11 only. The OD750 (optical density at 750 nm) was maintained at a constant level of 0.2.

extract_protocol:
Extraction was prepared as described previously by Vijayan et al 2009. Briefly, frozen cells were lysed in 65° C phenol/SDS by vortexing. Total RNA was extracted with phenol/chloroform followed by isopropanol precipitation. Then, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. To assess integrity total RNA was analyzed on an agarose gel.
Ribosomal RNA was depleted from 6 μg of total RNA using the MICROBExpress Bacterial mRNA enrichment kit (ThermoFisher Scientific), following the protocol provided by the manufacturer. RNA-sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) from 400 ng of rRNA-depleted RNA. Samples were multiplexed and sequenced on an Illumina HiSeq 2000 platform by the Bauer Core Facility at the Harvard FAS Center for Systems Biology.

treatment_protocol: The “clock rescue ” cells were exposed to two light/dark cycles (12 hours of dark, followed by 12 h of light, followed by 12 h of dark), while the rpaA- “clock rescue” cells were exposed to one light/dark cycle for entrainment. Cells were harvested by filtering and freezing in liquid-nitrogen at following time points: dusk (ZT=12h); 5 min, 15 min, 30 min, 1 h, 2 h, 4 h, 8 h and 11 h 50 min after exposure to expected darkness; and 5 min, 15 min and 30 min after re-exposure to light at dawn, and stored in -80º C.

value: rpaA- "clock rescue"

value: dawn 15 min


title: deltaR_dawn_30min

description: Expression_timecoursexls, column Z

value: dawn 30 min


title: Elav/TDP43:S12


title: T-REx cells with SKIV2L KD replicate C


title: T-REx cells with SKIV2L KD replicate A


title: muscle_d12_2

description:
rep2
trans-spliced RNA with tag-SL1


title: deltaR_dawn_5min

description: Expression_timecoursexls, column X

value: dawn 5 min


title: T-REx cells expressing control siRNA replicate C

value: control siRNA


title: deltaR_darkness_11h50min

description: Expression_timecoursexls, column W

value: darknes 11 h 50 min


title: T-REx cells with HBS1LV1 KD replicate C


title: I5

city: University Park

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

data_processing:
Basecalls performed using CASAVA version 1.7
Trimming performed using CLC Genomics WorkBech version 4.4, with default parameters
Assembly de novo performed using CLC Genomics WorkBech version 4.4, with default parameters
Genome_build: Amel_4.5

organism: Apis mellifera

source_name: newly emerged bee infested with three mites, sample 5

growth_protocol: L5 honeybee larvae were collected from comb cells sealed in the preceding 15 hours and artificially infested with one (H) , three (I) or no (G) Varroa destructor mites.

extract_protocol:
Samples for the analysis were transferred into liquid nitrogen and used for total RNA extraction using Tri-reagent (Ambion® Inc.). RNA was processed using the TruSeq mRNAseq sample prep kit (Illumina, Inc., CA, USA), starting from 2 micrograms of total RNA. The standard mRNA sample prep from Illumina was used to produce 36 base pairs long tags, 25-30 million per sample.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Prep Kit v2 (Part #15026495). Briefly, 0.1–1 μg of total RNA were purified using oligo-dT attached magnetic beads using two rounds of purification. During the second elution of the polyA RNA, the  RNA is also fragmented. Cleaved fragments are then primed with random hexamers into first strand cDNA using reverse transcriptase and random primers. Overhangs resulting from fragmentation are converted into blunt ends using an End Repair Mix. The 3' to 5' exonuclease activity of this mix removes the 3' overhangs and the polymerase activity fills in the 5' overhangs. A single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. A corresponding single ‘T’ nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragment. This strategy ensures a low rate of chimera (concatenated template). formation. PCR is used to enrich selectively DNA fragments that have adapter molecules on both ends, and the DNA  amount in the library is amplified. The PCR is performed with a PCR Primer Cocktail that anneals to the ends of the adapters. Library is validated by using Agilent Technologies 2100 Bioanalyzer using the Agilent DNA 1000 DNA-specific chip. Cluster density is optimized by quantify libraries using PCR according to the Illumina Sequencing Library qPCR Quantification Guide (part # 11322363). DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Bees were kept in 6.5 mm gelatine cells, at 35° and 75% R.H. and sampled after 12 days, at eclosion. Five bees from each experimental group were processed individually.

value: whole body

tag: agent

value: 3 mites


title: Repo/TDP43:S06


title: T-REx cells expressing control siRNA replicate A


title: deltaR_darkness_4h

description: Expression_timecoursexls, column U

tag: genotype

value: darkness 4h


title: Repo/TDP43:S05

tag: tissue


title: deltaR_darkness_8h

description: Expression_timecoursexls, column V

value: darkness 8 h


title: Repo/2U:S19_small RNA


title: I4

source_name: newly emerged bee infested with three mites, sample 4


title: deltaR_darkness_2h

description: Expression_timecoursexls, column T

value: darkness 2h


title: U2-3_2

description:
rep2
trans-spliced RNA with tag-SL1

value: mixed stage


title: SKIV2L rescue with SKIV2L KD replicate C

value: siRNA insensitive protein SKI2W

tag: cell line

value: HEK 293


title: SKIV2L rescue with SKIV2L KD replicate B


title: I3

source_name: newly emerged bee infested with three mites, sample 3


title: I2

source_name: newly emerged bee infested with three mites, sample 2


title: deltaR_darkness_15min

description: Expression_timecoursexls, column Q

tag: time point

value: darkness 15 min


title: deltaR_darkness_1h

description: Expression_timecoursexls, column S

value: darkness 1 h


title: deltaR_darkness_5min

description: Expression_timecoursexls, column P

value: darkness 5 min


title: I1

source_name: newly emerged bee infested with three mites, sample 1


title: H4

source_name: newly emerged bee infested with one mite, sample 4

value: 1 mites


title: Elav/TDP43:S11

value: head


title: deltaR_darkness_30min

description: Expression_timecoursexls, column R

value: rpaA- "clock rescue"

value: darkness 30 min


title: SKIV2L rescue with SKIV2L KD replicate A


title: H3

source_name: newly emerged bee infested with one mite, sample 3


title: T-REx cells expressing control siRNA replicate B

value: control siRNA


title: H2

source_name: newly emerged bee infested with one mite, sample 2


title: control_dawn_15min

description: Expression_timecoursexls, column M

value: "clock rescue"

value: dawn 15 min


title: control_dawn_30min

description: Expression_timecoursexls, column N

value: dawn 30 min


title: control_dawn_5min

description: Expression_timecoursexls, column L

value: dawn 5 min


title: 150NaCl.RAA026

city: Singapore

first: Neil

last: Clarke

address: 16 College Avenue West

country: Singapore

institute: Yale-NUS College

data_processing:
Read mapping. Reads were mapped using Bowtie (v0.12.8) agaiinst de novo assembled transcripts (submitteed to Transcriptome Shotgun Assembly; GEEU00000000).
Transcript abundances. Tag counts were determined using RSEM (v1.2.0)
Differential expression. edgeR (v3.0.8 from BioConductor), with TMM normalization and a dispersion value of 0.1; all comparisons were to the control conditio (sample name 9.0N.c2)
Transcript selection and merging: any transcript with an edgeR estimated FDR value of 0.05 or better for at least one of the nine comparisons to control was retained.  Scaffolds that share the first two identification numbers assigned by Trinity (i.e, differing only in the third number in ID’s that are of the form <num>_c<num>_seq<num>) were deemed to belong to the same scaffold family.  Although some of these may be authentic variants,  others are likely to be sequencing or assembly artifacts; consequently, we treated scaffold families as individual transcripts, summing their RPKM values for purposes of gene expression analysis
processed data files format and content: tab-delimited text (RPKM values)

organism: Ettlia oleoabundans

source_name: cell culture, phototrophic conditions, 6 days

growth_protocol: cells were grown photoautotrophically in modified Bold Basal Medium plus vitamins B1 and B12, and varying concentrations of nitrate and NaCl concentations. Cells were grown under constant light (22-28 µmol. photons m-2s-1) at 25 degrees for 6 days. Initial cell densities were 1x10^6 cells/ml.

extract_protocol:
hot phenol followed by poly-A selection using Dynal oligo-T beads
Illumina protocol using mRNA-Seq kit

treatment_protocol: varying nitrate and NaCl as described under samples

tag: condition

value: 150mM NaCl


title: G4

source_name: newly emerged bee not infested, sample 4

value: whole body

value: 0 mites


title: 75NaCl.c3

value: 75mM NaCl


title: control_darkness_8h

description: Expression_timecoursexls, column J

value: darkness 8 h


title: 600NaCl.c5

value: 600mM NaCl


title: G5

source_name: newly emerged bee not infested, sample 5


title: 300NaCl.c4

value: 300mM NaCl


title: control_darkness_11h50min

description: Expression_timecoursexls, column K

value: darknes 11 h 50 min


title: G3

source_name: newly emerged bee not infested, sample 3


title: control_darkness_4h

description: Expression_timecoursexls, column I

value: darkness 4h


title: H5

source_name: newly emerged bee infested with one mite, sample 5

value: 1 mites


title: 9.0N.c2

value: control (9mM nitrate, 42mM NaCl)


title: G2

source_name: newly emerged bee not infested, sample 2


title: 3.0N.c1

value: 3.0mM nitrate


title: 0.75N.c7

value: 0.75mM nitrate


title: deltaR_duskZT12

description: Expression_timecoursexls, column O

value: rpaA- "clock rescue"

value: dusk ZT=12


title: control_darkness_30min

description: Expression_timecoursexls, column F

value: "clock rescue"

value: darkness 30 min


title: control_darkness_1h

description: Expression_timecoursexls, column G

value: darkness 1 h


title: control_darkness_2h

description: Expression_timecoursexls, column H

value: darkness 2h


title: 0.38N.RAA025

value: 0.38mM nitrate


title: control_darkness_5min

description: Expression_timecoursexls, column D

value: darkness 5 min


title: G1

source_name: newly emerged bee not infested, sample 1

value: whole body

value: 0 mites


title: 0.00N.c6

value: 0mM nitrate


title: H1

source_name: newly emerged bee infested with one mite, sample 1


title: RNaseE_HTF_2

status: Public on Feb 14 2017

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: RNA from RNA-protein complexes

data_processing:
Library strategy: CLASH
hyb demultiplex M=1 code=BARCODES preprocess check detect db=SAKAI anti=1 analyse in=FASTQ. The hyb software package (Travis et al Methods 2014) was used to demultiplex, trim, quality filter, and align reads. BARCODES is a tab delimted file containing the barcodes  NNNACTCAGC and NNNGACTTAGC. SAKAI is the database generated from the fasta file (GeneBank Acc# NC_002695.1) using the command make_hyb_db. FASTQ is the input sequencing file.
The HYB file generated by hyb was annotated using the custom scripts and the GTF annotation file obtained from the UCSC microbial genome browser (below).
For analysis of RNase E binding sites (CRAC analysis), the pyCRAC software package was used (Webb et al Genome Biology 2014) and as previously described (Tree et al Mol Cell 2014) excepting clipped and quality filtered files generated by hyb were used for mapping and analysis.
novoalign -f NNNACTCAGC_L5Cc_RNaseE_1_clipped_qf.fastq -d NOVOINDEX -a TGGAATTCTCGGGTGCCAAGG -h 150 -F STDFQ -r Random > RNaseE_1.novo
pyReadCounters.py -f RNaseE_1.novo --gtf=Sakai.gtf -v --blocks
Processed data files for RNase E binding sites are presented as pyReadCounters GTF outputs
Genome_build: annotation = UCSC microbial genome (microbes.ucsc.edu) Escherichia coli O157H7 29/03/2000; sequence file = GeneBank Acc# NC_002695.1
Supplementary_files_format_and_content: HYB files generated by hyb software (Travis et al 2014 Methods). These files contain information on RNA-RNA interactions.
Supplementary_files_format_and_content: GTF files generated by pyReadCounters (pyCRAC). These files contain information on RNA-RNase E interactions.
Supplementary_files_format_and_content: RNaseE_peaks_threshold*.gtf: Annotation files that delimit peaks in the CRAC dataset.

organism: Escherichia coli O157:H7 str. Sakai

source_name: liquid culture

growth_protocol: E. coli O157:H7 rne-HTF was cultured overnight in LB broth and inoculated 1/100 into 2L of MEM-HEPES (+250nM Fe[NO3]3] + 0.1% glucose). Cultures were shaken at 200rpm and 37C untill the OD600 reached 0.8. Cultures were rapidly UV crosslinked, harvested, washed with PBS, harvested, and snap frozen in LN2.

extract_protocol:
Cells were treated with 1800mJ of UV-C and lyzed by vortexing with zirconia beads in lysis buffer. RNasE-RNA complexes were purified over M2 anti-FLAG resin, trimmed with RNase A/T1 and repurified under denaturing conditions using Ni-NTA resin. RNA 5' and 3' end were prepared for ligation by decapping 5' PPP with TAP, phosphorylation of 5'OH with 32P-ATP and PNK, and dephosphyorlation of 3'P with TSAP. RNA linkers were added using T4 RNA ligase. RNaseE-RNA complexes were eluted and seperated by SDS-PAGE, transferred to a nitrocelluose membrane and extracted. Protein was removed by Proteinase K digestion and RNAs purified by phenol:chloroform extraction.
Extracted RNAs were converted to cDNA using Superscript III and PCR amplified. PCR products between ~150 and 250 bp were gel extracted and submitted for Illumina sequencing.

value: Sakai

tag: media

value: MEM-HEPES supplemented with 250nM FeIII and 0.1% glucose


title: RNaseE_HTF_1

description: RNA from RNA-protein complexes