title: 665X_d42_young_cDNA190916_C5


title: 665X_d42_young_cDNA190916_C9

status: Public on Mar 05 2021

type: SRA

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 platform.
Demultiplexed fastq reads were trimmed with trimgalore (v0.6.6, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), using default parameters.
Trimmed reads were mapped to Ensembl build GRCh38.87 using HISAT2 (v2.1.0) with the options --sp 1000,1000.
Aligned reads were quantified using featureCounts, as implemented in Rsubread (Subread v2.0.0).
Downstream analyses were performed using Bioconductor packages: scater and the SingleCellExperiment data infrastructure.
Genome_build: GRCh38
Supplementary_files_format_and_content: GEO_supporting_processed_data_file_raw_count_matrix.csv.gz - the Rsubread count matrix as a gzipped comma separated values file.

molecule: polyA RNA

organism: Homo sapiens

source_name: Haemagglutinin specific B cell

extract_protocol:
Index sorting of haemagluttin (HA) specific B cells was performed with samples from days 0 and 42. B cells were negatively selected magnetically from cryopreserved peripheral blood mononuclear cells, after 1 hour rest at 37C. Individual HA specific B cells were isolated using FACS and fluorescently labelled recombinant haemagglutinin. Sorts were performed into 96 well plates.
Single HA specific B cells were index sorted in RNA lysis buffer, and samples were processed using plate-based SMART-Seq (SMART-Seq HT kit, Takara-Clontech). cDNA libraries were generated using Nextera XT adaptors, following the Takara-Clontech HT kit instructions. After library creation, libraries were pooled for clean-up.
scRNASeq (SMART-Seq) of haemagglutinin specific B cell flow sorted from PBMC

tag: treament

value: trivalent influenza vaccination

tag: time

value: day 42

tag: age

tag: cell type

value: PBMC

tag: cell type_sorted

value: haemagglutinin specific B cell


title: 665X_d42_young_cDNA190916_D11


title: 665X_d42_young_cDNA190916_D10


title: 665X_d42_young_cDNA190916_D9


title: 665X_d42_young_cDNA190916_E5


title: 665X_d42_young_cDNA190916_E4


title: 665X_d42_young_cDNA190916_D3


title: 665X_d42_young_cDNA190916_C2


title: 665X_d42_young_cDNA190916_C1


title: 665X_d42_young_cDNA190916_C4


title: 665X_d42_young_cDNA190916_C3


title: 665X_d42_young_cDNA190916_C12


title: 665X_d42_young_cDNA190916_C11


title: 665X_d42_young_cDNA190916_E6


title: 665X_d42_young_cDNA190916_E10


title: 665X_d42_young_cDNA190916_C10


title: 665X_d42_young_cDNA190916_B9


title: 665X_d42_young_cDNA190916_B6


title: 665X_d42_young_cDNA190916_B12


title: 665X_d42_young_cDNA190916_B4


title: 665X_d42_young_cDNA190916_B5


title: 665X_d42_young_cDNA190916_C6


title: 665X_d42_young_cDNA190916_B11


title: 665X_d42_young_cDNA190916_B3


title: 665X_d42_young_cDNA190916_A12


title: 665X_d42_young_cDNA190916_A5


title: 665X_d42_young_cDNA190916_B10


title: 665X_d42_young_cDNA190916_A9


title: 665X_d42_young_cDNA190916_A11


title: 665X_d0_young_cDNA190916_G8

value: control

value: day 0


title: 665X_d0_young_cDNA190916_F8


title: 665X_d0_young_cDNA190916_G7


title: 665X_d42_young_cDNA190916_A10


title: 665X_d0_young_cDNA190916_E8


title: 665X_d0_young_cDNA190916_E7


title: 665X_d0_young_cDNA190916_F7


title: 665X_d0_young_cDNA190916_D7


title: 665X_d0_young_cDNA190916_C8


title: 665X_d0_young_cDNA190916_B7


title: 665X_d0_young_cDNA190916_C7


title: 665X_d0_young_cDNA190916_D8


title: 665X_d0_young_cDNA190916_B8


title: 665X_d0_young_cDNA190916_A8


title: 660R_d42_old_cDNA190921_H9


title: 660R_d42_old_cDNA190921_H12


title: 665X_d0_young_cDNA190916_A7


title: 660R_d42_old_cDNA190921_H11


title: 660R_d42_old_cDNA190921_G10


title: 660R_d42_old_cDNA190921_H10


title: 660R_d42_old_cDNA190921_G12


title: 660R_d42_old_cDNA190921_G9


title: 660R_d42_old_cDNA190921_G11


title: 665X_d42_young_cDNA190916_A6


title: 660R_d42_old_cDNA190921_F11


title: 660R_d42_old_cDNA190921_F10


title: 660R_d42_old_cDNA190921_E9


title: 660R_d42_old_cDNA190921_E12


title: 660R_d42_old_cDNA190921_E11


title: 660R_d42_old_cDNA190921_F12


title: 660R_d42_old_cDNA190921_E10


title: 660R_d42_old_cDNA190921_D11


title: 660R_d42_old_cDNA190921_D12


title: 660R_d42_old_cDNA190921_D9


title: 660R_d42_old_cDNA190921_C12


title: 660R_d42_old_cDNA190921_D10


title: 660R_d42_old_cDNA190921_C9


title: 660R_d42_old_cDNA190921_C10


title: 660R_d42_old_cDNA190921_C11


title: 660R_d42_old_cDNA190921_B9


title: 660R_d42_old_cDNA190921_B12


title: 660R_d42_old_cDNA190921_B10


title: 660R_d42_old_cDNA190921_A9


title: 660R_d42_old_cDNA190921_A10


title: 660R_d0_old_cDNA190921_D8


title: 660R_d0_old_cDNA190921_C7


title: 660R_d0_old_cDNA190921_C8


title: 660R_d42_old_cDNA190921_A11


title: 660R_d42_old_cDNA190921_F9


title: 660R_d0_old_cDNA190921_B8


title: 660R_d0_old_cDNA190921_B7


title: 660R_d0_old_cDNA190921_A7


title: 652H_d42_old_cDNA190916_A4


title: 660R_d0_old_cDNA190921_D7


title: 652H_d42_old_cDNA190916_A3


title: 652H_d0_old_cDNA190916_B1


title: 652H_d0_old_cDNA190916_B2


title: 660R_d42_old_cDNA190921_B11


title: 652H_d0_old_cDNA190916_A2


title: 643Y_d42_old_cDNA190917_D12


title: 652H_d0_old_cDNA190916_A1


title: 643Y_d42_old_cDNA190917_C9


title: 643Y_d42_old_cDNA190917_C11


title: 660R_d42_old_cDNA190921_A12


title: 643Y_d42_old_cDNA190917_B12


title: 643Y_d42_old_cDNA190917_B11


title: 643Y_d42_old_cDNA190917_B9


title: 643Y_d42_old_cDNA190917_B10


title: 643Y_d42_old_cDNA190917_A9


title: 660R_d0_old_cDNA190921_E7


title: 643Y_d42_old_cDNA190917_A11


title: 660R_d0_old_cDNA190921_A8


title: 643Y_d42_old_cDNA190917_A10


title: 643Y_d0_old_cDNA190917_C8


title: 643Y_d0_old_cDNA190917_B8


title: 643Y_d0_old_cDNA190917_C7


title: 643Y_d0_old_cDNA190917_B7


title: 637R_d42_young_cDNA190921_H6


title: 643Y_d42_old_cDNA190917_C12


title: 643Y_d0_old_cDNA190917_A8


title: 643Y_d42_old_cDNA190917_C10


title: 637R_d42_young_cDNA190921_H5


title: 643Y_d0_old_cDNA190917_A7


title: 637R_d42_young_cDNA190921_H3


title: 637R_d42_young_cDNA190921_G6


title: 637R_d42_young_cDNA190921_G3


title: 637R_d42_young_cDNA190921_F6


title: 637R_d42_young_cDNA190921_F5


title: 637R_d42_young_cDNA190921_G5


title: 637R_d42_young_cDNA190921_F4


title: 637R_d42_young_cDNA190921_F3


title: 637R_d42_young_cDNA190921_E6


title: 643Y_d42_old_cDNA190917_A12


title: 637R_d42_young_cDNA190921_E3


title: 637R_d42_young_cDNA190921_D6


title: 637R_d42_young_cDNA190921_D5


title: 637R_d42_young_cDNA190921_E4


title: 637R_d42_young_cDNA190921_D4


title: 637R_d42_young_cDNA190921_D3


title: 637R_d42_young_cDNA190921_C6


title: 637R_d42_young_cDNA190921_C4


title: 637R_d42_young_cDNA190921_C5


title: 637R_d42_young_cDNA190921_C3


title: 637R_d42_young_cDNA190921_B6


title: 637R_d42_young_cDNA190921_B5


title: 637R_d42_young_cDNA190921_H4


title: 637R_d42_young_cDNA190921_B4


title: 637R_d42_young_cDNA190921_B3


title: 637R_d42_young_cDNA190921_G4


title: 637R_d42_young_cDNA190921_A4


title: 637R_d42_young_cDNA190921_A5


title: 637R_d42_young_cDNA190921_A6


title: 637R_d42_young_cDNA190921_A3


title: 637R_d42_young_cDNA190921_E5


title: 637R_d0_young_cDNA190921_H7


title: 637R_d0_young_cDNA190921_H8


title: 637R_d0_young_cDNA190921_G8


title: 637R_d0_young_cDNA190921_F7


title: 627F_d42_young_cDNA190917_H9


title: 627F_d42_young_cDNA190917_H5


title: 637R_d0_young_cDNA190921_F8


title: 627F_d42_young_cDNA190917_H4


title: 627F_d42_young_cDNA190917_H3


title: 627F_d42_young_cDNA190917_G9


title: 627F_d42_young_cDNA190917_G5


title: 627F_d42_young_cDNA190917_G4


title: 627F_d42_young_cDNA190917_G3


title: 627F_d42_young_cDNA190917_G12


title: 627F_d42_young_cDNA190917_G10


title: 627F_d42_young_cDNA190917_F9


title: 627F_d42_young_cDNA190917_F5


title: 627F_d42_young_cDNA190917_F6


title: 627F_d42_young_cDNA190917_F4


title: 627F_d42_young_cDNA190917_F12


title: 627F_d42_young_cDNA190917_F10


title: 627F_d42_young_cDNA190917_F11


title: 627F_d42_young_cDNA190917_E9


title: 637R_d0_young_cDNA190921_G7


title: 627F_d42_young_cDNA190917_E6


title: 627F_d42_young_cDNA190917_E5


title: 627F_d42_young_cDNA190917_E3


title: 627F_d42_young_cDNA190917_G6


title: 627F_d42_young_cDNA190917_H6


title: 627F_d42_young_cDNA190917_E12


title: 627F_d42_young_cDNA190917_E10


title: 627F_d42_young_cDNA190917_D5


title: 627F_d42_young_cDNA190917_D6


title: 627F_d42_young_cDNA190917_D9


title: 627F_d42_young_cDNA190917_E11


title: 627F_d42_young_cDNA190917_G11


title: 627F_d42_young_cDNA190917_D3


title: 627F_d42_young_cDNA190917_D10


title: 627F_d42_young_cDNA190917_D4


title: 627F_d42_young_cDNA190917_C6


title: 627F_d42_young_cDNA190917_F3


title: 627F_d42_young_cDNA190917_C3


title: 627F_d42_young_cDNA190917_B5


title: 627F_d42_young_cDNA190917_B6


title: 627F_d42_young_cDNA190917_B4


title: 627F_d42_young_cDNA190917_B3


title: 627F_d42_young_cDNA190917_A6


title: 627F_d42_young_cDNA190917_E4


title: 627F_d42_young_cDNA190917_C4


title: 627F_d42_young_cDNA190917_A5


title: 627F_d42_young_cDNA190917_A4


title: 627F_d0_young_cDNA190917_H2


title: 627F_d0_young_cDNA190917_H1


title: 627F_d42_young_cDNA190917_A3


title: 627F_d0_young_cDNA190917_G1


title: 627F_d0_young_cDNA190917_F2


title: 627F_d42_young_cDNA190917_D11


title: 627F_d0_young_cDNA190917_E2


title: 627F_d0_young_cDNA190917_F1


title: 627F_d0_young_cDNA190917_D2


title: 627F_d0_young_cDNA190917_E1


title: 627F_d0_young_cDNA190917_D1


title: 627F_d0_young_cDNA190917_C2


title: 627F_d42_young_cDNA190917_C5


title: 627F_d0_young_cDNA190917_C1


title: 627F_d0_young_cDNA190917_B1


title: 627F_d0_young_cDNA190917_B2


title: 627F_d0_young_cDNA190917_A1


title: 627F_d0_young_cDNA190917_A2


title: 622A_d42_young_cDNA190821_H9


title: 622A_d42_young_cDNA190821_H12


title: 622A_d42_young_cDNA190821_G9


title: 622A_d42_young_cDNA190821_H10


title: 627F_d0_young_cDNA190917_G2


title: 622A_d42_young_cDNA190821_G12


title: 622A_d42_young_cDNA190821_F9


title: 622A_d42_young_cDNA190821_G10


title: 622A_d42_young_cDNA190821_F11


title: 622A_d42_young_cDNA190821_E9


title: 622A_d42_young_cDNA190821_E12


title: 622A_d42_young_cDNA190821_E11


title: 622A_d42_young_cDNA190821_E10


title: 622A_d42_young_cDNA190821_D9


title: 622A_d42_young_cDNA190821_D10


title: 622A_d42_young_cDNA190821_C12


title: 622A_d42_young_cDNA190821_D12


title: 622A_d42_young_cDNA190821_C9


title: 622A_d42_young_cDNA190821_H11


title: 622A_d42_young_cDNA190821_C10


title: 622A_d42_young_cDNA190821_B11


title: 622A_d42_young_cDNA190821_B10


title: 622A_d42_young_cDNA190821_B9


title: 622A_d42_young_cDNA190821_A12


title: 622A_d42_young_cDNA190821_A11


title: 622A_d42_young_cDNA190821_A9


title: 622A_d42_young_cDNA190821_B12


title: 622A_d42_young_cDNA190821_G11


title: 622A_d42_young_cDNA190821_F12


title: 622A_d0_young_cDNA190821_H8


title: 622A_d0_young_cDNA190821_H7


title: 622A_d0_young_cDNA190821_G8


title: 622A_d0_young_cDNA190821_G7


title: 622A_d0_young_cDNA190821_F8


title: 622A_d42_young_cDNA190821_A10


title: 622A_d0_young_cDNA190821_F7


title: 622A_d0_young_cDNA190821_E8


title: 622A_d0_young_cDNA190821_E7


title: 622A_d42_young_cDNA190821_F10


title: 622A_d0_young_cDNA190821_D7


title: 622A_d0_young_cDNA190821_C8


title: 622A_d42_young_cDNA190821_D11


title: 622A_d42_young_cDNA190821_C11


title: 622A_d0_young_cDNA190821_B8


title: 622A_d0_young_cDNA190821_D8


title: 622A_d0_young_cDNA190821_A7


title: 622A_d0_young_cDNA190821_C7


title: 602D_d42_young_cDNA190920_H12


title: 622A_d0_young_cDNA190821_A8


title: 602D_d42_young_cDNA190920_H9


title: 622A_d0_young_cDNA190821_B7


title: 602D_d42_young_cDNA190920_H10


title: 602D_d42_young_cDNA190920_F9


title: 602D_d42_young_cDNA190920_G11


title: 602D_d42_young_cDNA190920_F12


title: 602D_d42_young_cDNA190920_H11


title: 602D_d42_young_cDNA190920_G9


title: 602D_d42_young_cDNA190920_F11


title: 602D_d42_young_cDNA190920_F10


title: 602D_d42_young_cDNA190920_G12


title: 602D_d42_young_cDNA190920_E10


title: 602D_d42_young_cDNA190920_E12


title: 602D_d42_young_cDNA190920_E9


title: 602D_d42_young_cDNA190920_E11


title: 602D_d42_young_cDNA190920_D9


title: 602D_d42_young_cDNA190920_D11


title: 602D_d42_young_cDNA190920_D10


title: 602D_d42_young_cDNA190920_D12


title: 602D_d42_young_cDNA190920_C12


title: 602D_d42_young_cDNA190920_C9


title: 602D_d42_young_cDNA190920_C11


title: 602D_d42_young_cDNA190920_C10


title: 602D_d42_young_cDNA190920_B9


title: 602D_d42_young_cDNA190920_B11


title: 602D_d42_young_cDNA190920_B10


title: 602D_d42_young_cDNA190920_B12


title: 602D_d42_young_cDNA190920_A10


title: 602D_d42_young_cDNA190920_A12


title: 602D_d42_young_cDNA190920_A9


title: 602D_d42_young_cDNA190920_A11


title: 602D_d0_young_cDNA190920_A8


title: 602D_d0_young_cDNA190920_A7


title: 594V_d42_young_cDNA190917_G7


title: 594V_d42_young_cDNA190917_G8


title: 594V_d42_young_cDNA190917_H7


title: 594V_d42_young_cDNA190917_F8


title: 594V_d42_young_cDNA190917_F7


title: 594V_d42_young_cDNA190917_E7


title: 594V_d42_young_cDNA190807_H12


title: 594V_d42_young_cDNA190807_H10


title: 594V_d42_young_cDNA190917_E8


title: 594V_d42_young_cDNA190807_H9


title: 594V_d42_young_cDNA190807_H11


title: 594V_d42_young_cDNA190807_G9


title: 594V_d42_young_cDNA190807_G12


title: 594V_d42_young_cDNA190807_G11


title: 594V_d42_young_cDNA190807_G10


title: 594V_d42_young_cDNA190807_F9


title: 594V_d42_young_cDNA190807_F12


title: 594V_d42_young_cDNA190807_F11


title: 594V_d42_young_cDNA190807_E9


title: 594V_d42_young_cDNA190807_E11


title: 594V_d42_young_cDNA190807_F10


title: 594V_d42_young_cDNA190807_E12


title: 594V_d42_young_cDNA190917_H8


title: 594V_d42_young_cDNA190807_E10


title: 594V_d42_young_cDNA190807_D12


title: 594V_d42_young_cDNA190807_D10


title: 594V_d42_young_cDNA190807_C12


title: 594V_d42_young_cDNA190807_D11


title: 594V_d42_young_cDNA190807_B9


title: 594V_d42_young_cDNA190807_B12


title: 594V_d42_young_cDNA190807_C9


title: 594V_d42_young_cDNA190807_B10


title: 594V_d42_young_cDNA190807_C10


title: 594V_d42_young_cDNA190807_B11


title: 594V_d42_young_cDNA190807_D9


title: 594V_d0_young_cDNA190917_H11


title: 594V_d0_young_cDNA190807_F7


title: 594V_d0_young_cDNA190807_G8


title: 594V_d42_young_cDNA190807_A10


title: 594V_d0_young_cDNA190917_H10


title: 594V_d0_young_cDNA190917_H12


title: 594V_d0_young_cDNA190807_E7


title: 594V_d42_young_cDNA190807_A9


title: 594V_d42_young_cDNA190807_A12


title: 594V_d0_young_cDNA190807_F8


title: 594V_d0_young_cDNA190807_H8


title: 594V_d0_young_cDNA190807_G7


title: 594V_d0_young_cDNA190807_C7


title: 594V_d0_young_cDNA190807_C8


title: 594V_d0_young_cDNA190807_H7


title: 594V_d42_young_cDNA190807_C11


title: 594V_d0_young_cDNA190807_E8


title: 594V_d0_young_cDNA190807_B8


title: 594V_d0_young_cDNA190807_D7


title: 594V_d0_young_cDNA190807_D8


title: 594V_d0_young_cDNA190807_B7


title: 594V_d42_young_cDNA190807_A11


title: 568R_d42_young_cDNA190919_H12


title: 594V_d0_young_cDNA190807_A7


title: 594V_d0_young_cDNA190807_A8


title: 568R_d42_young_cDNA190919_H9


title: 568R_d42_young_cDNA190919_G9


title: 568R_d42_young_cDNA190919_H11


title: 568R_d42_young_cDNA190919_H10


title: 568R_d42_young_cDNA190919_G12


title: 568R_d42_young_cDNA190919_G11


title: 568R_d42_young_cDNA190919_G10


title: 568R_d42_young_cDNA190919_F12


title: 568R_d42_young_cDNA190919_E10


title: 568R_d42_young_cDNA190919_F9


title: 568R_d42_young_cDNA190919_D9


title: 568R_d42_young_cDNA190919_E11


title: 568R_d42_young_cDNA190919_C9


title: 568R_d42_young_cDNA190919_C12


title: 568R_d42_young_cDNA190919_F11


title: 568R_d42_young_cDNA190919_D10


title: 568R_d42_young_cDNA190919_C11


title: 602D_d42_young_cDNA190920_G10


title: 568R_d42_young_cDNA190919_B12


title: 568R_d42_young_cDNA190919_D12


title: 568R_d42_young_cDNA190919_D11


title: 568R_d42_young_cDNA190919_C10


title: 568R_d42_young_cDNA190919_B10


title: 568R_d42_young_cDNA190919_A11


title: 568R_d42_young_cDNA190919_A9


title: 568R_d42_young_cDNA190919_E9


title: 568R_d42_young_cDNA190919_A12


title: 568R_d42_young_cDNA190919_B9


title: 568R_d0_young_cDNA190919_G8


title: 568R_d0_young_cDNA190919_H8


title: 568R_d0_young_cDNA190919_G7


title: 568R_d0_young_cDNA190919_F7


title: 568R_d0_young_cDNA190919_D7


title: 568R_d0_young_cDNA190919_E7


title: 568R_d0_young_cDNA190919_C8


title: 568R_d42_young_cDNA190919_E12


title: 568R_d0_young_cDNA190919_C7


title: 568R_d0_young_cDNA190919_H7


title: 568R_d0_young_cDNA190919_F8


title: 568R_d42_young_cDNA190919_A10


title: 568R_d0_young_cDNA190919_A8


title: 568R_d0_young_cDNA190919_A7


title: 568R_d0_young_cDNA190919_D8


title: 562K_d42_young_cDNA190921_C1


title: 568R_d0_young_cDNA190919_B8


title: 568R_d0_young_cDNA190919_B7


title: 562K_d42_young_cDNA190921_D1


title: 562K_d42_young_cDNA190819_H9


title: 562K_d42_young_cDNA190819_H12


title: 562K_d42_young_cDNA190819_H11


title: 568R_d0_young_cDNA190919_E8


title: 568R_d42_young_cDNA190919_F10


title: 562K_d42_young_cDNA190819_G9


title: 562K_d42_young_cDNA190819_H10


title: 568R_d42_young_cDNA190919_B11


title: 562K_d42_young_cDNA190819_G12


title: 562K_d42_young_cDNA190819_F9


title: 562K_d42_young_cDNA190819_G10


title: 562K_d42_young_cDNA190819_G11


title: 562K_d42_young_cDNA190819_F12


title: 562K_d42_young_cDNA190819_F11


title: 562K_d42_young_cDNA190819_E9


title: 562K_d42_young_cDNA190819_F10


title: 562K_d42_young_cDNA190819_E12


title: 562K_d42_young_cDNA190921_B1


title: 562K_d42_young_cDNA190921_A1


title: 562K_d42_young_cDNA190819_D9


title: 562K_d42_young_cDNA190819_D12


title: 562K_d42_young_cDNA190819_D11


title: 562K_d42_young_cDNA190819_D10


title: 562K_d42_young_cDNA190819_C12


title: 562K_d42_young_cDNA190819_B9


title: 562K_d42_young_cDNA190819_C11


title: 562K_d42_young_cDNA190819_C10


title: 562K_d42_young_cDNA190819_B10


title: 562K_d42_young_cDNA190819_B11


title: 562K_d42_young_cDNA190819_A9


title: 562K_d0_young_cDNA190920_H8


title: 562K_d0_young_cDNA190920_G8


title: 562K_d0_young_cDNA190920_F8


title: 562K_d42_young_cDNA190819_E10


title: 562K_d42_young_cDNA190819_E11


title: 562K_d0_young_cDNA190920_B8


title: 562K_d0_young_cDNA190819_H8


title: 562K_d0_young_cDNA190920_E8


title: 562K_d0_young_cDNA190819_H7


title: 562K_d0_young_cDNA190920_D8


title: 562K_d0_young_cDNA190819_F8


title: 562K_d0_young_cDNA190819_G8


title: 562K_d0_young_cDNA190819_F7


title: 562K_d0_young_cDNA190819_G7


title: 562K_d0_young_cDNA190819_E8


title: 562K_d0_young_cDNA190819_E7


title: 562K_d42_young_cDNA190819_B12


title: 562K_d0_young_cDNA190819_D8


title: 562K_d0_young_cDNA190819_B7


title: 562K_d0_young_cDNA190819_B8


title: 562K_d42_young_cDNA190819_A10


title: 562K_d0_young_cDNA190819_C7


title: 562K_d0_young_cDNA190819_C8


title: 562K_d0_young_cDNA190819_A8


title: 562K_d0_young_cDNA190819_D7


title: 559G_d42_young_cDNA190919_H2


title: 562K_d0_young_cDNA190819_A7


title: 562K_d42_young_cDNA190819_A12


title: 559G_d42_young_cDNA190919_H1


title: 562K_d42_young_cDNA190819_A11


title: 562K_d0_young_cDNA190920_C8


title: 559G_d42_young_cDNA190919_F2


title: 559G_d42_young_cDNA190919_G1


title: 559G_d42_young_cDNA190820_H9


title: 559G_d42_young_cDNA190919_F1


title: 559G_d42_young_cDNA190820_H12


title: 559G_d42_young_cDNA190820_H11


title: 559G_d42_young_cDNA190820_G12


title: 559G_d42_young_cDNA190820_G11


title: 559G_d42_young_cDNA190820_H10


title: 559G_d42_young_cDNA190820_G9


title: 559G_d42_young_cDNA190820_G10


title: 559G_d42_young_cDNA190820_F9


title: 559G_d42_young_cDNA190820_F11


title: 559G_d42_young_cDNA190820_F10


title: 559G_d42_young_cDNA190820_E9


title: 559G_d42_young_cDNA190820_E11


title: 559G_d42_young_cDNA190820_D12


title: 559G_d42_young_cDNA190820_C12


title: 559G_d42_young_cDNA190820_C11


title: 559G_d42_young_cDNA190820_C9


title: 559G_d42_young_cDNA190820_C10


title: 559G_d42_young_cDNA190919_G2


title: 559G_d42_young_cDNA190820_B9


title: 559G_d42_young_cDNA190820_A9


title: 559G_d42_young_cDNA190820_B12


title: 559G_d42_young_cDNA190820_B10


title: 559G_d42_young_cDNA190820_D9


title: 559G_d0_young_cDNA190820_H8


title: 559G_d42_young_cDNA190820_A10


title: 559G_d42_young_cDNA190820_F12


title: 559G_d0_young_cDNA190820_H7


title: 559G_d0_young_cDNA190820_G8


title: 559G_d0_young_cDNA190820_G7


title: 559G_d0_young_cDNA190820_F8


title: 559G_d42_young_cDNA190820_E12


title: 559G_d42_young_cDNA190820_E10


title: 559G_d0_young_cDNA190820_F7


title: 559G_d42_young_cDNA190820_D11


title: 562K_d42_young_cDNA190819_C9


title: 559G_d0_young_cDNA190820_D8


title: 559G_d0_young_cDNA190820_C8


title: 559G_d0_young_cDNA190820_C7


title: 559G_d0_young_cDNA190820_B7


title: 559G_d0_young_cDNA190820_A8


title: 559G_d0_young_cDNA190820_A7


title: 559G_d0_young_cDNA190820_D7


title: 559G_d42_young_cDNA190820_A11


title: 545R_d42_old_cDNA190807_H2


title: 545R_d42_old_cDNA190807_G2


title: 545R_d42_old_cDNA190807_G3


title: 545R_d42_old_cDNA190807_H1


title: 545R_d42_old_cDNA190807_G1


title: 545R_d42_old_cDNA190807_G5


title: 545R_d42_old_cDNA190807_G4


title: 545R_d42_old_cDNA190807_F6


title: 559G_d0_young_cDNA190820_E7


title: 545R_d42_old_cDNA190807_F4


title: 545R_d42_old_cDNA190807_F5


title: 545R_d42_old_cDNA190807_F3


title: 559G_d0_young_cDNA190820_E8


title: 545R_d42_old_cDNA190807_F2


title: 545R_d42_old_cDNA190807_F1


title: 559G_d0_young_cDNA190820_B8


title: 545R_d42_old_cDNA190807_E6


title: 545R_d42_old_cDNA190807_E5


title: 545R_d42_old_cDNA190807_E4


title: 545R_d42_old_cDNA190807_E1


title: 545R_d42_old_cDNA190807_D6


title: 545R_d42_old_cDNA190807_E3


title: 545R_d42_old_cDNA190807_E2


title: 545R_d42_old_cDNA190807_H6


title: 545R_d42_old_cDNA190807_G6


title: 545R_d42_old_cDNA190807_D4


title: 545R_d42_old_cDNA190807_D3


title: 545R_d42_old_cDNA190807_C5


title: 545R_d42_old_cDNA190807_C4


title: 545R_d42_old_cDNA190807_C3


title: 559G_d42_young_cDNA190820_D10


title: 545R_d42_old_cDNA190807_B5


title: 559G_d42_young_cDNA190820_A12


title: 545R_d42_old_cDNA190807_A6


title: 545R_d42_old_cDNA190807_B3


title: 545R_d42_old_cDNA190807_A5


title: 545R_d42_old_cDNA190807_B4


title: 545R_d42_old_cDNA190807_A4


title: 545R_d0_old_cDNA190807_D2


title: 545R_d0_old_cDNA190807_D1


title: 545R_d42_old_cDNA190807_A3


title: 545R_d0_old_cDNA190807_C2


title: 545R_d0_old_cDNA190807_B2


title: 545R_d42_old_cDNA190807_D5


title: 545R_d0_old_cDNA190807_C1


title: 545R_d0_old_cDNA190807_B1


title: 544Q_d42_old_cDNA190821_H5


title: 545R_d0_old_cDNA190807_A1


title: 545R_d0_old_cDNA190807_A2


title: 544Q_d42_old_cDNA190821_H6


title: 544Q_d42_old_cDNA190821_H4


title: 545R_d42_old_cDNA190807_C6


title: 544Q_d42_old_cDNA190821_H3


title: 545R_d42_old_cDNA190807_B6


title: 544Q_d42_old_cDNA190821_G6


title: Nor rep3

city: Shenzhen

first: Yuqi

last: Wu

state: Guangdong

address: Xueyuan Road 1098

country: China

institute: Shenzhen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (TPM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for miRNAs by calculating TPM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Testicular tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Testicular tissue

tag: strain

value: Sprague-Dawley

tag: condition

value: normal


title: Nor rep1


title: Nor rep2


title: DM rep3

value: STZ-induced diabetes


title: DM rep2


title: 544Q_d42_old_cDNA190821_G5


title: DM rep1


title: 544Q_d42_old_cDNA190821_G3


title: 544Q_d42_old_cDNA190821_G4


title: 544Q_d42_old_cDNA190821_F4


title: 544Q_d42_old_cDNA190821_F5


title: 544Q_d42_old_cDNA190821_F6


title: 544Q_d42_old_cDNA190821_F3


title: 544Q_d42_old_cDNA190821_E6


title: Pulmonary TB (UK) EBUS028

type: RNA

city: Salisbury

first: Karen

middle: Elizabeth

last: Kempsell

state: Wiltshire

address: Porton Down

department: Science Group

institute: UK Health Security Agency

description:
Pulmonary TB (UK)
UKPTB

data_processing: Normalisation was performed to the average of three housekeeping gene prior to data export using the Roche lightcycler 480 software.

label: FAM

source_name: Whole blood

label_protocol: RT-qPCR assays were performed using predesigned or bespoke Real-Time ready assays, designed using the RTR assay design configurator (configuration numbers 100059401, 100059386 and 100059377) and arrayed in 384 well format. Reverse transcription was performed using Transcriptor First Strand cDNA synthesis Kit (Roche) following manufacturer's instructions.  PCR was performed in duplicate using the following cycling conditions: 1 cycle at 95C for 10 minutes, 45 cycles of 95C for 10s, 60C for 30s, 72C for 1s, 40C for 10s.

extract_protocol: Total RNA was extracted using PAXgene Blood RNA kit or Tempus Spin RNA Isolation Kit

tag: disease status

tag: quantiferon

value: ND

tag: tspot

tag: tst skin test

tag: recruiting site

value: UCL, Royal Free NHS UK


title: Pulmonary TB (UK) EBUS032

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_E4


title: Pulmonary TB (UK) EBUS020

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS031

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS023

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_E5


title: 544Q_d42_old_cDNA190821_D6


title: Pulmonary TB (UK) EBUS021

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_E3


title: Pulmonary TB (UK) EBUS024

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_D5


title: 544Q_d42_old_cDNA190821_D4


title: 544Q_d42_old_cDNA190821_D3


title: 544Q_d42_old_cDNA190821_C6


title: Pulmonary TB (UK) EA49

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA41

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS018

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_C5


title: 544Q_d42_old_cDNA190821_C3


title: Pulmonary TB (UK) EA44

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA45

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA43

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_C4


title: Pulmonary TB (UK) EA40

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_B6


title: Pulmonary TB (UK) EA38

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA37

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_B5


title: 544Q_d42_old_cDNA190821_B4


title: 544Q_d42_old_cDNA190821_A5


title: 544Q_d42_old_cDNA190821_B3


title: 544Q_d42_old_cDNA190821_A6


title: Pulmonary TB (UK) EA36

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA30

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d42_old_cDNA190821_A3


title: Pulmonary TB (UK) EA35

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA34

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA29

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_H2


title: Pulmonary TB (UK) EA27

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA39

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA25

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA26

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_G2


title: 544Q_d0_old_cDNA190821_F2


title: 544Q_d0_old_cDNA190821_G1


title: Pulmonary TB (UK) EA17

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA22

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EA16

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL093

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL094

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_E2


title: Pulmonary TB (UK) BAL092

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_E1


title: 544Q_d42_old_cDNA190821_A4


title: 544Q_d0_old_cDNA190821_D2


title: 544Q_d0_old_cDNA190821_D1


title: 544Q_d0_old_cDNA190821_H1


title: 559G_d42_young_cDNA190820_B11


title: 544Q_d0_old_cDNA190821_B2


title: Pulmonary TB (UK) BAL089

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_A2


title: 544Q_d0_old_cDNA190821_C1


title: Pulmonary TB (UK) BAL088

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL083

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_A1


title: 544Q_d0_old_cDNA190821_F1


title: 543P_d42_old_cDNA190921_H2


title: 544Q_d0_old_cDNA190821_C2


title: Pulmonary TB (UK) BAL082

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL083-2

description:
Pulmonary TB (UK)
UKPTB


title: 543P_d42_old_cDNA190921_H1


title: Pulmonary TB (UK) BAL077

description:
Pulmonary TB (UK)
UKPTB


title: 543P_d42_old_cDNA190921_G2


title: Pulmonary TB (UK) BAL075

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL087

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL079

description:
Pulmonary TB (UK)
UKPTB


title: 544Q_d0_old_cDNA190821_B1


title: Pulmonary TB (UK) BAL074

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL091

description:
Pulmonary TB (UK)
UKPTB


title: 543P_d42_old_cDNA190921_G1


title: Pulmonary TB (UK) BAL080

description:
Pulmonary TB (UK)
UKPTB


title: 543P_d42_old_cDNA190921_F2


title: Pulmonary TB (UK) BAL073

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) BAL072

description:
Pulmonary TB (UK)
UKPTB


title: 543P_d42_old_cDNA190921_F1


title: High incidence control (UK) 19944

description:
High incidence control (UK)
CNTRL B

value: NPR

value: Negative

value: PHE, NMRS-South UK


title: 543P_d42_old_cDNA190921_E2


title: Latent TB 10714

description:
Latent TB
LTBI

value: Positive


title: 543P_d42_old_cDNA190921_D2


title: 543P_d42_old_cDNA190921_E1


title: 543P_d42_old_cDNA190921_C2


title: 543P_d42_old_cDNA190921_B2


title: High incidence control (UK) 10100

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 10441

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190921_A2


title: 543P_d42_old_cDNA190920_G7


title: Latent TB 9974

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190920_H7


title: 543P_d42_old_cDNA190920_D7


title: High incidence control (UK) 10094

description:
High incidence control (UK)
CNTRL B


title: Latent TB 9476

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190920_C7


title: High incidence control (UK) 9521

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190920_E7


title: High incidence control (UK) 9870

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 9873

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190920_B7


title: High incidence control (UK) 9508

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_H6


title: Latent TB 9148

description:
Latent TB
LTBI


title: Latent TB 9123

description:
Latent TB
LTBI


title: Latent TB 8998

description:
Latent TB
LTBI


title: High incidence control (UK) 9084

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 8991

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_H5


title: 543P_d42_old_cDNA190819_H4


title: Latent TB 8982

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_G6


title: 543P_d42_old_cDNA190819_H3


title: 543P_d42_old_cDNA190920_F7


title: High incidence control (UK) 8979

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_G5


title: Latent TB 8970

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_G3


title: 543P_d42_old_cDNA190819_G4


title: High incidence control (UK) 8961

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 8818

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_F6


title: 543P_d42_old_cDNA190819_F5


title: 543P_d42_old_cDNA190819_E5


title: 543P_d42_old_cDNA190819_E4


title: High incidence control (UK) 8506

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 8693

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_F3


title: Latent TB 8685

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_E6


title: Latent TB 8478

description:
Latent TB
LTBI


title: High incidence control (UK) 8746

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_E3


title: Latent TB 8467

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_D6


title: Latent TB 8411

description:
Latent TB
LTBI


title: High incidence control (UK) 8399

description:
High incidence control (UK)
CNTRL B


title: Latent TB 8370

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_D5


title: High incidence control (UK) 8365

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_D4


title: High incidence control (UK) 8859

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_D3


title: 543P_d42_old_cDNA190819_F4


title: High incidence control (UK) 8259

description:
High incidence control (UK)
CNTRL B


title: Latent TB 8271

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_C6


title: Latent TB 8212

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_C5


title: Latent TB 8118

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_C3


title: Latent TB 8202

description:
Latent TB
LTBI


title: 543P_d42_old_cDNA190819_B6


title: 543P_d42_old_cDNA190819_B5


title: 543P_d42_old_cDNA190819_B3


title: High incidence control (UK) 7265

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_B4


title: 543P_d42_old_cDNA190819_A5


title: Latent TB 7222

description:
Latent TB
LTBI


title: High incidence control (UK) 7244

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_A4


title: 543P_d42_old_cDNA190819_C4


title: High incidence control (UK) 6909

description:
High incidence control (UK)
CNTRL B


title: 543P_d42_old_cDNA190819_A3


title: Latent TB 6736

description:
Latent TB
LTBI


title: Latent TB 6995

description:
Latent TB
LTBI


title: Latent TB 7213

description:
Latent TB
LTBI


title: 543P_d0_old_cDNA190920_G2


title: 543P_d0_old_cDNA190920_H2


title: Latent TB 7572

description:
Latent TB
LTBI


title: 543P_d0_old_cDNA190920_H1


title: High incidence control (UK) 6640

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 7751

description:
High incidence control (UK)
CNTRL B


title: Latent TB 6750

description:
Latent TB
LTBI


title: High incidence control (UK) 6731

description:
High incidence control (UK)
CNTRL B


title: 543P_d0_old_cDNA190819_G1


title: 543P_d0_old_cDNA190819_H2


title: Latent TB 6709

description:
Latent TB
LTBI

value: PR


title: 543P_d0_old_cDNA190920_F1


title: Latent TB 6947

description:
Latent TB
LTBI


title: Latent TB 6642

description:
Latent TB
LTBI


title: 543P_d0_old_cDNA190819_H1


title: 543P_d42_old_cDNA190819_A6

value: trivalent influenza vaccination


title: Latent TB 6155

description:
Latent TB
LTBI


title: 543P_d0_old_cDNA190819_F2


title: High incidence control (UK) 6572

description:
High incidence control (UK)
CNTRL B


title: 543P_d0_old_cDNA190819_E2


title: 543P_d0_old_cDNA190819_F1


title: 543P_d0_old_cDNA190920_G1


title: Latent TB 6406

description:
Latent TB
LTBI


title: High incidence control (UK) 6030

description:
High incidence control (UK)
CNTRL B


title: Latent TB 6316

description:
Latent TB
LTBI


title: Latent TB 6282

description:
Latent TB
LTBI


title: High incidence control (UK) 6006

description:
High incidence control (UK)
CNTRL B


title: 543P_d0_old_cDNA190819_E1


title: 543P_d0_old_cDNA190819_D2


title: High incidence control (UK) 5784

description:
High incidence control (UK)
CNTRL B


title: 543P_d0_old_cDNA190819_G2


title: 543P_d0_old_cDNA190819_D1


title: 543P_d0_old_cDNA190819_C2


title: High incidence control (UK) 6097

description:
High incidence control (UK)
CNTRL B


title: 543P_d0_old_cDNA190819_C1


title: High incidence control (UK) 5723

description:
High incidence control (UK)
CNTRL B


title: 543P_d0_old_cDNA190819_B2


title: Latent TB 5684

description:
Latent TB
LTBI


title: Latent TB 5682

description:
Latent TB
LTBI


title: 543P_d0_old_cDNA190819_A1


title: 543P_d0_old_cDNA190819_A2


title: High incidence control (UK) 5627

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_H5

value: day 42


title: Latent TB 5664

description:
Latent TB
LTBI


title: 541M_d42_old_cDNA190920_H6

value: PBMC


title: High incidence control (UK) 5439

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 5432

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_H4

value: haemagglutinin specific B cell


title: 541M_d42_old_cDNA190920_G6


title: Latent TB 5375

description:
Latent TB
LTBI


title: High incidence control (UK) 5301

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 5231

description:
High incidence control (UK)
CNTRL B


title: Latent TB 5180

description:
Latent TB
LTBI


title: 541M_d42_old_cDNA190920_G3


title: 541M_d42_old_cDNA190920_F6


title: 541M_d42_old_cDNA190920_G4


title: 543P_d0_old_cDNA190819_B1

value: control


title: Latent TB 5138

description:
Latent TB
LTBI


title: High incidence control (UK) 5072

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_F5


title: 541M_d42_old_cDNA190920_F4


title: High incidence control (UK) 5073

description:
High incidence control (UK)
CNTRL B


title: Latent TB 5076

description:
Latent TB
LTBI


title: High incidence control (UK) 4966

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_E6


title: High incidence control (UK) 5472

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_E4


title: 541M_d42_old_cDNA190920_E5


title: Latent TB 4932

description:
Latent TB
LTBI


title: 541M_d42_old_cDNA190920_H3


title: 541M_d42_old_cDNA190920_G5


title: 541M_d42_old_cDNA190920_E3


title: Latent TB 4870

description:
Latent TB
LTBI


title: High incidence control (UK) 4748

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_D5


title: High incidence control (UK) 4744

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 4738

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_D4


title: 541M_d42_old_cDNA190920_D3


title: High incidence control (UK) 4734

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_C6


title: 541M_d42_old_cDNA190920_F3


title: 541M_d42_old_cDNA190920_C5


title: 541M_d42_old_cDNA190920_C4


title: High incidence control (UK) 4685

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 4733

description:
High incidence control (UK)
CNTRL B


title: Latent TB 4931

description:
Latent TB
LTBI


title: 541M_d42_old_cDNA190920_C3


title: 541M_d42_old_cDNA190920_B6


title: Latent TB 4599

description:
Latent TB
LTBI


title: High incidence control (UK) 4907

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_B3


title: High incidence control (UK) 4539

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 4237

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_B4


title: 541M_d42_old_cDNA190920_D6


title: Latent TB 4039

description:
Latent TB
LTBI


title: High incidence control (UK) 4672

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_A6


title: 541M_d42_old_cDNA190920_A5


title: High incidence control (UK) 3850

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_A4


title: High incidence control (UK) 3843

description:
High incidence control (UK)
CNTRL B


title: 541M_d42_old_cDNA190920_A3


title: 541M_d0_old_cDNA190920_F2

value: day 0


title: 541M_d0_old_cDNA190920_E2


title: Latent TB 4706

description:
Latent TB
LTBI


title: Latent TB 3811

description:
Latent TB
LTBI


title: High incidence control (UK) 3769

description:
High incidence control (UK)
CNTRL B


title: 541M_d0_old_cDNA190920_E1


title: 541M_d42_old_cDNA190920_B5


title: 541M_d0_old_cDNA190920_D2


title: 541M_d0_old_cDNA190920_D1


title: 541M_d0_old_cDNA190920_C2


title: Latent TB 3768

description:
Latent TB
LTBI


title: High incidence control (UK) 3767

description:
High incidence control (UK)
CNTRL B


title: Latent TB 4127

description:
Latent TB
LTBI


title: High incidence control (UK) 3740

description:
High incidence control (UK)
CNTRL B


title: 541M_d0_old_cDNA190920_B1


title: 541M_d0_old_cDNA190920_B2


title: 541M_d0_old_cDNA190920_C1


title: High incidence control (UK) 4011

description:
High incidence control (UK)
CNTRL B


title: Latent TB 3673

description:
Latent TB
LTBI


title: Latent TB 3550

description:
Latent TB
LTBI


title: High incidence control (UK) 3651

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 3641

description:
High incidence control (UK)
CNTRL B


title: 536G_d42_old_cDNA190919_H6


title: 541M_d0_old_cDNA190920_A1


title: Latent TB 3560

description:
Latent TB
LTBI


title: Latent TB 3792

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_H5


title: Latent TB 3372

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_H4


title: High incidence control (UK) 3239

description:
High incidence control (UK)
CNTRL B


title: 536G_d42_old_cDNA190919_G6


title: 536G_d42_old_cDNA190919_H3


title: High incidence control (UK) 3195

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2978

description:
Latent TB
LTBI


title: High incidence control (UK) 3015

description:
High incidence control (UK)
CNTRL B


title: 536G_d42_old_cDNA190919_G5


title: 536G_d42_old_cDNA190919_G4


title: Latent TB 3192

description:
Latent TB
LTBI


title: 541M_d0_old_cDNA190920_A2


title: 536G_d42_old_cDNA190919_G3


title: 536G_d42_old_cDNA190919_F6


title: 536G_d42_old_cDNA190919_F4


title: 536G_d42_old_cDNA190919_F5


title: High incidence control (UK) 2868

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2863

description:
Latent TB
LTBI


title: Latent TB 2870

description:
Latent TB
LTBI


title: Latent TB 2871

description:
Latent TB
LTBI


title: Latent TB 2871-2

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_F3


title: 536G_d42_old_cDNA190919_E6


title: 536G_d42_old_cDNA190919_E5


title: 536G_d42_old_cDNA190919_E4


title: Latent TB 3370

description:
Latent TB
LTBI


title: High incidence control (UK) 2859

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2847

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_E3


title: Latent TB 2636

description:
Latent TB
LTBI


title: Latent TB 2626

description:
Latent TB
LTBI


title: High incidence control (UK) 2846

description:
High incidence control (UK)
CNTRL B


title: 536G_d42_old_cDNA190919_D6


title: 536G_d42_old_cDNA190919_D5


title: 536G_d42_old_cDNA190919_D4


title: Latent TB 2624

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_C5


title: 536G_d42_old_cDNA190919_D3


title: 536G_d42_old_cDNA190919_C6


title: High incidence control (UK) 2609

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 2614

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2604

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_C4


title: 536G_d42_old_cDNA190919_B6


title: Latent TB 2603

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_C3


title: Latent TB 2595

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_B4


title: High incidence control (UK) 2565

description:
High incidence control (UK)
CNTRL B


title: 536G_d42_old_cDNA190919_B5


title: 536G_d42_old_cDNA190919_B3


title: Latent TB 2571

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_A6


title: High incidence control (UK) 2589

description:
High incidence control (UK)
CNTRL B


title: 536G_d42_old_cDNA190919_A4


title: Latent TB 2488

description:
Latent TB
LTBI


title: 536G_d42_old_cDNA190919_A5


title: High incidence control (UK) 2625

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2467

description:
Latent TB
LTBI


title: High incidence control (UK) 2564

description:
High incidence control (UK)
CNTRL B


title: 536G_d0_old_cDNA190919_E2


title: Latent TB 2439

description:
Latent TB
LTBI


title: Latent TB 2404

description:
Latent TB
LTBI


title: Latent TB 2562

description:
Latent TB
LTBI


title: Latent TB 2359

description:
Latent TB
LTBI


title: 536G_d0_old_cDNA190919_D2


title: 536G_d0_old_cDNA190919_C1


title: High incidence control (UK) 2358

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2357

description:
Latent TB
LTBI


title: 536G_d0_old_cDNA190919_C2


title: Latent TB 2354

description:
Latent TB
LTBI


title: 536G_d0_old_cDNA190919_B1


title: Latent TB 2462

description:
Latent TB
LTBI


title: High incidence control (UK) 2298

description:
High incidence control (UK)
CNTRL B


title: 536G_d0_old_cDNA190919_A2


title: 536G_d0_old_cDNA190919_B2


title: 536G_d42_old_cDNA190919_A3


title: 536G_d0_old_cDNA190919_A1


title: High incidence control (UK) 2296

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_H12


title: Latent TB 2242

description:
Latent TB
LTBI


title: 536G_d0_old_cDNA190919_E1


title: High incidence control (UK) 2217

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2194

description:
Latent TB
LTBI


title: Latent TB 2173

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_H11


title: High incidence control (UK) 2405

description:
High incidence control (UK)
CNTRL B


title: Latent TB 2198

description:
Latent TB
LTBI


title: 536G_d0_old_cDNA190919_D1


title: 526W_d42_old_cDNA190910_H10


title: Latent TB 2161

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_G9


title: 526W_d42_old_cDNA190910_G12


title: 526W_d42_old_cDNA190910_G11


title: 526W_d42_old_cDNA190910_G10


title: Latent TB 2064

description:
Latent TB
LTBI


title: High incidence control (UK) 2060

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_F9


title: 526W_d42_old_cDNA190910_H9


title: High incidence control (UK) 1886

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_F12


title: Latent TB 2041

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_F11


title: 526W_d42_old_cDNA190910_F10


title: Latent TB 2056

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_E9


title: High incidence control (UK) 1865

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1867

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_E12


title: High incidence control (UK) 1864

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1773

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1868

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_D9


title: 526W_d42_old_cDNA190910_E10


title: 526W_d42_old_cDNA190910_D12


title: 526W_d42_old_cDNA190910_E11


title: High incidence control (UK) 1772

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1771

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1770

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1728

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_D11


title: High incidence control (UK) 1727

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_D10


title: 526W_d42_old_cDNA190910_C9


title: Latent TB 1710

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_C12


title: High incidence control (UK) 1628

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_C11


title: High incidence control (UK) 1516

description:
High incidence control (UK)
CNTRL B


title: 526W_d42_old_cDNA190910_B9


title: High incidence control (UK) 1488

description:
High incidence control (UK)
CNTRL B


title: High incidence control (UK) 1399

description:
High incidence control (UK)
CNTRL B


title: Latent TB 1313

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_C10


title: Latent TB 1314

description:
Latent TB
LTBI


title: Latent TB 1249

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_A9


title: 526W_d42_old_cDNA190910_B12


title: 526W_d42_old_cDNA190910_B11


title: Latent TB 1241

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_B10


title: 526W_d42_old_cDNA190910_A12


title: 526W_d42_old_cDNA190910_A11


title: Latent TB 1223

description:
Latent TB
LTBI


title: 526W_d42_old_cDNA190910_A10


title: 526W_d0_old_cDNA190910_H8


title: Latent TB 1192

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_H7


title: Latent TB 1178

description:
Latent TB
LTBI


title: High incidence control (UK) 1067

description:
High incidence control (UK)
CNTRL B


title: Latent TB 1244

description:
Latent TB
LTBI


title: Latent TB 1055

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_G8


title: 526W_d0_old_cDNA190910_F8


title: 526W_d0_old_cDNA190910_G7


title: High incidence control (UK) 1053

description:
High incidence control (UK)
CNTRL B


title: Latent TB 758

description:
Latent TB
LTBI


title: Latent TB 748

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_F7


title: High incidence control (UK) 982

description:
High incidence control (UK)
CNTRL B


title: 526W_d0_old_cDNA190910_E8


title: 526W_d0_old_cDNA190910_D8


title: Latent TB 706

description:
Latent TB
LTBI


title: Latent TB 728

description:
Latent TB
LTBI


title: Latent TB 726

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_C8


title: 526W_d0_old_cDNA190910_D7


title: Latent TB 617

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_B8


title: 526W_d0_old_cDNA190910_B7


title: Latent TB 513

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_A8


title: High incidence control (UK) 547

description:
High incidence control (UK)
CNTRL B


title: 526W_d0_old_cDNA190910_A7


title: Latent TB 347

description:
Latent TB
LTBI


title: 520P_d42_old_cDNA190820_H6


title: High incidence control (UK) 477

description:
High incidence control (UK)
CNTRL B


title: Latent TB 342

description:
Latent TB
LTBI


title: 520P_d42_old_cDNA190820_H5


title: 520P_d42_old_cDNA190820_H4


title: Low incidence control (UK) 234

description:
Low incidence control (UK)
CNTRL A

value: PHE, Porton  UK


title: 520P_d42_old_cDNA190820_H3


title: Latent TB 730

description:
Latent TB
LTBI


title: 526W_d0_old_cDNA190910_E7


title: Low incidence control (UK) 232

description:
Low incidence control (UK)
CNTRL A

value: PHE, Porton UK


title: Low incidence control (UK) 233

description:
Low incidence control (UK)
CNTRL A


title: 526W_d0_old_cDNA190910_C7


title: High incidence control (UK) 622

description:
High incidence control (UK)
CNTRL B


title: 520P_d42_old_cDNA190820_G5


title: 520P_d42_old_cDNA190820_G3


title: 520P_d42_old_cDNA190820_F6


title: 520P_d42_old_cDNA190820_F5


title: Latent TB 228

description:
Latent TB
LTBI


title: Latent TB 227

description:
Latent TB
LTBI


title: 520P_d42_old_cDNA190820_G4


title: 520P_d42_old_cDNA190820_F4


title: Low incidence control (UK) 226

description:
Low incidence control (UK)
CNTRL A


title: Low incidence control (UK) 224

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_F3


title: 520P_d42_old_cDNA190820_G6


title: 520P_d42_old_cDNA190820_E6


title: 520P_d42_old_cDNA190820_E4


title: Low incidence control (UK) 231

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_E5


title: Low incidence control (UK) 179

description:
Low incidence control (UK)
CNTRL A


title: Low incidence control (UK) 177

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_D5


title: 520P_d42_old_cDNA190820_E3


title: 520P_d42_old_cDNA190820_D6


title: Latent TB 229

description:
Latent TB
LTBI


title: Low incidence control (UK) 176

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_D4


title: Low incidence control (UK) 178

description:
Low incidence control (UK)
CNTRL A


title: Low incidence control (UK) 171

description:
Low incidence control (UK)
CNTRL A


title: Low incidence control (UK) 174

description:
Low incidence control (UK)
CNTRL A


title: Low incidence control (UK) 173

description:
Low incidence control (UK)
CNTRL A


title: Low incidence control (UK) 225

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_D3


title: 520P_d42_old_cDNA190820_C5


title: Low incidence control (UK) 163

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_C6


title: Low incidence control (UK) 170

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_C4


title: Low incidence control (UK) 161

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_C3


title: 520P_d42_old_cDNA190820_B6


title: Low incidence control (UK) 160

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_B5


title: Latent TB 99

description:
Latent TB
LTBI


title: 520P_d42_old_cDNA190820_B3


title: Low incidence control (UK) 172

description:
Low incidence control (UK)
CNTRL A


title: 520P_d42_old_cDNA190820_B4


title: Latent TB 73

description:
Latent TB
LTBI


title: 520P_d42_old_cDNA190820_A6


title: 520P_d42_old_cDNA190820_A5


title: Extra-pulmonary TB 20

description:
Extra-pulmonary TB
IEPTB

value: JIPMER, Pondicherry, India


title: 520P_d42_old_cDNA190820_A4


title: 520P_d42_old_cDNA190820_A3


title: Extra-pulmonary TB 16

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 17

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_H2


title: 520P_d0_old_cDNA190820_H1


title: Extra-pulmonary TB 14

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_G2


title: 520P_d0_old_cDNA190820_G1


title: Extra-pulmonary TB 18

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 13

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 12

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_F2


title: 520P_d0_old_cDNA190820_F1


title: Low incidence control (UK) 162

description:
Low incidence control (UK)
CNTRL A


title: High incidence control (UK) 80

description:
High incidence control (UK)
CNTRL B


title: Extra-pulmonary TB 10

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_E1


title: Extra-pulmonary TB 9

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 19

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_D2


title: Extra-pulmonary TB 8

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_D1


title: Extra-pulmonary TB 7

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 15

description:
Extra-pulmonary TB
IEPTB


title: 520P_d0_old_cDNA190820_C2


title: 520P_d0_old_cDNA190820_C1


title: 520P_d0_old_cDNA190820_B2


title: Extra-pulmonary TB 1

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 4

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB 2

description:
Extra-pulmonary TB
IEPTB


title: P4879-2

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

country: USA

institute: Northwestern University

data_processing:
Reads were demultiplexed using with cellranger mkfastq command (v3.1.0). Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v3.1.0), producing raw and filtered gene expression matrices.
Genome_build: custom (human GRCh38.93 and SARS-CoV-2 NC_045512.2)
Supplementary_files_format_and_content: gene expression count matrices

source_name: Bronchial brushing

extract_protocol:
https://www.protocols.io/view/cell-dissociation-from-nasal-and-bronchial-brushin-qubdwsn
Libraries were prepared with 10x Genomics 5' gene expression (GEX) reagents according to the manufacturer protocol (CG000086_RevM).

tag: patient id

tag: tissue/sample type

value: Bronchial brushing


title: P2635-1


title: Extra-pulmonary TB 11

description:
Extra-pulmonary TB
IEPTB

value: ND


title: 520P_d0_old_cDNA190820_B1


title: 520P_d0_old_cDNA190820_E2


title: P5074-1


title: colostrum fed 12 h after birth rep6

city: Edmonton

first: Yang

last: Song

state: Alberta

department: AFNS

country: Canada

institute: University of Alberta

description:
all_counts_ileum.txt
4147_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Filtered reads were aligned to the reference bovine genome (UMD 3.1) using Tophat 2.1.1.
The BAM alignment files generated from Tophat were sorted using Samtools (v1.4) and converted to SAM files.
The SAM files were analyzed using HTSeq-count to obtain gene read counts based on the annotation from ENSEMBL bovine genes.
Genome_build: UMD3.1
Supplementary_files_format_and_content: a text file includes raw counts number for each sample

organism: Bos taurus

source_name: Ileum

extract_protocol:
Tissues were collected after dissection of calves, flash frozen on liquid nitrogen, and RNA was harvested using a mirVana total RNA Isolation Kit (Ambion, Carlsbad, CA, USA).
TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA, USA) was used with 100 ng of total RNA for the construction of sequencing libraries.The RNA libraries were prepared using standard Illumina protocols

value: Ileum

tag: developmental stage

value: newborn

value: 51 h of age

tag: feeding strategy

value: colostrum fed 12 h after birth


title: colostrum fed 12 h after birth rep9

description:
all_counts_ileum.txt
4168_3


title: colostrum fed 12 h after birth rep8

description:
all_counts_ileum.txt
4159_3


title: colostrum fed 12 h after birth rep5

description:
all_counts_ileum.txt
4145_3


title: P9151-4

value: Positive


title: 520P_d0_old_cDNA190820_A2

tag: treament


title: colostrum fed 12 h after birth rep3

description:
all_counts_ileum.txt
4128_3


title: colostrum fed 12 h after birth rep2

description:
all_counts_ileum.txt
4126_3


title: P9151-3


title: 501T_d42_young_cDNA190910_H6

tag: time


title: P2635-2


title: colostrum fed 12 h after birth rep1

description:
all_counts_ileum.txt
4117_3

tag: age


title: colostrum fed 6 h after birth rep9

description:
all_counts_ileum.txt
4154_2

value: colostrum fed 6 h after birth


title: P4879-1


title: P9151-2


title: 501T_d42_young_cDNA190910_H5

value: trivalent influenza vaccination

tag: cell type


title: colostrum fed 6 h after birth rep8

description:
all_counts_ileum.txt
4151_2


title: P9151-1


title: colostrum fed 6 h after birth rep7

description:
all_counts_ileum.txt
4146_2


title: colostrum fed 6 h after birth rep6

description:
all_counts_ileum.txt
4144_2


title: colostrum fed 12 h after birth rep7

description:
all_counts_ileum.txt
4158_3


title: 501T_d42_young_cDNA190910_H4

value: day 42

tag: cell type_sorted


title: 501T_d42_young_cDNA190910_H3

value: PBMC


title: colostrum fed 6 h after birth rep5

description:
all_counts_ileum.txt
4140_2

tag: tissue


title: colostrum fed 6 h after birth rep4

description:
all_counts_ileum.txt
4134_2


title: colostrum fed 6 h after birth rep3

description:
all_counts_ileum.txt
4125_2


title: colostrum fed 12 h after birth rep4

description:
all_counts_ileum.txt
4139_3


title: colostrum fed 6 h after birth rep2

description:
all_counts_ileum.txt
4122_2


title: RS411_PolIIS5P_1_(20201201_SH_Hs_RS411_PolS5hex_1123)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUTAC for PolIIS5P 10 min in cross-linked SEM cells at home

library_source: genomic

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.3.4.3 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

molecule: genomic DNA

source_name: CUT&TAG-direct

extract_protocol:
CUTnTag-direct_v3_Protocols.io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: antibody

value: cell signaling technologies; phospho-rpb1 ctd (ser5) #13523

value: RS411 human immortalised mixed-lineage leukemia cell line


title: KOPN8_PolIIS5P_1_(20201201_SH_Hs_KOPN8x_PolS5hex_1123)

description: CUTAC for PolIIS5P 10 min in cross-linked KOPN8 cells at home

value: KOPN8 human immortalised mixed-lineage leukemia cell line


title: 501T_d42_young_cDNA190910_G5

value: haemagglutinin specific B cell


title: colostrum fed immediately after birth rep9

description:
all_counts_ileum.txt
4164_1

value: colostrum fed immediately after birth


title: 520P_d0_old_cDNA190820_A1

value: control

value: day 0


title: colostrum fed 6 h after birth rep1

description:
all_counts_ileum.txt
4114_2


title: colostrum fed immediately after birth rep8

description:
all_counts_ileum.txt
4149_1


title: 501T_d42_young_cDNA190910_G4


title: K562_PolIIS5P_con_(20201230_SH_Hs_PolS5_con10_1220)

description: CUTAC for PolIIS5P 10 min in K562 cells at home

value: H1 human embryonic stem cell line


title: K562_PolIIS5P_Xlinked_6k_(20201216_SH_Hs_K5x_PolS5h_6k_1212)

description: CUTAC for PolIIS5P 20 min in 6,000 cross-linked K562 cells at home

source_name: CUT&TAG


title: colostrum fed immediately after birth rep7

description:
all_counts_ileum.txt
4143_1

value: Ileum


title: 501T_d42_young_cDNA190910_G3


title: colostrum fed immediately after birth rep5

description:
all_counts_ileum.txt
4135_1

value: newborn


title: K562_PolIIS5P_Xlinked_60k_(20201216_SH_Hs_K5x_PolS5h_60k_1212)

description: CUTAC for PolIIS5P 20 min in 60,000 cross-linked K562 cells at home


title: 501T_d42_young_cDNA190910_F6


title: SEM_PolIIS5P_1_(20201201_SH_Hs_SEM_PolS5hex_1123)

description: CUTAC for PolIIS5P 10 min in cross-linked RS411 cells at home

value: SEM human immortalised mixed-lineage leukemia cell line


title: 501T_d42_young_cDNA190910_F5


title: K562_PolIIS5P_Xlinked_600_(20201216_SH_Hs_K5x_PolS5h_600_1212)

description: CUTAC for PolIIS5P 20 min in 600 cross-linked K562 cells at home


title: 501T_d42_young_cDNA190910_G6


title: colostrum fed immediately after birth rep1

description:
all_counts_ileum.txt
4108_1

value: 51 h of age


title: colostrum fed immediately after birth rep2

description:
all_counts_ileum.txt
4124_1


title: K562_PolIIS5P_Xlinked_2k_(20201216_SH_Hs_K5x_PolS5h_2k_1212)

description: CUTAC for PolIIS5P 20 min in 2,000 cross-linked K562 cells at home


title: K562_PolIIS5P_Xlinked_20k_(20201216_SH_Hs_K5x_PolS5h_20k_1212)

description: CUTAC for PolIIS5P 20 min in 20,000 cross-linked K562 cells at home


title: 501T_d42_young_cDNA190910_F3


title: 501T_d42_young_cDNA190910_F4


title: 501T_d42_young_cDNA190910_E6


title: K562_PolIIS5P_Xlinked_200_(20201216_SH_Hs_K5x_PolS5h_200_1212)

description: CUTAC for PolIIS5P 20 min in 200 cross-linked K562 cells at home


title: Pulmonary TB (India) P8

description:
Pulmonary TB (India)
IPTB

value: ND

value: AIIMS, New Delhi, India


title: Pulmonary TB (India) P5

description:
Pulmonary TB (India)
IPTB


title: K562_PolIIS5P_3_(20201230_SH_Hs_PolS10_1220)

description: CUT&Tag for PolIIS5P in K562 cells at home

source_name: CUT&Tag

value: K562 human immortalised myelogenous leukemia cell line


title: colostrum fed immediately after birth rep6

description:
all_counts_ileum.txt
4138_1


title: Pulmonary TB (India) P7

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P47

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P6

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_E5

value: trivalent influenza vaccination

value: day 42


title: Pulmonary TB (India) P9

description:
Pulmonary TB (India)
IPTB


title: colostrum fed immediately after birth rep4

description:
all_counts_ileum.txt
4133_1


title: K562_PolIIS5P_2_(20201216_SH_Hs_K562x_PolS5hex_1211)

description: CUTAC for PolIIS5P 10 min in cross-linked K562 cells at home

value: cell signaling technologies; phospho-rpb1 ctd (ser5) #13523


title: 501T_d42_young_cDNA190910_E4

value: PBMC


title: colostrum fed immediately after birth rep3

description:
all_counts_ileum.txt
4127_1


title: Pulmonary TB (India) P46

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P45

description:
Pulmonary TB (India)
IPTB


title: K562_PolIIS5P_1_(20201216_SH_Hs_K562_PolS5hex_1211)


title: Pulmonary TB (India) P44

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P43

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_E3


title: K562_PolIIS2S5P_con_(20201230_SH_Hs_PolS2_con10_1220)

description: CUTAC for PolIIS2S5P 10 min in K562 cells at home

value: cell signaling technologies; phospho-rpb1 ctd (ser2/ser5) (d1g3k) #1354


title: 501T_d42_young_cDNA190910_D6

value: haemagglutinin specific B cell


title: Pulmonary TB (India) P42

description:
Pulmonary TB (India)
IPTB


title: K562_PolIIS2S5P_1_(20201230_SH_Hs_PolS2S10_1220)

description: CUT%Tag for PolIIS2S5P in K562 cells at home


title: Pulmonary TB (India) P40

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P41

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P4

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_D5


title: 501T_d42_young_cDNA190910_D4


title: K562_PolIIS2P_con_(20201230_SH_Hs_PolS2S5_con10_1220)

description: CUTAC for PolIIS2P 10 min in K562 cells at home

value: cell signaling technologies; phospho-rpb1 ctd (ser2) (e1z3g) rabbit mab #13499


title: Pulmonary TB (India) P39

description:
Pulmonary TB (India)
IPTB


title: K562_PolIIS2P_1_(20201230_SH_Hs_PolS2_1220)

description: CUT&Tag for PolIIS2P in K562 cells at home


title: 501T_d42_young_cDNA190910_C6


title: 501T_d42_young_cDNA190910_D3


title: Pulmonary TB (India) P37

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P38

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P36

description:
Pulmonary TB (India)
IPTB


title: K562_H3K4me2_CnT_4_(20201230_SH_Hs_K4me2_1220)

description: CUT&Tag for K4me2 in K562 cells at home

value: H3K4me2 Epicypher cat# 13-0027


title: Pulmonary TB (India) P33

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P35

description:
Pulmonary TB (India)
IPTB


title: H1_PolIIS5P_Xlinked_6k_(20201216_SH_Hs_H1x_PolS5h_6k_1212)

description: CUTAC for PolIIS5P 20 min in 6,000 cross-linked H1 cells at home


title: Pulmonary TB (India) P34

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P31

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P32

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_C5


title: Pulmonary TB (India) P30

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_C4


title: H1_PolIIS5P_Xlinked_60k_(20201216_SH_Hs_H1x_PolS5h_60k_1212)

description: CUTAC for PolIIS5P 20 min in 60,000 cross-linked H1 cells at home


title: 501T_d42_young_cDNA190910_C3


title: Pulmonary TB (India) P3

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P29

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P28

description:
Pulmonary TB (India)
IPTB


title: H1_PolIIS5P_Xlinked_600_(20201216_SH_Hs_H1x_PolS5h_600_1212)

description: CUTAC for PolIIS5P 20 min in 600 cross-linked H1 cells at home


title: 501T_d42_young_cDNA190910_B6


title: H1_PolIIS5P_Xlinked_2k_(20201216_SH_Hs_H1x_PolS5h_2k_1212)

description: CUTAC for PolIIS5P 20 min in 2,000 cross-linked H1 cells at home


title: K562_H3K4me2_rem10_1_(20201230_SH_Hs_K4me2_con10_1220)

description: CUTAC for K4me2 10 min in K562 cells at home


title: Pulmonary TB (India) P25

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P26

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P27

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_B5


title: H1_PolIIS5P_Xlinked_20k_(20201216_SH_Hs_H1x_PolS5h_20k_1212)

description: CUTAC for PolIIS5P 20 min in 20,000 cross-linked H1 cells at home


title: Pulmonary TB (India) P24

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P23

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P22

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_B3


title: Pulmonary TB (India) P21

description:
Pulmonary TB (India)
IPTB


title: H1_PolIIS5P_Native_60k_(20201216_SH_Hs_H1_PolS5h_60k_1212)

description: CUTAC for PolIIS5P 20 min in 60,000 H1 cells at home


title: 501T_d42_young_cDNA190910_A6


title: Pulmonary TB (India) P20

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_A5


title: H1_PolIIS5P_Native_600_(20201216_SH_Hs_H1_PolS5h_600_1212)

description: CUTAC for PolIIS5P 20 min in 600 H1 cells at home


title: Pulmonary TB (India) P2

description:
Pulmonary TB (India)
IPTB


title: H1_PolIIS5P_Native_2k_(20201216_SH_Hs_H1_PolS5h_2k_1212)

description: CUTAC for PolIIS5P 20 min in 2,000 H1 cells at home


title: 501T_d42_young_cDNA190910_A4


title: Pulmonary TB (India) P17

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P16

description:
Pulmonary TB (India)
IPTB


title: Pulmonary TB (India) P15

description:
Pulmonary TB (India)
IPTB


title: H1_PolIIS5P_Native_20k_(20201216_SH_Hs_H1_PolS5h_20k_1212)

description: CUTAC for PolIIS5P 20 min in 20,000 H1 cells at home


title: Pulmonary TB (India) P14

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_A3


title: Pulmonary TB (India) P13

description:
Pulmonary TB (India)
IPTB


title: 501T_d42_young_cDNA190910_B4


title: H1_PolIIS5P_Native_200_(20201216_SH_Hs_H1_PolS5h_200_1212)

description: CUTAC for PolIIS5P 20 min in 200 H1 cells at home


title: H1_PolIIS5P_Native_6k_(20201216_SH_Hs_H1_PolS5h_6k_1212)

description: CUTAC for PolIIS5P 20 min in 6,000 H1 cells at home


title: Pulmonary TB (India) P12

description:
Pulmonary TB (India)
IPTB


title: RPE Patient Rep3

city: Madrid

first: Alberto

last: Benguria

address: Melchor Fernadez Almagro

country: Spain

institute: Centro Nacional Investigaciones Cardiovasculares

description:
RPEPaciente
Sequencing batch 2

data_processing:
Base-calling: :
Trimming: cutadapt (v2.5, --discard-trimmed): Removal of reads including adapters.
Alignment: STAR (v2.7.3a): Splice-aware mapping to the human genome.
Gene expression quantification: HTSeq (htseq-count, v0.11.0): Gene-level quantification using ENSEMBL transcriptome, release 87.
Normalization of expression: edgeR (TMM method): Library size normalization.
Batch effect correction: NOISeq (ARSyN method): Removal of batch effects between sequencing batches.
Isoform expression quantification: RSEM (v1.3.0): Isoform-level quantification using RefSeq transcriptome, release 96. Generation of isoform-level TPM values, necessary for SUPPA2.
Splicing event quantification: SUPPA2 (v2.3): Percentage Spliced-In (PSI) and differential splicing (dPSI) calculations for splicing events.
Genome_build: Human NCBI genome build 38 (GRCh38.p7 for gene expression, GRCh38.p13 for isoform expression): :
Supplementary_files_format_and_content: gene-counts_ENSEMBL_raw.tsv: Raw gene counts (ENSEMBL IDs) for each sample (sample ID column names).:
Supplementary_files_format_and_content: gene-counts_ENSEMBL_normalized_batch-corrected.tsv: TMM-normalized and batch-corrected gene counts (ENSEMBL IDs) for each sample (sample ID column names):
Supplementary_files_format_and_content: condition_factors.tsv: Matrix indicating the corresponding condition, replicate and sequencing batch for each sample, in the same order of the columns from the count matrix.:
Supplementary_files_format_and_content: id-table_ENSEMBL_symbol_RefSeq.tsv: Table containing ENSEMBL IDs, RefSeq isoform IDs, and gene symbol names.:
Supplementary_files_format_and_content: isoform-counts_RefSeq-RSEM_raw.tsv: Raw isoform expected counts (RefSeq IDs) for each sample (sample ID column names) output by RSEM.:
Supplementary_files_format_and_content: isoform-TPM_RefSeq-RSEM.tsv: Isoform TPMs (RefSeq IDs) for each sample (sample ID column names) output by RSEM.:
Supplementary_files_format_and_content: id-table_RefSeq-gene_RefSeq-transcripts.tsv: Table containing RefSeq gene IDs and RefSeq isoform IDs.:

source_name: iPSC-RPE

growth_protocol: Fibroblasts cell lines derived from skin biopsies and cultured at 37 °C under 5% CO2. Fibroblasts at passages 6-8 were used in this study. iPSC cell lines were induced to differentiate toward RPE: the iPSC were grown in  suspension in the absence of bFGF until the dark patches appeared. The dark patches were excised, trypsinized and plated on collagen type IV/LN- 521coated plastic cell culture dishes where they acquired the RPE morphology within 4-8 weeks. Another passage of RPE-like cells passing the cells through 70 µm cell strainer in order to reach homogeneous highly pigmented RPE-like monolayer with characteristic uniform polygonal cell morphology.

extract_protocol:
RNA was extracted by RNeasy mini kit (Qiagen, Germany) and quantified by Agilent 2100 Bioanalyser.
Libraries were prepared from 200 ng of total RNA using the NEBNext Ultra RNA Library Prep kit (New England Biolabs, Ref E7530L) with the NebNext poly A isolation magnetic module (New England Biolabs, Ref E7530L)

value: iPSC-RPE

tag: disease state

value: autosomal dominant retinitis pigmentosa


title: 501T_d0_young_cDNA190910_H2

value: control

value: day 0


title: Pulmonary TB (India) P11

description:
Pulmonary TB (India)
IPTB

tag: disease status


title: Pulmonary TB (India) P10

description:
Pulmonary TB (India)
IPTB

tag: quantiferon


title: 501T_d0_young_cDNA190910_H1


title: Pulmonary TB (India) P1

description:
Pulmonary TB (India)
IPTB

tag: tspot


title: RPE Patient Rep2

description:
RPEPaciente6
Sequencing batch 1


title: 501T_d0_young_cDNA190910_G2


title: Pulmonary TB (India) P19

description:
Pulmonary TB (India)
IPTB

tag: tst skin test


title: RPE Patient Rep1

description:
RPEPaciente5
Sequencing batch 1


title: Pulmonary TB (India) P18

description:
Pulmonary TB (India)
IPTB

tag: recruiting site


title: Extra-pulmonary TB EP8

description:
Extra-pulmonary TB
IEPTB


title: 501T_d0_young_cDNA190910_F2


title: 501T_d0_young_cDNA190910_G1


title: Extra-pulmonary TB EP7

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP9

description:
Extra-pulmonary TB
IEPTB


title: 501T_d0_young_cDNA190910_F1


title: Fibroblasts Patient Rep3

description:
FibroPaciente
Sequencing batch 2

source_name: Dermal skin fibroblasts

value: Dermal skin fibroblasts


title: Extra-pulmonary TB EP5

description:
Extra-pulmonary TB
IEPTB


title: Fibroblasts Patient Rep2

description:
FibroblPaciente2
Sequencing batch 1


title: Extra-pulmonary TB EP4

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP3

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP6

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP25

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP24

description:
Extra-pulmonary TB
IEPTB


title: Fibroblasts Patient Rep1

description:
FibroblPaciente1
Sequencing batch 1


title: 501T_d0_young_cDNA190910_E2


title: RPE Control Rep3

description:
RPESano
Sequencing batch 2

value: Healthy individual


title: 501T_d0_young_cDNA190910_E1


title: Extra-pulmonary TB EP23

description:
Extra-pulmonary TB
IEPTB

value: ND


title: Extra-pulmonary TB EP22

description:
Extra-pulmonary TB
IEPTB

value: AIIMS, New Delhi, India


title: Extra-pulmonary TB EP21

description:
Extra-pulmonary TB
IEPTB


title: RPE Control Rep2

description:
RPESano8
Sequencing batch 1


title: 501T_d0_young_cDNA190910_D2


title: Extra-pulmonary TB EP20

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP2

description:
Extra-pulmonary TB
IEPTB


title: RPE Control Rep1

description:
RPESano7
Sequencing batch 1


title: Extra-pulmonary TB EP19

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP18

description:
Extra-pulmonary TB
IEPTB


title: Fibroblasts Control Rep3

description:
FibroSano
Sequencing batch 2


title: 501T_d0_young_cDNA190910_D1


title: 501T_d0_young_cDNA190910_C2


title: Extra-pulmonary TB EP17

description:
Extra-pulmonary TB
IEPTB


title: Fibroblasts Control Rep2

description:
FibroblSano4
Sequencing batch 1


title: Fibroblasts Control Rep1

description:
FibroblSano3
Sequencing batch 1


title: 501T_d0_young_cDNA190910_C1


title: Extra-pulmonary TB EP16

description:
Extra-pulmonary TB
IEPTB


title: 501T_d0_young_cDNA190910_B2


title: Extra-pulmonary TB EP15

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP12

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP14

description:
Extra-pulmonary TB
IEPTB


title: AhR-LNA-7, Rep 2

city: Princeton

first: Thomas

middle: E

last: Shenk

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
Illumina Casava1.7 software used for basecalling.
Concatenated human/HCMV fasta and annotation (.gtf) files were created for mapping and feature counting by combining sequences and annotations from gencode human genome Release 24 (GRCh38.p5) and AD169-HHV5 (FJ527563.1).
Align sequencing fragments were mapped to the concatenated genome using HISAT2 version 2.0.3 (Kim et al., 2015)
Strand-specific fragment counts were generated at the gene level using featureCounts (Liao et al., 2014), requiring a minimum mapping quality score of 10 and concordantly mapped fragment ends on the same chromosome.
In order to eliminate compositional bias, HCMV counts were removed prior to normalization and ratio determination.
Ratio determination and significance calling was performed using DESeq2 (Love et al., 2014) with dispersion estimates fit with local regression.
Genome_build: gencode human genome Release 24 (GRCh38.p5) and AD169-HHV5 (FJ527563.1)
Supplementary_files_format_and_content: Tab-delimited count matrix (gene.id vs. Sample) containing gene-level summarized raw counts from featureCounts. This file contains human and HCMV counts.

source_name: Foreskin

growth_protocol: DMEM supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, 2 mM glutamax (Gibco), 10 mM Hepes pH 7.4, 0.1 mM MEM Non-Essential Amino Acids (Gibco), 100 units/ml Penicillin G, and 100 μg/ml Streptomycin Sulfate.

extract_protocol:
Trizol fractionation followed by Rneasy column and Dnase treatment.
According to manufacturer's instructions using a KAPA Stranded RNA-Seq Kit with RiboErase (Kappa Biosytems).

treatment_protocol: 6h infection at 3 MOI based on IE1-titering (fluorescent focus assay)

value: Fibroblasts

tag: locked nucleic acid (lna) name

value: AhR-Targeting 7

tag: lna sequence

tag: hcmv strain

value: infected with AD169 HCMV at 6 hpi


title: Extra-pulmonary TB EP13

description:
Extra-pulmonary TB
IEPTB


title: Extra-pulmonary TB EP11

description:
Extra-pulmonary TB
IEPTB


title: AhR-LNA-7, Rep 1


title: Extra-pulmonary TB EP10

description:
Extra-pulmonary TB
IEPTB


title: 501T_d0_young_cDNA190910_B1


title: 501T_d0_young_cDNA190910_A2


title: Extra-pulmonary TB EP1

description:
Extra-pulmonary TB
IEPTB


title: AhR-LNA-4, Rep 2

value: AhR-Targeting 4


title: Pulmonary TB (UK) EBUS066

description:
Pulmonary TB (UK)
UKPTB

value: UCL, Royal Free NHS UK


title: AhR-LNA-4, Rep 1


title: Pulmonary TB (UK) EBUS064

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS063

description:
Pulmonary TB (UK)
UKPTB


title: 501T_d0_young_cDNA190910_A1

value: PBMC


title: input_24hpi_Rep2

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: bigWig files

source_name: input_24hpi GFP+

growth_protocol: Kasumi-3 were grown in RPMI-1640 medium (ATCC 30-2001) supplemented with 20% fetal bovine serum (Corning) and 1,000 Units/ml Penicillin-Streptomycin (Gibco)

extract_protocol:
After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bio Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells. Cells were then fixed with 1% of Formaldehyde in PBS fand quenched with 0.125 M glycine.

tag: treatment

value: live GFP+ infected, 24hpi

tag: chip antibody

tag: cell line


title: NC-LNA, Rep 2

value: Non-Targeting/Negative Control


title: Pulmonary TB (UK) EBUS062

description:
Pulmonary TB (UK)
UKPTB


title: NC-LNA, Rep 1


title: Pulmonary TB (UK) EBUS060

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS057

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS059

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS056

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS055

description:
Pulmonary TB (UK)
UKPTB


title: Total_RNA_Uninfected_K3_Rep1

description: RNA-seq

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: tab-delimited file with read counts per gene
Supplementary_files_format_and_content: bigWig files

source_name: Total RNA Uninfected K3

extract_protocol:
The cDNA was quantitated by qubit and processed into NGS libraries using the Swift BioSciences ACCEL-NGS® 1S PLUS DNA LIBRARY KIT in combination with the Swift BioSciences 1S Unique Dual Indexing Kit. Library QC (quality and quantity) was done by Bio-analyzer and the pool of libraries was sequenced on the Illumina NextSeq using Illumina reagents and protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 24 hr post-infection, HCMV infected cells were sorted for GFP expression and live cells while mock-infected cells were sorted for live cells. Newly synthesized RNA was labeled for 4 hr with 5-ethynyl uridine.   A portion of the RNA was saved for analysis of steady state RNA, and the nascent RNA was purified by biotinylation of EU-labeled RNA and selection on Streptavidin beads.  cDNA was prepared from each of the four RNA populations and the cDNA was purified with a Qiagen minElute PCR purification kit.

value: mock-infected, 24 hr, EU-labeled total RNA

tag: rna type

value: steady state RNA


title: ERB-transduced_ERB_100nM_ICI_II (P7469_507)

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

description:
Estrogen receptor beta transduced cells treated with 100nM with ICI for 24 hour
count_table.txt
fpkm_table.txt
P7469_507

data_processing:
Mapping:  Reads were mapped with Tophat/2.0.4 to the Human genome assembly, build GRCh37.
Merging:  Bamfiles from samples run on different lanes were merged with samtools.
Sorting and Marking duplicates:  Merged bam files were sorted and duplicates removed using picard-tools/1.29.
Counts for genes:  Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts: FPKMs for genes and transcripts were generated using  cufflinks/2.1.1 on bamfiles with duplicates included.
Genome_build: Homo Sapiens, GRch37
Supplementary_files_format_and_content: tab-delimited text files with counts and FPKM values for each sample and each gene.

source_name: Colon

growth_protocol: DMEM/10 FBS media was used to culture both cell lines

extract_protocol:
Qiagen RNAasy kit. We have done an extra on-colum DNAase treatment step.
RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA). The protocol was modified and automated using an Agilent NGS workstation (Agilent, CA, USA) using purification steps as described in S.Lundin et al. 2011 PLoS ONE.

tag: erb transduced

value: Yes

tag: transduced with empty vector

value: No

value: Treated with 100nM ICI for 24 hours


title: Total_RNA_Uninfected_K3_Rep2

description: RNA-seq


title: ERB-transduced_ERB_100nM_ICI_III (P7469_508)

description:
Estrogen receptor beta transduced cells treated with 100nM with ICI for 24 hour
count_table.txt
fpkm_table.txt
P7469_508


title: Pulmonary TB (UK) EBUS053

description:
Pulmonary TB (UK)
UKPTB


title: input_24hpi_Rep1


title: Pulmonary TB (UK) EBUS054

description:
Pulmonary TB (UK)
UKPTB


title: Nascent_RNA_Uninfected_K3_Rep1

description: RNA-seq

source_name: Nascent RNA Uninfected K3

value: mock infected, 24 hr, EU-labeled, biotinylated RNA purified

value: nascent RNA


title: Pulmonary TB (UK) EBUS058

description:
Pulmonary TB (UK)
UKPTB

value: ND


title: Nascent_RNA_Uninfected_K3_Rep2

description: RNA-seq


title: Empty_vector-transduced_1uM-G1-24hr_I (P7469_505)

description:
Empty vector transduced treated with 1 uM G1 for 24 hours
count_table.txt
fpkm_table.txt
P7469_505

value: Treated with 1uM G1 for 24 hours


title: Pulmonary TB (UK) EBUS047

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS050

description:
Pulmonary TB (UK)
UKPTB


title: Empty_vector-transduced_10nM-E2-24HR_II  (P7469_504)

description:
Empty vector transduced treated with 10nM estradiol for 24 hours
count_table.txt
fpkm_table.txt
P7469_504

value: Treated with 10nM Estradiol for 24 hours


title: 24hr_K3_Uninfected_Rep3

description: ATACseq

source_name: Mock infected

extract_protocol:
Cells were collected and resuspended in 50 μl of a transposase mix that included 25 μl of 2x Nextera Tagment DNA buffer (Illumina), 2.5 μl Nextera Tn5 transposase (Illumina), 0.5 μl digitonin 5% (Invitrogen), and 22μl of H2O. The reaction was carried at 37°C for 30 min. DNA was purified with Qiagen MinElute PCR purification kit and eluted in 10μl of buffer EB.
DNA libraries were amplified by using NEBNext High-Fidelity (New England Biolabs) and barcoded primers. The number of amplification cycles were calculated by qPCR and kept under 11 to prevent saturation. Libraries were purified with Qiagen MinElute PCR purification kit and sized selected with AMPure XB beads (Beckman Coulter) . Library quality control was assessed by Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and the libraries were sequenced with Illumina NextSeq technology (75bp single-end reads, 100 million reads/sample).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells.

value: mock-infected, 24 hr

tag: barcode


title: Pulmonary TB (UK) EBUS061

description:
Pulmonary TB (UK)
UKPTB


title: Pulmonary TB (UK) EBUS033

description:
Pulmonary TB (UK)
UKPTB


title: Small_intestine_tissue_T1L-SD33S08

city: New York

first: Simone

last: Dallari

state: NY

address: 550 1st Ave

institute: New York University Grossman School of Medicine

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the mm10 reference genome
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample, obtained from DESeq2

organism: Mus musculus

source_name: Small Intestine

growth_protocol: Piece of colonic (colon mid-section) and small intestinal (duodenum, jejunum, and ileum mid-section combined) were collected, snap frozen, and conserved at -80 until extraction

extract_protocol:
RNA for each sample was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Germ free mice were left uninfected or mono infected with several enteric viruses. Tissues were collected 28 days post infection

tag: tissue

value: Small Intestine

tag: infection


title: Pulmonary TB (UK) EBUS042

description:
Pulmonary TB (UK)
UKPTB

tag: disease status


title: Small_intestine_tissue_T1L-SD33S07


title: 24hr_K3_Uninfected_Rep1

description: ATACseq


title: Small_intestine_tissue_T1L-SD33S06


title: Small_intestine_tissue_T1L-SD31S05


title: Small_intestine_tissue_T1L-SD31S04


title: Empty_vector-transduced-DMSO-II (P7469_502)

description:
Empty vector transduced treated with DMSO for 24 hours
count_table.txt
fpkm_table.txt
P7469_502

value: DMSO


title: Empty_vector-transduced_1uM-G1-24hr_II (P7469_506)

description:
Empty vector transduced treated with 1 uM G1 for 24 hours
count_table.txt
fpkm_table.txt
P7469_506


title: Small_intestine_tissue_T1L-SD31S03


title: Small_intestine_tissue_RRV-SD42S06

value: RRV


title: 24hr_K3_Uninfected_Sorted_Rep1

description: RNA-seq

source_name: Total RNA_mock-infected K3 cells_24hpi

extract_protocol:
Infected Kasumi-3 cells were collected and lysed in Trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion step according to the manufacturer’s instructions.
RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads)

value: mock- infected, 24 hr

value: total RNA


title: 24hr_K3_Uninfected_Sorted_Rep2

description: RNA-seq


title: Small_intestine_tissue_RRV-SD42S05


title: Pulmonary TB (UK) EBUS046

description:
Pulmonary TB (UK)
UKPTB

tag: quantiferon

value: UCL, Royal Free NHS UK


title: Small_intestine_tissue_RRV-SD33S05


title: RPP-A_rep2

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing data were aligned to hg19 version of the human genome or mm10 version of the mouse genome with Star aligner (v. 2.6.1).
Viper RNA-seq processing pipeline (Cornwell et al., 2018; PMID: 29649993) was used to generate normalized expression values.
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: 631RPP-A cell line

growth_protocol: RPP-A cells were derived from RPP cells after selection for adherent cell growth on tissue-culture treated plastic cell culture dishes.

extract_protocol:
RNA was isolated  the Qiagen RNeasy isolation kit (Cat# 8028). RNA libraries were prepared from 250 ng total RNA.
RNA libraries were constructed using the Illumina Exome Capture kit per manufacturer’s instructions. RNA-sequencing (RNA-seq) was performed per the standard protocols at the Dana-Farber Molecular Biology Core Facilities with Illumina NextSeq 500 instrument.

treatment_protocol: H69M cells were derived from H69 cells as in Canadas et al. 2014 (PMID 24284055). H69EZ cells were derived from H69 cells after transient (6 day) EZH2 inhibitor exposure, and continued routine culture without inhibitor, with selection for adherent populations on tissue-culture treated plastic cell culture dishes.

tag: mhc class i status

value: high

tag: sorted population


title: 24hr_K3_Uninfected_Rep2

description: ATACseq


title: Small_intestine_tissue_RRV-SD33S03


title: RPP-A_rep3


title: RPP-A_rep1


title: ERB-transduced-10nM_E2/24HR_treated-I (P5501-215)

description:
Estrogen receptor beta transduced cells treated with 10nM estradiol for 24 hour
count_table.txt
fpkm_table.txt
P5501-215


title: ERB-transduced-10nM_E2/24HR_treated-II (P5501-216)

description:
Estrogen receptor beta transduced cells treated with 10nM estradiol for 24 hour
count_table.txt
fpkm_table.txt
P5501-216


title: Small_intestine_tissue_MVMp-SD45S05

value: MVMp


title: ERB-transduced-DMSO/24HR_treated-I (P5501-213)

description:
Estrogen receptor beta transduced cells treated with DMSO for 24 hour
count_table.txt
fpkm_table.txt
P5501-213

value: Yes

value: DMSO treated


title: Small_intestine_tissue_MVMp-SD45S04


title: RPP_rep3

source_name: 631RPP cell line

value: low/neg


title: Small_intestine_tissue_RRV-SD33S04


title: ERB-transduced-DMSO/24HR_treated-II (P5501-214)

description:
Estrogen receptor beta transduced cells treated with DMSO for 24 hour
count_table.txt
fpkm_table.txt
P5501-214

value: No


title: Empty_vector-transduced_10nM-E2-24HR_I (P7469_503)

description:
Empty vector transduced treated with 10nM estradiol for 24 hours
count_table.txt
fpkm_table.txt
P7469_503


title: Small_intestine_tissue_MVMp-SD45S06


title: Small_intestine_tissue_MVMp-SD24S05


title: Empty_vector-transduced-DMSO-I (P7469_501)

description:
Empty vector transduced treated with DMSO for 24 hours
count_table.txt
fpkm_table.txt
P7469_501


title: Empty_vector-transduced-II (P5501-212)

description:
Cells transduced with empty vector
count_table.txt
fpkm_table.txt
P5501-212

value: No treatment


title: Small_intestine_tissue_MVMp-SD24S04


title: RPP_rep2


title: Small_intestine_tissue_RRV-SD42S04


title: Small_intestine_tissue_MVMp-SD24S03


title: Empty_vector-transduced-I (P5501-211)

description:
Cells transduced with empty vector
count_table.txt
fpkm_table.txt
P5501-211


title: RPP_rep1