title: skm_683s_N17


title: skm_683s_N1

status: Public on Jun 18 2020

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: total RNA

organism: Mus musculus

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol
single-cell RNA-seq

tag: tissue

value: skeletal muscle

tag: starin

tag: age

value: 10-20 weeks

tag: cluster


title: skm_683s_N14


title: skm_683s_N12


title: skm_683s_M8


title: skm_683s_M6


title: skm_683s_M4


title: skm_683s_M23


title: skm_683s_M24


title: skm_683s_M22


title: skm_683s_M21


title: skm_683s_M2


title: skm_683s_M14


title: skm_683s_M11


title: skm_683s_M15


title: skm_683s_M5


title: skm_683s_M10


title: skm_683s_L4


title: skm_683s_L9


title: skm_683s_L5


title: skm_683s_M20


title: skm_683s_L3


title: skm_683s_M1


title: skm_683s_L18


title: skm_683s_L20


title: skm_683s_L19


title: skm_683s_L2


title: skm_683s_L17


title: skm_683s_L16


title: skm_683s_L12


title: skm_683s_L24


title: skm_683s_L1


title: skm_683s_L6


title: skm_683s_L15


title: skm_683s_L13


title: skm_683s_K8


title: skm_683s_L11


title: skm_683s_L21


title: skm_683s_K6


title: skm_683s_K5


title: skm_683s_L14


title: skm_683s_L23


title: skm_683s_K4


title: skm_683s_L22


title: skm_683s_K3


title: skm_683s_K24


title: skm_683s_K21


title: skm_683s_K2


title: skm_683s_K23


title: skm_683s_K20


title: skm_683s_K19


title: skm_683s_K17


title: skm_683s_K15


title: skm_683s_K18


title: skm_683s_K11


title: skm_683s_K14


title: skm_683s_K13


title: skm_683s_K12


title: skm_683s_K1


title: skm_683s_J9


title: skm_683s_K10


title: skm_683s_J8


title: skm_683s_J4


title: skm_683s_J3


title: skm_683s_J24


title: skm_683s_J21


title: skm_683s_J23


title: skm_683s_J20


title: skm_683s_J19


title: skm_683s_J2


title: skm_683s_J22


title: skm_683s_J18


title: skm_683s_J17


title: skm_683s_J16


title: skm_683s_J12


title: skm_683s_J14


title: skm_683s_J15


title: skm_683s_I8


title: skm_683s_I6


title: skm_683s_J1


title: skm_683s_I9


title: skm_683s_J5


title: skm_683s_I3


title: skm_683s_I5


title: skm_683s_I21


title: skm_683s_I22


title: skm_683s_I24


title: skm_683s_I19


title: skm_683s_I18


title: skm_683s_I13


title: skm_683s_I16


title: skm_683s_I14


title: skm_683s_I15


title: skm_683s_I11


title: skm_683s_I17


title: skm_683s_J13


title: skm_683s_J10


title: skm_683s_I1


title: skm_514s_P9

value: PdgfrbGFP


title: skm_683s_I23


title: skm_514s_P8


title: skm_514s_P7


title: skm_683s_I10


title: skm_514s_P4


title: skm_514s_P5


title: skm_514s_P3


title: skm_514s_P20


title: skm_514s_P22


title: skm_514s_P19


title: skm_514s_P21


title: skm_683s_I20


title: skm_514s_P2


title: skm_514s_P17


title: skm_683s_I12


title: skm_514s_P18


title: skm_514s_P16


title: skm_514s_P15


title: skm_514s_P13


title: skm_514s_P14


title: skm_514s_P10


title: skm_514s_P12


title: skm_514s_P6


title: skm_514s_O9


title: skm_514s_P11


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title: skm_514s_O24


title: skm_514s_O22


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title: skm_514s_O23


title: skm_514s_O6


title: skm_514s_O7


title: skm_514s_O3


title: skm_514s_O21


title: skm_514s_O5


title: skm_514s_O20


title: skm_514s_O2


title: skm_514s_O17


title: skm_514s_O19


title: skm_514s_O12


title: skm_514s_O16


title: skm_514s_O18


title: skm_514s_O15


title: skm_514s_O14


title: skm_514s_N9


title: skm_514s_N8


title: skm_514s_N7


title: skm_514s_O13


title: skm_514s_O11


title: skm_514s_N5


title: skm_514s_N6


title: skm_514s_N4


title: skm_514s_N23


title: skm_514s_N3


title: skm_514s_N22


title: skm_514s_N21


title: skm_514s_N20


title: skm_514s_N24


title: skm_683s_I7


title: skm_514s_N18


title: skm_514s_N17


title: skm_514s_N19


title: skm_514s_N16


title: skm_514s_N14


title: skm_514s_N15


title: skm_514s_O10


title: skm_514s_N13


title: skm_514s_N11


title: skm_514s_N10


title: skm_514s_M9


title: skm_514s_M6


title: skm_514s_M7


title: skm_514s_M5


title: skm_514s_M8


title: skm_514s_M4


title: skm_514s_M3


title: skm_514s_M23


title: skm_514s_M24


title: skm_514s_N2


title: skm_514s_M22


title: skm_514s_M20


title: skm_514s_M21


title: skm_514s_M16


title: skm_514s_M18


title: skm_514s_M15


title: skm_514s_N12


title: skm_514s_M17


title: skm_514s_M14


title: skm_514s_N1


title: skm_514s_M10


title: skm_514s_M11


title: skm_514s_L9


title: skm_514s_L7


title: skm_514s_M1


title: skm_514s_L6


title: skm_514s_L4


title: skm_514s_L5


title: skm_514s_L23


title: skm_514s_L24


title: skm_514s_M2


title: skm_514s_L22


title: skm_514s_M13


title: skm_514s_L21


title: skm_514s_M12


title: skm_514s_L2


title: skm_514s_L18


title: skm_514s_L20


title: skm_514s_L16


title: skm_514s_L17


title: skm_514s_L8


title: skm_514s_L15


title: skm_514s_L11


title: skm_514s_L13


title: skm_514s_K9


title: skm_514s_L1


title: skm_514s_L10


title: skm_514s_L12


title: skm_514s_K6


title: skm_514s_L3


title: skm_514s_K5


title: skm_514s_K8


title: skm_514s_K24


title: skm_514s_K21


title: skm_514s_K20


title: skm_514s_K2


title: skm_514s_L14


title: skm_gastroc_520s_D1

value: skeletal muscle - gastrocnemius


title: skm_514s_K18


title: skm_514s_K19


title: skm_514s_L19


title: skm_514s_K16


title: skm_514s_K15


title: skm_514s_K7


title: skm_514s_K11


title: skm_514s_K13


title: skm_514s_K17


title: skm_514s_K14


title: skm_514s_J9


title: skm_514s_K12


title: skm_514s_K10


title: skm_514s_K1


title: skm_514s_K4


title: skm_514s_J8


title: skm_514s_K3


title: skm_514s_J6


title: skm_514s_J5


title: skm_514s_J7


title: skm_514s_K23


title: skm_514s_J4


title: skm_514s_J24


title: skm_514s_J3


title: skm_514s_J23


title: skm_514s_J22


title: skm_514s_J21


title: skm_514s_J19


title: skm_514s_J20


title: skm_514s_J17


title: skm_514s_J18


title: skm_514s_J15


title: skm_514s_J2


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title: skm_514s_J14


title: skm_514s_J11


title: skm_514s_J10


title: skm_514s_I8


title: skm_514s_J1


title: skm_514s_I6


title: skm_514s_I5


title: skm_514s_J16


title: skm_514s_I22


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title: skm_514s_I4


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title: skm_514s_I24


title: skm_514s_I9


title: skm_514s_I23


title: skm_514s_I18


title: skm_514s_I20


title: skm_514s_I19


title: skm_514s_I16


title: skm_514s_I17


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title: skm_514s_I13


title: skm_514s_I15


title: skm_514s_I12


title: skm_514s_I10


title: skm_514s_I11


title: skm_514s_H9


title: skm_514s_H6


title: skm_514s_H7


title: skm_514s_H5


title: skm_514s_H3


title: skm_514s_H4


title: skm_514s_H24


title: skm_514s_I1


title: skm_514s_H23


title: skm_514s_H22


title: skm_514s_H21


title: skm_514s_H20


title: skm_514s_I2


title: skm_514s_H19


title: skm_514s_H16


title: skm_514s_H18


title: skm_514s_H13


title: skm_514s_H15


title: skm_514s_H11


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title: skm_514s_H12


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title: skm_514s_D8


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title: skm_514s_D23


title: skm_514s_D9


title: skm_514s_D20


title: skm_514s_D24


title: skm_514s_D19


title: skm_514s_D2


title: skm_514s_E15


title: skm_514s_D22


title: skm_514s_D18


title: skm_514s_D12


title: skm_514s_D15


title: skm_514s_D14


title: skm_514s_D16


title: skm_514s_D13


title: skm_514s_D17


title: skm_514s_C7


title: skm_514s_C8


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title: skm_514s_C24


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title: skm_514s_C2


title: skm_514s_C16


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title: skm_514s_C18


title: skm_514s_C19


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title: skm_514s_C6


title: skm_514s_C12


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title: skm_514s_C10


title: skm_514s_B9


title: skm_514s_B8


title: skm_514s_B7


title: skm_514s_C20


title: skm_514s_B5


title: skm_514s_C21


title: skm_514s_B3


title: skm_514s_C14


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title: skm_514s_B24


title: skm_514s_B2


title: skm_514s_B22


title: skm_514s_B23


title: skm_514s_B15


title: skm_514s_B20


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title: skm_514s_B13


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title: skm_514s_B11


title: skm_514s_B17


title: skm_514s_A9


title: skm_514s_B18


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title: skm_514s_A7


title: skm_514s_A20


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title: skm_514s_A19


title: skm_514s_A18


title: skm_514s_A16


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title: skm_514s_A12


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title: skm_514s_A14


title: skm_351s_O6


title: skm_351s_O18


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title: skm_351s_O14


title: skm_351s_O12


title: skm_351s_O22


title: skm_351s_N8


title: skm_351s_N5


title: skm_514s_A1


title: skm_351s_N4


title: skm_351s_N23


title: skm_351s_O13


title: skm_351s_N24


title: skm_351s_N21


title: skm_351s_N22


title: skm_351s_N2


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title: skm_351s_N18


title: skm_351s_N17


title: skm_351s_N14


title: skm_351s_N13


title: skm_514s_A10


title: skm_351s_N9


title: skm_351s_M9


title: skm_351s_M8


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title: skm_351s_M6


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title: skm_351s_G6


title: skm_351s_I11


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title: skm_351s_F4


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title: skm_351s_F20


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title: skm_351s_F22


title: skm_351s_F2


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title: skm_351s_F9


title: skm_351s_F18


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title: skm_351s_F14


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title: skm_351s_F11


title: skm_351s_F10


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title: skm_351s_E9


title: skm_351s_E8


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title: skm_351s_E20


title: skm_351s_E10


title: skm_351s_E1


title: skm_351s_E12


title: skm_205s_P9


title: skm_205s_P8


title: skm_205s_P7


title: skm_205s_P3


title: skm_351s_E18


title: skm_351s_E16


title: skm_205s_P5


title: skm_205s_P4


title: skm_205s_P20


title: skm_205s_P2


title: skm_205s_P15


title: skm_205s_P19


title: skm_205s_P16


title: skm_205s_P17


title: skm_351s_E3


title: skm_351s_N15


title: skm_205s_P6


title: skm_205s_P12


title: skm_205s_P10


title: skm_205s_P11


title: skm_205s_P1


title: skm_205s_O9


title: skm_205s_O7


title: skm_205s_O8


title: skm_205s_O4


title: skm_205s_P22


title: skm_205s_O3


title: skm_205s_O5


title: skm_205s_O24


title: skm_205s_O23


title: skm_205s_O21


title: skm_205s_P18


title: skm_205s_P13


title: skm_205s_O19


title: skm_205s_O17


title: skm_205s_O20


title: skm_205s_O11


title: skm_205s_O15


title: skm_205s_O12


title: skm_205s_N8


title: skm_205s_O1


title: skm_205s_O10


title: skm_205s_O18


title: skm_205s_O14


title: skm_205s_N5


title: skm_205s_O13


title: skm_205s_N6


title: skm_205s_N9


title: skm_205s_N7


title: skm_205s_N4


title: skm_205s_N3


title: skm_205s_N23


title: skm_205s_N21


title: skm_205s_N24


title: skm_205s_N22


title: skm_205s_N20


title: skm_205s_N19


title: skm_205s_N18


title: skm_205s_N15


title: skm_205s_N14


title: skm_205s_N17


title: skm_205s_N13


title: skm_205s_N16


title: skm_205s_N12


title: skm_205s_N11


title: skm_205s_M6


title: skm_205s_M3


title: skm_205s_M4


title: skm_205s_N10


title: skm_205s_M9


title: skm_205s_M5


title: skm_205s_M17


title: skm_205s_M8


title: skm_205s_M19


title: skm_205s_M20


title: skm_205s_M23


title: skm_205s_M22


title: skm_205s_M21


title: skm_205s_M15


title: skm_205s_M13


title: skm_205s_M14


title: skm_205s_M12


title: skm_205s_M7


title: skm_205s_N1


title: skm_205s_M1


title: skm_205s_L7


title: skm_205s_L9


title: skm_205s_L8


title: skm_205s_M24


title: skm_205s_L6


title: skm_205s_L4


title: skm_205s_L23


title: skm_205s_L24


title: skm_205s_L3


title: skm_205s_L19


title: skm_205s_L2


title: skm_205s_L22


title: skm_205s_M16


title: skm_205s_M11


title: skm_205s_L17


title: skm_205s_L16


title: skm_205s_L14


title: skm_205s_L15


title: skm_205s_L21


title: skm_205s_M10


title: skm_205s_L18


title: skm_205s_L10


title: skm_205s_L13


title: skm_205s_L11


title: skm_205s_L5


title: skm_205s_L1


title: skm_205s_K9


title: skm_205s_L12


title: skm_205s_K3


title: skm_205s_K4


title: skm_205s_K23


title: skm_205s_L20


title: skm_205s_K7


title: skm_205s_K22


title: skm_205s_K5


title: skm_205s_K8


title: skm_205s_K2


title: skm_205s_K18


title: skm_205s_K20


title: skm_205s_K13


title: skm_205s_K19


title: skm_205s_K17


title: skm_205s_K12


title: skm_205s_K15


title: skm_205s_J9


title: skm_205s_K11


title: skm_205s_K10


title: skm_205s_J6


title: skm_205s_J5


title: skm_205s_K1


title: skm_205s_K16


title: skm_205s_J3


title: skm_205s_K14


title: skm_205s_J8


title: skm_205s_J23


title: skm_205s_J21


title: skm_205s_J4


title: skm_205s_K21


title: skm_205s_J22


title: skm_205s_J20


title: skm_205s_J19


title: skm_205s_J2


title: skm_205s_J18


title: skm_205s_J17


title: skm_205s_J16


title: skm_205s_J15


title: skm_205s_J14


title: skm_205s_J7


title: skm_205s_J12


title: skm_205s_J13


title: skm_205s_J24


title: skm_205s_J10


title: skm_205s_I23


title: skm_205s_I3


title: skm_205s_I7


title: skm_205s_I2


title: skm_205s_I9


title: skm_205s_I6


title: skm_205s_I24


title: skm_205s_J1


title: skm_205s_J11


title: skm_205s_I22


title: skm_205s_I20


title: skm_205s_I15


title: skm_205s_I17


title: skm_205s_I16


title: skm_205s_I19


title: skm_205s_I21


title: skm_205s_I14


title: skm_205s_I8


title: skm_205s_I4


title: skm_205s_I5


title: skm_205s_I10


title: skm_205s_H8


title: skm_205s_I12


title: skm_205s_I1


title: skm_205s_I18


title: skm_205s_H7


title: skm_205s_I13


title: skm_205s_I11


title: skm_205s_H6


title: skm_205s_H23


title: skm_205s_H5


title: skm_205s_H9


title: skm_205s_H20


title: skm_205s_H1


title: skm_205s_H18


title: skm_205s_H12


title: skm_205s_H16


title: skm_205s_G8


title: skm_205s_H21


title: skm_205s_H15


title: skm_205s_H24


title: skm_205s_H19


title: skm_205s_H3


title: skm_205s_H2


title: skm_205s_H11


title: skm_205s_H10


title: skm_205s_G5


title: skm_205s_H22


title: skm_205s_H4


title: skm_205s_G9


title: skm_205s_H14


title: skm_205s_G3


title: skm_205s_G24


title: skm_205s_H13


title: skm_205s_G23


title: skm_205s_G6


title: skm_205s_G22


title: skm_205s_G2


title: skm_205s_G15


title: skm_205s_G11


title: skm_205s_G13


title: skm_205s_G18


title: skm_205s_G19


title: skm_205s_G12


title: skm_205s_G1


title: skm_205s_F9


title: skm_205s_F6


title: skm_205s_G14


title: skm_205s_G7


title: skm_205s_G10


title: skm_205s_G4


title: skm_205s_F23


title: skm_205s_F8


title: skm_205s_F4


title: skm_205s_F3


title: skm_205s_F20


title: skm_205s_F19


title: skm_205s_F21


title: skm_205s_F22


title: skm_205s_F24


title: skm_205s_G20


title: skm_205s_G17


title: skm_205s_F17


title: skm_205s_F18


title: skm_205s_G21


title: skm_205s_F5


title: skm_205s_F2


title: skm_205s_F14


title: skm_205s_F16


title: skm_205s_F12


title: skm_205s_F11


title: skm_205s_F1


title: skm_205s_E8


title: skm_205s_E7


title: skm_205s_F15


title: skm_205s_E5


title: skm_205s_F10


title: skm_205s_E4


title: skm_205s_E3


title: skm_205s_E23


title: skm_205s_E21


title: skm_205s_E22


title: skm_205s_E2


title: skm_205s_E20


title: skm_205s_E19


title: skm_205s_E16


title: skm_205s_E18


title: skm_205s_E15


title: skm_205s_E14


title: skm_205s_E17


title: skm_205s_E12


title: skm_205s_F13


title: skm_205s_E13


title: skm_205s_E10


title: skm_205s_E9


title: skm_205s_E11


title: skm_205s_D9


title: skm_205s_E1


title: skm_205s_E6


title: skm_205s_D8


title: skm_205s_D7


title: skm_205s_D5


title: skm_205s_E24


title: skm_205s_D3


title: skm_205s_D24


title: skm_205s_D4


title: skm_205s_D23


title: skm_205s_D6


title: skm_205s_D22


title: skm_205s_D21


title: skm_205s_D20


title: skm_205s_D17


title: skm_205s_D13


title: skm_205s_D16


title: skm_205s_D12


title: skm_205s_D14


title: skm_205s_D18


title: skm_205s_D19


title: skm_205s_D15


title: skm_205s_C8


title: skm_205s_C6


title: skm_205s_C7


title: skm_205s_D1


title: skm_205s_C9


title: skm_205s_D10


title: skm_205s_D11


title: skm_205s_C3


title: skm_205s_C5


title: skm_205s_C4


title: skm_205s_C24


title: skm_205s_C23


title: skm_205s_C22


title: skm_205s_C21


title: skm_205s_C2


title: skm_205s_C17


title: skm_205s_C18


title: skm_205s_D2


title: skm_205s_C16


title: skm_205s_C20


title: skm_205s_C15


title: skm_205s_C19


title: skm_205s_C14


title: skm_205s_C13


title: skm_205s_B6


title: skm_205s_C11


title: skm_205s_B9


title: skm_205s_C10


title: skm_205s_B8


title: skm_205s_B24


title: skm_205s_B23


title: skm_205s_B3


title: skm_205s_B5


title: skm_205s_B22


title: skm_205s_B19


title: skm_205s_B21


title: skm_205s_B4


title: skm_205s_B16


title: skm_205s_B14


title: skm_205s_B15


title: skm_205s_B11


title: skm_205s_B20


title: skm_205s_B2


title: skm_205s_B10


title: skm_205s_B13


title: skm_205s_A9


title: skm_205s_C1


title: skm_205s_A8


title: skm_205s_A7


title: skm_205s_B1


title: skm_205s_A6


title: skm_205s_A24


title: skm_205s_A5


title: skm_205s_A4


title: skm_205s_A3


title: skm_205s_A23


title: skm_205s_B18


title: skm_205s_A22


title: skm_205s_B12


title: skm_205s_A2


title: skm_205s_B17


title: skm_205s_A16


title: skm_205s_A15


title: skm_205s_A19


title: skm_205s_A21


title: skm_205s_A17


title: skm_205s_A20


title: skm_205s_A11


title: skm_205s_A18


title: skm_205s_A10


title: skm_205s_A1


title: skm_205s_A14


title: skm_205s_A13


title: skm_205s_A12


title: heart_683s_H3

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol

value: heart

tag: Sex

value: male


title: heart_683s_H20


title: heart_683s_H19


title: heart_683s_H8


title: heart_683s_H1


title: heart_683s_H22


title: heart_683s_H7


title: heart_683s_H5


title: heart_683s_H24


title: heart_683s_H23


title: heart_683s_H9


title: heart_683s_H21


title: heart_683s_H18


title: heart_683s_H17


title: heart_683s_H15


title: heart_683s_G5


title: heart_683s_H16


title: heart_683s_H12


title: heart_683s_H10


title: heart_683s_G24


title: heart_683s_G23


title: heart_683s_H11


title: heart_683s_G6


title: heart_683s_G3


title: heart_683s_G7


title: heart_683s_G4


title: heart_683s_G8


title: heart_683s_G20


title: heart_683s_G1


title: heart_683s_G15


title: heart_683s_G19


title: heart_683s_G16


title: heart_683s_G17


title: heart_683s_G22


title: heart_683s_F8


title: heart_683s_G11


title: heart_683s_F5


title: heart_683s_G14


title: heart_683s_F6


title: heart_683s_G18


title: heart_683s_G13


title: heart_683s_G10


title: heart_683s_F3


title: heart_683s_F21


title: heart_683s_F23


title: heart_683s_F9


title: heart_683s_G21


title: heart_683s_F20


title: heart_683s_F18


title: heart_683s_F1


title: heart_683s_F17


title: heart_683s_F13


title: heart_683s_F24


title: heart_683s_F12


title: heart_683s_G12


title: heart_683s_F11


title: heart_683s_F10


title: heart_683s_E4


title: heart_683s_E2


title: heart_683s_E9


title: heart_683s_E3


title: heart_683s_E23


title: heart_683s_E8


title: heart_683s_E5


title: heart_683s_E6


title: heart_683s_E21


title: heart_683s_F15


title: heart_683s_F19


title: heart_683s_E1


title: heart_683s_E19


title: heart_683s_E22


title: heart_683s_E15


title: heart_683s_E18


title: heart_683s_E14


title: heart_683s_E24


title: heart_683s_D8


title: heart_683s_E12


title: heart_683s_F14


title: heart_683s_E11


title: heart_683s_D9


title: heart_683s_E16


title: heart_683s_D7


title: heart_683s_D6


title: heart_683s_E17


title: heart_683s_D5


title: heart_683s_E20


title: heart_683s_D3


title: heart_683s_D23


title: heart_683s_E13


title: heart_683s_D21


title: heart_683s_D22


title: heart_683s_D16


title: heart_683s_D19


title: heart_683s_D2


title: heart_683s_D15


title: heart_683s_D18


title: heart_683s_D1


title: heart_683s_D13


title: heart_683s_C7


title: heart_683s_D4


title: heart_683s_D24


title: heart_683s_D17


title: heart_683s_D12


title: heart_683s_D11


title: heart_683s_D10


title: heart_683s_C3


title: heart_683s_C9


title: heart_683s_C6


title: heart_683s_C5


title: heart_683s_C8


title: heart_683s_C2


title: heart_683s_C4


title: heart_683s_C22


title: heart_683s_C23


title: heart_683s_C1


title: heart_683s_C24


title: heart_683s_D14


title: heart_683s_C17


title: heart_683s_C21


title: heart_683s_C16


title: heart_683s_C19


title: heart_683s_C15


title: heart_683s_C14


title: heart_683s_C20


title: heart_683s_C13


title: heart_683s_C10


title: heart_683s_B6


title: heart_683s_B7


title: heart_683s_B5


title: heart_683s_B8


title: heart_683s_B4


title: heart_683s_B3


title: heart_683s_B2


title: heart_683s_B24


title: heart_683s_B22


title: heart_683s_C18


title: heart_683s_B23


title: heart_683s_B1


title: heart_683s_B21


title: heart_683s_B18


title: heart_683s_B16


title: heart_683s_C11


title: heart_683s_B15


title: heart_683s_B17


title: heart_683s_B13


title: heart_683s_B19


title: heart_683s_A8


title: heart_683s_A7


title: heart_683s_A5


title: heart_683s_C12


title: heart_683s_A4


title: heart_683s_A2


title: heart_683s_A3


title: heart_683s_A23


title: heart_683s_A22


title: heart_683s_B20


title: heart_683s_A21


title: heart_683s_A19


title: heart_683s_A20


title: heart_683s_A6


title: heart_683s_A1


title: heart_683s_A9


title: heart_683s_A16


title: heart_683s_A17


title: heart_683s_A15


title: heart_683s_B14


title: heart_683s_A18


title: heart_683s_A14


title: heart_517s_O24


title: heart_517s_O23


title: heart_683s_A10


title: heart_517s_P24


title: heart_683s_A24


title: heart_517s_O20


title: heart_517s_O21


title: heart_517s_N9


title: heart_517s_N6


title: heart_517s_N3


title: heart_683s_A13


title: heart_517s_N2


title: heart_517s_N24


title: heart_517s_N8


title: heart_517s_N20


title: heart_517s_N7


title: heart_517s_N22


title: heart_517s_N1


title: heart_517s_N17


title: heart_517s_N15


title: heart_517s_N10


title: heart_517s_N13


title: heart_517s_M5


title: heart_517s_M9


title: heart_517s_M4


title: heart_517s_M24


title: heart_517s_M17


title: heart_517s_M23


title: heart_517s_M16


title: heart_517s_M14


title: heart_517s_M22


title: heart_517s_M12


title: heart_517s_M20


title: heart_517s_M11


title: heart_517s_L4


title: heart_517s_L22


title: heart_517s_L5


title: heart_517s_L6


title: heart_517s_M1


title: heart_517s_N19


title: heart_517s_L23


title: heart_517s_L20


title: heart_517s_L9


title: heart_517s_L19


title: heart_517s_L7


title: heart_517s_M10


title: heart_517s_L18


title: heart_517s_L21


title: heart_517s_L15


title: heart_517s_L14


title: heart_517s_L13


title: heart_517s_K9


title: heart_517s_K8


title: heart_517s_K6


title: heart_517s_K5


title: heart_517s_K7


title: heart_517s_K22


title: heart_517s_K1


title: heart_517s_K15


title: heart_517s_K10


title: heart_517s_K11


title: heart_517s_K13


title: heart_517s_K19


title: heart_517s_J5


title: heart_517s_K17


title: heart_517s_K4


title: heart_517s_J6


title: heart_517s_K16


title: heart_517s_J2


title: heart_517s_K23


title: heart_517s_J24


title: heart_517s_J7


title: heart_517s_K21


title: heart_517s_J23


title: heart_517s_J20


title: heart_517s_L10


title: heart_517s_J17


title: heart_517s_L11


title: heart_517s_J14


title: heart_517s_J12


title: heart_517s_K20


title: heart_517s_I9


title: heart_517s_I8


title: heart_517s_I7


title: heart_517s_I6


title: heart_517s_I4


title: heart_517s_I5


title: heart_517s_I3


title: heart_517s_I2


title: heart_517s_I21


title: heart_517s_I20


title: heart_517s_I19


title: heart_517s_I14


title: heart_517s_I23


title: heart_517s_I16


title: heart_517s_H9


title: heart_517s_I10


title: heart_517s_I24


title: heart_517s_H8


title: heart_517s_J1


title: heart_517s_I18


title: heart_517s_I17


title: heart_517s_H7


title: heart_517s_I11


title: heart_517s_H5


title: heart_517s_H3


title: heart_517s_I22


title: heart_517s_H4


title: heart_517s_H23


title: heart_517s_H24


title: heart_517s_H20


title: heart_517s_H6


title: heart_517s_H1


title: heart_517s_H18


title: heart_517s_H19


title: heart_517s_H15


title: heart_517s_H16


title: heart_517s_H13


title: heart_517s_H14


title: heart_517s_H10


title: heart_517s_H11


title: heart_517s_G9


title: heart_517s_G8


title: heart_517s_G19


title: heart_517s_G24


title: heart_517s_G20


title: heart_517s_G5


title: heart_517s_G21


title: heart_517s_G4


title: heart_517s_G22


title: heart_517s_G18


title: heart_517s_G15


title: heart_517s_G11


title: heart_517s_G12


title: heart_517s_G10


title: heart_517s_F24


title: heart_517s_F23


title: heart_517s_F9


title: heart_517s_F8


title: heart_517s_F22


title: heart_517s_F21


title: heart_517s_H12


title: heart_517s_F20


title: heart_517s_G17


title: heart_517s_G13


title: heart_517s_F18


title: heart_517s_F19


title: heart_517s_F17


title: heart_517s_F11


title: heart_517s_E9


title: heart_517s_F10


title: heart_517s_E4


title: heart_517s_E8


title: heart_517s_E2


title: heart_517s_E23


title: heart_517s_E17


title: heart_517s_E20


title: heart_517s_E1


title: heart_517s_E22


title: heart_517s_E21


title: heart_517s_E16


title: heart_517s_E15


title: heart_517s_F1


title: heart_320s_P8


title: heart_320s_P5


title: heart_320s_P9


title: heart_517s_A22


title: heart_320s_P7


title: heart_320s_P22


title: heart_517s_A17


title: heart_320s_P3


title: heart_517s_E12


title: heart_320s_P2


title: heart_320s_P21


title: heart_320s_P19


title: heart_320s_P4


title: heart_320s_P18


title: heart_320s_P20


title: heart_320s_P15


title: heart_320s_P17


title: heart_320s_P10


title: heart_320s_P11


title: heart_320s_P16


title: heart_320s_P1


title: heart_320s_O9


title: heart_320s_O8


title: heart_320s_P12


title: heart_320s_O6


title: heart_320s_O7


title: heart_320s_O5


title: heart_320s_O4


title: heart_320s_O3


title: heart_320s_O24


title: heart_320s_O2


title: heart_320s_O21


title: heart_320s_O23


title: heart_320s_O19


title: heart_320s_P13


title: heart_320s_O22


title: heart_320s_O20


title: heart_320s_O16


title: heart_320s_O15


title: heart_320s_O12


title: heart_320s_P14


title: heart_320s_O11


title: heart_320s_O10


title: heart_320s_N7


title: heart_320s_N6


title: heart_320s_O17


title: heart_320s_N5


title: heart_320s_N9


title: heart_320s_N21


title: heart_320s_O13


title: heart_320s_N4


title: heart_320s_N8


title: heart_320s_N20


title: heart_320s_O18


title: heart_320s_N24


title: heart_320s_O14


title: heart_320s_N15


title: heart_320s_N13


title: heart_320s_N16


title: heart_320s_N23


title: heart_320s_N3


title: heart_320s_N19


title: heart_320s_N14


title: heart_320s_N22


title: heart_320s_N12


title: heart_320s_N1


title: heart_320s_N18


title: heart_320s_N11


title: heart_320s_M8


title: heart_320s_M9


title: heart_320s_M23


title: heart_320s_M24


title: heart_320s_M20


title: heart_320s_M5


title: heart_320s_M2


title: heart_320s_M22


title: heart_320s_M18


title: heart_320s_M17


title: heart_320s_M14


title: heart_320s_M16


title: heart_320s_N10


title: heart_320s_M19


title: heart_320s_M6


title: heart_320s_M4


title: heart_320s_M3


title: heart_320s_M21


title: heart_320s_M15


title: heart_320s_L7


title: heart_320s_L6


title: heart_320s_L8


title: heart_320s_M1


title: heart_320s_M10


title: heart_320s_L5


title: heart_320s_L9


title: heart_320s_L3


title: heart_320s_M11


title: heart_320s_M7


title: heart_320s_M13


title: heart_320s_L23


title: heart_320s_L19


title: heart_320s_L18


title: heart_320s_L4


title: heart_320s_N2


title: DNMT3B_N779A_eRRBS, biological replicate 1

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

country: USA

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

description:
counts_matrix.txt.gz
DNMT3B_N779A_eRRBS_iNA2

library_source: genomic

data_processing:
Sequence reads from bisulfite-treated libraries were identified using standard Illumina base-calling software.
Reads were filtered to retain only those with average base quality score >=20.
Adapter sequence was trimmed from the 3’ end of reads via Cutadapt v1.12 (parameters -a AGATCGGAAGAG -O 5 -q 0 -f fastq).  Reads shorter than 30nt after trimming were discarded.
Filtered and trimmed reads were mapped with Bismark v0.18.1 (parameters: -X 1000 --non_bs_mm), using Bowtie v1.2 as the underlying alignment tool against a reference including the genome sequence of enterobacteria phage λ (NC_001416.1) concatenated to the mm10 reference assembly (GRCm38).
To avoid bias in quantification of methylation status, any redundant mapped bases due to overlapping read ends from the same read pair were trimmed.
Read pairs in which either read end had 3 more or methylated cytosines in non-CpG context were discarded, as they were assumed to have escaped bisulfite conversion.
Methylated and total cytosine base counts per CpG site per sample were tabulated, with data summed over both genomic strands.
Percent methylation per CpG site per sample was calculated as methylated cytosine bases / total cytosine bases, filtered for sites with minimum read depth >=5 for the purposes of genome browser visualization tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Percent methylation at CpG sites with depth 5+ reads; format = bigWig.
Supplementary_files_format_and_content: Count of methylated and total cytosines per CpG site per sample; format = tab-delimited text.

molecule: genomic DNA

source_name: DNMT TKO ES Cells

growth_protocol: Dnmt3a, Dnmt3b and Dnmt1 triple knockout (TKO) mouse ES cells were cultivated on gelatin-coated dishes in the high-glucose DMEM base medium (Invitrogen) supplemented with 15% of fetal bovine serum (FBS, Invitrogen), 1 x nonessential amino acids (Invitrogen), 0.1 mM 2-mercaptoethanol, and 1000 U/ml leukemia inhibitory factor (ESGRO).

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen). eRRBS analysis of different cell samples was carried out in parallel to generate datasets for across-sample comparisons (such as WT DNMT3A1 versus DNMT3B1, or WT DNMT3B vs. its mutant).
eRRBS was carried out with a previously described protocol with slight modification (Garrett-Bakelman et al., 2015). Briefly, ~300 ng of genomic DNA were digested with three different enzymes (~80 units of MspI, 40 units of BfaI and 40 units of MseI) to enhance genomic fragmentation and coverage. The produced fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine, followed by overhang fill-in, 3’-terminal-A extension and purification. Bisulfite treatment of the fragments was done using the EZ DNA Methylation–Lightning kit (Zymo Research). Amplified eRRBS libraries was quality checked with Agilent 2200 TapeStation, followed by deep sequencing on the Illumina brand genome analyzer with 150 bp paired end (150xPE) parameters.

treatment_protocol: TKO ES cells were transfected by Lipofectamine 2000 (Invitrogen) with the pPyCAGIZ empty vector (EV) or that carrying wild-type (WT) or mutant DNMT3A or DNMT3B. At 48 hours following transfection, the transduced ES cells were selected out in 50 µg/ml Zeocin (Invitrogen) for 10 days and continuously maintained in the medium with 25 µg/ml Zeocin.

tag: cell type

value: ES Cells

tag: genotype

value: DNMT TKO

tag: rescue with

value: DNMT3B N779A-mutated


title: eSF_SP_Neg_2

city: San Francisco

first: Nadia

last: Roan

state: California

address: 1650 Owens Street

institute: University of California at San Francisco

data_processing:
Trimmed reads were aligned to the Genome Reference Consortium Human Build 38 reference genome (GenBank Assembly Accession: GCA_000001405.15) using TopHat2 v2.1.0 with the following parameters: global alignment, no mismatch in the 20 base-pair seed, up to two mismatches in the read, library type Fr–unstranded, and mate inner distance 50.
Aligned reads were filtered by removing reads with low mapping quality (below 20) and keeping singletons.
Filtered reads were annotated to the Genome Reference Consortium Human Build 38 reference transcriptome (RefSeq Assembly Accession: GCF_000001405.26) using the Partek E/M annotation model (Partek Flow, build version 5.0.16.1128) with the following parameters: junction reads required to match introns: set to true; strict paired-end compatibility not required: set to false; and strand specificity not required: set to false. Filtered reads were normalized using TPM (Transcripts Per Kilobase Million).
Low-abundance transcripts were removed, with lowest maximum coverage set to 1.0.
Differential gene expression analysis was calculated by ANOVA in a paired test, with treatment as the fixed factor and ID as the random factor using the Partek Flow software (Partek Incorporated). Differentially expressed transcripts were identified based on fold change (³1.5), with significance set at P <0.05.
Genome_build: Human Build 38 reference genome (GenBank Assembly Accession: GCA_000001405.15)
Supplementary_files_format_and_content: Matrix tables (2) with normalized counts for every gene and every sample

organism: Homo sapiens

source_name: Endometrium

extract_protocol:
Total RNA was then extracted using the Nucleospin RNA purification kit (Machery Nagel) following the manufacturer´s protocol. DNase1 (Qiagen) was dissolved in the Elution Buffer of the Nucleospin kit, and used as instructed by the manufacturer (Machery Nagel) during the DNase treatment step. RNA samples were quantified using Nanodrop and integrity was assessed using the Bioanalyzer (Agilent).
Paired-end RNAseq, at > 20 million reads per sample was performed using the HiSeq platform (Illumina) by Novogene.

treatment_protocol: The MV fractions were assessed for their effects on endometrial stromal fibroblasts (eSFs) and endometrial epithelial cells (eECs) by RNAseq. Equal volumes of the microvesicle fractions and reconstituted seminal plasma were each pooled from 15 acutely-infected individuals and from 15 uninfected individuals. These four pooled fractions were used to treat eSFs or eECs from 3 different donors, at a final concentration equivalent to that of 1% reconstituted seminal plasma, for 5 hours, followed by 3 washes with media to remove surface-associated extracellular vesicles.

tag: cell tyoe

value: Endometrial stromal fibroblasts

tag: treatment

value: Seminal plasma from HIV-negative individuals


title: DNMT3B_N779A_eRRBS, biological replicate 2

description:
counts_matrix.txt.gz
DNMT3B_N779A_eRRBS_iNA3


title: heart_320s_L24


title: heart_320s_L22


title: eSF_SP_Neg_3


title: heart_320s_L20


title: heart_320s_L21


title: heart_320s_L2


title: DNMT3B_K777A_eRRBS, biological replicate 2

description:
counts_matrix.txt.gz
DNMT3B_K777A_eRRBS_iKA9

value: DNMT3B K777A-mutated


title: eSF_SP_Neg_1


title: heart_320s_L17


title: heart_320s_L13


title: heart_320s_L12


title: heart_320s_L16


title: heart_320s_L11


title: DNMT3B_K777A_eRRBS, biological replicate 1

description:
counts_matrix.txt.gz
DNMT3B_K777A_eRRBS_iKA7


title: eSF_SP_Acut_3

value: Seminal plasma from acutely-treated HIV-infected individuals


title: DNMT3B_N656I_eRRBS, biological replicate 2

description:
counts_matrix.txt.gz
DNMT3B_N656I_eRRBS_NI17

value: DNMT3B N656I-mutated


title: heart_320s_L15


title: DNMT3B_N656I_eRRBS, biological replicate 1

description:
counts_matrix.txt.gz
DNMT3B_N656I_eRRBS_NI13


title: DNMT3B_WT_eRRBS, biological replicate 2b

description:
counts_matrix.txt.gz
DNMT3B_WT_eRRBS_i3B4

value: DNMT3B WT


title: heart_320s_K8


title: heart_320s_K7


title: heart_320s_L10


title: heart_320s_K6


title: eSF_MV_Neg_1

value: Seminal plasma microvesicle fractions from HIV-negative individuals


title: heart_320s_K5


title: eSF_MV_Neg_3


title: eSF_SP_Acut_1


title: eSF_MV_Acut_3

value: Seminal plasma microvesicle fractions from acutely-treated HIV-infected individuals


title: DNMT3B_WT_eRRBS, biological replicate 1a

description:
counts_matrix.txt.gz
DNMT3B_WT_eRRBS_3B2


title: heart_320s_K9


title: heart_320s_L14


title: DNMT3B_WT_eRRBS, biological replicate 1b

description:
counts_matrix.txt.gz
DNMT3B_WT_eRRBS_i3B3


title: eSF_MV_Neg_2


title: heart_320s_K4


title: heart_320s_K3


title: heart_320s_L1


title: eSF_SP_Acut_2


title: DNMT3B_WT_eRRBS, biological replicate 2a

description:
counts_matrix.txt.gz
DNMT3B_WT_eRRBS_3B11


title: heart_320s_K22


title: DNMT3A_WT_eRRBS, biological replicate 2

description:
counts_matrix.txt.gz
DNMT3A_WT_eRRBS_3A9

value: DNMT3A WT


title: eSF_MV_Acut_2


title: DNMT3A_WT_eRRBS, biological replicate 1

description:
counts_matrix.txt.gz
DNMT3A_WT_eRRBS_3A8


title: heart_320s_K24

value: 10-20 weeks


title: heart_320s_K2

value: PdgfrbGFP


title: heart_320s_K23


title: 4T1 HIF1b-WT_Hif1bChIPseq_r3

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

data_processing:
FastQ files were mapped to the reference genome (mm10) using bowtie (version 0.12.8; settings -v 2 -m 1 -p --best -S).
Peaks were called by model-based analysis of ChIP-sequencing (MACS) using pooled data for each replicate
Genome_build: mm10
Supplementary_files_format_and_content: MACS called peaks for each cell line

source_name: 4T1 mouse breast cancer cell line

growth_protocol: cultured at 37 °C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5 mL of 100 U/mL Penicillin-Streptomycin (Pen Strep, Life Technologies), 10 µg/mL of blasticidin (ant-bl-05, Invivogen), puromycin (P9620, Sigma-Aldrich) 1.5 µg/mL medium and 5 mL of L-Glutamine 200 mM, 1 µM DMSO

extract_protocol:
Cells were incubated in hypoxic conditions for 16 hours. Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 mM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
One µg of input and all of the immunoprecipitated DNA were converted into sequencing libraries using the NEBNext Ultra DNA library prep kit.

value: murine breast tumour

tag: type of sample

value: ChIP

tag: chip antibody

tag: genotype/variation


title: heart_320s_K19

value: heart

value: male


title: heart_320s_K18


title: 4T1 HIF1b-WT_Hif1bChIPseq_r2

value: ARNT/HIF-1β monoclonal antibody (NB100-124, Novus)


title: heart_320s_K16


title: heart_320s_K15


title: 4T1 HIF1b-WT_Hif1bChIPseq_r1


title: heart_320s_K17


title: heart_320s_K14


title: eSF_Mock_1 (Seminal Plasma-Derived Extracellular-Vesicle control)

value: Mock treated


title: eEC_SP_Neg_3

value: Endometrial epithelial cells


title: mES Dnmt-TKO_HIF1bChIPseq_r4

description: ESC.Dnmt-TKO.macs.summits.txt

source_name: Mouse Embryonic Stem cells

growth_protocol: cultured in 0.1% Gelatin Solution in DMEM 4,500 mg /L glucose, 1% sodium pyruvate, 15% FBS, 1% Pen Strep, 0.1 mM of non-essential amino acids (EmbryoMax), 50 μM β-mercaptoethanol, 103 U LIF ESGRO (Millipore).

value: inner cell mass

value: mES-Dnmt-TKO


title: 4T1 HIF1b-WT_Hif1bChIPseq_r4


title: eEC_SP_Neg_2

value: Seminal plasma from HIV-negative individuals


title: heart_320s_K13


title: eSF_MV_Acut_1

value: Endometrial stromal fibroblasts


title: heart_320s_K12


title: mES Dnmt-TKO_HIF1bChIPseq_r3

description: ESC.Dnmt-TKO.macs.summits.txt


title: heart_320s_K21


title: eSF_Mock_3 (Seminal Plasma-Derived Extracellular-Vesicle control)


title: heart_320s_K20


title: heart_320s_J9


title: heart_320s_K11


title: mES Dnmt-TKO_HIF1bChIPseq_r1

description: ESC.Dnmt-TKO.macs.summits.txt


title: mES Dnmt-TKO_HIF1bChIPseq_r2

description: ESC.Dnmt-TKO.macs.summits.txt


title: eSF_Mock_2 (Seminal Plasma-Derived Extracellular-Vesicle control)


title: eEC_SP_Acut_2

value: Seminal plasma from acutely-treated HIV-infected individuals


title: heart_320s_K10


title: mES Dnmt-WT_HIF1bChIPseq_r4

description: ESC.Dnmt-TKO.macs.summits.txt

growth_protocol: cultured feeder-free in fibroblast-conditioned medium

value: mES-Dnmt-WT


title: heart_320s_J8


title: heart_320s_J7


title: eEC_SP_Acut_3


title: heart_320s_K1


title: heart_320s_J6


title: eEC_SP_Neg_1


title: heart_320s_J3


title: mES Dnmt-WT_HIF1bChIPseq_r3

description: ESC.Dnmt-TKO.macs.summits.txt


title: mES Dnmt-WT_HIF1bChIPseq_r2

description: ESC.Dnmt-TKO.macs.summits.txt


title: heart_320s_J4


title: eEC_MV_Neg_3

value: Seminal plasma microvesicle fractions from HIV-negative individuals


title: eEC_MV_Neg_2


title: heart_320s_J23


title: 4T1_tumour_RNAseq_aza_DC101_r4

description: 4T1 tumour aza 0.8mg/kg BW DC101 40mg/kg BW

data_processing:
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using tophat (version 2.0.10).
Counts were called byHTSeq (version 0.5.3p3)
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain raw read counts for each sample

molecule: polyA RNA

source_name: Breast tumour

extract_protocol:
PolyA mRNA capture by using KAPA Stranded mRNA-Seq Kit (Illumina)
Strand specific library preparation

value: breast

value: aza 0.8mg/kg BW, DC101 40mg/kg BW

tag: growth protocol

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: heart_320s_J24

value: PdgfrbGFP

value: 10-20 weeks


title: heart_320s_J22

value: heart


title: eEC_MV_Neg_1


title: heart_320s_J21

value: male


title: eEC_MV_Acut_3

value: Seminal plasma microvesicle fractions from acutely-treated HIV-infected individuals


title: 4T1_tumour_RNAseq_aza_DC101_r3


title: heart_320s_J2


title: heart_320s_J20


title: eEC_MV_Acut_2


title: heart_320s_J17


title: heart_320s_J19


title: eEC_SP_Acut_1


title: 4T1_tumour_RNAseq_aza_DC101_r2


title: heart_320s_J18


title: heart_320s_J5


title: eEC_Mock_3 (Seminal Plasma-Derived Extracellular-Vesicle control)

value: Mock treated


title: heart_320s_J16


title: heart_320s_J15


title: 4T1_tumour_RNAseq_aza_IgG_r4

description: 4T1 tumour aza 0.8mg/kg BW IgG 40mg/kg BW

value: aza 0.8mg/kg BW, IgG 40mg/kg BW


title: heart_320s_J14


title: 4T1_tumour_RNAseq_aza_DC101_r1


title: mES Dnmt-WT_HIF1bChIPseq_r1

description: ESC.Dnmt-TKO.macs.summits.txt

value: inner cell mass

value: ChIP

value: ARNT/HIF-1β monoclonal antibody (NB100-124, Novus)


title: eEC_Mock_1 (Seminal Plasma-Derived Extracellular-Vesicle control)

value: Endometrial epithelial cells


title: 4T1_tumour_RNAseq_aza_IgG_r3


title: heart_320s_J12


title: heart_320s_J13


title: heart_320s_J11


title: heart_320s_I9


title: heart_320s_J1


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r8

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW

value: aza 0.8mg/kg BW


title: 4T1_tumour_RNAseq_aza_IgG_r1

value: aza 0.8mg/kg BW, 40mg/kg BW IgG


title: heart_320s_J10


title: eEC_MV_Acut_1


title: heart_320s_I4


title: 4T1_tumour_RNAseq_aza_IgG_r2


title: Senescent HUVEC

city: Dongguan

first: weipeng

last: Wu

state: Guangdong

address: Xin Cheng Avenue 1#, Songshan Lake

country: China

institute: Guangdong Medical University

data_processing:
illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCH38/hg38 using HISAT2 with parameters HWI-ST1276 71 C1162ACXX  1 1101 1208 2458 1 N CGATGT
Transcripts Per Million (TPM) were calculated using a protocol from Zhou et al.,  PLoS One, 2010.
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Senescent HUVEC

extract_protocol:
RNA was harvested from young and senescent endothelial cells (HUVECs and HCAECs)using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Senescent HUVEC

value: untreated


title: Senescent HCAEC

source_name: Senescent HCAEC

value: Senescent HCAEC


title: heart_320s_I6


title: Young HCAEC

source_name: Young HCAEC

value: Young HCAEC


title: heart_320s_I3

value: PdgfrbGFP


title: MCF7_control_HIF1bChIPseq_r1

description:
MCF7 DMSO
processed data file: MCF7.dmso.macspeaks.txt

data_processing:
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using bowtie (version 0.12.8; settings -v 2 -m 1 -p --best -S).
Peaks were called by model-based analysis of ChIP-sequencing (MACS) using pooled data for each cell line and using the correspondent input as background set.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: MACS called peaks for each cell line

growth_protocol: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.

extract_protocol:
Cells were incubated in hypoxic conditions for 16 hours. Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 µM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
Five µg of input and all of the immunoprecipitated DNA were converted into sequencing libraries using the NEBNext Ultra DNA library prep kit.

tag: tissue source

value: breast

tag: cell line

value: Breast cancer cell line


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r7

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: heart_320s_I5

value: heart

value: male

value: 10-20 weeks


title: Young HUVEC

source_name: Young HUVEC

value: Young HUVEC


title: eEC_Mock_2 (Seminal Plasma-Derived Extracellular-Vesicle control)

value: Mock treated


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r5

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW


title: heart_320s_I24


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r4

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW


title: heart_320s_I19


title: heart_320s_I22


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r6

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW


title: MCF7_control_Input_r1

value: Input


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r2

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW


title: MCF7_AZA-treated_SeqCapEpi_BSseq_r1

description: MCF7 aza-treated

data_processing:
FastQ files were mapped to the human genome (build GRCh37/hg19) using bismark (version 0.10.1).
Methylation status were extract using bismark, replicated were pooled for the extraction.
Genome_build: hg19
Supplementary_files_format_and_content: Methylation status for all C's in the captured region.

source_name: Brest cancer cell line

extract_protocol:
cultured cells were washed on ice with ice-cold phosphate-buffer saline (PBS), detached using cell scrapers and collected by centrifugation (400 ×G, 4°C). Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, dissolved in 80 µL PBS with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit, eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. Libraries were bisulfite-converted using the EZ DNA Methylation-Lightning™ kit (Zymo) as recommended, and PCR amplified for 12 cycles using barcoded primers (NEB) and the KAPA HiFi HS Uracil+ ready mix (Sopachem, Eke, Belgium) according to manufacturers instructions. Fragments were selected from these libraries using the SeqCap Epi CpGiant Enrichment Kit (Roche) following the manufacturers instructions, sequenced from both ends for 100 bases on a HiSeq 2000.

value: 1uM 5-Aza-2′-deoxycytidine (aza) for 72h


title: MCF7_HIF1B KO_SeqCapEpi_BSseq_r2

description: MCF7 HIF1B KO


title: MCF7_AZA-treated_SeqCapEpi_BSseq_r2

description: MCF7 aza-treated


title: heart_320s_I15


title: heart_320s_I23


title: heart_320s_I18


title: heart_320s_I2


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r1

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW

value: aza 0.8mg/kg BW


title: heart_320s_I13


title: 4T1 HIF1B-KO_tumour_RNAseq_aza_r3

description: 4T1 HIF1B-KO tumour aza 0.8mg/kg BW


title: heart_320s_I14


title: MCF7_HIF1B KO_SeqCapEpi_BSseq_r1

description: MCF7 HIF1B KO


title: heart_320s_I16


title: heart_320s_I20


title: heart_320s_I12


title: heart_320s_I17


title: heart_320s_I10


title: SK-MEL-28_SeqCapEpi_BSseq_r2

description:
SK-MEL-28
BT931.methylation.status.bedGraph

source_name: Melanoma cell line

extract_protocol:
cultured cells were washed on ice with ice-cold phosphate-buffer saline (PBS), detached using cell scrapers and collected by centrifugation (400 ×G, 4°C). Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, dissolved in 80 µL PBS with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit, eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. Libraries were bisulfite-converted using the Imprint DNA modification kit (Sigma) as recommended, and PCR amplified for 12 cycles using barcoded primers (NEB) and the KAPA HiFi HS Uracil+ ready mix (Sopachem, Eke, Belgium) according to manufacturers instructions. Fragments were selected from these libraries using the SeqCap Epi CpGiant Enrichment Kit (Roche) following the manufacturers instructions, sequenced from both ends for 100 bases on a HiSeq 2000.

value: skin

value: cultured at 37°C in Roswell Park Memorial Institut 1640 Medium (RPMI) 10% FBS 1% Pen Strep and 1% L-Glutamine.


title: heart_320s_I11


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r7

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: heart_320s_I1


title: heart_320s_H9


title: SK-MEL-28_SeqCapEpi_BSseq_r1


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r6

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: RCC4_SeqCapEpi_BSseq_r2

description:
RCC4
BT929.methylation.status.bedGraph

source_name: Renal cell carcinoma cell line

value: kidney


title: heart_320s_H8


title: heart_320s_H7


title: heart_320s_H5


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r4

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: heart_320s_H4


title: F

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq 2500 instrument.
The raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using the Illumina bcl2fastq program version 2.17. One mis-match was allowed for index sequence identification.
Adapter trimming was performed using BBDuk (https://jgi.doe.gov/data-andtools/bbtools/), and read pairs were merged with BBmerge (https://jgi.doe.gov/data-and-tools/bbtools/) in order to increase base call quality and generate long, whole fragment reads.
Reads were aligned to the mouse genome (GRCm38) using Hisat2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated values files were generated using Sleuth; wt.b scores represent differential gene (or transcript) expression.

source_name: Transfected NIH/3T3 cells

growth_protocol: NIH/3T3 cells were cultured in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin. All cell lines were grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
48h after transfection, cells were washed with 1x PBS and lysed. The RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer’s instructions.
The multiplexed RNA sequencing library was prepared using the TruSeq Stranded  mRNA Library Prep kit following the manufacturer’s protocol (Illumina, Cat# 20020594).

treatment_protocol: NIH/3T3 cells were seeded in a 6 well plate and transfected at a confluency of 80%. NIH/3T3 cells were transfected using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions using 3.75 µl Lipofectamine 3000 and appropriate siRNA(s) at a final concentration of 10 nM.

value: Wild type

tag: replicate


title: heart_320s_H3

tag: tissue


title: heart_320s_H24

tag: starin


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r5

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: heart_320s_H23

tag: age


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r8

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: heart_320s_H22

tag: cluster


title: B

value: Knockdown


title: heart_320s_H20

value: PdgfrbGFP

tag: Sex


title: RCC4_SeqCapEpi_BSseq_r1

description:
RCC4
BT929.methylation.status.bedGraph


title: A

tag: cell type


title: 4T1 HIF1B-KO_tumour_RNAseq_PBS_r6

description: 4T1 HIF1B-KO tumour PBS 0.8mg/kg BW

value: breast

value: PBS 0.8mg/kg BW


title: heart_320s_H2


title: E


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r3

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r2

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: Tet-TKO_HIF1bChIP-BSseq

data_processing:
FastQ files were mapped to the mouse genome ((human:build GRCh37/hg19; mouse:mm10) using bismark (version 0.10.1).
Read counts at HIF peak areas were quantified in each sample using SeqMonk, and background-normalized to enable enrichment assessment.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain read numbers overlapping HIF peaks both in MCF7 and Tet-TKO mouse

source_name: Embryonic Stem Cells

extract_protocol:
Cells were incubated in hypoxic conditions for 16 hours. Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 µM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. DNA libraries were bisulfite converted using the EZ DNA Methylation-Lightning™ kit (Zymo) prior to library amplification using HiFi Uracil+ (KAPA).

value: Embryonic Stem Cells

value: ChIP-BS


title: heart_320s_H17

value: heart

value: male

value: 10-20 weeks


title: heart_320s_H19


title: 4T1 HIF1B-KO_tumour_RNAseq_PBS_r5

description: 4T1 HIF1B-KO tumour PBS 0.8mg/kg BW


title: heart_320s_H15


title: 4T1 HIF1B-KO_tumour_RNAseq_PBS_r4

description: 4T1 HIF1B-KO tumour PBS 0.8mg/kg BW


title: heart_320s_H14


title: heart_320s_H21


title: 4T1 HIF1B-WT_tumour_RNAseq_aza_r1

description: 4T1 HIF1B-WT tumour aza 0.8mg/kg BW


title: Di_ZT12_1; ZT12, disome footprint, rep2

city: Lasuanne

first: David

last: Gatfield

address: UNIL CIG

department: CIG

country: Switzerland

institute: University of Lausanne

description:
Di12_2
GSM1644089

data_processing:
Library strategy: ribosome profiling
Base-calling: Casava 1.82
Adapter trimming: Adapter sequences were removed using cutadapt utility with following options: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --match-read-wildcards -m 6
Insert size filtering: Trimmed read sequences were filtered by their size using an in-house Python script with following inclusive ranges: [45,70]
Alignment: Trimmed and filtered insert sequences were mapped sequentially to following databases: mouse rRNA, human rRNA, mt-tRNA, mouse tRNA, mouse cDNA (Ensembl.v.91) and mouse genome (GRCm38.p2). All but last one were mapped using bowtie (version 2.3.0) using following parameters: -p 2 -L 15 -k 20 –no-unal. After each alignment, only reads that were not aligned were used in the following mapping. For further analysis (processed data files), only alignments against mouse cDNA were used.
Post-alignment filtering: For each query sequence, only alignments with maximum score were kept. Expressed transcript models were estimated using STAR (genomic map) + Stringtie. Resulting FPKM tracking information was parsed with an in-house Python script to filter out transcripts which were not found to have an FPKM > 0.1, and %isoform expression > 0.05 in at least 2 samples. A database of expressed transcripts was used in further analysis.
Abundance measurement: disome footprint levels were estimated per locus. An in-house Python script was used to count uniquely (by gene) mapped reads within each annotation feature (5'UTR, CDS, 3'UTR). For multi-isoform loci, preference order used was CDS, 5'UTR, 3'UTR.
Normalization: Read counts of disome footprints were normalized with upper quantile method of R package edgeR. Prior to normalization, transcripts which did not have at least 10 counts in at least one third of the samples were removed from the datasets.
Normalization: RPKM values were calculated as the number of counted reads per 1000 mappable and countable bases per geometric mean of normalized read counts per million.
Genome_build: Genome Reference Consortium GRCm38.p2 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files. RPKM values for disome footprints calculated for CDS regions. Per gene; gene ids are Ensembl IDs

source_name: liver

extract_protocol:
Livers were homogenized in 3 volumes of lysis buffer (150 mM NaCl, 20 mM Tris-HCl pH7.4, 5 mM MgCl2, 5 mM DTT, 100 μg ml-1 cycloheximide, 1% Triton X-100, 0.5% Sodium deoxycholate, complete EDTA-free protease inhibitors (Roche) and 40 U ml-1 RNasin plus (Promega)) using a Teflon homogenizer. Lysates were incubated for 10 min on ice and cleared by centrifugation at 1000 x g, 4°C for 3 min in a tabletop centrifuge. Supernatants were flash-frozen and stored in liquid nitrogen. Lysates of two mice per timepoint were pooled. Disome profiling libraries, lysate pools (15 OD260) were digested with 650 U RNase I (Ambion) for 45 min at room temperature and passed over size exclusion columns for ribosome purification prior to RNA extraction and library preparation.
Sequencing libraries were generated using Ribo-Zero (Epicentre) and ARTseq ribosome profiling kits (Epicentre).

value: liver

tag: timepoint

tag: strain

tag: gender

value: 11-12 weeks

tag: molecule subtype

value: ribosome protected RNA


title: heart_320s_H10


title: 4T1 HIF1B-KO_tumour_RNAseq_PBS_r3

description: 4T1 HIF1B-KO tumour PBS 0.8mg/kg BW

tag: treatment


title: heart_320s_H18


title: heart_320s_H1


title: Di_ZT2_1; ZT2, disome footprint, rep2

description:
Di02_2
GSM1644079


title: 4T1 HIF1B-KO_tumour_RNAseq_PBS_r2

description: 4T1 HIF1B-KO tumour PBS 0.8mg/kg BW


title: Di_ZT2_1; ZT2, disome footprint, rep1

description:
Di02_1
GSM1644078


title: heart_320s_G9


title: heart_320s_G7


title: heart_320s_H11


title: heart_320s_G4


title: heart_320s_G23


title: Di_ZT0_1; ZT0, disome footprint, rep2

description:
Di00_2
GSM1644077


title: heart_320s_G8


title: Di_ZT0_1; ZT0, disome footprint, rep1

description:
Di00_1
GSM1644076


title: heart_320s_G5


title: heart_320s_G6


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r7

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW


title: Di_ZT12_1; ZT12, disome footprint, rep1

description:
Di12_1
GSM1644088


title: heart_320s_G21


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r6

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW


title: heart_320s_G22


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r5

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW


title: 4T1 HIF1B-KO_tumour_RNAseq_PBS_r1

description: 4T1 HIF1B-KO tumour PBS 0.8mg/kg BW


title: heart_320s_G20


title: Gata2 rescue replicate 4

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description:
mutant expressing Gata2
Gata2 -77 enhancer knockout mouse

data_processing:
Sequencing reads were aligned by STAR (version 2.5.2b) to mouse genome (mm10, chromosomes 1 to 19, X, Y, and M) with GENCODE comprehensive gene annotation (version M16) on the reference chromosomes only. Command line options for STAR followed ENCODE RNA-seq processing protocol (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/dnanexus/quant-rsem/resources/usr/bin/lrna_rsem_quantification.sh)
Gene expression levels were quantified by RSEM (version 1.3.0) with command line options following ENCODE RNA-seq processing protocol (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/blob/master/dnanexus/quant-rsem/resources/usr/bin/lrna_rsem_quantification.sh).
Genome_build: mm10
Supplementary_files_format_and_content: TSV: RSEM quantification results at the gene level

source_name: mutant expressing Gata2

growth_protocol: All cells were grown in IMDM medium supplemented with 20% FBS, penicillin-streptomycin, 4% of IL3-CM, and 4% of SCF-CM for 3 days

extract_protocol:
total RNA
standard NuGEN Ovation protocol

treatment_protocol: Lin-negative hematopoietic progenitor cells were isolated from WT or -77KO fetal livers. Cells were infected with high-titer pMSCV-Gata2 retroviral vector or control retroviral vector immediately after isolation. After infection, cells were cultured for 3 days and RNA was harvested.

tag: genotype

value: Gata2 rescue

value: Lin- hematopoietic progenitor cells

value: fetal liver

tag: background strain


title: Gata2 rescue replicate 3


title: heart_320s_G2

source_name: male mouse


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r4

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW

tag: growth protocol


title: Gata2 rescue replicate 2


title: heart_320s_G19


title: heart_320s_G18


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r3

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW


title: Gata2 rescue replicate 1


title: heart_320s_G17


title: heart_320s_G15


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r1

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW


title: heart_320s_G13


title: heart_320s_G14


title: 4T1 HIF1B-WT_tumour_RNAseq_PBS_r2

description: 4T1 HIF1B-WT tumour PBS 0.8mg/kg BW


title: 4T1 HIF1B-KO_RNAseq_control_1day-Hypoxia_r3b

description: 4T1 HIF1B-KO DMSO 1day-Hypoxia

source_name: Breast tumor


title: WT replicate 4

description: wild-type control

source_name: wild-type control

value: wild type


title: WT replicate 3

description: wild-type control


title: heart_320s_G11


title: WT replicate 2

description: wild-type control


title: 4T1 HIF1B-KO_RNAseq_control_1day-Hypoxia_r3a

description: 4T1 HIF1B-KO DMSO 1day-Hypoxia


title: heart_320s_G1


title: heart_320s_G12


title: WT replicate 1

description: wild-type control


title: heart_320s_G10


title: heart_320s_F9


title: heart_320s_F8


title: 4T1 HIF1B-KO_RNAseq_control_1day-Hypoxia_r2b

description: 4T1 HIF1B-KO DMSO 1day-Hypoxia


title: heart_320s_F7


title: heart_320s_F6


title: Gata2 mutant replicate 3

description:
mutant control
Gata2 -77 enhancer knockout mouse

source_name: mutant control

value: Gata2 mutant


title: heart_320s_F5

value: PdgfrbGFP


title: heart_320s_G16


title: Gata2 mutant replicate 2


title: 4T1 HIF1B-KO_RNAseq_control_1day-Hypoxia_r1a

description: 4T1 HIF1B-KO DMSO 1day-Hypoxia

value: breast


title: heart_320s_F4


title: 4T1 HIF1B-KO_RNAseq_control_1day-Hypoxia_r1b

description: 4T1 HIF1B-KO DMSO 1day-Hypoxia


title: heart_320s_F3


title: heart_320s_F23


title: heart_320s_F24


title: CBE_2_duplicate ATAC-Seq

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

data_processing:
The single-end ATAC-seq reads were trimmed to remove adaptor content using Trimmomatic and aligned to mouse genome mm9 using bowtie2.
Reads with mapping quality score (MAPQ) < 10 were filtered out using samtools and PCR duplicates were removed using Picard.
Chromatin accessible sites (i.e., peaks) were identified using MACS with q-value < 0.05 as cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: MACS narrowPeak files that contain the peak calling results.

source_name: Pro-B cell line

growth_protocol: Pro-B cell lines were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol)

extract_protocol:
Assay for transposase-accessible chromatin (ATAC) was performed as previously described (Bossen et al., 2015; Buenrostro et al., 2013).  Briefly, 200,000 RAG2-deficient pro-B cells with WT or IGCR1-mutated (CBE-/-(1) and CBE-/-(2)) IgH alleles were collected by centrifugation and washed once with 100μl PBS.  Cell pellets were then resuspended in 50μl lysis buffer (10mM Tris-HCl, pH 7.4, 3mM MgCl2, 10mM NaCl, 0.1% NP-40 (Igepal CA-630)) and immediately centrifuged at 500g for 10 min at 4 °C.  Nuclei-containing pellets were resuspended in 50μl transposition buffer (25μl 2 × TD buffer, 22.5μl dH20, 2.5μl Illumina Tn5 transposase) and incubated at 37 °C for 30 min.  Transposed DNA was purified with DNA Clean and Concentrator columns (ZymoResearch).  Library fragments were amplified with 1× NEB Next PCR Master Mix and custom Nextera PCR primers 1–6.  The number of cycles was 11.  Libraries were purified with DNA Clean and Concentrator columns.
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on a HiSeq 2500 system as single reads.

treatment_protocol: ATAC-Seq method was employed to analyze chromatin accessibility of different pro-B cell lines without any treatment.

value: Pro-B cell line

value: Bone marrow


title: heart_320s_F21


title: heart_320s_F22


title: Gata2 mutant replicate 1


title: heart_320s_F2


title: CBE_2_ATAC-Seq


title: heart_320s_F20


title: heart_320s_F17


title: heart_320s_F16


title: heart_320s_F19


title: Gata2 mutant replicate 4


title: CBE_1_duplicate ATAC-Seq


title: 4T1 HIF1B-KO_RNAseq_control_1day-Normoxia_r2a

description: 4T1 HIF1B-KO DMSO 1day-Normoxia

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: heart_320s_F15


title: 4T1 HIF1B-KO_RNAseq_control_1day-Hypoxia_r2a

description: 4T1 HIF1B-KO DMSO 1day-Hypoxia


title: heart_320s_F13


title: 4T1 HIF1B-KO_RNAseq_control_1day-Normoxia_r1b

description: 4T1 HIF1B-KO DMSO 1day-Normoxia


title: WT duplicate ATAC-Seq

value: Wild type


title: 4T1 HIF1B-KO_RNAseq_control_1day-Normoxia_r1a

description: 4T1 HIF1B-KO DMSO 1day-Normoxia


title: heart_320s_F14

value: heart


title: 4T1 HIF1B-KO_RNAseq_control_1day-Normoxia_r3b

description: 4T1 HIF1B-KO DMSO 1day-Normoxia


title: heart_320s_F12

value: male


title: WT ATAC-Seq


title: heart_320s_F10

value: 10-20 weeks


title: 4T1 HIF1B-KO_RNAseq_control_1day-Normoxia_r3a

description: 4T1 HIF1B-KO DMSO 1day-Normoxia


title: 4T1 HIF1B-WT_RNAseq_control_1day-Normoxia_r3b

description: 4T1 HIF1B-WT DMSO 1day-Normoxia


title: 4T1 HIF1B-KO_RNAseq_control_1day-Normoxia_r2b

description: 4T1 HIF1B-KO DMSO 1day-Normoxia


title: heart_320s_F1


title: 4T1_tumour_RNAseq_AZA_r4

description: 4T1 tumour aza 0.8mg/kg BW

source_name: Breast tumour

value: aza 0.8mg/kg BW


title: CBE_1_ATAC-Seq


title: heart_320s_E9


title: heart_320s_E8


title: 4T1 HIF1B-WT_RNAseq_control_1day-Normoxia_r3a

description: 4T1 HIF1B-WT DMSO 1day-Normoxia


title: heart_320s_E7


title: 4T1_tumour_RNAseq_AZA_r3

description: 4T1 tumour aza 0.8mg/kg BW


title: 4T1_tumour_RNAseq_AZA_r2

description: 4T1 tumour aza 0.8mg/kg BW


title: heart_320s_E6


title: 4T1 HIF1B-WT_RNAseq_control_1day-Normoxia_r2a

description: 4T1 HIF1B-WT DMSO 1day-Normoxia


title: heart_320s_E5


title: heart_320s_E4


title: 4T1_tumour_RNAseq_AZA_r1

description: 4T1 tumour aza 0.8mg/kg BW


title: heart_320s_E3


title: 4T1 HIF1B-WT_RNAseq_control_1day-Normoxia_r1b

description: 4T1 HIF1B-WT DMSO 1day-Normoxia


title: heart_320s_E23


title: heart_320s_E22


title: 4T1_tumour_RNAseq_PBS_r4

description: 4T1 tumour PBS 0.8mg/kg BW

value: PBS 0.8mg/kg BW


title: heart_320s_E24


title: heart_320s_E21


title: 4T1_RNAseq_aza_1day-Hypoxia_r3b

description: 4T1 aza 1day-Hypoxia


title: heart_320s_E2


title: heart_320s_E20


title: 4T1 HIF1B-WT_RNAseq_control_1day-Normoxia_r1a

description: 4T1 HIF1B-WT DMSO 1day-Normoxia


title: 4T1_tumour_RNAseq_PBS_r5

description: 4T1 tumour PBS 0.8mg/kg BW


title: 4T1_tumour_RNAseq_PBS_r3

description: 4T1 tumour PBS 0.8mg/kg BW


title: 4T1_RNAseq_aza_1day-Hypoxia_r3a

description: 4T1 aza 1day-Hypoxia


title: 4T1 HIF1B-WT_RNAseq_control_1day-Normoxia_r2b

description: 4T1 HIF1B-WT DMSO 1day-Normoxia


title: heart_320s_E19


title: 4T1_tumour_RNAseq_PBS_r2

description: 4T1 tumour PBS 0.8mg/kg BW


title: heart_320s_E17


title: 4T1_RNAseq_aza_1day-Hypoxia_r2b

description: 4T1 aza 1day-Hypoxia


title: heart_320s_E18


title: 4T1_tumour_RNAseq_PBS_r1

description: 4T1 tumour PBS 0.8mg/kg BW


title: heart_320s_E16


title: heart_320s_E15


title: mES Tet-TKO_WGBS 8

description:
Tet-TKO
TKO.methylation.inHIPPeaks.WGBS.txt

data_processing:
FastQ files were mapped to the mouse genome (build mm10) using bismark (version 0.10.1).
Read counts at HIF peak areas were quantified in each sample using SeqMonk, and background-normalized to enable enrichment assessment.
Genome_build: mm10
Supplementary_files_format_and_content: file contains read numbers overlaping with HIF peaks in TET TKO mouse

extract_protocol:
cultured cells were washed on ice with ice-cold phosphate-buffer saline (PBS), detached using cell scrapers and collected by centrifugation (400 ×G, 4°C). Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, dissolved in 80 µL PBS with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit, eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. Libraries were bisulfite-converted using the Imprint DNA modification kit (Sigma) as recommended, and PCR amplified for 12 cycles using barcoded primers (NEB) and the KAPA HiFi HS Uracil+ ready mix (Sopachem, Eke, Belgium) according to manufacturers instructions.

value: inner cell mass


title: 4T1_RNAseq_aza_1day-Hypoxia_r1b

description: 4T1 aza 1day-Hypoxia


title: heart_320s_E13


title: heart_320s_E12


title: mES Tet-TKO_WGBS 7


title: heart_320s_E11


title: mES Tet-TKO_WGBS 6


title: heart_320s_E10


title: mES Tet-TKO_WGBS 5


title: 4T1_RNAseq_aza_1day-Normoxia_r3b

description: 4T1 aza 1day-Normoxia


title: heart_320s_D9


title: 4T1_RNAseq_aza_1day-Hypoxia_r1a

description: 4T1 aza 1day-Hypoxia


title: mES Tet-TKO_WGBS 4


title: 4T1_RNAseq_aza_1day-Normoxia_r2b

description: 4T1 aza 1day-Normoxia


title: heart_320s_D7


title: 4T1_RNAseq_aza_1day-Normoxia_r3a

description: 4T1 aza 1day-Normoxia


title: heart_320s_E1


title: heart_320s_D8


title: heart_320s_D5


title: 4T1_RNAseq_aza_1day-Hypoxia_r2a

description: 4T1 aza 1day-Hypoxia


title: heart_320s_E14


title: mES Tet-TKO_WGBS 3


title: heart_320s_D6


title: mES Tet-TKO_WGBS 2


title: heart_320s_D24


title: 4T1_RNAseq_aza_1day-Normoxia_r1b

description: 4T1 aza 1day-Normoxia


title: 4T1_RNAseq_aza_1day-Normoxia_r2a

description: 4T1 aza 1day-Normoxia


title: heart_320s_D4


title: heart_320s_D3


title: 4T1_RNAseq_aza_1day-Normoxia_r1a

description: 4T1 aza 1day-Normoxia


title: heart_320s_D21


title: heart_320s_D22


title: 4T1_RNAseq_control_1day-Hypoxia_r3b

description: 4T1 DMSO 1day-Hypoxia


title: Femoral homogenate - DO mouse 414

city: Charlottesville

first: Basel

last: Al-Barghouthi

state: VA

institute: University of Virginia

data_processing:
Basecalls were performed using the Real-Time Analysis (RTA) software version 2.4.11
Each sample/run combination was aligned to GRCm38 using HISAT2 version 2.0.5, using the GRCm38_snp index. HISAT2 was run with the following parameters: --dta --trim3 1
Aligned files were sorted, merged by sample for all runs, and sorted again using samtools version 1.10
Assembly and quantification was performed with StringTie version 1.3.3, using the GRCm38.98 GTF annotation. The following StringTie parameters were used: -e -G
A single GTF was generated with all common transcripts, using StringTie --merge -G. Assembly and quantification were repeated as before, but using the merged GTF, with the -eB -G parameters.
A gene count matrix was generated using the prepDE.py script, sourced from the StringTie website (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual)
Gene counts were filtered to include genes that had more than 0.1 TPM and more than 6 reads in more than 38 samples (20%).
Gene read counts were transformed using the variance stabilizing transformation (VST) from the DESeq2 package (version 1.20.0). This was followed by a quantile- based inverse Normal transformation , as performed in Yang et al., Nature,  2012.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file containing filtered gene read counts for all 192 samples
Supplementary_files_format_and_content: CSV file containing transformed filtered gene read counts

source_name: Femur

extract_protocol:
Femurs were homogenated in TRIzol, and total RNA was extracted from homogenates using mirVana miRNA isolation kit (Life Technologies, Carlsbad, CA).
Libraries were prepared using the Illumina TruSeq Stranded Total RNA HT sample prep kits

treatment_protocol: Ends of femurs were cut, and marrow was flushed out.

value: Marrow-depleted left femur - homogenate

value: Diversity Outbred (J:DO)

value: 86 days


title: heart_320s_D20


title: heart_320s_D2


title: Femoral homogenate - DO mouse 413


title: heart_320s_D19


title: 4T1_RNAseq_control_1day-Hypoxia_r3a

description: 4T1 DMSO 1day-Hypoxia


title: heart_320s_D17


title: Femoral homogenate - DO mouse 408

value: 85 days


title: Femoral homogenate - DO mouse 410


title: 4T1_RNAseq_control_1day-Hypoxia_r2b

description: 4T1 DMSO 1day-Hypoxia


title: Femoral homogenate - DO mouse 407

value: 84 days


title: heart_320s_D16

value: PdgfrbGFP


title: 4T1_RNAseq_control_1day-Hypoxia_r2a

description: 4T1 DMSO 1day-Hypoxia

value: breast


title: mES Tet-TKO_WGBS 1


title: 4T1_RNAseq_control_1day-Hypoxia_r1b

description: 4T1 DMSO 1day-Hypoxia


title: heart_320s_D23


title: heart_320s_D14


title: heart_320s_D15


title: heart_320s_D1


title: Femoral homogenate - DO mouse 406


title: heart_320s_C9


title: 4T1_RNAseq_control_1day-Normoxia_r3b

description: 4T1 DMSO 1day-Normoxia


title: heart_320s_C8


title: 4T1_RNAseq_control_1day-Normoxia_r3a

description: 4T1 DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 402

value: 83 days


title: heart_320s_D18


title: 4T1_RNAseq_control_1day-Normoxia_r2b

description: 4T1 DMSO 1day-Normoxia


title: heart_320s_C5


title: heart_320s_C6


title: Femoral homogenate - DO mouse 401


title: Femoral homogenate - DO mouse 403


title: heart_320s_C3


title: 4T1_RNAseq_control_1day-Normoxia_r2a

description: 4T1 DMSO 1day-Normoxia


title: heart_320s_C7


title: heart_320s_D11


title: heart_320s_D13


title: Femoral homogenate - DO mouse 404


title: heart_320s_D10


title: heart_320s_C23


title: Femoral homogenate - DO mouse 400


title: 4T1_RNAseq_control_1day-Hypoxia_r1a

description: 4T1 DMSO 1day-Hypoxia


title: 4T1_RNAseq_control_1day-Normoxia_r1b

description: 4T1 DMSO 1day-Normoxia


title: Femoral homogenate - DO mouse 399


title: 4T1_RNAseq_control_1day-Normoxia_r1a

description: 4T1 DMSO 1day-Normoxia


title: heart_320s_C21


title: heart_320s_C20


title: Femoral homogenate - DO mouse 398


title: heart_320s_C2


title: heart_320s_C22


title: heart_320s_C19


title: B16_tumour_RNAseq_IgG_r5

description: B16 tumour IgG 40mg/kg BW

source_name: Melanoma tumour

value: skin

value: IgG 40mg/kg BW


title: B16_tumour_RNAseq_IgG_r4

description: B16 tumour IgG 40mg/kg BW

value: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.


title: heart_320s_C16

value: heart


title: heart_320s_C17

value: male


title: B16_tumour_RNAseq_IgG_r3

description: B16 tumour IgG 40mg/kg BW


title: heart_320s_C15

value: 10-20 weeks


title: heart_320s_C18


title: heart_320s_C14


title: heart_320s_C12


title: Femoral homogenate - DO mouse 393


title: B16_tumour_RNAseq_IgG_r1

description: B16 tumour IgG 40mg/kg BW


title: heart_320s_C24


title: Femoral homogenate - DO mouse 394


title: Femoral homogenate - DO mouse 392


title: heart_320s_C11


title: mES Hif1b-KO_WGBS

data_processing:
FastQ files were mapped to the mouse genome (build mm10) using bismark (version 0.10.1).
Read counts at HIF peak areas were quantified in each sample using SeqMonk, and background-normalized to enable enrichment assessment.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read file contains read numbers overlaping with HIF peaks in mES cells; Mathylation status for all C's in the captured region.

source_name: Embyonic Stem Cells


title: heart_320s_C10


title: Femoral homogenate - DO mouse 397


title: heart_320s_C1


title: heart_320s_C13


title: B16_tumour_RNAseq_IgG_r2

description: B16 tumour IgG 40mg/kg BW


title: heart_320s_B9


title: mES Hif1b-WT_WGBS


title: heart_320s_B6


title: heart_320s_B8


title: Femoral homogenate - DO mouse 391


title: Femoral homogenate - DO mouse 396


title: heart_320s_B7


title: Femoral homogenate - DO mouse 390


title: heart_320s_B3


title: heart_320s_B4


title: Femoral homogenate - DO mouse 389


title: RCC4_SeqCapEpi_Bsseq_hypoxia

description: RCC4 Hypoxia

data_processing:
Default trim_galore (0.6.4_dev) quality trimming were performed on FastQ files. Then they were mapped to the human genome (hg19)  using bismark (version v0.22.3).
Genome_build: hg19
Supplementary_files_format_and_content: Bismark coverage files containing DNA methylation calls for every CpG measured

extract_protocol:
Cultured cells were subsequently immediately fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly in the medium and incubating for 8 minutes. Fixed cells were incubated with 150 µM of glycine for 5 min to revert the cross-links, washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 ×G 5min at 4°C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The chromatin was sonicated for 3 min by using a Branson 250 Digital Sonifier with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 ×G at 4°C) and the supernatant were transferred in a new eppendorf tube. The protein concentration was assessed using a BCA assay. Fifty µL of shared chromatin was used as “input” and 1.4 µg of primary ARNT/HIF-1β monoclonal antibody (NB100-124, Novus) per 1 mg of protein was added to the remainder of the chromatin, and incubated overnight at 4°C in a rotator. Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples in a volume that is 4X the volume of the primary Ab and incubated at 4°C for at least 5 hours. A/G Magnetic Beads were collected and the samples were washed 5 times with the washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNAse A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37°C. After addition of 1.5 µL of proteinase K (200 units) and overnight incubation at 65°C, the DNA was purified using 1.8´ volume of Agencourt AMPure XP (Beckman Coulter) according to the manufactory instructions
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. DNA libraries were bisulfite converted using the EZ DNA Methylation-Lightning™ kit (Zymo) prior to library amplification using HiFi Uracil+ (KAPA).

treatment_protocol: Cells were incubated in hypoxic conditions (0.5% oxygen) for 16 hours.

tag: oxygen status

value: 16 hours of 0.5% oxygen (hypoxia)


title: MCF7_SeqCapEpi_Bsseq_hypoxia

description: MCF7 Hypoxia

tag: cell line


title: heart_320s_B5

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol


title: Femoral homogenate - DO mouse 388


title: heart_320s_B23


title: heart_320s_B22


title: Femoral homogenate - DO mouse 385


title: heart_320s_B21


title: heart_320s_B20


title: heart_320s_B24


title: Femoral homogenate - DO mouse 387


title: Femoral homogenate - DO mouse 386


title: heart_320s_B2


title: heart_320s_B19


title: heart_320s_B16


title: heart_320s_B14


title: heart_320s_B13


title: Femoral homogenate - DO mouse 383


title: Femoral homogenate - DO mouse 384


title: heart_320s_B11


title: Femoral homogenate - DO mouse 382


title: SK-MEL-28_SeqCapEpi_BSseq_Hypoxia

description: SK-MEL-28 Hypoxia


title: heart_320s_B17


title: Femoral homogenate - DO mouse 381


title: heart_320s_B15


title: heart_320s_B12


title: Femoral homogenate - DO mouse 380


title: heart_320s_B10


title: heart_320s_B1


title: heart_320s_A9


title: Femoral homogenate - DO mouse 379


title: Femoral homogenate - DO mouse 378


title: heart_320s_A6


title: heart_320s_B18


title: heart_320s_A8


title: Femoral homogenate - DO mouse 375

value: 87 days


title: heart_320s_A22


title: heart_320s_A23


title: heart_320s_A7


title: Femoral homogenate - DO mouse 377


title: heart_320s_A2


title: heart_320s_A4


title: heart_320s_A20


title: heart_320s_A3


title: heart_320s_A17


title: Femoral homogenate - DO mouse 376


title: Femoral homogenate - DO mouse 373


title: heart_320s_A15


title: Femoral homogenate - DO mouse 372


title: Femoral homogenate - DO mouse 371


title: heart_320s_A14


title: heart_320s_A21


title: Femoral homogenate - DO mouse 370


title: heart_320s_A16


title: heart_320s_A12


title: rJDS033

data_processing:
FastQ files were mapped to the reference genome (hg38) using STAR (version 2.4.2).
Counts were called by HTSeq (version 0.11.0)
Genome_build: hg38
Supplementary_files_format_and_content: Raw read files contain raw read counts for each sample

extract_protocol:
For PolyA mRNA capture system, RNA was extracted using TRIzol (Invitrogen) according to manufacture instructions. RNA was subsiquently used for PolyA capture.
Strand specific library preparation (KAPA stranded mRNA seq kit)


title: Femoral homogenate - DO mouse 369


title: heart_320s_A13


title: heart_320s_A5


title: heart_320s_A10


title: heart_316s_P9


title: rJDS031


title: heart_320s_A1


title: Femoral homogenate - DO mouse 367


title: heart_320s_A19


title: heart_320s_A18


title: heart_316s_P22


title: rJDS030


title: heart_316s_P4


title: Femoral homogenate - DO mouse 365


title: heart_320s_A11


title: Femoral homogenate - DO mouse 368


title: heart_316s_P3


title: heart_316s_P21


title: heart_316s_P20


title: Femoral homogenate - DO mouse 363


title: Femoral homogenate - DO mouse 361


title: rJDS028


title: Femoral homogenate - DO mouse 362


title: heart_316s_P16


title: heart_316s_P19


title: heart_316s_P18


title: rJDS027


title: Femoral homogenate - DO mouse 360


title: heart_316s_P15


title: rJDS024


title: Femoral homogenate - DO mouse 359


title: rJDS026


title: heart_316s_P14


title: heart_316s_P13


title: heart_316s_P11


title: heart_316s_P1


title: Femoral homogenate - DO mouse 357


title: Femoral homogenate - DO mouse 358


title: heart_316s_P10


title: heart_316s_O9


title: rJDS029


title: rJDS023


title: Femoral homogenate - DO mouse 355


title: rJDS021


title: heart_316s_O6


title: heart_316s_O5


title: heart_316s_O8


title: Femoral homogenate - DO mouse 356


title: heart_316s_O7


title: rJDS018


title: heart_316s_O3


title: Femoral homogenate - DO mouse 354


title: rJDS020


title: heart_316s_O24


title: heart_316s_O4


title: rJDS017


title: Femoral homogenate - DO mouse 353


title: rJDS015


title: Femoral homogenate - DO mouse 351


title: heart_316s_O21


title: heart_316s_O22


title: rJDS019


title: heart_316s_O23


title: Femoral homogenate - DO mouse 349


title: heart_316s_O2


title: heart_316s_O19


title: rJDS014


title: heart_316s_O18


title: heart_316s_O20


title: Femoral homogenate - DO mouse 348


title: rJDS011


title: heart_316s_O16


title: rJDS010


title: Femoral homogenate - DO mouse 347


title: heart_316s_O17


title: heart_316s_O15


title: Femoral homogenate - DO mouse 345


title: rJDS009


title: heart_316s_O14


title: heart_316s_O11


title: heart_316s_O12


title: heart_316s_O13


title: Femoral homogenate - DO mouse 342


title: MCF7_RNAseq_DMOG_aza_1day-Hypoxia_r3b

description: MCF7 DMOG aza 1day-Normoxia

source_name: Breast cancer cell line

value: 2mM DMOG 24h, 1 µM aza 72h, 21% O2 24h


title: heart_316s_O1


title: Femoral homogenate - DO mouse 340

value: Marrow-depleted left femur - homogenate


title: MCF7_RNAseq_DMOG_aza_1day-Hypoxia_r3a

description: MCF7 DMOG aza 1day-Normoxia


title: heart_316s_N7


title: Femoral homogenate - DO mouse 338

value: Diversity Outbred (J:DO)