title: 28dpci [H430_D8]


title: 28dpci [H430_I9]

status: Public on Feb 21 2022

type: SRA

city: Stockholm

first: Kenneth

last: Chien

state: State...

address: A6 Biomedicum

department: CMB

country: Sweden

institute: Karolinska Insitute

library_source: transcriptomic

data_processing:
Single-end 43 bp reads were mapped using STAR (v.2.5.3a) to the Pleurodeles waltl reference coding sequences consolidated in orthology groups (Elewa et al.). Reads mapping uniquely to one orthology group were assigned to that group and a final matrix of unique read counts per orthology group was used for downstream analysis.
Elewa, A., Wang, H., Talavera-López, C., Joven, A., Brito, G., Kumar, A., Hameed, L.S., Penrad-Mobayed, M., Yao, Z., Zamani, N., et al. (2017) Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.
Genome_build: Regarding the feature of the processed table, the BBLXXXX is the id generated by OrthoMCL, as described in the paper "Elewa, et al. (2017) Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration". There is no  published* Pleurodeles waltl *genome or annotation.
Supplementary_files_format_and_content: Final matrix of unique read counts per orthology group. Cell identities are labeled in scRNA_meta_data_suppleTable1.csv and scRNA_meta_data_suppleTable2.csv

molecule: total RNA

organism: Pleurodeles waltl

source_name: Dissociated single cell from heart

extract_protocol: Single cell RNA libraries were prepared for sequencing using Smart-Seq2 protocol

tag: strain

value: wild type

tag: tissue

value: whole ventricle

tag: treatment

value: untreated

tag: dissociation

value: Standard

tag: staining

value: Live


title: 28dpci [H430_N11]


title: 28dpci [H430_F17]


title: 28dpci [H430_H22]


title: 28dpci [H430_G3]


title: 28dpci [H430_E5]


title: 28dpci [H430_A22]


title: 28dpci [H430_H9]


title: 28dpci [H430_C5]


title: 28dpci [H430_G6]


title: sham [H431_K24]


title: 28dpci [H430_M22]


title: 28dpci [H430_J22]


title: 28dpci [H430_C14]


title: 28dpci [H430_M11]


title: 28dpci [H430_E8]


title: 28dpci [H430_I20]


title: 28dpci [H430_I23]


title: 28dpci [H430_C11]


title: 28dpci [H430_J5]


title: 28dpci [H430_H3]


title: 28dpci [H430_C9]


title: 28dpci [H430_L19]


title: 28dpci [H430_D21]


title: 28dpci [H430_H21]


title: 28dpci [H430_H8]


title: 28dpci [H430_F5]


title: 28dpci [H430_L21]


title: 28dpci [H430_G7]


title: 28dpci [H430_J14]


title: 28dpci [H430_B20]


title: 28dpci [H430_D20]


title: 28dpci [H430_F4]


title: 28dpci [H430_M14]


title: 28dpci [H430_A13]


title: 28dpci [H430_L17]


title: 28dpci [H430_F10]


title: 28dpci [H430_B22]


title: 28dpci [H430_P11]


title: 28dpci [H430_I14]


title: 28dpci [H430_D7]


title: 28dpci [H430_K6]


title: 28dpci [H430_B21]


title: 28dpci [H430_B23]


title: 28dpci [H430_F11]


title: 28dpci [H430_C15]


title: 28dpci [H430_D14]


title: 28dpci [H430_B8]


title: 28dpci [H430_C13]


title: 28dpci [H430_G20]


title: 28dpci [H430_N19]


title: 28dpci [H430_D10]


title: 28dpci [H430_O7]


title: 28dpci [H430_I13]


title: 28dpci [H430_C2]


title: 28dpci [H430_A14]


title: 28dpci [H430_C16]


title: 28dpci [H430_O19]


title: 28dpci [H430_B6]


title: 28dpci [H430_K2]


title: 28dpci [H430_I8]


title: 28dpci [H430_G18]


title: 28dpci [H430_M9]


title: 28dpci [H430_K24]


title: 28dpci [H430_A1]


title: 28dpci [H430_J15]


title: 28dpci [H430_E11]


title: 28dpci [H430_L15]


title: 28dpci [H430_A24]


title: 28dpci [H430_E22]


title: 28dpci [H430_H1]


title: 28dpci [H430_M15]


title: 28dpci [H430_E16]


title: 28dpci [H430_H2]


title: 28dpci [H430_O9]


title: 28dpci [H430_J1]


title: 28dpci [H430_B16]


title: 28dpci [H430_L24]


title: 28dpci [H430_E19]


title: 28dpci [H430_M17]


title: 28dpci [H430_E1]


title: 28dpci [H430_J23]


title: 28dpci [H430_C19]


title: 28dpci [H430_K21]


title: 28dpci [H430_J24]


title: 28dpci [H430_G16]


title: 28dpci [H430_H15]


title: 28dpci [H430_M24]


title: 28dpci [H430_E9]


title: 28dpci [H430_N8]


title: 28dpci [H430_M16]


title: 28dpci [H430_D4]


title: 28dpci [H430_D9]


title: 28dpci [H430_L9]


title: 28dpci [H430_L23]


title: 28dpci [H430_C1]


title: 28dpci [H430_K4]


title: 28dpci [H430_F13]


title: 28dpci [H430_B11]


title: 28dpci [H430_E14]


title: 28dpci [H430_I6]


title: 28dpci [H430_A9]


title: 28dpci [H430_D2]


title: 28dpci [H430_K12]


title: 28dpci [H430_H11]


title: 28dpci [H430_I17]


title: 28dpci [H430_K8]


title: 28dpci [H430_L22]


title: 28dpci [H430_H17]


title: 28dpci [H430_I4]


title: 28dpci [H430_L13]


title: 28dpci [H430_D24]


title: 28dpci [H430_G1]


title: 28dpci [H430_M12]


title: 28dpci [H430_G21]


title: 28dpci [H430_J19]


title: 28dpci [H430_F7]


title: 28dpci [H430_H10]


title: 28dpci [H430_H7]


title: 28dpci [H430_G17]


title: 28dpci [H430_D22]


title: 28dpci [H430_F3]


title: 28dpci [H430_B7]


title: 28dpci [H430_D23]


title: 28dpci [H430_C6]


title: 28dpci [H430_M3]


title: 28dpci [H430_J18]


title: 28dpci [H430_P14]


title: 28dpci [H430_N24]


title: 28dpci [H430_O21]


title: 28dpci [H430_P20]


title: 28dpci [H430_L10]


title: 28dpci [H430_C12]


title: 28dpci [H430_G9]


title: 28dpci [H430_D3]


title: 28dpci [H430_K14]


title: 28dpci [H430_L1]


title: 28dpci [H430_N1]


title: 28dpci [H430_B3]


title: 28dpci [H430_N3]


title: 28dpci [H430_J12]


title: 28dpci [H430_A2]


title: 28dpci [H430_O14]


title: 28dpci [H430_H16]


title: 28dpci [H430_J4]


title: 28dpci [H430_B19]


title: 28dpci [H430_G19]


title: 28dpci [H430_H13]


title: 28dpci [H430_G10]


title: 28dpci [H430_K20]


title: 28dpci [H430_J9]


title: 28dpci [H430_H5]


title: 28dpci [H430_K7]


title: 28dpci [H430_C24]


title: 28dpci [H430_J7]


title: 28dpci [H430_B2]


title: 28dpci [H430_B4]


title: 28dpci [H430_A21]


title: 28dpci [H430_O11]


title: 28dpci [H430_B12]


title: 28dpci [H430_G4]


title: 28dpci [H430_H23]


title: 28dpci [H430_I3]


title: 28dpci [H430_O12]


title: 28dpci [H430_H14]


title: 28dpci [H430_C18]


title: 28dpci [H430_G5]


title: 28dpci [H430_E18]


title: 28dpci [H430_O2]


title: 28dpci [H430_E15]


title: 28dpci [H430_H18]


title: 28dpci [H430_D19]


title: 28dpci [H430_K16]


title: 28dpci [H430_K13]


title: 28dpci [H430_K17]


title: 28dpci [H430_D13]


title: 28dpci [H430_B18]


title: 28dpci [H430_H19]


title: 28dpci [H430_A17]


title: 28dpci [H430_K18]


title: 28dpci [H430_B10]


title: 28dpci [H430_I19]


title: 28dpci [H430_L8]


title: 28dpci [H430_K3]


title: 28dpci [H430_I12]


title: 28dpci [H430_E21]


title: 28dpci [H430_K22]


title: 28dpci [H430_C17]


title: 28dpci [H430_G22]


title: 28dpci [H430_A18]


title: 28dpci [H430_A10]


title: 28dpci [H430_I10]


title: 28dpci [H430_F20]


title: 28dpci [H430_O22]


title: 28dpci [H430_F23]


title: 28dpci [H430_D16]


title: 28dpci [H430_I21]


title: 28dpci [H430_P10]


title: 28dpci [H430_A5]


title: 28dpci [H430_F24]


title: 28dpci [H430_F16]


title: 28dpci [H429_E6]

value: apex/ventricle


title: 28dpci [H429_J7]


title: 28dpci [H429_C17]


title: 28dpci [H429_E22]


title: 28dpci [H429_J22]


title: 28dpci [H429_E13]


title: 28dpci [H429_K3]


title: 28dpci [H429_H8]


title: 28dpci [H429_F17]


title: 28dpci [H429_C22]


title: 28dpci [H429_H20]


title: 28dpci [H429_K22]


title: 28dpci [H429_M12]


title: 28dpci [H430_K11]


title: 28dpci [H429_J4]


title: 28dpci [H429_G1]


title: 28dpci [H429_P7]


title: 28dpci [H430_I24]


title: 28dpci [H429_M4]


title: 28dpci [H429_C16]


title: 28dpci [H429_M18]


title: 28dpci [H429_C9]


title: 28dpci [H429_C23]


title: 28dpci [H429_J12]


title: 28dpci [H429_I9]


title: 28dpci [H429_A23]


title: 28dpci [H429_H9]


title: 28dpci [H429_E9]


title: 28dpci [H429_P11]


title: 28dpci [H429_L14]


title: 28dpci [H429_F9]


title: 28dpci [H429_H11]


title: 28dpci [H429_F1]


title: 28dpci [H429_A7]


title: 28dpci [H429_K23]


title: 28dpci [H429_K15]


title: 28dpci [H429_F23]


title: 28dpci [H429_C6]


title: 28dpci [H429_F12]


title: 28dpci [H429_C21]


title: 28dpci [H429_F5]


title: 28dpci [H429_D18]


title: 28dpci [H429_D22]


title: 28dpci [H429_B22]


title: 28dpci [H429_J23]


title: 28dpci [H429_B24]


title: 28dpci [H429_I4]


title: 28dpci [H429_F7]


title: 28dpci [H429_H18]


title: 28dpci [H429_G22]


title: 28dpci [H429_N11]


title: 28dpci [H429_D14]


title: 28dpci [H429_N16]


title: 28dpci [H429_B20]


title: 28dpci [H429_N17]


title: 28dpci [H429_G19]


title: 28dpci [H429_B4]


title: 28dpci [H429_P4]


title: 28dpci [H429_A10]


title: 28dpci [H429_F13]


title: 28dpci [H429_I21]


title: 28dpci [H429_H21]


title: 28dpci [H429_G12]


title: 28dpci [H429_D9]


title: 28dpci [H429_M13]


title: 28dpci [H429_G3]


title: 28dpci [H429_M1]


title: 28dpci [H429_L22]


title: 28dpci [H429_L12]


title: 28dpci [H429_D20]


title: 28dpci [H429_L13]


title: 28dpci [H429_B19]


title: 28dpci [H429_N7]


title: 28dpci [H429_N9]


title: 28dpci [H429_P20]


title: 28dpci [H429_L23]


title: 28dpci [H429_A5]


title: 28dpci [H429_A3]


title: 28dpci [H429_F11]


title: 28dpci [H429_J10]


title: 28dpci [H429_D1]


title: 28dpci [H429_B12]


title: 28dpci [H429_I19]


title: 28dpci [H429_M6]


title: 28dpci [H429_B3]


title: 28dpci [H429_A11]


title: 28dpci [H429_N18]


title: 28dpci [H429_J24]


title: 28dpci [H429_E8]


title: 28dpci [H429_P6]


title: 28dpci [H429_N23]


title: 28dpci [H429_N20]


title: 28dpci [H429_P17]


title: 28dpci [H429_A19]


title: 28dpci [H429_H19]


title: 28dpci [H429_C1]


title: 28dpci [H429_B9]


title: 28dpci [H429_K6]


title: 28dpci [H429_M11]


title: 28dpci [H429_A20]


title: 28dpci [H429_J1]


title: 28dpci [H429_B16]


title: 28dpci [H429_L5]


title: 28dpci [H429_P18]


title: 28dpci [H429_N8]


title: 28dpci [H429_H5]


title: 28dpci [H429_L24]


title: 28dpci [H429_I11]


title: 28dpci [H429_C2]


title: 28dpci [H429_K1]


title: 28dpci [H429_F21]


title: 28dpci [H429_C12]


title: 28dpci [H429_I16]


title: 28dpci [H429_D17]


title: 28dpci [H429_J13]


title: 28dpci [H429_G17]


title: 28dpci [H429_N5]


title: 28dpci [H429_B21]


title: 28dpci [H429_G4]


title: 28dpci [H429_D10]


title: 28dpci [H429_D23]


title: 28dpci [H429_O13]


title: 28dpci [H429_E5]


title: 28dpci [H429_A21]


title: 28dpci [H429_K8]


title: 28dpci [H429_D13]


title: 28dpci [H429_G23]


title: 28dpci [H429_F6]


title: 28dpci [H429_C18]


title: 28dpci [H429_G15]


title: 28dpci [H429_N10]


title: 28dpci [H429_O10]


title: 28dpci [H429_A22]


title: 28dpci [H429_H17]


title: 28dpci [H429_J18]


title: 28dpci [H429_E14]


title: 28dpci [H429_A14]


title: 28dpci [H429_H2]


title: 28dpci [H429_M8]


title: 28dpci [H429_G21]


title: 28dpci [H429_C3]


title: 28dpci [H429_M17]


title: 28dpci [H429_D21]


title: 28dpci [H429_G11]


title: 28dpci [H429_C19]


title: 28dpci [H429_J2]


title: 28dpci [H429_N12]


title: 28dpci [H429_F8]


title: 28dpci [H429_A18]


title: 28dpci [H429_B17]


title: 28dpci [H429_F10]


title: 28dpci [H429_B18]


title: 28dpci [H429_O1]


title: 28dpci [H429_B15]


title: 28dpci [H429_A2]


title: 28dpci [H429_A12]


title: 28dpci [H429_P8]


title: 28dpci [H429_K17]


title: 28dpci [H429_J17]


title: 28dpci [H429_K19]


title: 28dpci [H429_E3]


title: 28dpci [H429_E20]


title: 28dpci [H429_K11]


title: 28dpci [H429_C8]


title: 28dpci [H429_E12]


title: 28dpci [H429_G2]


title: 28dpci [H429_J5]


title: 28dpci [H429_M22]


title: 28dpci [H429_G8]


title: 28dpci [H429_M2]


title: 28dpci [H429_F16]


title: 28dpci [H429_L9]


title: 28dpci [H429_J3]


title: 28dpci [H429_M19]


title: 28dpci [H429_F14]


title: 28dpci [H429_G16]


title: 28dpci [H429_L16]


title: 28dpci [H429_F20]


title: 28dpci [H429_M23]


title: 28dpci [H429_M15]


title: 28dpci [H429_K20]


title: 28dpci [H429_D6]


title: 28dpci [H429_I24]


title: 28dpci [H429_L21]


title: 28dpci [H429_I17]


title: 28dpci [H429_O23]


title: 28dpci [H429_D3]


title: 28dpci [H429_O14]


title: 28dpci [H429_H12]


title: 28dpci [H429_O21]


title: 28dpci [H429_K7]


title: 28dpci [H429_B7]


title: 28dpci [H429_O19]


title: 28dpci [H429_N21]


title: 28dpci [H429_J19]


title: 28dpci [H429_I3]


title: 28dpci [H429_K18]


title: 28dpci [H429_I15]


title: 28dpci [H429_D15]


title: 28dpci [H429_B8]


title: 28dpci [H429_P5]


title: 28dpci [H429_J8]


title: 28dpci [H429_A24]


title: 28dpci [H429_D11]


title: 28dpci [H429_O20]


title: 28dpci [H429_A17]


title: 28dpci [H429_I2]


title: 28dpci [H429_K5]


title: 28dpci [H429_H7]


title: 28dpci [H429_K10]


title: 28dpci [H429_L11]


title: 28dpci [H429_G6]


title: 28dpci [H429_K12]


title: 28dpci [H429_B5]


title: 28dpci [H429_L3]


title: 28dpci [H429_D12]


title: 28dpci [H429_P1]


title: 28dpci [H429_C7]


title: 28dpci [H429_M14]


title: 28dpci [H429_L1]


title: 28dpci [H430_G14]


title: 28dpci [H429_I12]


title: 28dpci [H429_M10]


title: 28dpci [H429_I7]


title: 28dpci [H429_E7]


title: 28dpci [H429_J14]


title: 28dpci [H429_C14]


title: 28dpci [H429_M9]


title: 28dpci [H429_L7]


title: 28dpci [H429_H13]


title: 28dpci [H429_E16]


title: 28dpci [H429_G13]


title: 28dpci [H429_L19]


title: 28dpci [H429_L15]


title: 28dpci [H429_M3]


title: 28dpci [H429_B13]


title: 28dpci [H429_C13]


title: 28dpci [H429_D8]


title: 28dpci [H429_A13]


title: 28dpci [H429_B1]


title: 28dpci [H429_F2]


title: 28dpci [H429_A15]


title: 28dpci [H429_I1]


title: 28dpci [H429_B11]


title: 28dpci [H429_F22]


title: 28dpci [H429_M20]


title: 28dpci [H429_E10]


title: 28dpci [H429_C4]


title: 28dpci [H429_N15]


title: 28dpci [H429_G24]


title: 28dpci [H429_L4]


title: 28dpci [H429_K4]


title: 28dpci [H429_B6]


title: 28dpci [H429_O22]


title: 28dpci [H429_E15]


title: 28dpci [H429_O24]


title: 28dpci [H429_E11]


title: 28dpci [H429_A9]


title: 28dpci [H429_E21]


title: 28dpci [H429_H23]


title: 28dpci [H429_G5]


title: 28dpci [H429_H6]


title: 28dpci [H429_E2]


title: 28dpci [H429_F19]


title: 28dpci [H429_L8]


title: 28dpci [H429_J6]


title: 28dpci [H429_I5]


title: 28dpci [H429_I13]


title: 28dpci [H429_C15]


title: 28dpci [H429_D24]


title: 28dpci [H429_M7]


title: 28dpci [H429_L18]


title: 28dpci [H429_F15]


title: 28dpci [H429_N4]


title: 28dpci [H429_G20]


title: 28dpci [H429_N19]


title: 28dpci [H429_E1]


title: 28dpci [H429_D7]


title: 28dpci [H429_J16]


title: 28dpci [H429_B2]


title: 28dpci [H429_K2]


title: 28dpci [H429_L6]


title: 28dpci [H429_K13]


title: 28dpci [H429_E24]


title: 28dpci [H429_C24]


title: 28dpci [H429_O2]


title: 28dpci [H429_D4]


title: 28dpci [H429_H1]


title: 28dpci [H429_F4]


title: 28dpci [H429_K9]


title: 28dpci [H429_O3]


title: 28dpci [H429_N22]


title: 28dpci [H429_C5]


title: 28dpci [H429_L2]


title: 28dpci [H429_P9]


title: 28dpci [H429_K24]


title: 28dpci [H429_C11]


title: 28dpci [H429_I22]


title: 28dpci [H429_E19]


title: 28dpci [H429_D19]


title: 28dpci [H429_E17]


title: 28dpci [H429_H16]


title: 28dpci [H429_M24]


title: 28dpci [H429_K21]


title: 28dpci [H429_E23]


title: 28dpci [H429_H22]


title: 28dpci [H429_G10]


title: 28dpci [H429_P12]


title: 28dpci [H429_G14]


title: 28dpci [H429_J11]


title: 28dpci [H429_I20]


title: 28dpci [H429_F18]


title: 28dpci [H429_O18]


title: 28dpci [H429_G18]


title: 28dpci [H429_H24]


title: 28dpci [H429_P13]


title: 28dpci [H429_D5]


title: 28dpci [H429_I10]


title: 28dpci [H429_P14]


title: 28dpci [H429_B23]


title: 28dpci [H429_H10]


title: 28dpci [H429_M5]


title: 28dpci [H429_P15]


title: 28dpci [H429_N6]


title: 28dpci [H429_A1]


title: 28dpci [H429_F24]


title: 28dpci [H429_P10]


title: 28dpci [H429_J20]


title: 28dpci [H429_I14]


title: 7dpci [H262_A1]

value: apex


title: 28dpci [H429_A16]


title: 7dpci [H262_N3]


title: 28dpci [H429_C10]


title: 7dpci [H262_G6]


title: 7dpci [H262_N2]


title: 7dpci [H262_F9]


title: 7dpci [H262_L14]


title: 28dpci [H429_K14]


title: 7dpci [H262_F20]


title: 7dpci [H262_F21]


title: 7dpci [H262_A24]


title: 7dpci [H262_M4]


title: 7dpci [H262_G14]


title: 7dpci [H262_A15]


title: 7dpci [H262_A18]


title: 7dpci [H262_M3]


title: 28dpci [H429_N3]


title: 28dpci [H429_A8]


title: 7dpci [H262_N11]


title: 7dpci [H262_J3]


title: 7dpci [H262_I1]


title: 7dpci [H262_F4]


title: 7dpci [H262_J22]


title: 7dpci [H262_B17]


title: 7dpci [H262_J10]


title: 7dpci [H262_L24]


title: 7dpci [H262_H12]


title: 7dpci [H262_G13]


title: 7dpci [H262_N5]


title: 7dpci [H262_L5]


title: 7dpci [H262_N1]


title: 7dpci [H262_H22]


title: 7dpci [H262_D5]


title: 7dpci [H262_I6]


title: 7dpci [H262_G16]


title: 7dpci [H262_K23]


title: 7dpci [H262_G7]


title: 7dpci [H262_H14]


title: 7dpci [H262_F17]


title: 7dpci [H262_M23]


title: 7dpci [H262_A22]


title: 7dpci [H262_E12]


title: 7dpci [H262_J8]


title: 7dpci [H262_I16]


title: 7dpci [H262_K19]


title: 7dpci [H262_L17]


title: 7dpci [H262_E16]


title: 7dpci [H262_G17]


title: 7dpci [H262_K9]


title: 7dpci [H262_M18]


title: 7dpci [H262_B10]


title: 7dpci [H262_E21]


title: 7dpci [H262_K10]


title: 7dpci [H262_H11]


title: 7dpci [H262_I10]


title: 7dpci [H262_A2]


title: 7dpci [H262_F10]


title: 7dpci [H262_G20]


title: 7dpci [H262_D11]


title: 7dpci [H262_L12]


title: 28dpci [H429_L10]


title: 7dpci [H262_C8]


title: 7dpci [H262_E11]


title: 7dpci [H262_M14]


title: 7dpci [H262_H20]


title: 7dpci [H262_D18]


title: 7dpci [H262_A17]


title: 7dpci [H262_A7]


title: 7dpci [H262_J2]


title: 7dpci [H262_I15]


title: 7dpci [H262_A14]


title: 7dpci [H262_D24]


title: 7dpci [H262_H9]


title: 7dpci [H262_J19]


title: 7dpci [H262_E5]


title: 7dpci [H262_I2]


title: 7dpci [H262_G18]


title: 7dpci [H262_F1]


title: 7dpci [H262_M22]


title: 7dpci [H262_D13]


title: 7dpci [H262_B19]


title: 7dpci [H262_L11]


title: 7dpci [H262_J5]


title: 7dpci [H262_C22]


title: 7dpci [H262_J7]


title: 7dpci [H262_F2]


title: 7dpci [H262_L18]


title: 7dpci [H262_D12]


title: 7dpci [H262_L1]


title: 7dpci [H262_I24]


title: 7dpci [H262_F23]


title: 7dpci [H262_I8]


title: 7dpci [H262_B18]


title: 7dpci [H262_D9]


title: 7dpci [H262_F19]


title: 7dpci [H262_J23]


title: 7dpci [H262_H6]


title: 7dpci [H262_N18]


title: 7dpci [H262_C5]


title: 7dpci [H262_L8]


title: 7dpci [H262_B16]


title: 7dpci [H262_M16]


title: 7dpci [H262_M2]


title: 7dpci [H262_M20]


title: 7dpci [H262_K7]


title: 7dpci [H262_B9]


title: 7dpci [H262_D2]


title: 7dpci [H262_G8]


title: 7dpci [H262_D19]


title: 7dpci [H262_H7]


title: 7dpci [H262_D14]


title: 7dpci [H262_E4]


title: 7dpci [H262_C10]


title: 7dpci [H262_B13]


title: 7dpci [H262_M9]


title: 7dpci [H262_C9]


title: 7dpci [H262_I19]


title: 7dpci [H262_F6]


title: 7dpci [H262_C18]


title: 7dpci [H262_H4]


title: 7dpci [H262_N19]


title: 7dpci [H262_E24]


title: 7dpci [H262_B12]


title: 7dpci [H262_C20]


title: 7dpci [H262_A8]


title: 7dpci [H262_H17]


title: 7dpci [H262_I5]


title: 7dpci [H262_J18]


title: 7dpci [H262_A23]


title: 7dpci [H262_K14]


title: 7dpci [H262_A9]


title: 7dpci [H262_K18]


title: 7dpci [H262_F13]


title: 7dpci [H262_K12]


title: 7dpci [H262_N10]


title: 7dpci [H262_F12]


title: 7dpci [H262_M5]


title: 7dpci [H262_E2]


title: 7dpci [H262_A10]


title: 7dpci [H262_M6]


title: 7dpci [H262_C24]


title: 7dpci [H262_E23]


title: 7dpci [H262_I4]


title: 7dpci [H262_N8]


title: 7dpci [H262_L6]


title: 7dpci [H262_D3]


title: 7dpci [H262_L21]


title: 7dpci [H262_K13]


title: 7dpci [H262_K22]


title: 7dpci [H262_G3]


title: 7dpci [H262_B24]


title: 7dpci [H262_D6]


title: 7dpci [H262_H1]


title: 7dpci [H262_E17]


title: 7dpci [H262_K1]


title: 7dpci [H262_H2]


title: 7dpci [H262_D10]


title: 7dpci [H262_A11]


title: 7dpci [H262_C1]


title: 7dpci [H262_M8]


title: 7dpci [H262_J24]


title: 7dpci [H262_J15]


title: 7dpci [H262_C23]


title: 7dpci [H262_H21]


title: 7dpci [H262_E10]


title: 7dpci [H262_K2]


title: 7dpci [H262_C4]


title: 7dpci [H262_J20]


title: 7dpci [H262_D16]


title: 7dpci [H262_M21]


title: 7dpci [H262_L16]


title: 7dpci [H262_L9]


title: 7dpci [H262_E7]


title: 7dpci [H262_E3]


title: 7dpci [H262_A21]


title: 7dpci [H262_M1]


title: 7dpci [H262_D21]


title: 7dpci [H262_E15]


title: 7dpci [H262_I22]


title: 7dpci [H262_G23]


title: 7dpci [H262_E20]


title: 7dpci [H262_E18]


title: 7dpci [H262_M12]


title: 7dpci [H262_M7]


title: 7dpci [H262_G21]


title: 7dpci [H262_K20]


title: 7dpci [H262_G15]


title: 7dpci [H262_H13]


title: 7dpci [H262_F7]


title: 7dpci [H262_K21]


title: 7dpci [H262_D20]


title: 7dpci [H262_M19]


title: 7dpci [H262_N7]


title: 7dpci [H262_H10]


title: 7dpci [H262_H8]


title: 7dpci [H262_K6]


title: 7dpci [H262_N9]


title: 7dpci [H262_A20]


title: 7dpci [H262_M13]


title: 7dpci [H262_M15]


title: 7dpci [H262_E8]


title: 7dpci [H262_N17]


title: 7dpci [H262_M24]


title: 7dpci [H262_I7]


title: 7dpci [H262_J13]


title: 7dpci [H262_G2]


title: 7dpci [H262_D8]


title: 7dpci [H262_C7]


title: 7dpci [H262_G12]


title: 7dpci [H262_H19]


title: 7dpci [H262_I12]


title: 7dpci [H262_K11]


title: 7dpci [H262_L13]


title: 7dpci [H262_I17]


title: 7dpci [H262_D7]


title: 7dpci [H262_H16]


title: 7dpci [H262_N13]


title: 7dpci [H262_E13]


title: 7dpci [H262_E1]


title: 7dpci [H262_K17]


title: 7dpci [H262_F8]


title: 7dpci [H262_K16]


title: 7dpci [H262_H5]


title: 7dpci [H262_J21]


title: 7dpci [H262_B21]


title: 7dpci [H262_G11]


title: 7dpci [H262_N16]


title: 7dpci [H262_N6]


title: 7dpci [H262_E19]


title: 7dpci [H262_I18]


title: 7dpci [H262_C15]


title: 7dpci [H262_L4]


title: 7dpci [H262_J12]


title: 7dpci [H262_L10]


title: 7dpci [H262_C19]


title: 7dpci [H262_J9]


title: 7dpci [H262_L7]


title: 7dpci [H262_A3]


title: 7dpci [H262_F24]


title: 7dpci [H262_K5]


title: 7dpci [H262_K24]


title: 7dpci [H262_J16]


title: 7dpci [H262_E14]


title: 7dpci [H262_C6]


title: 7dpci [H262_E6]


title: 7dpci [H262_I9]


title: 7dpci [H262_G5]


title: 7dpci [H262_F11]


title: 7dpci [H262_J17]


title: 7dpci [H262_A16]


title: 7dpci [H262_N12]


title: 7dpci [H262_K3]


title: 7dpci [H262_F5]


title: 7dpci [H262_H18]


title: 7dpci [H262_F16]


title: 7dpci [H262_C14]


title: 7dpci [H262_I11]


title: 7dpci [H262_G9]


title: 7dpci [H262_I13]


title: 7dpci [H262_G4]


title: 7dpci [H262_I21]


title: 7dpci [H262_K4]


title: 7dpci [H262_J14]


title: 7dpci [H262_F14]


title: 7dpci [H262_F3]


title: 7dpci [H262_G24]


title: 7dpci [H262_M11]


title: 7dpci [H262_L23]


title: 7dpci [H262_H3]


title: 7dpci [H262_C11]


title: 7dpci [H262_A6]


title: 7dpci [H262_D17]


title: 7dpci [H262_H23]


title: 7dpci [H262_E9]


title: 7dpci [H262_J6]


title: 7dpci [H262_C12]


title: 7dpci [H262_C13]


title: 7dpci [H262_C3]


title: 7dpci [H262_C21]


title: 7dpci [H262_C17]


title: 7dpci [H262_A19]


title: 7dpci [H262_B15]


title: 7dpci [H262_N14]


title: 7dpci [H262_G10]


title: 7dpci [H262_F15]


title: 7dpci [H262_M17]


title: 7dpci [H262_G19]


title: 7dpci [H262_D4]


title: 7dpci [H262_H15]


title: 7dpci [H262_B14]


title: 7dpci [H262_F22]


title: 7dpci [H262_A12]


title: 7dpci [H262_J4]


title: 7dpci [H262_B20]


title: 7dpci [H262_L22]


title: 7dpci [H262_F18]


title: 7dpci [H262_I3]


title: 7dpci [H262_B22]


title: 7dpci [H262_J11]


title: 7dpci [H262_J1]


title: 7dpci [H262_N15]


title: 7dpci [H262_K15]


title: 7dpci [H262_H24]


title: 7dpci [H262_D15]


title: 7dpci [H262_D1]


title: 7dpci [H262_I14]


title: 7dpci [H262_L15]


title: 7dpci [H262_N4]


title: 7dpci [H262_K8]


title: 7dpci [H262_M10]


title: 7dpci [H262_A13]


title: 7dpci [H262_C16]


title: 7dpci [H262_L3]


title: 7dpci [H262_G1]


title: 7dpci [H261_P16]


title: 7dpci [H262_I23]


title: 7dpci [H261_B16]


title: 7dpci [H261_I7]


title: 7dpci [H261_L24]


title: 7dpci [H261_D2]


title: 7dpci [H261_I12]


title: 7dpci [H262_L2]


title: 7dpci [H261_G15]


title: 7dpci [H261_O5]


title: 7dpci [H262_A4]


title: 7dpci [H261_M24]


title: 7dpci [H261_J2]


title: 7dpci [H261_M18]


title: 7dpci [H261_D20]


title: 7dpci [H261_K5]


title: 7dpci [H261_G19]


title: 7dpci [H261_L23]


title: 7dpci [H261_N16]


title: 7dpci [H261_F15]


title: 7dpci [H261_H20]


title: 7dpci [H261_I8]


title: 7dpci [H261_C2]


title: 7dpci [H261_E2]


title: 7dpci [H261_C15]


title: 7dpci [H261_J16]


title: 7dpci [H261_J19]


title: 7dpci [H261_P20]


title: 7dpci [H261_O1]


title: 7dpci [H261_O16]


title: 7dpci [H261_O20]


title: 7dpci [H261_I19]


title: 7dpci [H261_M7]


title: 7dpci [H261_I17]


title: 7dpci [H261_B21]


title: 7dpci [H261_L15]


title: 7dpci [H261_J13]


title: 7dpci [H261_I18]


title: 7dpci [H261_F23]


title: 7dpci [H261_H12]


title: 7dpci [H261_L20]


title: 7dpci [H261_G8]


title: 7dpci [H261_G3]


title: 7dpci [H261_E15]


title: 7dpci [H261_F17]


title: 7dpci [H261_M6]


title: 7dpci [H261_J3]


title: 7dpci [H261_H11]


title: 7dpci [H261_J23]


title: 7dpci [H261_K19]


title: 7dpci [H261_B5]


title: 7dpci [H261_P9]


title: 7dpci [H261_B20]


title: 7dpci [H261_P10]


title: 7dpci [H261_D4]


title: 7dpci [H261_I21]


title: 7dpci [H261_E21]


title: 7dpci [H261_F7]


title: 7dpci [H261_C1]


title: 7dpci [H261_N10]


title: 7dpci [H261_J1]


title: 7dpci [H261_G13]


title: 7dpci [H261_H24]


title: 7dpci [H261_P14]


title: 7dpci [H261_J8]


title: 7dpci [H261_D10]


title: 7dpci [H261_L8]


title: 7dpci [H261_N23]


title: 7dpci [H261_K1]


title: 7dpci [H261_J7]


title: 7dpci [H261_C20]


title: 7dpci [H261_L13]


title: 7dpci [H261_G11]


title: 7dpci [H261_M19]


title: 7dpci [H261_P1]


title: 7dpci [H261_O6]


title: 7dpci [H261_E13]


title: 7dpci [H261_M5]


title: 7dpci [H261_M14]


title: 7dpci [H261_P7]


title: 7dpci [H261_K22]


title: 7dpci [H261_D24]


title: 7dpci [H261_P2]


title: 7dpci [H261_J11]


title: 7dpci [H261_N15]


title: 7dpci [H261_M17]


title: 7dpci [H261_C13]


title: 7dpci [H261_O8]


title: 7dpci [H261_I2]


title: 7dpci [H261_F8]


title: 7dpci [H261_I6]


title: 7dpci [H261_F18]


title: 7dpci [H261_A16]


title: 7dpci [H261_G7]


title: 7dpci [H261_A17]


title: 7dpci [H261_K9]


title: 7dpci [H261_O14]


title: 7dpci [H261_D16]


title: 7dpci [H261_A4]


title: 7dpci [H261_C24]


title: 7dpci [H261_D1]


title: 7dpci [H261_B4]


title: 7dpci [H261_A11]


title: 7dpci [H261_D14]


title: 7dpci [H261_A12]


title: 7dpci [H261_K2]


title: 7dpci [H261_I5]


title: 7dpci [H261_M2]


title: 7dpci [H261_L22]


title: 7dpci [H261_B8]


title: 7dpci [H261_G14]


title: 7dpci [H261_N17]


title: 7dpci [H261_G6]


title: 7dpci [H261_D15]


title: 7dpci [H261_C8]


title: 7dpci [H261_A10]


title: 7dpci [H261_D8]


title: 7dpci [H261_E1]


title: 7dpci [H261_L17]


title: 7dpci [H261_D13]


title: 7dpci [H261_B13]


title: 7dpci [H261_I13]


title: 7dpci [H261_L7]


title: 7dpci [H261_H6]


title: 7dpci [H261_A2]


title: 7dpci [H261_F20]


title: 7dpci [H261_D11]


title: 7dpci [H261_E20]


title: 7dpci [H261_A15]


title: 7dpci [H261_D17]


title: 7dpci [H261_D23]


title: 7dpci [H261_A19]


title: 7dpci [H261_H8]


title: 7dpci [H261_N14]


title: 7dpci [H261_E8]


title: 7dpci [H261_H18]


title: 7dpci [H261_J4]


title: 7dpci [H261_J20]


title: 7dpci [H261_L10]


title: 7dpci [H261_E12]


title: 7dpci [H261_J5]


title: 7dpci [H261_O17]


title: 7dpci [H261_C5]


title: 7dpci [H261_K8]


title: 7dpci [H261_E4]


title: 7dpci [H261_B7]


title: 7dpci [H261_O3]


title: 7dpci [H261_E19]


title: 7dpci [H261_F22]


title: 7dpci [H261_N7]


title: 7dpci [H261_I15]


title: 7dpci [H261_G18]


title: 7dpci [H261_B3]


title: 7dpci [H261_N20]


title: 7dpci [H261_H17]


title: 7dpci [H261_C7]


title: 7dpci [H261_D7]


title: 7dpci [H261_F5]


title: 7dpci [H261_C14]


title: 7dpci [H261_G24]


title: 7dpci [H261_C19]


title: 7dpci [H261_J18]


title: 7dpci [H261_L3]


title: 7dpci [H261_P11]


title: 7dpci [H261_J22]


title: 7dpci [H261_D12]


title: 7dpci [H261_A18]


title: 7dpci [H261_G10]


title: 7dpci [H261_L4]


title: 7dpci [H261_P6]


title: 7dpci [H261_O21]


title: 7dpci [H261_M21]


title: 7dpci [H261_F2]


title: 7dpci [H261_K13]


title: 7dpci [H261_D18]


title: 7dpci [H261_N1]


title: 7dpci [H261_D21]


title: 7dpci [H261_P19]


title: 7dpci [H261_K15]


title: 7dpci [H261_E10]


title: 7dpci [H261_M10]


title: 7dpci [H261_I9]


title: 7dpci [H261_N6]


title: 7dpci [H261_E14]


title: 7dpci [H261_G12]


title: 7dpci [H261_E9]


title: 7dpci [H261_B12]


title: 7dpci [H261_F13]


title: 7dpci [H261_J9]


title: 7dpci [H261_F4]


title: 7dpci [H261_M22]


title: 7dpci [H261_C10]


title: 7dpci [H261_N24]


title: 7dpci [H261_A6]


title: 7dpci [H261_A7]


title: 7dpci [H261_B1]


title: 7dpci [H261_N9]


title: 7dpci [H261_F3]


title: 7dpci [H261_L1]


title: 7dpci [H261_K16]


title: 7dpci [H261_A20]


title: 7dpci [H261_B10]


title: 7dpci [H261_H23]


title: 7dpci [H261_F21]


title: 7dpci [H261_G21]


title: 7dpci [H261_B23]


title: 7dpci [H261_M20]


title: 7dpci [H261_B17]


title: 7dpci [H261_D9]


title: 7dpci [H261_P4]


title: 7dpci [H261_N3]


title: 7dpci [H261_N5]


title: 7dpci [H261_K23]


title: 7dpci [H261_P13]


title: 7dpci [H261_O18]


title: 7dpci [H261_E3]


title: 7dpci [H261_M13]


title: 7dpci [H261_M15]


title: 7dpci [H261_F1]


title: 7dpci [H261_I1]


title: 7dpci [H261_E16]


title: 7dpci [H261_E17]


title: 7dpci [H261_M23]


title: 7dpci [H261_O7]


title: 7dpci [H261_L14]


title: 7dpci [H261_H7]


title: 7dpci [H261_K11]


title: 7dpci [H261_L2]


title: 7dpci [H261_O15]


title: 7dpci [H261_O2]


title: 7dpci [H261_C9]


title: 7dpci [H261_M9]


title: 7dpci [H261_K14]


title: 7dpci [H261_I11]


title: 7dpci [H261_C12]


title: 7dpci [H261_A24]


title: 7dpci [H261_B18]


title: 7dpci [H261_P3]


title: 7dpci [H261_N19]


title: 7dpci [H261_M11]


title: 7dpci [H261_C3]


title: 7dpci [H261_E18]


title: 7dpci [H261_F16]


title: 7dpci [H261_K21]


title: 7dpci [H261_H3]


title: 7dpci [H261_J15]


title: 7dpci [H261_H21]


title: 7dpci [H261_L12]


title: 7dpci [H261_G1]


title: 7dpci [H261_H13]


title: 7dpci [H261_F19]


title: 7dpci [H261_K7]


title: 7dpci [H261_L11]


title: 7dpci [H261_D6]


title: 7dpci [H261_M16]


title: 7dpci [H261_A1]


title: 7dpci [H261_I16]


title: 7dpci [H261_O12]


title: 7dpci [H261_K12]


title: 7dpci [H261_B22]


title: 7dpci [H261_J21]


title: 7dpci [H261_H1]


title: 7dpci [H261_O13]


title: 7dpci [H261_A3]


title: 7dpci [H261_O19]


title: 7dpci [H261_H16]


title: 7dpci [H261_H2]


title: 7dpci [H261_A5]


title: 7dpci [H261_H14]


title: 7dpci [H261_M12]


title: 7dpci [H261_A14]


title: 7dpci [H261_M8]


title: 7dpci [H261_I14]


title: 7dpci [H261_N2]


title: 7dpci [H261_C16]


title: 7dpci [H261_N12]


title: 7dpci [H261_B9]


title: 7dpci [H261_N18]


title: 7dpci [H261_I10]


title: 7dpci [H261_J24]


title: 7dpci [H261_J17]


title: 7dpci [H261_K17]


title: 7dpci [H261_F9]


title: 7dpci [H261_I22]


title: 7dpci [H261_P17]


title: 7dpci [H261_G16]


title: 7dpci [H261_F12]


title: 7dpci [H261_P22]


title: 7dpci [H261_N13]


title: 7dpci [H261_E23]


title: 7dpci [H261_C21]


title: 7dpci [H261_J14]


title: 7dpci [H261_L9]


title: 7dpci [H261_I20]


title: 7dpci [H261_D5]


title: 7dpci [H261_G2]


title: 7dpci [H261_P15]


title: 7dpci [H261_O10]


title: 7dpci [H261_P21]


title: 7dpci [H261_B19]


title: 7dpci [H261_K4]


title: 7dpci [H261_H22]


title: 7dpci [H261_O23]


title: 7dpci [H261_C23]


title: 7dpci [H261_E7]


title: 7dpci [H261_N8]


title: 7dpci [H261_I3]


title: 7dpci [H261_F24]


title: 7dpci [H261_B24]


title: 7dpci [H261_K24]


title: 7dpci [H261_E24]


title: 7dpci [H261_H15]


title: 7dpci [H261_G23]


title: 7dpci [H261_O9]


title: 7dpci [H261_C18]


title: 7dpci [H261_E6]


title: 7dpci [H261_G5]


title: 7dpci [H261_J6]


title: 7dpci [H261_D19]


title: 7dpci [H261_E5]


title: 7dpci [H261_C6]


title: 7dpci [H261_P18]


title: 7dpci [H261_A13]


title: 7dpci [H261_H4]


title: 7dpci [H261_O11]


title: 7dpci [H261_F14]


title: 7dpci [H261_J12]


title: 7dpci [H261_N4]


title: 7dpci [H261_P8]


title: 7dpci [H261_A8]


title: 7dpci [H261_B6]


title: 7dpci [H261_L19]


title: 7dpci [H261_C11]


title: 7dpci [H261_A22]


title: 7dpci [H261_C22]


title: 7dpci [H261_L5]


title: 7dpci [H261_K20]


title: 7dpci [H261_M1]


title: 7dpci [H261_O4]


title: 7dpci [H261_L6]


title: 7dpci [H261_N21]


title: 7dpci [H261_H10]


title: 7dpci [H261_K10]


title: 7dpci [H261_G20]


title: 7dpci [H261_F11]


title: 7dpci [H261_C17]


title: 7dpci [H261_D3]


title: 7dpci [H261_N22]


title: 7dpci [H261_H19]


title: 7dpci [H261_O24]


title: 7dpci [H261_H5]


title: 7dpci [H261_J10]


title: 7dpci [H261_F10]


title: 7dpci [H261_B15]


title: 7dpci [H261_I24]


title: 7dpci [H261_K18]


title: 7dpci [H261_O22]


title: 7dpci [H261_M3]


title: 7dpci [H261_E22]


title: 7dpci [H261_M4]


title: 7dpci [H261_L21]


title: 7dpci [H261_B14]


title: 7dpci [H261_A21]


title: 7dpci [H261_I23]


title: 7dpci [H261_K3]


title: 7dpci [H261_G17]


title: 7dpci [H261_G4]


title: 7dpci [H261_E11]


title: 7dpci [H261_B11]


title: Single_cut_product_sequencing_set1

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

description:
23296_shRNA_variant_sequences.txt
Single_cut_raw_count_set1.txt

library_source: genomic

data_processing:
First, we removed adapters from both ends in raw reads using cutadapt (34) (-a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC -m 10).  Then we joined the pair-end reads together using fastq-join. We used fastq_quality_filter (-q 20 -p 90) to collect the high quality reads. We removed the duplicated reads with the same 4 nt or 6 nt randomized barcodes in the both ends by using fastx_collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13). The randomized barcodes was removed by using cutadapt (cutadapt -u 4 -u -6 -m 32: 4 nt in 5p end and 6 nt in 3p end for original substrate sample; cutadapt -u 4 -u -4 -m 32: 4 nt in both ends for product sample).  The linkage of the 32-nt randomized barcodes and the original substrate or the cleaved product reads in each sample were extracted by using cutadapt (cutadapt -g GCTTGC...GCAAGC  -m 32 -M 32  --discard-untrimmed). Then, we used BWA to map the original substrate with the reference sequences containing 23,296 variants. The perfect alignments were collected. We generated the dictionary of variants with 32-nt randomized barcodes. In this dictionary, we only collected the unique barcode-variant pair so that a barcode belongs to only one variant. We used this dictionary to align the cleaved products to the reference sequences. For each repeat, we collected the variants containing at least 30 reads in the original substrate samples and 15 reads in the cleaved product samples for further analysis. We normalized the raw read counts as the counts per million in every sample.
Genome_build: n/a
Supplementary_files_format_and_content: 23296_shRNA_variant_sequences.txt: Tab-delimited text file contains the reference sequences of 23296 shRNA variants and the randomized nt in 9 DCS subgroups.
Supplementary_files_format_and_content: Dictionary_variant_and_unique_barcode_set1.txt: Tab-delimited text file contains the variant-unique barcode pairs and the number of each pair in the original substrate sample set 1.
Supplementary_files_format_and_content: Dictionary_variant_and_unique_barcode_set2.txt: Tab-delimited text file contains the variant-unique barcode pairs and the number of each pair in the original substrate sample set 2.
Supplementary_files_format_and_content: Dictionary_variant_and_unique_barcode_set3.txt: Tab-delimited text file contains the variant-unique barcode pairs and the number of each pair in the original substrate sample set 3.
Supplementary_files_format_and_content: Original_substrate_raw_count_all_sets.txt: Tab-delimited text file contains the raw count of variants in 3 sets of the original substrate sample.
Supplementary_files_format_and_content: Double_cut_raw_count_set1.txt: Tab-delimited text file contains the raw count of double cut products for each variant in double cut sample set 1. The reference sequences of variants do not contain 32 nt barcodes.
Supplementary_files_format_and_content: Double_cut_raw_count_set3.txt: Tab-delimited text file contains the raw count of double cut products for each variant in double cut sample set 3. The reference sequences of variants do not contain 32 nt barcodes.
Supplementary_files_format_and_content: Single_cut_raw_count_set1.txt: Tab-delimited text file contains the raw count of single cut products for each variant in single cut sample set 1. The reference sequences of variants do not contain 32 nt barcodes.
Supplementary_files_format_and_content: Single_cut_raw_count_set3.txt: Tab-delimited text file contains the raw count of single cut products for each variant in single cut sample set 3. The reference sequences of variants do not contain 32 nt barcodes.

molecule: genomic DNA

organism: synthetic construct

source_name: synthetic

extract_protocol:
Illumina adapter sequences were incorporated to the libraries using PCR.
Nine single-stranded DNA (ssDNA) oligos were obtained from Integrated DNA Technologies (IDT). Each ssDNA contained a region containing 32 nt, which served as a random barcode for data analysis. We also introduced the randomized nt in the loop and upper stem region of pre-miRNAs in these ssDNA. Each synthesized ssDNA was annealed to R-set6(PsiI) through a 23 bp complementary region. The single-stranded region of the partial duplex DNA resulting from the previous annealing step was filled with complementary ssDNA using Klenow (Thermo Scientific) at 37°C for 120 min, resulting in the perfect duplex DNA. Next, we amplified the Klenow-synthesized double-stranded DNAs (dsDNAs) using F-T7-noGGG and R-set6 (PsiI) primers in the PCR reactions to obtain  dsDNAs containing T7 promoter. Subsequently, we treated 500 ng of T7-containing dsDNAs with PsiI restriction enzyme (Thermo Scientific) at 37°C for 120 min to remove the unnecessary region from the dsDNAs. Finally, 200 ng of the PsiI-digested dsDNAs were used in a 20 µl in vitro transcription (IVT) reaction using the MEGAscript T7 transcription kit (Ambion). Synthesized RNA substrates (DCS) were gel-purified and quantified with NanoDrop 2000 spectrophotometer (Thermo Scientific). Subsequently, we collected a total of 9 groups of DCS, naming DCS_1 to DCS_9, with different randomized sequences. Obtained purified RNAs were stored at -80°C for long time uses.  To perform high-throughput DICER processing assays, five pmol of each of the nine DCS RNA substrates (from DCS_1 to DCS_9) were incubated with four pmol of purified DICER proteins in 10 μl of cleavage assay reaction buffer. The control reaction was added with a T500-plus buffer DICER. After 120 min incubation at 37°C, all the reactions were stopped by adding 11 μl of 2X-TBE buffer plus 20 μg of proteinase K. These resulting mixtures were incubated at 37°C for 15 min, 50°C for 15 min, heated at 95°C for 5 min, and immediately chilled on ice. The chilled reaction samples were finally analyzed on 12% urea-PAGE which were later stained with SYBR™ Green II RNA gel stain (Invitrogen) in 10 min. The original substrates and cleaved products, which were visualized in gel with the stain, were cut separately and gel-purified. We collected the original substrate (C) and cleaved products (DC) from gel . The purified RNAs were ligated to the 4N-RA3 adapter (/5rApp/NN NNT GGA ATT CTC GGG TGC CAA GG/3ddC/) using T4 RNA Ligase 2, truncated KQ enzyme (NEB, M0373L). The 4N-RA3-ligated C and SC were first precipitated using isopropanol. The precipitated RNAs were added in reverse transcription (RT) mixture using cirRTP primer (/5Phos/NNN NNN GAT CGT CGG ACT GTA GAA CTC TGA AC/iSp18/CCT TGG CAC CCG AGA ATT CCA) and Superscript IV Reverse Transcriptase (Invitrogen). After 60 min incubation at 50°C, the RT reaction mixture was supplemented with 0.1 M NaOH, and heated at 98°C for 10 min to degrade the RNAs. The NaOH-treated RT mixture was loaded onto 12% urea-PAGE gel to separate cDNAs from cirRTP primer. The cDNAs were cut from gel and gel-purified. The purified cDNAs were next circulalized using CircLigase ssDNA ligase (Epicentre). The circulalized cDNAs were separated from linear cDNAs in 18% urea-PAGE gel and gel-purified. The purified circularized DNAs of C or SC were finally amplified by PCR using RP1 (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG TTC AGA GTT CTA CAG TCC GA) and RPI1 (CAA GCA GAA GAC GGC ATA CGA GAT CGT GAT GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA) or RPI2 (CAA GCA GAA GAC GGC ATA CGA GAT ACA TCG GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA), respectively.   The 4N-RA3-ligated DC RNAs were separated from unligated DC RNAs and free 4N-RA3 in 12% Urea-PAGE and gel-purified. The purified 4N-RA3-ligated DC RNAs were ligated with the 4N-RA5 primer (GUU CAG AGU UCU ACA GUC CGA CGA UCN NNN) using T4 RNA ligase 1 enzyme. The double ligated DC RNAs were reverse transcribed using Superscript IV Reverse Transcriptase and RTP primer (CAA GCA GAA GAC GGC ATA CGA). Finally, the cDNA were amplified by PCR using RP1 and RPI10 (CAA GCA GAA GAC GGC ATA CGA GAT AAG CTA GTG ACT GGA GTT CCT TGG CAC CCG AGA ATT CCA).   As a result, we obtained three DNA libraries that were sequenced by Illumina Novaseq 6000 in 150 bp paired-end mode.

tag: barcode

value: CGATGT

tag: set

tag: type sample

value: Single cut product


title: 7dpci [H261_P5]


title: 7dpci [H261_F6]


title: Original_substrate_sequencing_set3

description:
23296_shRNA_variant_sequences.txt
Original_substrate_raw_count_all_sets.txt

value: CAGATC

value: Original substrate


title: Double_cut_product_sequencing_set1

description:
23296_shRNA_variant_sequences.txt
Double_cut_raw_count_set1.txt

value: TAGCTT

value: Double cut product


title: Original_substrate_sequencing_set1

value: ATCACG


title: 7dpci [H261_C4]


title: Double_cut_product_sequencing_set3

description:
23296_shRNA_variant_sequences.txt
Double_cut_raw_count_set3.txt

value: GATCAG


title: 7dpci [H261_L16]


title: 7dpci [H261_G22]


title: 7dpci [H261_A23]


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 15

city: Rochester

first: Mrinal

middle: M.

last: Patnaik

state: MN

address: 200 First Street SW

department: Division of Hematology

country: USA

institute: Mayo Clinic

description:
Human bone marrow mononuclear cells ChIP-seq Input
ASXL1_MT_5hmC_Consensus_Peaks.bw

data_processing:
FastQC (v0.11.8) pre-alignment quality and adapter trimming, Bowtie2 (v2.3.3.1) / BWA (v0.7.17) alignment, post-alignment quality control, MACS2 (v3.0.0a6), MSPC(v5.4.0), ChromHMM (v1.20)
Genome_build: GRCh38 / hg38
Supplementary_files_format_and_content: Consensus peaks in BW file generated by subjecting the peaks called by MACS2 to a second selection step by MSPC; Chromatin states (7-state model) in BW file generated by ChromHMM

organism: Homo sapiens

source_name: Bone marrow mononuclear cells

extract_protocol:
Viable bone marrow mononuclear cells were were cross-linked with 1% formaldehyde for 10 min, followed by quenching with 125 mM glycine for 5 min at room temperature. Fixed cells were washed twice with TBS, resuspended in cell lysis buffer (10 mM Tris- HCl, pH 7.5, 10 mM NaCl, 0.5% NP-40), and incubated on ice for 10 min. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) and incubated for 20 min at 37 °C in the presence of MNase (2000 gel units/4× 106 cells, New England Biolabs, Ipswich, MA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH 8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysate was sonicated for 15 cycles (30 s on, 30 s off) using a Diagenode Bioruptor and centrifuged at 15,000 rpm for 10 min. The cleared supernatant equivalent to 4 × 106 cells was incubated with 2 g of antibody at 4 °C on a rocker overnight. Full protocol in Zhong et  al. Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application. BMC Genomics 2017;18(1):985. (PMID: 29268714; PMCID: PMC5740926).
N-CHIP, MeDIP, ATAC
ChIP-seq, DIP-seq, ATAC-seq

value: Bone marrow

tag: cell type

value: Bone marrow mononuclear cells

tag: cell selection

value: Ficoll-gradient selected mononuclear cells

tag: genotype

tag: chip antibody


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 16

description:
Human bone marrow mononuclear cells DIP-seq Input
ASXL1_MT_5hmC_Consensus_Peaks.bw

tag: dip antibody


title: 7dpci [H261_L18]

value: wild type

value: whole ventricle


title: 7dpci [H261_B2]

value: untreated

value: Standard


title: Single_cut_product_sequencing_set3

description:
23296_shRNA_variant_sequences.txt
Single_cut_raw_count_set3.txt

value: ACTTGA


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 16


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 15


title: Original_substrate_sequencing_set2


title: 7dpci [H261_P12]

value: Live


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 16


title: aspergillus_rgsE_3

city: Fuzhou

first: rui

last: xie

address: shangxiadian street

country: China

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling
Raw sequencing data was first filtered by Trimmomatic (version 0.36), then mapped to the reference genome of aspergillus flavus using STRA software (version 2.5.3a).
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Genome_build: https://fungidb.org/fungidb/app/downloads/Current_Release/AflavusNRRL3357/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...（
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Aspergillus flavus

source_name: Aspergillus flavus NRRL3357

growth_protocol: keep these strains at 29◦C for 48h and simultaneously need to be shook at 180rmp.

extract_protocol:
The harvested-mycelia (WT, ΔrgsA and ΔrgsE) were frozen in liquid nitrogen, and were lyophilized for 1day. The RNA of WT, ΔrgsA and ΔrgsE strains was extracted by TRIzol reagent  according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Add to the glucose minimal medium(spores of WT, ΔrgsA and ΔrgsE).

value: incubate for 10 days on GMM medium

value: [delta]rgsE

value: aspergillus flavus NRRL3357


title: 7dpci [H261_N11]


title: 7dpci [H261_I4]


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 14


title: 7dpci [H261_D22]


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 14


title: aspergillus_rgsE_1

value: incubate for 8 days on GMM medium


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 13


title: aspergillus_rgsA_3

value: incubate for 7 days on GMM medium

value: [delta]rgsA


title: aspergillus_rgsA_1

value: incubate for 5 days on GMM medium


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 12


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 14


title: aspergillus_WT_2

value: incubate for 3 days on GMM medium


title: aspergillus_WT_3

value: incubate for 4 days on GMM medium


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 12

value: Bone marrow

value: Bone marrow mononuclear cells


title: hCRC0087

city: Philadelphia

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

description: single cell RNA sequencing

data_processing:
Cellranger (10X Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix, barcode, and gene file

source_name: Colon and Colorectal Tumor (Hashed)

extract_protocol:
Paired human colon and tumor biopsies were obtained and made into single cell suspensions. Cells were encapsulated into droplets and libraries prepared using the 10X Genomics platform and libraries sequenced on an Illumina NextSeq
10X Genomics

value: Colon and Colorectal Tumor (Hashed)


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 12

value: Ficoll-gradient selected mononuclear cells


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 11


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 10


title: aspergillus_WT_1

value: incubate for 2 days on GMM medium

value: wild type


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 11


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 10


title: hCRC0086

description: single cell RNA sequencing


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 11


title: hCRC0084

description: single cell RNA sequencing


title: hCRC0083

description: single cell RNA sequencing


title: hCRC0081

description: single cell RNA sequencing


title: aspergillus_rgsE_2

value: incubate for 9 days on GMM medium


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 10


title: hCRC0080

description: single cell RNA sequencing


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 09


title: hCRC0049

description: single cell RNA sequencing


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 09


title: ColorectalTumor0040

description: single cell RNA sequencing

source_name: Colorectal Tumor

value: Colorectal Tumor


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 13


title: aspergillus_rgsA_2

value: incubate for 6 days on GMM medium


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 09


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 13


title: Colon0040

description: single cell RNA sequencing

source_name: Colon

value: Colon


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 08

description:
Human bone marrow mononuclear cells ChIP-seq Input
ASXL1_WT_5hmC_Consensus_Peaks.bw


title: ColorectalTumor0008

description: single cell RNA sequencing


title: Colon0008

description: single cell RNA sequencing


title: 7dpci [H261_G9]

value: whole ventricle

value: untreated

value: Standard

value: Live


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 08


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 08

description:
Human bone marrow mononuclear cells DIP-seq Input
ASXL1_WT_5hmC_Consensus_Peaks.bw


title: mismatch_repeat2

data_processing:
We removed the adapters from the raw reads using cutadapt (-a AGATCGGAAGAGCACACGTCT  -A GATCGTCGGACTGTAGAACTCTGAAC) and joined the pair-end reads using fastq-join. The low-quality reads were discarded using fastq_quality_filter (-q 20 -p 90). The remaining reads were then mapped to the transfected pri-miRNA reference sequences using Bowtie2.
Genome_build: GRCh38
Supplementary_files_format_and_content: primiRNA_transfection_reference_set2.txt: Tab-delimited text file contains the reference sequences of transfected pri-miRNA sequences
Supplementary_files_format_and_content: nobulge_rawcount.txt: Tab-delimited text file contains the raw read counts of the sample transfected pCDNA3 nobulge pri-miRNA plamsids.
Supplementary_files_format_and_content: bulge3p_rawcount.txt: Tab-delimited text file contains the raw read counts of the sample transfected pCDNA3 bulge-3p-containing pri-miRNA plamsids.
Supplementary_files_format_and_content: bulge5p_rawcount.txt: Tab-delimited text file contains the raw read counts of the sample transfected pCDNA3 bulge-5p-containing pri-miRNA plamsids.
Supplementary_files_format_and_content: mismatch_rawcount.txt: Tab-delimited text file contains the raw read counts of the sample transfected pCDNA3 mismatch-containing pri-miRNA plamsids.

source_name: HCT116 cells

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
HCT116 cells were transfected with pCDNA3 empty, pCDNA3 wild-type or SNP-containing pri-miRNA plasmids in 6-well plate using lipofectamine 3000 (Thermo Fisher Scientific). After 48 h, transfected cells were collected, and followed by total RNAs extraction using TRIzol reagent (Invitrogen). 5 μg of each total RNA was size separated in a 15% urea-PAGE, and the gel slices according to area within the 19–24 nt region were excised. Small RNA libraries from the gel-eluted small RNAs were cloned using NEBNext® Small RNA Library Prep Set for Illumina® (NEB). The resulting cDNAs were amplified using PCR with distinct index primers to produce DNA libraries.  The DNA libraries of the small RNAs were run using Illumina Nextseq 500.

tag: cell line

value: HCT116 cells

tag: disease state

value: colon carcinoma

tag: transfection

tag: repeat

value: repeat 2


title: bulge5p_repeat2

value: pCDNA3 bulge-5p-containing pri-miRNA plamsids


title: bulge3p_repeat1

value: pCDNA3 bulge-3p-containing pri-miRNA plamsids

value: repeat 1


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 07

value: Bone marrow

value: Bone marrow mononuclear cells

value: Ficoll-gradient selected mononuclear cells


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 07


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 06


title: bulge5p_repeat1


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 07


title: nobulge_repeat1

value: pCDNA3 nobulge pri-miRNA plamsids


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 06


title: nobulge_repeat2


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 06


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 05


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 05


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 04


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 04


title: KIPyV VLP-treated macrophages [kipvy_ix5]

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
The solo-in-drops pipeline (https://github.com/jsimonas/solo-in-drops), which is a wrapper around STARsolo (https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md), was used for obtain cells x genes expression matrices. STARsolo expects as input two fastq files per library, one containing the barcode information and the other the transcript information. Meanwhile, the custom scRNAseq protocol used in the current study outputs 3 fastq files per library: barcode half 1, barcode half 2, and transcript. Solo-in-drops prepares the data for compatibility with STARsolo. STAR (version 2.7.6a) was run with the following parameters: --soloType CB_UMI_Simple, -- soloUMIfiltering MultiGeneUMI, -- soloCBmatchWLtype 1MM_multi_pseudocounts. Homo sapiens (human) genome assembly GRCh38 (hg38) was used as the reference.
The Scanpy toolbox was used for data analysis. Transcriptomes with fewer than 900 total counts were excluded. No filtering on the fraction of mitochondrial counts was performed.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data files in each library consist of:
a mtx file with raw unfiltered gene counts (cells x genes)
a tsv file with gene names
a tsv file with barcode names
Series supplementary files:
Jupyter notebook showing how to load the filtered count data in Python: Load_data_from_GEO.ipynb
filtered counts concatenated across all samples: h5ad format mito_total_counts_filt_raw_32415x36601_210622_20h17.h5ad
Cell annotations of filtered concatenated counts: obs_info_32415x18_211010_11h51.npz"

molecule: polyA RNA

source_name: KIPyV VLP-treated macrophages

growth_protocol: Human macrophage cell cultures were prepared by differentiation of THP-1 cells (Chanput et al, 2014). The cells were seeded in the 24 well plate at a density of 0.125x106/well using RPMI 1640 medium supplemented with 10% FBS and 1% P/S and differentiated to macrophages using 100 ng/mL of PMA. After 48 h of differentiation the medium was replaced with the fresh medium without PMA and cells were left to rest for another 24 h. After the rest period the cells are differentiated into macrophages and were used in experiments with viral proteins. These macrophage-like cells were used in the study and called THP-1 macrophages.

extract_protocol:
After the treatment cells were washed with PBS and detached with TrypLE reagent after 15 min incubation at cell culture incubator (37 °C, 5% CO2). After centrifugation cells were washed twice with 1x RNase-free PBS (cat#AM9624, Invitrogen). After final centrifugation cells were resuspended in RNase-free PBS and kept on ice till cell preparation for RNA sequencing analysis.
Single-cell RNA sequencing (scRNAseq) was performed using a modified version of the inDrops method (Zilionis et al. 2017, Klein et al. 2015). While the original version is based on the CEL-Seq protocol (Hashimshony et al., 2012) that involves linear cDNA amplification by in vitro transcription, the modified version relies on template switching and cDNA amplification by PCR, as in the Smart-seq protocol (Ramsköld,2012). First, single cell transcriptomes were barcoded in 1-nl droplets by co-encapsulating: i) barcoding hydrogel beads; ii) the reverse-transcription/lysis (RT/lysis) mix; and iii) the cell suspension. Cell encapsulation was performed using the microfluidic device described in Zilionis et al. 2017 on an Onyx platform (Droplet Genomics). Maxima H- minus (ThermoFisher, cat. no. EP0751) was used for reverse-transcription with template switching. RT was performed for 1h at 42 ºC followed by heat inactivation for 5 min at 85 ºC. The emulsion was then broken and the pooled material was taken through library preparation for Illumina sequencing, which involves the following steps: i) cDNA amplification (Terra PCR direct Polymerase, Takara, cat. no. 639270), ii) fragmentation and adapter ligation (NEBNext® UltraTM II FS DNA Library Prep Kit for Illumina, NEB, cat. no. E7805S), and iii) indexing PCR (KAPA HiFi HotStart ReadyMix PCR Kit, Roche, cat. no. KK2601). Sequencing was performed on a single Illumina NextSeq run (NextSeq 500/550 High Output Kit v2.5 (75 Cycles), Illumina, cat. no. 20024906).

treatment_protocol: THP-1 macrophages were washed once with serum-free RPMI and treated with viral proteins (20 ug/ml) for 24 h. Viral proteins were prepared in PBS. PBS was used as control.

value: KI polyomavirus recombinant major capsid protein VP1 (KIPyV VLP)


title: KIPyV VLP-treated macrophages [kipyv_ix6]


title: MCPyV  VLP-treated macrophages [mcpyv_ix7]

source_name: MCPyV  VLP-treated macrophages

value: MC polyomavirus recombinant major capsid protein VP1 (MCPyV VLP)


title: MCPyV  VLP-treated macrophages [mcpyv_ix9]


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 04


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 03


title: MCPyV  VLP-treated macrophages [mcpyv_ix8]


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 03


title: mismatch_repeat1

value: pCDNA3 mismatch-containing pri-miRNA plamsids


title: DND41ResCas9_bioRep2_EBF1g7_RNAseq_rep3

first: YEQIAO

last: ZHOU

address: 421 Curie Boulevard

department: Pathology

data_processing:
RNA-seq data was aligned to Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using STAR (version 2.5) with parameters --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 100000 --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 25  --chimJunctionOverhangMin 25.
Strand-specific read counts were quantified using Subread (version 1.5.1) featureCounts with parameters -t exon -g gene_id -s 1 -T 6 and used as input to differential gene expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with read count; bigWig files for genome browser viewing

source_name: DND41 cell line

growth_protocol: DND41 (male) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

extract_protocol:
5x10^5 cells were washed with 1 x PBS and lysed with 350 μl RLT Plus buffer (Qiagen) supplemented with 2-mercaptoethanol, vortexed briefly and immediately proceeded to RNA isolation with RNeasy Plus Micro Kit (Qiagen #74034).
RNA integrity numbers were determined using TapeStation 4150 (Agilent), and all samples used for RNA-seq library preparation had RIN numbers greater than 9.5. 500-800 ng of total RNA was used, and libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian (Clontech cat# 634873). Libraries were paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.

treatment_protocol: To generate GSI-resistant DND41, parental DND41 was treated with 125nM gamma-secretase inhibitor (GSI) compound E (Calbiochem cat# 565790) for 7-12 weeks with regular refreshment of media and maintained in 125nM GSI. To generate GSI-resistant-reversed cells, GSI-resistant DND41 were cultured in media without GSI for 6-8 weeks.

value: DND41 cell line

value: T-ALL cell line

tag: lentiviral transduction

value: Cas9 and EBF1-targeting sgRNA

tag: drug treatment

value: GSI


title: Control macrophages [control_ix3]

source_name: Control macrophages

tag: treatment

value: PBS control


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 02

tag: tissue


title: DND41ResCas9_bioRep2_EBF1g7_RNAseq_rep2


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 02


title: Human bone marrow mononuclear cells, H3K4me1 H3K4me3 H3K27me3 Input Sample 01


title: DND41ResCas9_bioRep2_EBF1g7_RNAseq_rep1


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 02


title: Human bone marrow mononuclear cells, H3K27ac H2AK119ub Input Sample 01


title: DND41ResCas9_bioRep2_ctrl_RNAseq_rep3

value: Cas9 and control sgRNA


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 01


title: Human bone marrow mononuclear cells, H3K27me3 Sample 16

description:
Human bone marrow mononuclear cells H3K27me3 ChIP-seq
ASXL1_MT_H3K27me3_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw

value: H3K27me3-pAb-069-050 (Diagenode, Denville, United States)


title: Human bone marrow mononuclear cells, H3K27me3 Sample 15


title: DND41_GSIweek4_RNAseq_rep3


title: DND41ResCas9_bioRep2_ctrl_RNAseq_rep2


title: DND41ResCas9_bioRep2_ctrl_RNAseq_rep1


title: DND41_GSIweek4_RNAseq_rep2


title: Human bone marrow mononuclear cells, H3K27me3 Sample 14


title: Human bone marrow mononuclear cells, H3K27me3 Sample 13


title: Human bone marrow mononuclear cells, H3K27me3 Sample 12


title: DND41ResCas9_bioRep2_EBF1g7_day9_ATAC_rep3

data_processing:
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) and three replicates were performed for each condition. Briefly, 50,000 cells were pelleted at 800 x g and washed with 50 μl of ice cold 1 x PBS (Corning cat# 21031CV), followed by 2min treatment with 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% Igepal cat# CA-630). Pelleted nuclei were resuspended in 50 μl of transposition buffer (25 μl of 2 x TD buffer, 22.5ul of molecular biology grade water and 2.5 μl Tn5 transposase (Illumina cat# FC-121-1030) to tag the accessible chromatin for 45min at 37°C.
Tagmented DNA was purified with MinElute Reaction Cleanup kit (Qiagen cat# 28204) and amplified with 5 PCR cycles. Additional number of PCR cycles was determined from the side reaction and ranged from 10-12 total cycles of PCR. Libraries were purified using QiaQuick PCR purification kit (Qiagen cat# 28106) and eluted in 20 μl EB buffer. Indexed libraries were assessed for nucleosome patterning on TapeStation 4150 (Agilent) and paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.


title: DND41ResCas9_bioRep2_EBF1g7_day9_ATAC_rep4


title: Human bone marrow mononuclear cells, 5mC 5hmC Input Sample 03


title: Human bone marrow mononuclear cells, H3K27me3 Sample 11


title: Control macrophages [control_ix2]


title: DND41_GSIweek4_RNAseq_rep1


title: DND41ResCas9_bioRep2_EBF1g7_day9_ATAC_rep1


title: Human bone marrow mononuclear cells, H3K27me3 Sample 07

description:
Human bone marrow mononuclear cells H3K27me3 ChIP-seq
ASXL1_WT_H3K27me3_Consensus_Peaks.bw
ASXL1_WT_ChromHMM_States.bw


title: DND41ResCas9_bioRep2_EBF1g7_day6_ATAC_rep4


title: Human bone marrow mononuclear cells, H3K27me3 Sample 04


title: DND41ResCas9_bioRep2_EBF1g7_day6_ATAC_rep3


title: DND41ResCas9_bioRep2_EBF1g7_day3_ATAC_rep3


title: DND41ResCas9_bioRep2_EBF1g7_day6_ATAC_rep1


title: Human bone marrow mononuclear cells, H3K27me3 Sample 03


title: DND41ResCas9_bioRep2_EBF1g7_day6_ATAC_rep2


title: Human bone marrow mononuclear cells, H3K27me3 Sample 02


title: Human bone marrow mononuclear cells, H3K27ac Sample 14

description:
Human bone marrow mononuclear cells H3K27ac ChIP-seq
ASXL1_MT_H3K27ac_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw

value: H3K27ac-D5E4 (Cell Signaling Technology, Danvers, United States)


title: DND41ResCas9_bioRep2_EBF1g7_day3_ATAC_rep2


title: Human bone marrow mononuclear cells, H3K27ac Sample 15


title: Human bone marrow mononuclear cells, H3K27ac Sample 13


title: DND41ResCas9_bioRep2_EBF1g7_day3_ATAC_rep1


title: DND41ResCas9_bioRep2_ctrl_ATAC_rep4


title: DND41ResCas9_bioRep2_ctrl_ATAC_rep3


title: Human bone marrow mononuclear cells, H3K27ac Sample 11


title: Human bone marrow mononuclear cells, H3K27ac Sample 12


title: Human bone marrow mononuclear cells, H3K27ac Sample 10


title: DND41ResCas9_bioRep2_EBF1g7_day9_ATAC_rep2


title: DND41ResCas9_bioRep2_ctrl_ATAC_rep2


title: DND41_GSIweek4_ATAC_rep3


title: DND41ResCas9_bioRep2_ctrl_ATAC_rep1


title: DND41_GSIweek4_ATAC_rep1


title: Human bone marrow mononuclear cells, H3K27ac Sample 09


title: DND41_GSIweek4_ATAC_rep2


title: Human bone marrow mononuclear cells, H3K27me3 Sample 06


title: Human bone marrow mononuclear cells, H3K27ac Sample 08

description:
Human bone marrow mononuclear cells H3K27ac ChIP-seq
ASXL1_WT_H3K27ac_Consensus_Peaks.bw
ASXL1_WT_ChromHMM_States.bw


title: Human bone marrow mononuclear cells, H3K27ac Sample 07


title: Human bone marrow mononuclear cells, H3K27ac Sample 04


title: Human bone marrow mononuclear cells, H3K27ac Sample 02


title: Human bone marrow mononuclear cells, H3K27ac Sample 03


title: Human bone marrow mononuclear cells, H3K4me3 Sample 15

description:
Human bone marrow mononuclear cells H3K4me3 ChIP-seq
ASXL1_MT_H3K4me3_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw

value: H3K4me3-9751S (Cell Signaling Technology, Danvers, United States)


title: Human bone marrow mononuclear cells, H3K27ac Sample 06


title: Human bone marrow mononuclear cells, H3K4me3 Sample 14


title: Human bone marrow mononuclear cells, H3K4me3 Sample 16


title: LPS-RA FLSs EVs 2

city: Guangzhou

first: Yixiong

last: Chen

address: No. 600 Tianhe Road, Tianhe District

institute: The Third Affiliated Hospital of Sun Yat-sen University

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with bowtie software.
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) ).
Raw reads were normalized by calculated CPM value
Genome_build: miRBase Release 22
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample.

source_name: LPS-RA FLSs EVs

extract_protocol:
Total RNA was extracted from extracellular vesicles pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer(NanoDrop Technologies, Wilmington, DE). Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

tag: sample type

value: Fibroblast-like synoviocytes derived extracellular vesicles

value: LPS-RA


title: LPS-RA FLSs EVs 1


title: trauma FLSs EVs 3

source_name: trauma FLSs EVs

value: trauma


title: Human bone marrow mononuclear cells, H3K4me3 Sample 10

value: Bone marrow

value: Bone marrow mononuclear cells

value: Ficoll-gradient selected mononuclear cells


title: Human bone marrow mononuclear cells, H3K4me3 Sample 06

description:
Human bone marrow mononuclear cells H3K4me3 ChIP-seq
ASXL1_WT_H3K4me3_Consensus_Peaks.bw
ASXL1_WT_ChromHMM_States.bw


title: trauma FLSs EVs 2


title: trauma FLSs EVs 1


title: Human bone marrow mononuclear cells, H3K4me3 Sample 04


title: pcDNA3_primiRNA_SNP_repeat3

description:
processed data file:
pcDNA3_primiRNA_SNP_rawcount.txt

data_processing:
We removed the adapters from the raw reads using cutadapt (-a AGATCGGAAGAGCACACGTCT  -A GATCGTCGGACTGTAGAACTCTGAAC) and joined the pair-end reads using fastq-join. The low-quality reads were discarded using fastq_quality_filter (-q 20 -p 90). The remaining reads were then mapped to the transfected pri-miRNA reference sequences using Bowtie2.
Genome_build: GRCh38
Supplementary_files_format_and_content: primiRNA_transfection_reference.txt: Tab-delimited text file contains the reference sequences of transfected pri-miRNA sequences
Supplementary_files_format_and_content: Control_raw_count.txt: Tab-delimited text file contains the raw read counts of the sample transfected pCDNA3 empty plasmid.
Supplementary_files_format_and_content: pcDNA3_primiRNA_WT_rawcount.txt: Tab-delimited text file contains the raw read counts of the sample transfected pCDNA3 pri-miRNA WT.
Supplementary_files_format_and_content: pcDNA3_primiRNA_SNP_rawcount.txt: Tab-delimited text file contains the raw read counts of the sample transfected  pCDNA3 SNP-containing pri-miRNA.

value: colon carcinoma

value: pCDNA3 SNP-containing pri-miRNAs plamsids

value: repeat 3


title: Human bone marrow mononuclear cells, H3K4me1 Sample 16

description:
Human bone marrow mononuclear cells H3K4me1 ChIP-seq
ASXL1_MT_H3K4me1_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw

value: H3K4me1-C15410037 (Diagenode, Denville, United States)


title: Human bone marrow mononuclear cells, H3K27ac Sample 01


title: Human bone marrow mononuclear cells, H3K4me3 Sample 02


title: pcDNA3_primiRNA_WT_repeat3

description:
processed data file:
pcDNA3_primiRNA_WT_rawcount.txt

value: pCDNA3 wild-type pri-miRNAs plamsids


title: pcDNA3_primiRNA_SNP_repeat1

value: repeat 1


title: Human bone marrow mononuclear cells, H3K4me3 Sample 01


title: pcDNA3_primiRNA_WT_repeat2

value: repeat 2


title: Human bone marrow mononuclear cells, H3K4me1 Sample 15


title: LPS-RA FLSs EVs 3


title: pcDNA3_primiRNA_WT_repeat1


title: pcDNA3_primiRNA_SNP_repeat2


title: Human bone marrow mononuclear cells, H3K4me3 Sample 12


title: Human bone marrow mononuclear cells, H3K4me1 Sample 12


title: control_repeat1

description:
processed data file:
Control_rawcount.txt

value: pCDNA3 empty plasmid


title: control_repeat2


title: control_repeat3


title: Human bone marrow mononuclear cells, H3K4me1 Sample 13


title: Human bone marrow mononuclear cells, H3K4me1 Sample 11


title: shRNA_transfection_set2_repeat3

description:
shRNA_references_set2.txt
set2_raw_count.txt

data_processing:
We removed the adapters from the raw reads using cutadapt (-a AGATCGGAAGAGCACACGTCT  -A GATCGTCGGACTGTAGAACTCTGAAC) and joined the pair-end reads using fastq-join. The low-quality reads were discarded using fastq_quality_filter (-q 20 -p 90). The remaining reads were then mapped to the transfected shRNA reference sequences using Bowtie2. The reference sequences contain shRNA sequences followed by the 10-nt poly-T tails. The unique mapped reads were collected. The cleaved reads of DICER at the cleavage site x (CLx) was defined as the mapped reads starting at L - x and ending at L, in which x is ranging from 20 to 23, and L is the length of shRNAs without the poly-T tails. The cleavage accuracy of Dicer at CL21 was defined as [the cleaved reads at CL21]/[sum of the cleaved reads from CL20 to CL23]. The cleavage accuracy of Dicer at CL21 was averaged for 3 repeats.
Genome_build: GRCh38
Supplementary_files_format_and_content: shRNA_references_set1.txt: Tab-delimited text file contains the reference sequences of transfected shRNA sequences set 1.
Supplementary_files_format_and_content: shRNA_references_set2.txt: Tab-delimited text file contains the reference sequences of transfected shRNA sequences set 2.
Supplementary_files_format_and_content: set1_raw_count.txt: Tab-delimited text file contains the raw read counts of the transfected shRNAs set 1.
Supplementary_files_format_and_content: set2_raw_count.txt: Tab-delimited text file contains the raw read counts of the transfected shRNAs set 2.

source_name: HEK293T cells

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
The shRNA plasmids encoding for either 22-bulge or nobulge variants of shRNAs targeting GFP, SRSF7, SRSF3, HTT, TTR, and P53 were co-transfected into HEK293T cells in 6-well plate using lipofectamine 3000 (Thermo Fisher Scientific). After 48 h, transfected cells were collected, and followed by total RNAs extraction using TRIzol reagent (Invitrogen). 5 μg of each total RNA was size separated in a 15% urea-PAGE, and the gel slices according to area within the 19–24 nt region were excised. Small RNA libraries from the gel-eluted small RNAs were cloned using NEBNext® Small RNA Library Prep Set for Illumina® (NEB). The resulting cDNAs were amplified using PCR with distinct index primers to produce DNA libraries.  The DNA libraries of the small RNAs were run using Illumina Nextseq 500.

value: shRNAs set 2


title: Human bone marrow mononuclear cells, H3K4me1 Sample 08

description:
Human bone marrow mononuclear cells H3K4me1 ChIP-seq
ASXL1_WT_H3K4me1_Consensus_Peaks.bw
ASXL1_WT_ChromHMM_States.bw


title: Human bone marrow mononuclear cells, H3K4me1 Sample 09


title: Human bone marrow mononuclear cells, H3K4me1 Sample 07


title: Human bone marrow mononuclear cells, H3K4me3 Sample 03


title: shRNA_transfection_set2_repeat1


title: shRNA_transfection_set2_repeat2


title: Human bone marrow mononuclear cells, H3K4me1 Sample 06


title: Human bone marrow mononuclear cells, H3K4me1 Sample 05


title: shRNA_transfection_set1_repeat3

description:
shRNA_references_set1.txt
set1_raw_count.txt

value: shRNAs set 1


title: Human bone marrow mononuclear cells, H3K4me1 Sample 04


title: shRNA_transfection_set1_repeat2


title: Human bone marrow mononuclear cells, H3K4me1 Sample 03


title: shRNA_transfection_set1_repeat1


title: Human bone marrow mononuclear cells, H3K4me1 Sample 02


title: Human bone marrow mononuclear cells, H2AK119ub Sample 16

description:
Human bone marrow mononuclear cells H2AK119ub ChIP-seq
ASXL1_MT_H2AK119ub_Consensus_Peaks.bw

value: H2AK119ub-D27C4 (Cell Signaling Technology, Danvers, United States)


title: Human bone marrow mononuclear cells, H2AK119ub Sample 15


title: DND41_resistant_SMC1_HiChIP_rep1

data_processing:
Library strategy: HiChIP
Raw reads for each HiChIP sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE = GATCGATC and GENOME_FRAGMENT generated for MboI restriction enzyme.
The valid pairs (allValidPairs file) from HiC-Pro were used to generate .hic file using Juicer tools (version 1.7.6) ‘pre’ command.
Genome_build: hg19
Supplementary_files_format_and_content: .hic formatted file for juicebox viewing of contact matrices

extract_protocol:
SMC1 HiChIP was performed as previously described (Petrovic et al., 2019). Briefly, 2 x 107 cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific, cat# 28908) for 10 min and subsequently quenched with 0.125M glycine (Invitrogen, cat# 15527-013). Chromatin was digested using MboI restriction enzyme (NEB, cat# R0147), followed by biotin incorporation with Biotin-14-dATP (Invitrogen, cat# 19524-016 or Jena Bioscience cat# NU-835-BIO14-S). DNA was then ligated with T4 ligase (NEB cat# M0202L) and sonicated on Covaris LE220. Sheared chromatin was 4-fold diluted with ChIP dilution buffer (16.7mM Tris pH 7.5, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100), cleared with IgG (CST cat# 2729S) and then incubated with anti-SMC1 antibody (Bethyl, cat# A300-055A) at 4°C overnight. Chromatin-antibody complexes were captured by Protein-A magnetic beads (Pierce, cat# 88846) and subsequently washed with Low Salt Wash Buffer, High Salt Wash Buffer, LiCl Wash Buffer and eluted.
DNA was purified with MinElute PCR Purification Kit (Qiagen, cat# 28004) and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851). 50-150ng was used for capture with Dynabeads MyOne Streptavidin C-1 (Invitrogen, cat# 65001) and an appropriate amount of Tn5 enzyme was added to captured DNA to generate sequencing library. Paired-end sequencing (38 bp+38 bp) was performed on a NextSeq 550.

value: DND41 cell line

value: T-ALL cell line

value: GSI


title: DND41_resistant_SMC1_HiChIP_rep2


title: DND41_resistant_genomic_seq

data_processing: Single nucleotide variants and copy number alteration analyses were performed using CLIA-approved clinical pipeline used for analysis of cancer patients at the Hospital of the University of Pennsylvania. Very briefly, reads from cancer gene panel sequencing were aligned to GRCh38 using BWA (Li and Durbin, 2009) and subjected to GATK (McKenna et al., 2010) base quality score recalibration and duplicate read removal. Samples achieving an average of 500x mean coverage across the 505 targeted cancer associated genes were used in subsequent analyses. Small variant discovery and read filtration were performed according to GATK best practice recommendations (DePristo et al., 2011; Van der Auwera et al., 2013) and copy number segments were called using CNVKit (Talevich et al., 2016). Single nucleotide variations, insertions, deletions and copy number variations were then annotated using Variant Effect Predictor (McLaren et al., 2016). Resulting variations were further filtered with internally validated quality control metrics evaluating coding alterations greater than 50x coverage at a given loci and variant allele frequency higher than 4%, as well as any copy number alterations. Lastly, the variant call set was evaluated for clinical significance based on standards and guidelines by the Association for Molecular Pathology (Li et al., 2017), and manually assessed by a variant reviewer.

extract_protocol:
Genomic DNA of parental and GSI-resistant DND41 cells was extracted (296.6 and 293.5 ng respectively) using DNeasy Blood & Tissue Kits (Qiagen cat# 69506) and sheared with Covaris LE220-plus ultrasonicator to achieve an average length of 200 bp.
Whole genome libraries were generated with a Kapa Hyper Prep kit (Roche cat #07962363001) targeting the full-coding regions of 505 cancer-associated genes listed in Table S1. The target-enriched libraries were then PCR amplified and paired-end sequenced (150bp + 150bp) on Illumina NovaSeq 6000.


title: DND41_DMSO_SMC1_HiChIP_rep2

value: DMSO


title: Granta519_EBF1g7_ATAC_rep1

data_processing:
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
hg19
Genome_build: bigWig files for genome browser viewing

source_name: Granta-519 cell line

growth_protocol: Granta-519 (female) cells were grown in DMEM (Corning, cat# 10-013-CV) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03) and 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI).

value: Granta-519 cell line

value: Mantle cell lymphoma cell line

value: Cas9 and EBF1-targeting sgRNA


title: Granta519_EBF1g7_ATAC_rep2


title: DND41_DMSO_SMC1_HiChIP_rep1


title: DND41_parental_genomic_seq


title: Granta519Cas9_ctrl_ATAC_rep2

value: Cas9 and control sgRNA


title: Human bone marrow mononuclear cells, H2AK119ub Sample 12

value: Bone marrow

value: Bone marrow mononuclear cells

value: Ficoll-gradient selected mononuclear cells


title: Granta519Cas9_ctrl_ATAC_rep3


title: Human bone marrow mononuclear cells, H2AK119ub Sample 11


title: Human bone marrow mononuclear cells, H2AK119ub Sample 09


title: Human bone marrow mononuclear cells, H2AK119ub Sample 08

description:
Human bone marrow mononuclear cells H2AK119ub ChIP-seq
ASXL1_WT_H2AK119ub_Consensus_Peaks.bw


title: Human bone marrow mononuclear cells, H2AK119ub Sample 07


title: Human bone marrow mononuclear cells, H3K4me1 Sample 01

value: H3K4me1-C15410037 (Diagenode, Denville, United States)


title: Human bone marrow mononuclear cells, H2AK119ub Sample 06


title: JurkatCas9_LEF1_TCF1_KO_ATACseq_rep3

source_name: Jurkat E6-1 cell line

growth_protocol: Jurkat E6-1 (male) cells were grown in RPMI 1640 (Corning, cat# 10-040-CM) supplemented with 10% fetal bovine serum (Hyclone, cat# SH30070.03), 2 mM L-glutamine (Corning, cat# 25-005-CI), 100 U/mL and 100 μg/mL penicillin/streptomycin (Corning, cat# 30-002-CI), 100 mM nonessential amino acids (Gibco, cat# 11140-050), 1mM sodium pyruvate (Gibco, cat#11360-070) and 0.1mM of 2-mercaptoethanol (Sigma, cat# M6250).

value: Jurkat E6-1 cell line

value: Cas9 and LEF1+TCF1-targeting sgRNA


title: Granta519Cas9_ctrl_ATAC_rep1


title: JurkatCas9_LEF1_TCF1_KO_ATACseq_rep2


title: Human bone marrow mononuclear cells, H2AK119ub Sample 14


title: JurkatCas9_LEF1_TCF1_KO_ATACseq_rep1


title: Human bone marrow mononuclear cells, H2AK119ub Sample 04


title: Human bone marrow mononuclear cells, H2AK119ub Sample 03


title: Human bone marrow mononuclear cells, H2AK119ub Sample 02


title: Human bone marrow mononuclear cells, H2AK119ub Sample 10


title: Human bone marrow mononuclear cells, H2AK119ub Sample 13


title: JurkatCas9_TCF1g5_ATACseq_rep3

value: Cas9 and TCF1-targeting sgRNA


title: Human bone marrow mononuclear cells, H2AK119ub Sample 01


title: JurkatCas9_TCF1g5_ATACseq_rep2


title: JurkatCas9_TCF1g5_ATACseq_rep1


title: JurkatCas9_ctrl_ATACseq_rep3


title: JurkatCas9_ctrl_ATACseq_rep2


title: Human bone marrow mononuclear cells, ATAC Sample 15

description:
Human bone marrow mononuclear cells ATAC-seq
ASXL1_MT_ATAC_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw


title: Human bone marrow mononuclear cells, ATAC Sample 13


title: Human bone marrow mononuclear cells, ATAC Sample 12


title: Human bone marrow mononuclear cells, ATAC Sample 09


title: Human bone marrow mononuclear cells, ATAC Sample 08

description:
Human bone marrow mononuclear cells ATAC-seq
ASXL1_WT_ATAC_Consensus_Peaks.bw
ASXL1_WT_ChromHMM_States.bw


title: Human bone marrow mononuclear cells, ATAC Sample 07


title: DND41ResCas9_EBF1g7_RNAseq_rep2


title: DND41ResCas9_EBF1g7_RNAseq_rep1


title: Human bone marrow mononuclear cells, ATAC Sample 06


title: DND41ResCas9_EBF1g7_RNAseq_rep3


title: DND41ResCas9_ctrl_RNAseq_rep3


title: Granta519_EBF1g7_ATAC_rep3


title: DND41ResCas9_ctrl_RNAseq_rep2


title: Human bone marrow mononuclear cells, ATAC Sample 04


title: Human bone marrow mononuclear cells, 5mC Sample 16

description:
Human bone marrow mononuclear cells 5mC DIP-seq
ASXL1_MT_5mC_Consensus_Peaks.bw

value: 5mC-33D3 (Diagenode, Denville, United States)


title: Human bone marrow mononuclear cells, ATAC Sample 16


title: Human bone marrow mononuclear cells, 5mC Sample 13


title: Human bone marrow mononuclear cells, ATAC Sample 03


title: DND41_reverse_24hrGSI_RNAseq_rep1


title: DND41_reverse_24hrGSI_RNAseq_rep2


title: DND41_reverse_24hrGSI_RNAseq_rep3


title: DND41ResCas9_ctrl_RNAseq_rep1


title: Human bone marrow mononuclear cells, 5mC Sample 12


title: JurkatCas9_ctrl_ATACseq_rep1


title: Human bone marrow mononuclear cells, 5mC Sample 11


title: DND41_reverse_DMSO_RNAseq_rep2


title: DND41_reverse_DMSO_RNAseq_rep1


title: Human bone marrow mononuclear cells, 5mC Sample 14


title: Human bone marrow mononuclear cells, 5mC Sample 10


title: Human bone marrow mononuclear cells, 5mC Sample 08

description:
Human bone marrow mononuclear cells 5mC DIP-seq
ASXL1_WT_5mC_Consensus_Peaks.bw


title: Human bone marrow mononuclear cells, ATAC Sample 05


title: Human bone marrow mononuclear cells, 5mC Sample 07


title: DND41_reverse_DMSO_RNAseq_rep3


title: DND41_24hrGSI_RNAseq_rep3


title: DND41_resistant_RNAseq_rep3


title: Human bone marrow mononuclear cells, 5mC Sample 05


title: Human bone marrow mononuclear cells, 5mC Sample 06


title: DND41_resistant_RNAseq_rep1


title: Human bone marrow mononuclear cells, 5mC Sample 04


title: DND41_24hrGSI_RNAseq_rep1


title: DND41_24hrGSI_RNAseq_rep2


title: DND41_DMSO_RNAseq_rep3


title: DND41_DMSO_RNAseq_rep1


title: DND41_DMSO_RNAseq_rep2


title: Human bone marrow mononuclear cells, 5mC Sample 01


title: Human bone marrow mononuclear cells, 5mC Sample 03


title: DND41_reverse_24hrGSI_MYC_4C_rep3

data_processing:
Library strategy: UMI-4C
UMI 4C-seq data was processed with Juicer (version 1.5) (Durand et al., 2016) with parameters -g hg19 -s MboI to generate .hic files.
Genome_build: hg19

extract_protocol:
UMI 4C-seq was performed as previously described (Cho et al., 2018) with minor modifications. 5-10 x 10^6 cells were crosslinked with 1% formaldehyde and lysed with ice-cold Hi-C Lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40, 1X protease inhibitors) at 4°C for 30 minutes. Pelleted nuclei were resuspended in 0.5% SDS at 62°C for 10min and then quenched with Triton X-100 at 37°C for 15 min. Chromatin was then digested with MboI (NEB cat# R0147) at 37°C for 2 hours and ligated with T4 DNA Ligase (NEB cat# M0202) at room temperature for 4 hours with rotation. Pelleted nuclei were resuspended in 200 uL of Proteinase K Buffer (10 mM Tris pH 7.0, 100 mM NaCl, 1mM EDTA, 0.5% SDS) at 55°C for 1hr, reverse crosslinked at 67°C overnight, and treated with RNase A before DNA precipitation by ethanol and NaAc. 10 ug of eluted DNA was sonicated on Bioruptor for 5 cycles of 30sec on, 60sec off followed by sequential incubation with end repair mix (NEB cat# E6050), Klenow exo- (NEB cat# M0212) and CIP (NEB cat# M0290).
DNA was ligated with Illumina forked indexed adapters (Roche cat# 7141530001) with Quick Ligase (NEB cat# M2200L) at room temperature for 30min and denatured at 95°C for 2min to release the non-ligated strand of the adapter. Single-stranded DNA was quantified by Qubit ssDNA Assay Kit (Invitrogen cat# Q10212) and 200ng of 4C DNA template was amplified by nested PCR using primer sets targeting MYC promoter. 3-5 replicates were performed for each condition. Indexed libraries were validated for quality and size distribution using a TapeStation 4150 (Agilent), quantified by KAPA Library Quantification Kit (Roche #KK4824) and paired-end sequenced (38 bp+38 bp) on Illumina NextSeq 550.


title: Human bone marrow mononuclear cells, 5mC Sample 02


title: Human bone marrow mononuclear cells, 5mC Sample 09


title: Human bone marrow mononuclear cells, 5hmC Sample 16

description:
Human bone marrow mononuclear cells 5hmC DIP-seq
ASXL1_MT_5hmC_Consensus_Peaks.bw

value: 5hmC-IHD (Mayo Clinic Epigenomics Development Laboratory, Rochester, United States)


title: Human bone marrow mononuclear cells, 5hmC Sample 14


title: DND41_reverse_24hrGSI_MYC_4C_rep1

value: DND41 cell line


title: DND41_reverse_24hrGSI_MYC_4C_rep2

value: T-ALL cell line


title: DND41_reverse_DMSO_MYC_4C_rep3


title: DND41_reverse_DMSO_MYC_4C_rep2


title: Human bone marrow mononuclear cells, 5hmC Sample 13


title: Human bone marrow mononuclear cells, 5hmC Sample 11


title: Human bone marrow mononuclear cells, 5hmC Sample 12


title: DND41_resistant_RNAseq_rep2

value: GSI


title: DND41_reverse_DMSO_MYC_4C_rep1

value: DMSO


title: DND41_resistant_MYC_4C_rep3


title: Human bone marrow mononuclear cells, 5hmC Sample 10


title: DND41_resistant_MYC_4C_rep2


title: Human bone marrow mononuclear cells, 5hmC Sample 08

description:
Human bone marrow mononuclear cells 5hmC DIP-seq
ASXL1_WT_5hmC_Consensus_Peaks.bw


title: DND41_24hrGSI_MYC_4C_rep3


title: Human bone marrow mononuclear cells, 5hmC Sample 07


title: Human bone marrow mononuclear cells, 5hmC Sample 09


title: Human bone marrow mononuclear cells, 5hmC Sample 06


title: DND41_24hrGSI_MYC_4C_rep2


title: DND41_24hrGSI_MYC_4C_rep1


title: Human bone marrow mononuclear cells, 5hmC Sample 04


title: DND41_DMSO_MYC_4C_rep1


title: Human bone marrow mononuclear cells, 5hmC Sample 03


title: DND41_DMSO_MYC_4C_rep3


title: DND41_DMSO_MYC_4C_rep2


title: P-538

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description:
Tumor biopsy
Explorative_cohort_miRNA_counts_matrix.txt
Explorative_cohort_miRNA_normRPM_matrix.txt

data_processing:
Single-end sequencing of 50 bases of each cDNA
Real-time analysis, base calling, adapter clipping and filtering of low quality reads performed by Illumina software according to standard protocols.
Quality assessment was based on the reads using the FASTQC quality control
Read alignment software: miRDeep2 v.2.0.0.5 with mirBase v.21 for annotation of mature miRNAs
Genome_build: Hg19
Supplementary_files_format_and_content: Explorative_cohort_miRNA_counts_matrix.txt: matrix with raw counts for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.
Supplementary_files_format_and_content: Explorative_cohort_miRNA_normRPM_matrix.txt: matrix with normalized counts (RPM) for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.
Supplementary_files_format_and_content: Validation_cohort1_miRNA_counts_matrix.txt: matrix with raw counts for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.
Supplementary_files_format_and_content: Validation_cohort1_miRNA_normRPM_matrix.txt: matrix with normalized counts (RPM) for every miRNA in every sample in the Explorative cohort. Duplicate mature miRNA ID are included in the dataset due to annotation of identical mature miRNA IDs to different precursor miRNA ID by the miRDeep2 algorithm.

source_name: Cervical tumor

growth_protocol: 1-4 tumor samples were collected from each patient at the time of diagnosis

extract_protocol:
In the Explorative cohort, total RNA was extracted by use of the miRNeasy mini kit. In the validation cohort 1, total RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.
Small RNA preparation for sequencing was performed according to Illumina TruSeq Small RNA library protocols. Briefly, indexed 3’- and 5’end RNA adapters were ligated to 1 ug of isolated total RNA per sample followed by reverse transcription and library amplification. The cDNA was purified on a PAGE gel by cutting out bands corresponding to 140-160 bp (length of miRNA + adapter and index sequences), pooled and ethanol precipitated.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

tag: figo stage

tag: lymph node status (0=negative, 1=positive)

tag: tumor volume (mm3)

tag: histology

value: Squamous cell carcinoma

tag: cohort

value: Explorative cohort

tag: total number of reads from small rna seq.


title: Human bone marrow mononuclear cells, 5hmC Sample 02

tag: cell type

tag: cell selection

tag: genotype


title: P-536


title: DND41_resistant_Arima_HiC_rep1

data_processing:
Raw reads for each HiC sample were processed with HiC-Pro (version v2.5.0) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE and GENOME_FRAGMENT provided by Arima.
Genome_build: hg19
Supplementary_files_format_and_content: .hic formatted file for juicebox viewing of contact matrices

extract_protocol:
1-2x10^6 cells were washed with 1xPBS containing 3% BSA and fixed with 2% formaldehyde and proceeded with Arima-HiC Kit per manufacturer’s instructions.
Samples passing Arima-QC1 were used for library construction with Accel-NGS 2S Plus DNA Library Kit (Swift cat# 21024) and 2S SET A INDEXING KIT (Swift cat# 26148) and assessed with Arima-QC2. Samples passing Arima-QC2 were subsequently PCR amplified based on Arima-QC2 calculations, quantified with TapeStation 4150 (Agilent) and KAPA Library Quantification Kit (Roche cat# KK4824) and paired-end (38bp+38bp) sequenced on Illumina NextSeq 550.

tag: cell line


title: P-537


title: DND41ResCas9_EBF1g7_Arima_HiC_rep1

value: Cas9 and EBF1-targeting sgRNA


title: DND41ResCas9_ctrl_Arima_HiC_rep1

value: Cas9 and control sgRNA


title: Human bone marrow mononuclear cells, 5hmC Sample 01

value: Bone marrow

tag: dip antibody


title: P-533


title: P-535


title: DND41_resistant_H3K27me3_CnR_rep2

data_processing:
Library strategy: Cut&Run
Reads were trimmed with Trim Galore (version 0.4.1) with parameters -q 15 --phred33 --gzip --stringency 5 -e 0.1 --length 20. Trimmed reads were aligned to the Ensembl GRCh37.75 primary assembly including chromosome 1-22, chrX, chrY, chrM and contigs using BWA (version 0.7.13) (Li and Durbin, 2009) with parameters bwa aln -q 5 -l 32 -k 2 -t 6. Paired-end reads were group with bwa sampe -P -o 1000000. Reads mapped to contigs, ENCODE blacklist and marked as duplicates by Picard (version 2.1.0) were discarded and the remaining reads were used in downstream analyses and visualization.
Bedgraph of reads normalized to reads per million (RPM) were generated with bedtools (version 2.25.0) genomecov. Uploadable bigWig files were generated with UCSC bedGraphToBigWig (version 329).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for genome browser viewing

extract_protocol:
CUT & RUN was performed as described (Skene and Henikoff, 2017). Briefly, 5x10^5 cells were immobilized on Concanavalin-coated magnetic beads (Bangs Laboratories cat# cBP531) and incubated with Tri-Methyl-Histone H3 (Lys27) (C36B11) antibody (CST cat# 9733S) overnight at 4°C. Beads were washed with digitonin wash buffer and mixed in pA-MNase (gift from Henikoff lab) at 4°C for 1 hour. After activation by Ca2+ on wet ice for 30min, 2XSTOP buffer was added and incubated 37°C for 10min to release CUT & RUN fragments from the insoluble nuclear chromatin.
DNA was then extracted from the supernatant using Phenol-chloroform-isoamyl alcohol 25:24:1 (PCI; Invitrogen cat# 15593049) method. Library construction, quantification and sequencing were done as described above for ChIP-seq.

tag: chip antibody


title: DND41_resistant_MYC_4C_rep1


title: DND41_resistant_H3K27me3_CnR_rep1


title: P-529


title: DND41_24hrGSI_H3K27me3_CnR_rep2


title: Human bone marrow mononuclear cells, 5hmC Sample 05

data_processing:
FastQC (v0.11.8) pre-alignment quality and adapter trimming, Bowtie2 (v2.3.3.1) / BWA (v0.7.17) alignment, post-alignment quality control, MACS2 (v3.0.0a6), MSPC(v5.4.0), ChromHMM (v1.20)
Genome_build: GRCh38 / hg38
Supplementary_files_format_and_content: Consensus peaks in BW file generated by subjecting the peaks called by MACS2 to a second selection step by MSPC; Chromatin states (7-state model) in BW file generated by ChromHMM

value: Bone marrow mononuclear cells


title: DND41_24hrGSI_H3K27me3_CnR_rep1


title: P-527


title: P-526


title: P-525