title: SS2_Exp2_Uninfected_C3_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C3_B112556_B0000721


title: SS2_Exp2_Uninfected_B2_B112494_B001304

status: Public on Apr 20 2024

type: SRA

city: San Francisco

first: Leah

last: Dorman

state: CA

address: 499 Illinois St

department: Data Science

country: USA

institute: CZBiohub

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B2_B112494_B001304

library_source: transcriptomic single cell

data_processing:
De-multiplexed using bcl2fastq version 2.20 and aligned with Gencode v.M19 annotations using STAR version 2.5.2b with parameters TK
Assembly: mm10
Supplementary files format and content: h5ad: Processed complete data object from scanpy
Supplementary files format and content: csv: normalized counts and metadata table

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
For in vivo, 28 days post infection mice were sacrificed and single cell lung suspension stained for flow cytometry (see manuscript protocol for details).
For SmartSeq2, cells were sorted directly into 384 well plates containing gently lysis buffer and processed according to Picelli 2014 protocol.
scRNASeq (Smartseq2)

treatment_protocol: For in vivo mouse: mice were aerosol infected with H37Rv (50CFU) or H37Rv-deltaEccD (500CFU) and left for 28 days prior to sacrifice

tag: tissue

value: Lung

tag: cell type

value: Cd11b+ and-or Cd11c+

tag: infection

value: Control


title: SS2_Exp2_KO_Infected_N13_B112557_B0000731_S709

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: N13_B112557_B0000731_S709

value: Mycobacterium tuberculosis H37Rv_DeltaEccD_zsGreen aerosol infection


title: SS2_Exp2_KO_Infected_I21_B112557_B0000731_S597

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I21_B112557_B0000731_S597


title: SS2_Exp2_Uninfected_N18_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: N18_B112556_B0000721


title: SS2_Exp2_KO_Infected_H21_B112557_B0000731_S573

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: H21_B112557_B0000731_S573


title: SS2_Exp2_Uninfected_M11_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: M11_B112556_B0000721


title: SS2_Exp2_Uninfected_O17_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: O17_B112556_B0000721


title: SS2_Exp2_KO_Infected_H6_B112557_B0000731_S558

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: H6_B112557_B0000731_S558


title: SS2_Exp2_KO_Infected_I13_B112557_B0000731_S589

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I13_B112557_B0000731_S589


title: SS2_Exp2_KO_Infected_I15_B112557_B0000731_S591

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I15_B112557_B0000731_S591


title: SS2_Exp2_Uninfected_E15_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E15_B112559_B001942


title: SS2_Exp2_KO_Infected_I17_B112557_B0000731_S593

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I17_B112557_B0000731_S593


title: SS2_Exp2_KO_Infected_P9_B112557_B0000731_S753

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: P9_B112557_B0000731_S753


title: SS2_Exp2_Uninfected_D16_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D16_B112556_B0000721


title: SS2_Exp2_Uninfected_M21_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: M21_B112556_B0000721


title: SS2_Exp2_Uninfected_D2_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D2_B112556_B0000721


title: SS2_Exp2_Uninfected_O22_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: O22_B112556_B0000721


title: SS2_Exp2_KO_Infected_I22_B112557_B0000731_S598

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I22_B112557_B0000731_S598


title: SS2_Exp2_KO_Infected_H5_B112557_B0000731_S557

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: H5_B112557_B0000731_S557


title: SS2_Exp2_Uninfected_B18_B112561_B001994

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B18_B112561_B001994


title: SS2_Exp2_Uninfected_D10_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D10_B112556_B0000721


title: SS2_Exp2_KO_Infected_I3_B112557_B0000731_S579

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I3_B112557_B0000731_S579


title: SS2_Exp2_KO_Infected_I19_B112557_B0000731_S595

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I19_B112557_B0000731_S595


title: SS2_Exp2_Uninfected_D6_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D6_B112556_B0000721


title: SS2_Exp2_Uninfected_C13_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C13_B112556_B0000721


title: SS2_Exp2_KO_Infected_K13_B112557_B0000731_S637

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K13_B112557_B0000731_S637


title: SS2_Exp2_KO_Infected_I2_B112557_B0000731_S578

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I2_B112557_B0000731_S578


title: SS2_Exp2_Uninfected_D19_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D19_B112556_B0000721


title: SS2_Exp2_Uninfected_E10_B112561_B001994

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E10_B112561_B001994


title: SS2_Exp2_KO_Infected_K4_B112557_B0000731_S628

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K4_B112557_B0000731_S628


title: SS2_Exp2_KO_Infected_I23_B112557_B0000731_S599

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I23_B112557_B0000731_S599


title: SS2_Exp2_KO_Infected_I16_B112557_B0000731_S592

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I16_B112557_B0000731_S592


title: SS2_Exp2_Uninfected_M20_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: M20_B112556_B0000721


title: SS2_Exp2_KO_Infected_I4_B112557_B0000731_S580

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I4_B112557_B0000731_S580


title: SS2_Exp2_KO_Infected_K19_B112557_B0000731_S643

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K19_B112557_B0000731_S643


title: SS2_Exp2_Uninfected_B21_B112561_B001994

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B21_B112561_B001994


title: SS2_Exp2_Uninfected_B6_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B6_B112494_B001304


title: SS2_Exp2_Uninfected_B18_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B18_B112559_B001942


title: SS2_Exp2_KO_Infected_K16_B112557_B0000731_S640

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K16_B112557_B0000731_S640


title: SS2_Exp2_KO_Infected_K1_B112557_B0000731_S625

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K1_B112557_B0000731_S625


title: SS2_Exp2_KO_Infected_K17_B112557_B0000731_S641

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K17_B112557_B0000731_S641


title: SS2_Exp2_KO_Infected_K2_B112557_B0000731_S626

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K2_B112557_B0000731_S626


title: SS2_Exp2_KO_Infected_I18_B112557_B0000731_S594

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I18_B112557_B0000731_S594


title: SS2_Exp2_Uninfected_E14_B002059_B001303

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E14_B002059_B001303


title: SS2_Exp2_Uninfected_N21_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: N21_B112559_B001942


title: SS2_Exp2_KO_Infected_K14_B112557_B0000731_S638

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K14_B112557_B0000731_S638


title: SS2_Exp2_KO_Infected_K3_B112557_B0000731_S627

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K3_B112557_B0000731_S627


title: SS2_Exp2_Uninfected_B22_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B22_B112559_B001942


title: SS2_Exp2_KO_Infected_K5_B112557_B0000731_S629

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K5_B112557_B0000731_S629


title: SS2_Exp2_Uninfected_E16_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E16_B112494_B001304


title: SS2_Exp2_Uninfected_C12_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C12_B112556_B0000721


title: SS2_Exp2_Uninfected_P16_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: P16_B112556_B0000721


title: SS2_Exp2_Uninfected_B3_B112561_B001994

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B3_B112561_B001994


title: SS2_Exp2_KO_Infected_L10_B112557_B0000731_S658

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L10_B112557_B0000731_S658


title: SS2_Exp2_Uninfected_D18_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D18_B112556_B0000721


title: SS2_Exp2_KO_Infected_I11_B112557_B0000731_S587

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I11_B112557_B0000731_S587


title: SS2_Exp2_Uninfected_A18_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: A18_B112494_B001304


title: SS2_Exp2_Uninfected_E15_B112561_B001994

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E15_B112561_B001994


title: SS2_Exp2_KO_Infected_L17_B112557_B0000731_S665

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L17_B112557_B0000731_S665


title: SS2_Exp2_Uninfected_C21_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C21_B112556_B0000721


title: SS2_Exp2_KO_Infected_L22_B112557_B0000731_S670

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L22_B112557_B0000731_S670


title: SS2_Exp2_KO_Infected_L18_B112557_B0000731_S666

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L18_B112557_B0000731_S666


title: SS2_Exp2_Uninfected_D12_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D12_B112556_B0000721


title: SS2_Exp2_KO_Infected_L15_B112557_B0000731_S663

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L15_B112557_B0000731_S663


title: SS2_Exp2_Uninfected_E11_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E11_B112556_B0000721


title: SS2_Exp2_Uninfected_C18_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C18_B112556_B0000721


title: SS2_Exp2_KO_Infected_K9_B112557_B0000731_S633

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K9_B112557_B0000731_S633


title: SS2_Exp2_Uninfected_E12_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E12_B112556_B0000721


title: SS2_Exp2_Uninfected_M3_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: M3_B112556_B0000721


title: SS2_Exp2_KO_Infected_L16_B112557_B0000731_S664

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L16_B112557_B0000731_S664


title: SS2_Exp2_Uninfected_D14_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D14_B112556_B0000721


title: SS2_Exp2_KO_Infected_L1_B112557_B0000731_S649

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L1_B112557_B0000731_S649


title: SS2_Exp2_KO_Infected_I20_B112557_B0000731_S596

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: I20_B112557_B0000731_S596


title: SS2_Exp2_KO_Infected_K21_B112557_B0000731_S645

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: K21_B112557_B0000731_S645


title: SS2_Exp2_Uninfected_E11_B112561_B001994

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E11_B112561_B001994


title: SS2_Exp2_KO_Infected_L12_B112557_B0000731_S660

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L12_B112557_B0000731_S660


title: SS2_Exp2_KO_Infected_L21_B112557_B0000731_S669

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L21_B112557_B0000731_S669


title: SS2_Exp2_Uninfected_C15_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C15_B112556_B0000721


title: SS2_Exp2_Uninfected_E17_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E17_B112494_B001304


title: SS2_Exp2_KO_Infected_L20_B112557_B0000731_S668

description:
Illumina NextSeq 2000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-DeltaEccD-zsGreen positive infected cells Cell ID: L20_B112557_B0000731_S668


title: SS2_Exp2_Uninfected_D13_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D13_B112556_B0000721


title: WT_rep2

city: Piscataway

first: Ruth

last: Steward

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute of Microbiology

institute: Rutgers University

library_source: transcriptomic

data_processing:
Raw reads were filtered and trimmed by Trimmomatic 0.39
Then, the filtered reads will be mapped to Ensembl Drosophila melanogaster genome assembly BDGP6.22 using HISAT2
The mapping SAM files were converted to BAM using Samtools
The number of reads mapped to the individual gene is counted by featureCounts
Differential gene expression analysis was done by DESeq2. Then, the result was visualized by the Bioconductor package EnhancedVolcano
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes the matrix of raw count data for all samples, and the column names are equivalent to the library names.

molecule: total RNA

organism: Drosophila melanogaster

source_name: Pupal brain

growth_protocol: Fly stocks were cultured on the standard food medium at 25 °C.

extract_protocol:
Pupal brains were dissected in PBS and immediately frozen on dry ice. Totally, 30 brains per genotype were collected at 24h APF (After Puparium Formation). Three independent biological replicates per genotype were used for RNA isolation. Total RNA was isolated using RNeasy Plus Universal Kit (QIAGEN, USA) following the manufacturer’s instructions including DNase I treatment using RNase-Free DNase Set and on-column protocol (QIAGEN, USA). The isolated total RNAs were aliquoted for both RNA-seq and qRT-PCR.
Library preparation and sequencing were performed at Novogene. One microgram of total RNA was used as input for library preparation. Prior to library preparation, total RNA quality was validated for the following parameters:  degradation and contamination using 1% agarose gel electrophoresis, purity by NanoPhotometer® spectrophotometer (IMPLEN, USA), and integrity using Bioanalyzer 2100 and RNA Nano 6000 Kit (Agilent Technologies, USA). Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s instruction. mRNA was purified from total RNA using oligo dT magnetic beads. Purified mRNAs were fragmented by divalent cations. First-strand cDNA synthesis using random hexamer and M-MuLV RT (RNase H-). The dUTP method was used to synthesize the second strand and generate a strand-specific library. After 3’ A overhangs were cleaved by exonuclease, DNA fragments were ligated with NEBNext® hairpin loop adaptor to prepare for hybridization. AMPure XP system (Beckman Coulter, USA) was used for 150-200 bp size selection. The size selected and purified products were treated with USER® Enzyme to open up the NEBNext adapter. Then, PCR was performed with Phusion High-Fidelity DNA polymerase using Universal PCR primers and Index (X) prime. PCR products were purified using the AMPure XP system and quality was assessed by Agilent Bioanalyzer 2100. Clustering was done using cBot Cluster System using PE Cluster Kit cBot-HS (Illumina, USA) according to the manufacturer’s recommendation. Sequencing was performed on Illumina Novaseq 6000 (Illumina, USA) to generate paired-end reads.

treatment_protocol: The TetAXXC mutant was generated using the scarless gene editing approach which is mediated by CRISPR/Cas9 cut and homologous directed repair (HDR) of the designed DNA template harboring targeted mutations (7-9). Two gRNAs (gRNA1 and gRNA2) were designed to bind to both sides of the CXXC zinc finger domain flanking regions to guide the Cas9 cut. These gRNAs were synthesized (IDT, USA) and cloned to the pU6-BbsI-chiRNA expression vector (Addgene #45946)(8). The two homology arms were generated by PCR from the nos-Cas9 stock (BDSC # 54591) genomic DNA. The PCR was done using gene-specific and mutated primers to generate one wild-type homology arm and one mutated homology arm with at least 1000 bp overlap with the flanking genomic DNA from the cut site (Fig. S7). The homology arms were cloned to the pScarlessHD-DsRed donor vector (Addgene # 64703, gift from Kate O'Connor-Giles). The mixture of these vectors was injected into the nos-Cas9 stock and screened for the DsRed marker. DsRed positive lines were genetically crossed to remove the non-Cas9 chromosome. Then, these lines were crossed to a piggyBac recombinase stock 3xP3-ECFP, alpha-tub-piggyBacK10/TM6C, Sb1 (BDSC # 32072) to excise the DsRed marker. The mutant stocks were validated by PCR and Sanger sequencing.

value: Pupal brain

tag: cell line

value: Whole pupal brain

value: Brain cells

tag: genotype

value: WT

tag: developmental stage

value: 24h After puparium formation (APF)


title: WT_rep3


title: SS2_Exp2_Uninfected_E12_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E12_B112494_B001304


title: SS2_Exp2_Uninfected_B6_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B6_B112559_B001942


title: WT_rep1


title: SS2_Exp2_Uninfected_E17_B112361_B007833

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E17_B112361_B007833


title: TetAXXC_rep2

value: TetAXXC


title: TetAXXC_rep1


title: SS2_Exp2_Uninfected_E10_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E10_B112556_B0000721


title: SS2_Exp2_Uninfected_C16_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C16_B112556_B0000721


title: B6_BM_NK_nanoCAGE_Lib2

city: Saint Louis

first: Changxu

last: Fan

state: Missouri

address: 4515 McKinley Avenue, Room 5213

department: Genetics

institute: Washington University in St. Louis

data_processing:
Raw data were processed using a custom pipeline: Template-switching oligonucleotide (TSO) and unique molecular identifiers (UMIs) were identified using TagDust2 (v2.33). Reads that do not have the expected architecture were discarded. All libraries contain > 90% reads with the expected architecture; Sequencing adapters and TSO were trimmed using cutadapt (v1.18); STAR (v2.5.4b) was used to align trimmed reads to the genome; PCR duplicates were removed according to UMI using UMI-tools (v1.0.1); alignments were further filtered to remove secondary alignments and multimapping reads (samtools view -f 0x2 -F 0x900 -q 255);
a stringent secondary filter was applied to remove alignments satisfying any of the following criteria: a. template length > 10kb. In the Ly49 locus, these alignments represent cross-gene splicing; b. contain mismatches; c. contain > 3 bp soft clipping. This stringent filter was necessary because the 129 and NOD reference sequences contain gaps, in which additional Ly49 genes could exist. These “dark” Ly49 genes could be aligned to other Ly49 genes covered by the assembly. However, this type of alignment likely contains mismatches, extensive soft-clipping, and cross-gene splicing. This filter was also feasible because all samples were from inbred animals and each sample was aligned to the reference Ly49 sequence built from exactly the same strain. Therefore, we do not expect any mismatches arising from natural sequence, and any deviation from the reference genome likely represents errors in transcription, library prep or alignment.
Assembly: B6 reads were aligned to mm10. 129 and NOD reads were aligned to custom-built genomes, which were detailed in the “Ly49 and genome sequences and annotations” method section in the manuscript, and available from https://github.com/ChangxuFan/Ly49evolution
Supplementary files format and content: bedGraph.gz: TSS signals with no MAPQ filter or with MAPQ == 255 filter. Unnormalized. Signals are from both strands (represented by positive and negative values in the 4th column)

source_name: Bone Marrow

extract_protocol:
For all samples, total RNA was extracted using Quick-RNA Microprep Kit (Zymo Research, R1050).
For spleen NK cells: 20ng of total RNA was used for each library. cDNA was generated from the RNA template using Template Switching RT Enzyme Mix (NEB, M0466) with hexamer priming. nanoCAGE-seq libraries were then prepared following the previously described protocol (Poulain, S. et al. Promoter Associated RNA, Methods and Protocols. Methods Mol Biology Clifton N J 1543, 57–109 (2017).). For each of the two B6 samples (Ly49D+ and Ly49D-), we also generated one additional library where we used 250ng total RNA as input, extracted mRNA, and further depleted truncated mRNA with Terminator™ 5'-Phosphate-Dependent Exonuclease (TER51020), which gave similar results
For BM NK cells: A low-input protocol was used due to the low cell number (library 1: ~ 2000 cells; library 2: ~22,000 cells). Total RNA was extracted using Quick-RNA Microprep Kit (Zymo Research, R1050). cDNA was generated from the RNA template using NEBNext Single Cell/Low Input cDNA Synthesis & Amplification Module (NEB, E6421) with a Poly-T RT primer (20 µM): TAGTCGAACTGAAGGTCTCCGAACCGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTTVN and Template switching oligos (75 µM): TAGTCGAACTGAAGGTCTCCAGCA(N1:25252525)(N1)(N1)(N1)(N1)(N1)(N1)(N1)(N1)TATArGrGrG instead of the template switching oligos in the kit. (N1) represents one bp of the 8 bp UMI. 25252525 represents an equal mix of A/T/C/G. cDNA was then amplified using cDNA PCR primer forward and reverse (20 µM): TAGTCGAACTGAAGGTCTCCAGCA; TAGTCGAACTGAAGGTCTCCGAACC instead of the cDNA PCR primer in the kit. cDNA was quantified with Qubit and up to 0.5 ng of cDNA was applied for library preparation using Nextera XT library Prep Kit (Illumina, 15032350), following the previously described protocol (oulain, S. et al. Promoter Associated RNA, Methods and Protocols. Methods Mol Biology Clifton N J 1543, 57–109 (2017).). Libraries were size selected with double sided selection of 0.55x/0.95x Ampure beads and were sequenced on the Element AVITI machine to ~20 million reads (2 x 75 bp).

treatment_protocol: BM or Splenic NK cells were FACS-sorted from B6, 129, and NOD mice.

tag: strain

value: Bone Marrow

value: Natural killer cells

tag: marker

tag: treatment

value: ex vivo


title: B6_Spleen_NK_Ly49C_or_Ly49I_pos_rep2_ATAC

description: instrument model: Element AVITI

library_source: genomic

data_processing:
Mouse ATAC data were first processed using the AIAP (v1.1) pipeline. As a part of the pipeline: locations of Tn5 insertion events were inferred from properly paired, non-PCR duplicate reads with MAPQ >= 10; each Tn5 insertion event was extended from insertion site up and down 75 bp to generate a 150 bp “pseudo read”; pseudo reads were piled up to generate an ATAC signal profile, which was normalized against sequencing depth. The resulting normalized ATAC signal profile was used in genome browser views unless otherwise noted.
For Ly49 consensus views of mouse and rat ATAC data, we fine-tuned the alignment using a custom alignment pipeline (https://github.com/ChangxuFan/snakeATAC/): adaptors were removed using cutadapt (v1.18) with parameters “--quality-cutoff=15,10 --minimum-length=36”; reads were aligned to reference genomes using “bowtie2 --very-sensitive --xeq --dovetail --no-unal”; only reads with perfect match to the reference were kept (“sambamba view -f bam -F '[AS] == 0'”). This was applied because we aligned ATAC data against genomes assembled from exactly the same mouse/rat strains; when indicated, reads were filtered based on MAPQ (“sambamba view -f bam -F 'mapping_quality >= 8 '”); “methylQA48 atac -X 38 -Q 1 ” was used to remove PCR duplicates, identify Tn5 insertion sites, and generate smoothed ATAC signals through extending Tn5 insertion sites up and downstream 75 bp, similar to the AIAP package.
Assembly: B6 reads were aligned to mm10. Rat reads were aligned to rn7. 129 and NOD reads were aligned to custom-built genomes, which were detailed in the “Ly49 and genome sequences and annotations” method section in the manuscript, and available at https://github.com/ChangxuFan/Ly49evolution
Supplementary files format and content: bigwig: AIAPnorm.bw files are the normalized ATAC signals from the AIAP pipeline. unnorm.bw is the unnormalized ATAC signals from the snakeATAC pipeline (this study). MAPQ8 indicates that reads were filtered for MAPQ >= 8.

molecule: genomic DNA

source_name: Spleen

extract_protocol:
DNA was extracted according to a previously published protocol (Wu, J. et al. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Reports 33, 108395 (2020).)
libraries were constructed using a previously published protocol (Wu, J. et al. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Reports 33, 108395 (2020).)

treatment_protocol: Splenic NK cells or CD8 Tregs were FACS-sorted from mice or rats

value: Spleen

value: primary cells

tag: subset


title: B6_Spleen_NK_Ly49C_or_Ly49I_pos_rep1_ATAC

description: instrument model: Element AVITI


title: B6_BM_NK_nanoCAGE_Lib1


title: SS2_Exp2_Uninfected_E13_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E13_B112556_B0000721


title: SS2_Exp2_Uninfected_C20_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C20_B112556_B0000721


title: SS2_Exp2_Uninfected_E10_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E10_B112559_B001942


title: SS2_Exp2_WT_Bystander_C10_B112484_B0000720

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-zsGreen negative bystanders
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-zsGreen negative bystanders Cell ID: C10_B112484_B0000720

value: Mycobacterium tuberculosis H37Rv_zsGreen aerosol infection


title: SS2_Exp2_Uninfected_C14_B112556_B0000721

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C14_B112556_B0000721


title: B6_Spleen_CD8Treg_rep3_ATAC

value: CD8 Treg


title: SS2_Exp2_WT_Infected_A6_B001939_B001941

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-zsGreen positive infected cells Cell ID: A6_B001939_B001941

value: Lung


title: B6_Spleen_NK_Ly49C_and_Ly49I_neg_rep1_ATAC

description: instrument model: Element AVITI


title: SS2_Exp2_WT_Bystander_N8_B112571_B0000715

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-zsGreen negative bystanders
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-zsGreen negative bystanders Cell ID: N8_B112571_B0000715

value: Cd11b+ and-or Cd11c+


title: MAP8.B6.Ly49h_WT_homozygous_RNA_rep2

description:
GEX_MAP8.B6.Ly49H_KO_homozygous.tsv
gene expression values have been aggregated in supplementary files

data_processing:
STAR (v 2.5.4b) was used for alignment
“sambamba markdup” was used to remove PCR duplicates from paired-end libraries
reads with MAPQ < 30 were removed
"featureCounts -t exon --fracOverlap 0.5” from subread (v2.0.0) was used to count the number of reads overlapping the exons of each gene
Assembly: mm10
Supplementary files format and content: tsv: raw read counts for each gene in each sample

extract_protocol:
Total RNA from sorted cells was extracted using Quick-RNA Microprep Kit (Zymo Research, R1050).
50-100 ng of total RNA was processed with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760) to generate mRNA-seq libraries

treatment_protocol: Splenic NK cells were FACS-sorted from mice

tag: markers

value: total NK


title: SS2_Exp2_WT_Infected_A1_B001939_B001941

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-zsGreen positive infected cells Cell ID: A1_B001939_B001941


title: MAP8.B6.Ly49h_WT_homozygous_RNA_rep1


title: TetAXXC_rep3


title: B6_Spleen_CD8Treg_rep1_ATAC


title: SS2_Exp2_Uninfected_E16_B112361_B007833

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E16_B112361_B007833

value: Control


title: SS2_Exp2_WT_Infected_A9_B001939_B001941

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-zsGreen positive infected cells
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-zsGreen positive infected cells Cell ID: A9_B001939_B001941


title: MAP8.B6.Ly49h_KO_homozygous_RNA_rep1


title: SS2_Exp2_Uninfected_D21_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D21_B112494_B001304


title: SS2_Exp2_Uninfected_L10_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: L10_B112559_B001942


title: NOD_mRNA

description: singlet CD4-CD8-TCRβ-CD19-NKp46+CD49a-CD49b+

extract_protocol:
For all samples, total RNA was extracted using Quick-RNA Microprep Kit (Zymo Research, R1050).
20ng of total RNA was used for each library. cDNA was generated from the RNA template using Template Switching RT Enzyme Mix (NEB, M0466) with hexamer priming. nanoCAGE-seq libraries were then prepared following the previously described protocol (Poulain, S. et al. Promoter Associated RNA, Methods and Protocols. Methods Mol Biology Clifton N J 1543, 57–109 (2017).). For each of the two B6 samples (Ly49D+ and Ly49D-), we also generated one additional library where we used 250ng total RNA as input, extracted mRNA, and further depleted truncated mRNA with Terminator™ 5'-Phosphate-Dependent Exonuclease (TER51020), which gave similar results

treatment_protocol: Splenic NK cells were FACS-sorted from B6, 129, and NOD mice.

value: NOD/ShiLTJ


title: B6_Spleen_NK_Ly49C_and_Ly49I_neg_rep2_ATAC

description: instrument model: Element AVITI


title: 129_mRNA


title: SS2_Exp2_Uninfected_C13_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C13_B112559_B001942


title: B6_Ly49Dp_Terminator

description: singlet CD4-CD8-TCRβ-CD19-NK1.1+NKp46+CD49a-CD49b+


title: SS2_Exp2_Uninfected_N18_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: N18_B112559_B001942


title: B6_Spleen_CD8Treg_rep2_ATAC


title: SS2_Exp2_WT_Bystander_N22_B112571_B0000715

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: MTB-H37rv-zsGreen negative bystanders
Smartseq2 scRNAseq of mouse lung myeloid cells: MTB-H37rv-zsGreen negative bystanders Cell ID: N22_B112571_B0000715


title: rat_NK_ATAC_rep1

description: singlet CD3-CD45R-NKp46+NKR-p1+

organism: Rattus norvegicus

treatment_protocol: Splenic NK cells were FACS-sorted from mice or rats

value: BN/NHsdMcwi

value: singlet CD3-CD45R-NKp46+NKR-p1+


title: SS2_Exp2_Uninfected_D21_B112361_B007833

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D21_B112361_B007833


title: B6_Ly49Dn_mRNA

value: WT


title: B6_Ly49Dp_mRNA


title: rat_NK_ATAC_rep2

description: singlet CD3-CD45R-NKp46+NKR-p1+


title: B6_Ly49Dn_Terminator


title: B6_Ly49Dp_captureHiC_rep1

data_processing:
All capture Hi-C data were processed using the Juicer pipeline (version 1.6; -g mm10 -s Arima). Technical replicates were merged using the mega.sh script in Juicer.
Assembly: mm10
Supplementary files format and content: hic: interaction matrices (the inter.hic file from the juicer pipeline)

extract_protocol:
All Hi-C libraries were generated using the Arima Hi-C kit, following the vendor’s protocols.
To capture the Ly49 locus and its neighborhood, we designed oligos targeting chr6:128600000-130720000 (mm10) through https://earray.chem.agilent.com/suredesign, with 3x tiling density, moderately stringent repeat masking and boosting optimized for XT HS2. Capture was performed using SSEL XT HS2 DNA TE Kit (G9987A, Agilent), following the vendor’s protocol (G9983-900000, Agilent).


title: MAP8.B6.Ly49h_KO_homozygous_RNA_rep2


title: B6_Ly49Dp_captureHiC_rep2


title: SS2_Exp2_Uninfected_D2_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: D2_B112559_B001942


title: SS2_Exp2_Uninfected_B15_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: B15_B112494_B001304


title: B6_Ly49Dn_captureHiC_rep2


title: B6_Ly49Dn_captureHiC_rep1


title: SS2_Exp2_Uninfected_C14_B112361_B007833

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C14_B112361_B007833


title: NOD_NK_ATAC_rep2


title: 129_NK_ATAC_rep2


title: SS2_Exp2_Uninfected_K22_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: K22_B112559_B001942


title: 129_NK_ATAC_rep1


title: NOD_NK_ATAC_rep1


title: SS2_Exp2_Uninfected_C13_B112361_B007833

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C13_B112361_B007833


title: CAFs-rep2

city: Guangzhou

first: Chonghui

last: Hu

address: NA Zhongshan 2nd Road, Guangzhou

country: China

institute: Guangdong Provincial People’s Hospital

data_processing:
Clean reads were mapped to the genome (for example: Homo sapiens) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
Assembly: UCSC HG19
Supplementary files format and content: Excel file includes  include all gene expression

organism: Homo sapiens

source_name: CAFs

extract_protocol:
Cancer-associated fibroblasts (CAFs) and Primary normal fibroblasts (NFs) were isolated from pancreatic ductal carcinoma and paired non-cancerous tissues. Fibroblast populations were isolated by differential velocity adherent technique. Then the CAFs or NFs were treated with Trizol and extract the total RNA
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), ribosomal RNA was removed from 1 μg total RNA using Ribo-off® rRNA Depletion Kit (Human/Mouse/Rat, Vazyme, cat.N406-01, Nanjing, China) and purified using VAHTS® RNA Clean Beads (Vazyme, cat. N412, Nanjing, China). VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, cat.NR604-02, Nanjing, China) was used for lncRNA library construction following the manufacturer's protocol. The enriched ncRNAs were segmented with FRAG/PRIME Buffer. The first cDNA strand was generated by reverse transcription starting from -3 ’ , and the second cDNA strand with U was synthesized using the first cDNA strand. Single- or dual-index adapters were ligated to the fragments with ligase, and size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). The ligated products were amplified with PCR by the following conditions: Incubated at 37 ° C for 10 minutes to remove the U containing antisense chain, initial denaturation at 98℃ for 10 sec; 12-14 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, extension at 72℃ for 30 sec, and then final extension at 72 ℃ for 5 min. The average insert size for the final cDNA library was 290bp (±50 bp). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (Illumina Corporation， San Diego，USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

value: CAFs

value: primary cancer-associated firboblasts


title: NFs-rep3

source_name: NFs

value: NFs

value: primary normal fibroblasts


title: CAFs-rep3


title: CAFs-rep1


title: EL4_captureHiC

source_name: T lymphoblast

value: T lymphoblast


title: NFs-rep2


title: SS2_Exp2_Uninfected_N19_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: N19_B112494_B001304


title: B6_Ly49Dp_ATAC_rep1

value: Spleen

value: Natural killer cells

value: ex vivo


title: B6_Ly49Dn_ATAC_rep3

value: primary cells


title: B6_Ly49Dp_ATAC_rep3


title: SS2_Exp2_Uninfected_K3_B112559_B001942

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: K3_B112559_B001942

value: Lung


title: hHO_81

city: Shen Zhen

first: Yan

last: Wu

address: Tao Yuan

department: Department of biomedical engineering

institute: Southern University of Science and Technology

description: 10x genomics

data_processing:
Mapping to GRCh38 human genome, quality control and read counting of Ensemblgenes was performed by cellranger software with default parameter (v2.1.0). Cells with more than or equal 200 genes and less than or equal 10% percentage of mitochondrial genes detected were retained for subsequent analyses. Count matrix was used as the main input file for all downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampal organoid

extract_protocol:
4 day-70 hippocampal organoids were isolated to prepare sample #1. Organoids were dissected into fragments and plated on flasks. We cultured them for 2-4 days, then isolated them with a Pierce Primary Neuron Isolation Kit with papain enzyme. Single cells were isolated and lysed using the 10X Genomics Chromium platform. 10 day-81 hippocampal organoids were isolated to prepare sample #2. Organoids were isolated directly with a Pierce Primary Neuron Isolation Kit with papain enzyme, broken up by pipetting up and down.  The pre-sorting of live cells was completed using magnetic-activated cell sorting.  Single cells were isolated and lysed using the 10X Genomics Chromium platform.
Reverse transcription and library construction were performed using the 10X Chromium Single Cell 3' Reagent Kit

value: Hippocampal organoid

value: human pluripotent stem cell

value: neural cells

tag: time

value: 81 days

value: induced by growth factors


title: hHO70

description: 10x genomics

value: 70 days


title: B6_Ly49Dp_ATAC_rep2

value: WT


title: B6_Ly49Dn_ATAC_rep2


title: B6_Ly49Dn_ATAC_rep1


title: PANC-1 cells, YBX1 Input-rep2

data_processing:
Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated. Then these clean reads were aligned to human reference genome  (UCSC hg19) using bowtie2 software  (v2.2.4) with default parameters. Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).
Assembly: UCSC HG19
Supplementary files format and content: Excel file of the peak calling

source_name: pancreas

extract_protocol:
PANC-1 cells were pretreated with CAF-deirved Evs. Pretreated cells were UV-crosslinked (at 254nm, 400 mJ/cm2) and lysed with RIP lysis buffer. Lysed pellets were sonicated and treated with RNaseI (Life Technologies) Turbo DNase (Life Technologies). Then magnetic beads coated with 1 μg of YBX1 antibody were added into cell lysate and incubated overnight at 4 °C. The precipitated RNA was released with proteinase K and extracted 2 times with phenol chloroform isoamyl alcohol, followed by ethanol precipitation with a glycogen coprecipitant, 80% ethanol wash and final resuspension in TE.
Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Novaseq sequencer according to the manufacturer’s recommended protocol.

value: pancreas

value: Pancreatic cancer cells

value: pretreated with CAFs-derived Evs

tag: rip antibody


title: B6_Ly49Hp_ATAC_rep1


title: NFs-rep1

value: NFs

value: primary normal fibroblasts


title: B6_Ly49Hp_ATAC_rep2

value: Spleen


title: SS2_Exp2_Uninfected_C12_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C12_B112494_B001304

value: Cd11b+ and-or Cd11c+

value: Control


title: B6_Ly49Hn_ATAC_rep2

value: primary cells

value: Natural killer cells

value: ex vivo


title: B6_Ly49Hn_ATAC_rep1


title: SS2_Exp2_Uninfected_E14_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: E14_B112494_B001304

value: Lung


title: B6_Ly49Ap_ATAC_rep2


title: SS2_Exp2_Uninfected_N17_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: N17_B112494_B001304


title: PANC-1 cells, YBX1 Input-rep1


title: SS2_Exp2_Uninfected_C13_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: C13_B112494_B001304


title: B6_Ly49An_ATAC_rep2


title: B6_Ly49An_ATAC_rep1


title: B6_Ly49Ap_ATAC_rep1


title: MAP8.B6.Ly49m_WT_M9_RNA_rep2

value: total NK


title: MAP8.B6.Ly49m_KO_M9_RNA_rep2


title: MAP8.B6.Ly49m_KO_M9_RNA_rep1


title: MAP8.B6.Ly49m_WT_M9_RNA_rep1


title: SS2_Exp2_Uninfected_L10_B112494_B001304

description:
Illumina NovaSeq 6000
Smartseq2 scRNAseq of  mouse lung myeloid cells: Control
Smartseq2 scRNAseq of mouse lung myeloid cells: Control Cell ID: L10_B112494_B001304


title: MultiSeq10X_Invitro_Uninfected

description:
10X MultiSeq scRNAseq of matured BMDM cells: Uninfected control
Bone marrow derived macrophages were matured for 24 hours. THP-1 and PBMC cells included in this sample were for an unrelated project.

data_processing:
De-multiplexed using bcl2fastq version 2.20 and aligned with CellRanger v5.0.1
Assembly: mm10
Supplementary files format and content: h5ad: Processed complete data object from scanpy
Supplementary files format and content: csv: normalized counts and metadata table

source_name: Bone Marrow-derived Macrophage (BMDM)

growth_protocol: For invitro (MultiSeq): BMDM were isolated and grown in presence of mCSF. Differentiated cells were washed, and infected with H37Rv or H37Rv-deltaRD1 for 24 hours.

extract_protocol:
For in vitro, cells were washed, lifted, washed and stained to sort live/dead and presence of dsRed (bacteria).
For 10X, cells were sorted into tubes, washed, and processed according to 10X genomics protocol using 3'v3.1 kit. One exception was for in vitro study, cells were first labeled using lipid-tags (MultiSeq) prior to 10X processing.
10X Multiseq

value: Bone Marrow-derived Macrophage (BMDM)


title: MultiSeq10X_Invitro_Infected

description:
10X MultiSeq scRNAseqof MTB-mCherry infected matured BMDM cells: mCherry-positive infected cells
Bone marrow derived macrophages were matured and treated with MTB H37Rv-dsRed or MTB H37Rv-deltaRD1-dsRed for 24 hours and sorted for infected cells. THP-1 and PBMC cells included in this sample were for an unrelated project.


title: MultiSeq10X_Invitro_Bystander

description:
10X MultiSeq scRNAseq of MTB-mCherry infected matured BMDM cells: mCherry-negative bystander cells
Bone marrow derived macrophages were matured and treated with MTB H37Rv-dsRed or MTB H37Rv-deltaRD1-dsRed for 24 hours and sorted for uninfected and uninfected cells. THP-1 and PBMC cells included in this sample were for an unrelated project.


title: AntagomiR-141 treated cells

city: Mexico City

first: Federico

last: Castro-Muñozledo

address: Av Instituto Politecnico Nacional 2508, San Pedro Zacatenco

department: Cell Biology

country: Mexico

institute: CINVESTAV

data_processing:
Quality evaluation of raw reads, adapter removal and pairing of reads were carried out using the Geneious workflow software (Geneious version 9.1.8).
Paired reads were mapped to the reference genome OryCun2.0; GCF_000003625.3, using the Geneious for RNAseq mapper.
Differential expression (DE) analysis was carried out using the Geneious tools, calculating expression measures TPM, RPKM and FPKM normalized by the Median of Gene Expression Ratios method through the forth samples.
Assembly: oc2 GCF_000003625.3
Supplementary files format and content: tab-delimited text file including expression values for each sample

organism: Oryctolagus cuniculus

source_name: Corneal epithelium

growth_protocol: Cells were seeded at 2.7 x 103 cells/cm 2 together with mitomycin C-treated 3T3 cells plated at 2.2 x 104 cells/cm2, as previously described (Castro-Muñozledo, 1994, J Cell Sci 107, 2343-2351). Cells were cultured using the mixture DMEM-F12-Ham (3:1) supplemented with 5% fetal calf serum, 5 µg/ml insulin, 5 µg/ml transferrin,  0.4 µg/ml hydrocortisone, 2×10−9 M triiodothyronine, 1×10−10 M cholera toxin, 24.3 mg/l adenine and 10 ng/ml epidermal growth factor (EGF). Medium was changed every other day. Cultures were maintained at 36° C in a 10% CO2 and 90% air humidified atmosphere.

extract_protocol:
Before RNA isolation, the 3T3-feeder cells were removed by a 5-min incubation with 0.02% (w/v) EDTA  in PBS. Samples were washed twice with PBS; afterwards, total RNA was isolated at 4th, 6th and 10th days in culture, and 48 hrs after transfection of antagomiR-141, with Trizol reagent according to the instructions of the manufacturer, then resuspended in DNase/RNase free water.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: For miRNA inhibition experiments, RCE1(5T5) cells were seeded at previously indicated densities in the presence of 3T3 feeder cells. On day 4 of cell culture, feeder cells were detached from the culture plate using 0.02 % (w/v) EDTA in PBS wash. After that, epithelial cells were transfected with miRVana (Life Technologies, Carlsbad, Ca., USA) antagomiR-141-3p (MH10860) for miR-141-3p inhibition at 30 nM concentration. Transfection was made with Lipofectamine RNAiMAX (Invitrogen, Carlsbad, Ca., USA). The lipid-RNA complexes were added to the culture media according to the manufacturer's instructions. 24 hours after, fresh culture media was added, and 48 hours after transfection, cultures were washed with PBS, and RNA was subsequently isolated.

value: Corneal epithelium

value: antagomiR-141 transfection


title: Ev-treated PANC-1-rep2

data_processing:
Clean reads were mapped to the genome (for example: Homo sapiens) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
The expression level of mRNA were calculte using RSEM (RNA-Seq by Expectation Maximization) (v1.3.1) by normalized to FPKM (Fragments Per Kilobase Per Million reads)
Assembly: UCSC HG19
Supplementary files format and content: tab-delimited text file includes Fold change for samples

extract_protocol:
PANC-1 cells were pretreated with CAF-deirved Evs. The total RNA were extracted and sent for total RNA sequencing.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), mRNA with poly(A) is purified from 1μg total RNA using VAHTS® mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) through two rounds of purification. Subsequently, mRNA fragment was interrupted using VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃ 8min and reversed transcription into cDNA which would use to synthesise U-labeled second-stranded DNAs. An A-base was added to the blunt ends of each strand to ligase the indexed adapters which contains a T-base at the tail end. After UDG enzyme treatment of the U-labeled double-strand DNA, size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). Then the ligated products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 5 min; 12-17 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, and extension at 72℃ for 30 sec; final extension at 72℃ for 5 min. The average insert size of cDNA library was 280±80 bp. After purification by VAHTS® DNA Clean Beads (Vazyme,cat.N411-02, Nanjing, China), quality control of concentration and fragment size is performed by Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and Qubit assay tubes (Life, cat. 1604220, CA, USA). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 system (Illumina Corporation ， San Diego ， USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

value: Pancratic cancer cells

value: CAF-derived Evs


title: Ev-treated PANC-1-rep3


title: Ev-treated PANC-1-rep1


title: 10X_MTB_MouseLung_CTRL

description: 10X scRNAseq of mouse lung myeloid cells: Uninfected control

extract_protocol:
For in vivo, 28 days post infection mice were sacrificed and single cell lung suspension stained for flow cytometry (see manuscript protocol for details).
For 10X, cells were sorted into tubes, washed, and processed according to 10X genomics protocol using 3'v3.1 kit. One exception was for in vitro study, cells were first labeled using lipid-tags (MultiSeq) prior to 10X processing.

value: CD45+ myeloid cells


title: HUVEC_adhesion_RPF_B2

city: New Haven

first: Liana

last: Boraas

state: CT

address: 300 George Street, Room 752: Loria Center

institute: Yale University

description:
HUVEC_adhesion_RPF_B2
nicoli_adhesion_rpf2_run3_count_5_transcript_cds_v2

library_source: other

data_processing:
Raw reads were first trimmed using ReadKnead (https://github.com/vejnar/ReadKnead) using the “bktrim” algorithm. Trimmed reads were then filtered of small RNAs by mapping them onto sequences extracted from RepeatMasker (rRNA, snRNA, scRNA and tRNA types) and Ensembl (rRNA, snoRNA, snRNA, misc_RNA, Mt_rRNA and Mt_tRNA types) using STAR with the non-default parameters “–alignEndsType Local”, “–seedSearchStartLmaxOverLread 0.8” and “–outReadsUnmapped Fastx”. Unmapped reads (obtained from the last option above) were then mapped to human genome using STAR with the non-default options “–alignEndsType EndToEnd” and “–seedSearchStartLmaxOverLread 0.8”. The coding sequences (in genomic coordinates from FON1 file) were shifted of 12 nucleotides upstream to take into account the nucleotide separating the read start from the P-site of the translating ribosome. Read counts per mRNA were computed by summing the total number of reads overlapping at least 10 nucleotides the shifted mRNA annotation. Reads mapping to multiple loci (up to 5 loci) were accounted for by dividing 1 (each read) by the number of loci to which the read was mapped to.
Assembly: GRCh38
Supplementary files format and content: comma separated values file with raw counts for each sample
Library strategy: Ribo-Seq

molecule: other

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were maintained on on dishes coated with 0.1% w/v gelatin (10 min at room temperature in PBS; Sigma) in M199 medium (11150-059, Thermo Fisher) supplemented with 20% FBS (F0926-500 ML, Sigma), supplemented with 10 µg/mL endothelial cell growth supplement prepared from bovine hypothalamus, 50 µg/mL heparin filtered (H3149-100KU, Sigma), and 1% Penicillin-Streptomycin (15140122, Thermo Fisher). HDFs were  cultured in fibroblast growth medium (Fibroblast Growth Kit-Low Serum; ATCC, PCS-201–041) supplemented with 0.5 mL Phenol Red (ATCC, PCS-999-001, final concentration 33 µM) and 1% Penicillin-Streptomycin (ThermoFisher, 15140122).

extract_protocol:
Cell Lysis buffer from the RiboLace Kit from Immagina BioTECHNOLOGY (RL001) was used to collect whole cell or isolated FAs.
Ribo-Seq samples were prepared according to manufacturer’s instructions using the RiboLace Kit from Immagina BioTECHNOLOGY (RL001).

treatment_protocol: Both whole cell and isolated FA samples were seeded down on fibronectin. cells were treated for 5 minutes with 10 µg/mL cycloheximide (C4859-1ML, Sigma) at 37°C directly prior to focal adhesion isolation or collection of whole cell samples. Isolated FA samples were rinsed once with PBS and then treated for 3 minutes in a 2.5 mM triethanolamine (Sigma, 90279-100ML) low ionic strength buffer, pH 7.0. Immediately after the incubation, cell bodies were removed using hydrodynamic force (setting 1, Interplak, Conair) using PBS at ~0.5 cm from and ~90° to the surface of the dish. Isolated FA or whole cell samples were collected in trizol for RNA Extraction

value: Human Umbilical Vein Endothelial Cells

value: WT

tag: sample type

value: Isolated Focal Adhesions


title: HUVEC_adhesion_RPF_B1_2

description:
HUVEC_adhesion_RPF_B1_2
nicoli_adhesion_rpf2_run3_count_5_transcript_cds_v2


title: MAP8.B6.Ly49m_WT_M6_RNA_rep2

description: singlet CD4-CD8-TCRβ-CD19-NK1.1+NKp46+CD49a-CD49b+

value: Spleen


title: MAP8.B6.Ly49m_WT_M6_RNA_rep1


title: PANC-1 cells, YBX1 IP-rep2

value: pancreas

value: Pancreatic cancer cells

value: pretreated with CAFs-derived Evs

value: YBX1 antibody


title: PANC-1 cells, Control-rep3


title: 10X_MTB_MouseLung_NEG

description: 10X scRNAseq of MTB-mCherry infected mouse lung myeloid cells: mCherry-negative bystander cells


title: HUVEC_adhesion_RPF_B1

description:
HUVEC_adhesion_RPF_B1
nicoli_adhesion_rpf2_run3_count_5_transcript_cds_v2


title: MAP8.B6.Ly49m_KO_M6_RNA_rep2

value: Natural killer cells

value: ex vivo


title: PANC-1 cells, Control-rep1


title: HDF_adhesion_RPF_B1_2

description:
HDF_adhesion_RPF_B1_2
nicoli_adhesion_rpf2_run3_count_5_transcript_cds_v2

source_name: Human Dermal Fibroblasts

value: Human Dermal Fibroblasts


title: PANC-1 cells, YBX1 IP-rep1


title: PANC-1 cells, Control-rep2


title: m5C Input-rep2

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Assembly: UCSC HG19
Supplementary files format and content: bed

extract_protocol:
PANC-1 cells were pretreated with CAF-deirved Evs. The total RNA were extracted via GenSeqTM m5C RNA IP Kit (GenSeq Inc., China)
Both the input samples without immunoprecipitation and the m5C IP samples were used for RNA-seq library geneMouseion with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
MeRIP-seq


title: in9_3

city: Nanjing

first: Xinyue

last: Gu

address: Chunhua Street

institute: China pharmaceutical university

data_processing:
Sequencing on Illumina NovaSeq 6000 platform.
Qubit 4.0 quantitative, mixed by the proportion of data on the machine
Bridge PCR amplification on cBot to generate clusters
Illumina NovaSeq 6000 platform sequencing
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: 4T1 breast cancer cells were cultured in 1640 medium containing 10 % fetal bovine serum ( FBS ) and antibiotics at 37 °C and 5 % CO2 saturated humidity.

extract_protocol:
Total RNA was extracted from tissue samples, and the concentration and purity of the extracted RNA were detected using Nanodrop2000. 1ug of total RNA was used for the construction of sequencing libraries.
Eukaryotic mRNA sequencing is based on the Illumina platform to sequence all mRNAs transcribed from specific tissues or cells of eukaryotes at a certain period. The sequencing experiment uses the Illumina NovaSeq Reagent Kit method for library construction.

value: breast cancer cells


title: in9_2


title: m5C IP-rep2

value: m5c antibody


title: MAP8.B6.Ly49h_WT_Hn_RNA


title: HDF_adhesion_RPF_B2

description:
HDF_adhesion_RPF_B2
nicoli_adhesion_rpf2_run3_count_5_transcript_cds_v2


title: HDF_adhesion_RPF_B1

description:
HDF_adhesion_RPF_B1
nicoli_adhesion_rpf2_run3_count_5_transcript_cds_v2


title: m5C Input-rep1


title: MAP8.B6.Ly49h_KO_Hn_RNA_rep2


title: HUVECs - Isolated FA S4

data_processing:
Raw reads were processed using LabxPipe (https://github.com/vejnar/LabxPipe): first reads were trimmed using ReadKnead (https://github.com/vejnar/ReadKnead) using the “bktrim” algorithm using the sequence AAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. They were then mapped to the human genome using STAR with non-default parameters “–alignEndsType Local” and “–seedSearchStartLmaxOverLread 0.8”. FON1 files containing genes (or “metagenes”) were generated by concatenating the isoforms of each gene together using the “–method union” option of the ”fon_transform” tool. Read counts per gene were computed by summing the total number of reads overlapping at least 10 nucleotides of the gene (i.e. metagene) annotation. Reads mapping to multiple loci were accounted for by dividing 1 (each read) by the number of loci to which the read was mapped to. To identify differentially expressed genes, genes with at least 1 count in both conditions in any of the replicates were first selected, and input to the “DESeq” function. The “results” function with parameters “pAdjustMethod=”fdr”, independentFiltering=FALSE” returned the differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: comma separated values file with raw counts for each sample

extract_protocol:
Trizol was used to extract RNA.The quality was verified using the 2100 Bioanalyzer.
500 ng of total RNA was used to prepare Lexogen QuantSeq 3′ mRNA-Seq FWD libraries for Illumina deep-sequencing according to the manufacturer’s protocols. Libraries were amplified for 13-14 PCR cycles.

treatment_protocol: Both whole cell and isolated FA samples were seeded down on fibronectin. Isolated FA samples were rinsed once with PBS and then treated for 3 minutes in a 2.5 mM triethanolamine (Sigma, 90279-100ML) low ionic strength buffer, pH 7.0. Immediately after the incubation, cell bodies were removed using hydrodynamic force (setting 1, Interplak, Conair) using PBS at ~0.5 cm from and ~90° to the surface of the dish. Isolated FA or whole cell samples were collected in trizol for RNA Extraction

value: Endothelial Cells


title: m5C IP-rep1


title: in9_1


title: MAP8.B6.Ly49h_KO_Hn_RNA_rep1


title: LV2_3


title: HUVECs - Isolated FA S3


title: LV2_2


title: HDF_whole_cell_RPF_B2

description:
HDF_whole_cell_RPF_B2
nicoli_adhesion_rpf_wc_run1_count_5_transcript_cds_v2

value: Whole Cell


title: LV2_1


title: HDF_whole_cell_RPF_B1

description:
HDF_whole_cell_RPF_B1
nicoli_adhesion_rpf_wc_run1_count_5_transcript_cds_v2


title: KPC LM2 cells biological replicate 2

city: New York

first: Norihiro

last: Yamaguchi

state: Ny

address: 1230 York Avenue, Box 16

department: Systems Cancer Biology

institute: The Rockefeller University

description: KPC liver metastatic 2nd generation (KPC LM2) 2

data_processing:
mRNA reads were aligned to human or mouse reference genome (hg19 or mm39) with STAR 2.7.6a using the default setting (Dobin et al., 2013). To quantify gene expression, we counted sequenced reads mapping to exon regions using featureCounts v2.0.0 (Liao et al., 2014). The sequencing and mapping quality were examined with MultiQC v1.9 (Ewels et al., 2016). Differential expression analysis was performed using DESeq2 v1.24 (Love et al., 2014).
Assembly: hg19 and mm39
Supplementary files format and content: excel spread sheet with the differential gene expression analysis results

source_name: liver metastasizing pancreatic ductal carcinoma

growth_protocol: 500,000 cells of each were injected into the spleen on day 1 and liver metastazing tumors were harvested on day 21

extract_protocol:
RNA was extracted from ex vivo liver metastasizing tumors using Norgen's total RNA purification kit
Using Truseq RNA library prep kit Ver2, the manufacture's protocol has been followed

value: KPC LM2

value: pancreatic cancer


title: KPC LM2 cells biological replicate 3

description: KPC liver metastatic 2nd generation (KPC LM2) 3

value: liver metastasizing pancreatic ductal carcinoma


title: 10X_MTB_MouseLung_POS

description: 10X scRNAseq of MTB-mCherry infected mouse lung myeloid cells: mCherry-positive infected cells

value: Lung

value: CD45+ myeloid cells


title: HUVECs - Isolated FA S1

value: Human Umbilical Vein Endothelial Cells

value: WT


title: MAP8.B6.Ly49m_KO_M6_RNA_rep1

value: Spleen

value: total NK


title: KPC LM2 cells biological replicate 1

description: KPC liver metastatic 2nd generation (KPC LM2) 1


title: B6_Ly49DpHp_ampliconBS

data_processing:
samples were processed using a custom pipeline publicly available at https://github.com/ChangxuFan/wgbs/tree/fanc
Briefly: trimgalore was used to remove adaptors and low-quality bases; trimmed reads were aligned to the lambda genome using Bismark to assess bisulfite conversion rates. All libraries have > 99.5% conversion rates; trimmed reads were then aligned to the mm10 genome using Bismark, which also calculates the coverage and methylation level of each CpG across the genome; A custom script was used to convert Bismark outputs to methylC tracks, which were visualized using WashU Epigenome Browser.
Amplicon data were processed similar to WGBS. The percentage of reads with a given number of protected cytosines were counted using GenomicAlignments::stackStringsFromBam() in R.
Assembly: mm10
Supplementary files format and content: methylC.gz: methylC tracks for the visualization of the methylation level and sequencing depth at each CpG across the genome
Supplementary files format and content: csv: columns: each CpG covered by the amplicon-based bisulfite sequencing; rows: reads; entries: nucleotide

extract_protocol:
Genome DNA was extracted using Quick-DNA Microprep Kit (Zymo Research, R3020).
WGBS: DNA was sheared to produce 350 bp DNA fragments. 100 ng of DNA fragments were then bisulfite converted using EZ DNA Methylation-Gold Kit (Zymo, D5005) for subsequent WGBS library construction, with xGen Methyl-Seq DNA Library Prep Kit (IDT, 10009860). Amplicon bisulfite: 500ng of genomic DNA was bisulfite-converted using EZ DNA Methylation-Gold Kit (Zymo Research, D5005). The bisulfite-converted DNA was then amplified with target-specific primers using ZymoTaq PreMix (Zymo Research, E2003). Amplicon libraries were then generated using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645).


title: HUVECs - Whole Cell S4


title: NCI-H1299 cells, Adenoviral CYB5R3 3

city: Daejeon

first: Misun

last: Won

address: 125 Kwahag-ro, Yuseong-gu

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
The raw fastq file reads were trimmed using 'Trim galore!' (v.0.6.4) to remove adapters and low-quality reads.
The reads were then mapped to human genome (hg38) using 'STAR' (v.2.7.3a).
gene expression was quantified using the count module in 'STAR'.
The edgeR package (v.3.32.0) was employed to select differentially expressed genes (DEGs) from RNA-seq count data.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes CPM values for all Sample

growth_protocol: NCI-H1299 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: NCI-H1299 cells were infected with adenovirus at a mode of infection (MOI) of 100.

value: Non-small cell lung cancer

value: CYB5R3 overexpression

value: Adenoviral CYB5R3 treatment

value: 24 hours


title: KPC cells biological replicate 3

description: KPC parental 3

value: KPC


title: B6_Ly49DpHn_ampliconBS

value: Natural killer cells

value: ex vivo


title: NCI-H1299 cells, Adenoviral CYB5R3 2


title: HUVECs - Whole Cell S3

value: Endothelial Cells

value: Whole Cell


title: B6_Ly49DnHp_ampliconBS


title: KPC cells biological replicate 2

description: KPC parental 2

value: pancreatic cancer


title: NCI-H1299 cells, Adenoviral CYB5R3 1


title: HUVECs - Whole Cell S2


title: B6_Ly49DnHn_ampliconBS


title: HUVECs - Whole Cell S1

value: Human Dermal Fibroblasts

value: Fibroblasts

value: Isolated Focal Adhesions


title: HUVECs - Isolated FA S2

value: Human Umbilical Vein Endothelial Cells


title: B6_Ly49DpHp_WGBS

value: WT


title: HDFs - Isolated FA S4


title: NCI-H1299 cells, Adenoviral Empty Vector 3

value: Lung

value: Adenoviral EV treatment


title: scRNA-Seq of skin, CE

first: Jiao

last: Qu

address: Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China

institute: Nanjing University

description: The CE group was treated with celastrol and imiquimod

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines  (v3.1.0,10X Genomics).
Assembly: mm10  (GRCm38)
Supplementary files format and content: barcodes.tsv; features.tsv; matrix.mtx

source_name: Skin

extract_protocol:
The mice project from dorsal skin
RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR

value: Skin

tag: age

value: post natal 7 weeks

value: celastrol and imiquimod

tag: condition

value: imiquimod-induced psoriasis


title: KPC cells biological replicate 1

description: KPC parental 1

value: liver metastasizing pancreatic ductal carcinoma

value: KPC


title: B6_Ly49DpHn_WGBS

value: Spleen

value: Natural killer cells

value: ex vivo


title: scRNA-Seq of skin, IMQ

description: The IMQ  group was treated with imiquimod

value: imiquimod


title: HDFs - Isolated FA S3

value: Human Dermal Fibroblasts


title: scRNA-Seq of skin, Normal

description: The normal group was treated with glycerin

value: control


title: B6_Ly49DnHp_WGBS


title: NCI-H1299 cells, Adenoviral Empty Vector 1

value: Non-small cell lung cancer

value: 24 hours


title: NCI-H1299 cells, PBS 3

value: WT

value: PBS treatment


title: HDFs - Isolated FA S2

value: Fibroblasts

value: Isolated Focal Adhesions


title: B6_Ly49DnHn_WGBS


title: PANC1 LM3 cells shNPTX1_4 biological replicate 4

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_4 4

data_processing:
mRNA reads were aligned to human or mouse reference genome (hg19 or mm39) with STAR 2.7.6a using the default setting (Dobin et al., 2013). To quantify gene expression, we counted sequenced reads mapping to exon regions using featureCounts v2.0.0 (Liao et al., 2014). The sequencing and mapping quality were examined with MultiQC v1.9 (Ewels et al., 2016). Differential expression analysis was performed using DESeq2 v1.24 (Love et al., 2014).
Assembly: hg19
Supplementary files format and content: excel spread sheet with the differential gene expression analysis results

growth_protocol: 500,000 cells of each cells (shCTRL, shNPTX1_3, and shNPTX1_4 expressing PANC1 LM3 cells) were injected into the spleen on day 1 and liver metastazing tumors were harvested on day 21

value: PANC1 LM3

value: pancreatic cancer

value: NPTX1 knock down


title: HDFs - Isolated FA S1

value: Whole Cell


title: HDFs - Whole Cell S3


title: NCI-H1299 cells, PBS 1

value: Lung


title: PANC1 LM3 cells shNPTX1_4 biological replicate 3

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_4 3

value: liver metastasizing pancreatic ductal carcinoma


title: PANC1 LM3 cells shNPTX1_4 biological replicate 2

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_4 2


title: HDFs - Whole Cell S2


title: NCI-H1299 cells, Adenoviral Empty Vector 2

value: Adenoviral EV treatment


title: HDFs - Whole Cell S1


title: D45_Un_S1

city: Izmir

first: Burak

last: Kahveci

address: Izmir

country: Turkey

institute: Izmir Biomedicine and Genome Center

data_processing:
All the samples were sequenced on the NovaSeq 6000 System
Fastq files quality check was performed using FASTQC quality control tool.
Sequences were trimmed using Trimmomatic.
Assembly: hg38
Supplementary files format and content: csv file includes count values for each samples
Supplementary files format and content: csv file includes fpkm values for each samples

source_name: hiPSC-derived eye cells

extract_protocol:
NovaSeq Reagent Kits v1.5
Illumina Stranded Total RNA Prep with with Ribo-Zero Plus

value: induced pluripotent stem cells

value: Day 45 Untreated

value: Ocular Differentiation


title: PANC1 LM3 cells shNPTX1_3 biological replicate 3

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_3 3


title: PANC1 LM3 cells shNPTX1_4 biological replicate 1

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_4 1


title: PANC1 LM3 cells shNPTX1_3 biological replicate 2

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_3 2


title: D45_C+_S2

value: Day 45 Carbachol Treated (24 h)


title: iPSC_S2

source_name: Induced pluripotent stem cells

value: Undifferentiated iPSC


title: D45_Un_S2


title: NCI-H1299 cells, PBS 2

source_name: Lung

value: Non-small cell lung cancer

value: 24 hours


title: PANC1 LM3 cells shNPTX1_3 biological replicate 1

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_3 1


title: NM5

type: RNA

city: Chengdu

first: Ningyuan

last: Wen

address: No.37 GuoXueXiang, Wuhou district, Chengdu, China

institute: West China Hospital, Sichuan University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 10 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.  When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 2.0 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.
The significantly differentially expressed circRNAs were defined as normalized log2 ratios>1.5 and p-values <= 0.05).

source_name: Total RNA from human bile exosome samples

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Bile samples were obtained from patients undergoing preoperative biliary drainage, collected within 6 hours after emptying the drainage bag and immediately stored at -80℃ until further processing and testing. The isolation of exosomes was conducted via differential ultracentrifugation. Total RNA was extracted using an improved TRIzol-based method.

value: bile exosome

tag: disease

value: benign biliary obstruction

tag: patient

value: patient No.5


title: NM3

tag: tissue

value: patient No.3


title: PANC1 LM3 cells shCTRL biological replicate 4

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shCTRL 4

value: PANC1 LM3

tag: cell type

value: pancreatic cancer

value: WT


title: D45_C+_S1


title: SNU-449 cells transfected with USP48, rep3

city: Nanning

first: Bo

last: Tang

address: No. 6 Shuangyong Road

institute: The First Affiliated Hospital of Guangxi Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The conversion of image signals (.DAT files) to digital signals (.CEL files) was performed by the AGCC software, while fluorescence signal intensity at the probe level was recorded in .CEL files. The .CEL files served as the primary source files for data preprocessing, which involved background correction, integration of probe signals into probeset signals, and inter-slice normalization to eliminate non-biological inter-sample variability. Data preprocessing typically employed the RMA algorithm. Subsequently, sample correlation analysis, including cluster analysis and principal component analysis, was conducted on the data processed by the RMA algorithm to the similarity and grouping of the samples.

label: biotin

source_name: SNU-449 cells transfected with USP48

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The SNU-449 cell line was grown in Roswell Park Memorial Institute (RPMI) - 1640 medium (Gibco, USA). By supplementing the medium with 10% fetal bovine serum (FBS, Gibco), penicillin, and streptomycin, we reduced microbial contamination and provided nutrition.

extract_protocol: After harvesting SNU-449 cells transfected by USP48, Trizol was used for total RNA extraction.

treatment_protocol: Cells were inoculated into 24-well plates at a density of 3 × 105 cells/mL for viral infections, and cultured until cell fusion reached 20%-30%. Lenti-USP48 viruses with a MOI ≥ 90 were transduced into the cells for 24 hours in serum-free medium using HiTransG A. Subsequently, the cells were further cultured in complete medium for 4-6 days before puromycin was added for concentration screening and stable expression strain cell screening.

tag: cell line

value: USP48 OE


title: NM2

value: patient No.2


title: PANC1 LM3 cells shCTRL biological replicate 3

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shCTRL 3

value: liver metastasizing pancreatic ductal carcinoma

tag: genotype


title: D45_F+_S1

value: induced pluripotent stem cells

value: Day 45 Forskolin Treated (24 h)


title: SNU-449 cells transfected with USP48, rep2


title: SNU-449 cells transfected with USP48, rep1


title: NM1

value: patient No.1


title: PANC1 LM3 cells shCTRL biological replicate 2

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shCTRL 2


title: NM4

value: patient No.4


title: DAY21_S2

value: Day 21

value: Ocular Differentiation


title: M5

value: malignant biliary obstruction


title: iPSC_S1

value: Undifferentiated iPSC


title: PANC1 LM3 cells shCTRL biological replicate 1

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) shCTRL


title: MAP8.B6.Ly49m_KO_nanopore

data_processing:
Base-calling from raw sequencing data was perform using Guppy (v6.4.6) with the dna_r10.4.1_e8.2_400bps_sup model. Base-called reads (fastq file) were aligned to the mouse genome (mm10) using minimap2 (v2.24, -ax map-ont).
We then filtered the fastq file for reads mapped to the Ly49 locus (chr6:129800001-130500000), irrespective of their mapping status (primary, secondary, or supplementary). These reads were used to perform de novo assembly of the Ly49 locus using flye (v2.9.2, --nano-hq -g 700k).
Assembly: mm10
Supplementary files format and content: fa: assembled Ly49 locus
Library strategy: DNA-Seq

source_name: Spleen

extract_protocol:
High molecular weight DNA was extracted from ~5 million splenocytes of 1 MAP8.B6.Ly49h or MAP8.B6.Ly49m KO mouse, using Gentra Puregene Cell Kit (8 x 10^8) (catalog # 158767).
8 ug of DNA was then fragmented using Covaris g-TUBE (catalog 520079), which was spun at 4200 rpm to fragment the DNA to an average size of 50 Kb. The 7.7 ug DNA recovered after fragmentation was subsequently cleaned using Short Fragment Eliminator (Oxford Nanopore EXP-SFE001). The sequencing library was prepared using Ligation Sequencing Kit V14 (ONT SQK-LSK114) with 2 ug DNA as input, and 22 fmol of the library was run on a single PromethION flow cell (FLO-PRO114M) for 42 hours without reloading.

treatment_protocol: Total splenocytes were isolated from mice

value: Spleen

value: Splenocytes


title: M3

value: bile exosome

value: patient No.3


title: DAY30_S2

value: Day 30


title: left ventricular myocardial tissue of USP29-KO mice induced by 4weeks TAC replicate 3

city: Shenyang

first: Xi

last: Jiang

address: Shengjing Hospital of China Medical University, No.39 Huaxiang Road

institute: Shengjing Hospital of China Medical University department   Department of Cardiology

data_processing:
To align the sequence fragments to the reference genome for mice (mm10/GRCm38), we employed HISAT2 software. The resulting files were then converted to binary BAM format using SAMtools. Following this, StringTie was used with default parameters to calculate Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) for identified genes. DESeq2 was applied to identify differentially expressed genes (DEGs) based on two criteria: (1) fold change greater than 2; and (2) adjusted P value <0.05." The RNA-seq data has been deposited in GEO, and the accession key is PRJNA1081174.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: left ventricular myocardial tissue

extract_protocol:
TRIzol reagent (15596-026, Invitrogen) was utilized to isolate total RNA from LV tissues or cell samples. Two micrograms RNA were reverse-transcribed into first-strand cDNA utilizing Transcriptor 1st Strand cDNA Synthesis reagent (04896866001, Roche). Subsequently, PCR amplification was conducted utilizing SYBR Green Mix PCR Master (04887352001, Roche). Target gene expression levels were standardized against GAPDH, and Table S2 presents the related gene primer sequences.
We isolated total RNA from cardiac tissues of USP29-KO and WT mice that were subjected to four weeks of TAC. Subsequently, a cDNA library was generated and sequenced using the MGISEQ-2000 RS system with 50-bp single-end reads.

value: left ventricular myocardial tissue

value: Primary cardiomyocytes of rat Suckling rats

value: transverse aortic constriction


title: SNU-449 cells transfected with vector, rep3

source_name: SNU-449 cells transfected with vector

value: Ctrl


title: D45_F+_S2

value: induced pluripotent stem cells


title: PANC1 LM3 cells biological replicate 3

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) 3

value: liver metastasizing pancreatic ductal carcinoma

value: PANC1 LM3

value: pancreatic cancer

value: WT


title: left ventricular myocardial tissue of USP29-KO mice induced by 4weeks TAC replicate 2


title: SNU-449 cells transfected with vector, rep2


title: SNU-449 cells transfected with vector, rep1


title: DAY35_S2

value: Day 35

value: Ocular Differentiation


title: M1

value: malignant biliary obstruction

value: patient No.1


title: PANC1 LM3 cells biological replicate 2

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) 2


title: PANC1 LM3 cells biological replicate 1

description: PANC1 liver metastatic 3rd generation (PANC1 LM3) 1


title: left ventricular myocardial tissue of USP29-KO mice induced by 4weeks TAC replicate 1


title: left ventricular myocardial tissue of WT mice induced by 4weeks TAC replicate 3


title: M4

value: patient No.4


title: DAY30_S1


title: left ventricular myocardial tissue of WT mice induced by 4weeks TAC replicate 2


title: PANC1 cells biological replicate 3

description: PANC1 parental 3


title: DAY35_S1


title: PANC1 cells biological replicate 2

description: PANC1 parental 2


title: MAP8.B6.Ly49h_KO_nanopore

extract_protocol:
High molecular weight DNA was extracted from ~5 million splenocytes of 1 MAP8.B6.Ly49h KO mouse, using Gentra Puregene Cell Kit (8 x 10^8) (catalog # 158767).
8 ug of DNA was then fragmented using Covaris g-TUBE (catalog 520079), which was spun at 4200 rpm to fragment the DNA to an average size of 50 Kb. The 7.7 ug DNA recovered after fragmentation was subsequently cleaned using Short Fragment Eliminator (Oxford Nanopore EXP-SFE001). The sequencing library was prepared using Ligation Sequencing Kit V14 (ONT SQK-LSK114) with 2 ug DNA as input, and 22 fmol of the library was run on a single PromethION flow cell (FLO-PRO114M) for 42 hours without reloading.

value: Spleen

value: Splenocytes


title: DAY21_S1

value: Day 21


title: PANC1 cells biological replicate 1

description: PANC1 parental 1


title: left ventricular myocardial tissue of WT mice induced by 4weeks TAC replicate 1

value: left ventricular myocardial tissue


title: RNA sequencing of Priestia megaterium CL-1 without salt stress ( 2)

city: Noida

first: Rajnish

middle: Prakash

last: Singh

address: A 10, A Block, Block A, Industrial Area, Sector 62, Noida

country: India

institute: Jaypee Institute of Information Technology

data_processing:
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using trimgalore (Phred score threshold of 20)
Trimmed sequence reads were mapped to reference genome using Bowtie2 aligner.
Read count extraction was done using featureCounts and normalization and DEG identification was done using DESeq2.
Assembly: GCF_009935415.1,  GCF_002220285.1
Supplementary files format and content: Tab delimited text file includes normalized counts for each sample

organism: Priestia megaterium

source_name: bacteria

extract_protocol:
The bacterial cells were lysed using Qiagen bacterial lysis buffer, the lysate containing RNA was passed to silica membrane of Qiagen RNeasy spin column, and the total RNA was eluted using nuclease free water. The quality of the RNA was analysed through Agilent Bioanalyzer.
QIAseqFastSelect – 5S/16S/23S Kit for Bacterial Ribodepletion and QIAseq Stranded RNA Library Kit for Library preparation following manufacturer's protocols.

value: bacteria

value: without salt stress


title: RNA sequencing of Priestia megaterium CL-1 without salt stress ( 1)


title: M2

value: bile exosome

value: patient No.2


title: RNA sequencing of Priestia megaterium CL-1 at 8% salt stress ( 2)

value: with 8% salt stress


title: RNA sequencing of Priestia megaterium CL-1 at 8% salt stress ( 1)


title: Neu54yo_ZT30_replicate2

status: Public on Apr 19 2024

type: genomic

city: Vilnius

first: Karolis

last: Koncevičius

address: Saulėtekio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

description: neutrophils purified with magnetically activated cell sorting

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylationEPIC v1.0 Beadchip using standard Infinium HD Methylation Assay protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing:
Processeing was done using the R “minfi” package. First, all samples having more than 3% of probes with poor detection p-values (detection p < 0.05) using an alternative detection p-value approach(Heiss and Just 2019) were removed as outliers. Then array normalization was performed using “noob” background correction followed by functional normalization, and signals from the methylated and unmethylated channels were combined to obtain the methylation beta values. Additional outliers were identified by measuring Pearson’s correlations among all the sample pairs and removing samples with an average inter-sample correlation value more than three standard deviations below the mean. Finally, for the datasets that contained technical replicates for every sample, all the samples with only a single replicate remaining after quality control were discarded.
R "minfi" package computed Average Beta values after "noob" background correction and "functional" normalization

label: Cy3 and Cy5

source_name: Neutrophils

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Neutrophils were isolated from whole blood by immunomagnetic negative selection with EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL) according to the manufacturer's protocol. The remaining fraction of white blood cells depleted of neutrophils were snap-frozen and stored in -80 °C before DNA extractionDNA was extracted with NucleoSpin® Tissue kit using the standard protocol

tag: Sex

value: male

tag: ct


title: Neu54yo_ZT30_replicate1


title: Neu54yo_ZT27_replicate2


title: Neu54yo_ZT27_replicate1


title: Neu54yo_ZT30


title: Neu54yo_ZT27


title: Neu54yo_ZT24_replicate2