title: Exp1_DMC19_Plate1_E3P1_B01_N723_S513, Older adult

description:
CAI7246A1_241
genes.fpkm_table
genes.attr_table
samples.table

tag: phenotype


title: 708768 Control

status: Public on Aug 16 2023

type: SRA

city: Baltimore

first: Rasika

middle: M

last: Mathias

state: MD

address: 5501 Bayview Cir

department: Allergy and Clinical Immunology

country: USA

institute: Johns Hopkins University

library_source: transcriptomic

data_processing:
Trimming: FastQC0.11.9, BBDuk Version 38.90
Alignment: HISAT2 Version 2.2.21
Read Count Extraction: CoCo Version 2.0.2
Normalization: LIMMA Version 3.50.3, sva Version 3.42.0, edgeR Version 3.36.0
Filtering Genes: DESeq2_1.34.0
Assembly: GrCh38
Supplementary files format and content: full_n536__21831_voom_norm_counts_with_RandomID.csv
Supplementary files format and content: full_n536__raw_counts_with_RandomID.csv

molecule: total RNA

organism: Homo sapiens

source_name: Nasal Epithelium

extract_protocol: Total RNA with Ribo-Zero kit was used to prepare libraries from nasal epithelial cells depleting the ribosomal RNA

tag: tissue

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Control

tag: rnaseq inclusion

tag: site

value: Chicago

tag: age

tag: asthma

value: Not Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: Exp1_DMC19_Plate1_E3P1_C01_N723_S515, Older adult

city: Sydney

first: Fabio

last: Luciani

state: NSW

address: Kensington Campus

country: Australia

institute: UNSW Sydney

description:
CAI7246A1_242
genes.fpkm_table
genes.attr_table
samples.table

library_source: transcriptomic single cell

data_processing:
VDJPuzzle was run to extract TCR and quantify gene expression (FPKM)
Assembly: hg38
Supplementary files format and content: Matrix of FPKM values per sample, per gene
Supplementary files format and content: List of gene names in matrix
Supplementary files format and content: List of sample names in matrix

source_name: PBMCs

extract_protocol:
Single influenza A2/M158-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope

value: Older adult

value: Tem


title: Exp1_KK42_Plate3_A2P3_G10_N722_S522, Adult

description:
CAI7246A1_240
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: Adult

tag: phenotype

value: Tnaive


title: Exp1_KK42_Plate3_A2P3_F10_N722_S521, Adult

description:
CAI7246A1_239
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: Exp1_DMC19_Plate1_E3P1_A04_N724_S513, Older adult

description:
CAI7246A1_249
genes.fpkm_table
genes.attr_table
samples.table

tag: cell line

value: Bulk C1R

value: Bulk C1R cell line


title: Exp1_KK42_Plate3_A2P3_E10_N722_S520, Adult

description:
CAI7246A1_238
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: Exp1_KK42_Plate3_A2P3_A10_N722_S518, Adult

description:
CAI7246A1_237
genes.fpkm_table
genes.attr_table
samples.table


title: 845423 Control

tag: Sex

tag: case control_definition

tag: rnaseq inclusion


title: 723142 Control

tag: site

tag: age

tag: asthma


title: 680730 Control

value: Male

value: Denver

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: denver pc1

tag: denver pc2


title: 241786 Control

value: Nasal Epithelium

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: Exp1_DMC19_Plate1_E3P1_A03_N723_S520, Older adult

description:
CAI7246A1_246
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

tag: epitope


title: Exp1_KK42_Plate3_A2P3_G09_N722_S517, Adult

description:
CAI7246A1_236
genes.fpkm_table
genes.attr_table
samples.table

tag: phenotype


title: 366700 Control

tag: Sex

value: Female

tag: case control_definition


title: Exp1_KK42_Plate3_A2P3_E09_N722_S516, Adult

description:
CAI7246A1_235
genes.fpkm_table
genes.attr_table
samples.table


title: 367100 Control

value: Control

tag: rnaseq inclusion

tag: site


title: Exp1_KK42_Plate3_A2P3_G08_N722_S515, Adult

description:
CAI7246A1_234
genes.fpkm_table
genes.attr_table
samples.table

tag: age


title: 906069 Control

tag: asthma

tag: active asthma


title: 889140 Control

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch


title: Exp1_KK42_Plate3_A2P3_D08_N721_S522, Adult

description:
CAI7246A1_232
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_A08_N721_S521, Adult

description:
CAI7246A1_231
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells


title: Exp1_KK42_Plate3_A2P3_G07_N721_S520, Adult

description:
CAI7246A1_230
genes.fpkm_table
genes.attr_table
samples.table


title: 908637 Control

value: Chicago

value: Not Asthmatic

tag: chicago pc1

tag: chicago pc2


title: Exp1_KK42_Plate3_A2P3_E07_N721_S517, Adult

description:
CAI7246A1_228
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: CD8+ T cell


title: 319221 Control

tag: rnaseq cg_content

tag: full pc1

tag: denver pc1

tag: denver pc2


title: Exp1_KK42_Plate3_A2P3_F07_N721_S518, Adult

description:
CAI7246A1_229
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

tag: epitope

value: Tem


title: 755306 NA

tag: Sex

tag: case control_definition

tag: full pc2


title: Exp1_KK42_Plate3_A2P3_D07_N721_S516, Adult

description:
CAI7246A1_227
genes.fpkm_table
genes.attr_table
samples.table

tag: age

value: Adult

tag: phenotype


title: Exp1_KK42_Plate3_A2P3_B07_N721_S515, Adult

description:
CAI7246A1_226
genes.fpkm_table
genes.attr_table
samples.table


title: 289084 Control

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma


title: Exp1_KK42_Plate3_A2P3_G06_N720_S522, Adult

description:
CAI7246A1_224
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_A07_N721_S513, Adult

description:
CAI7246A1_225
genes.fpkm_table
genes.attr_table
samples.table


title: 152053 Control

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch


title: 970199 Control

tag: rnaseq cg_content

tag: full pc1


title: Exp1_KK42_Plate3_A2P3_E08_N722_S513, Adult

description:
CAI7246A1_233
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_E06_N720_S520, Adult

description:
CAI7246A1_222
genes.fpkm_table
genes.attr_table
samples.table


title: 850104 Control

tag: denver pc1

tag: denver pc2


title: Exp1_KK42_Plate3_A2P3_C06_N720_S517, Adult

description:
CAI7246A1_220
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type


title: Exp1_KK42_Plate3_A2P3_B06_N720_S516, Adult

description:
CAI7246A1_219
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope


title: Exp1_KK42_Plate3_A2P3_D06_N720_S518, Adult

description:
CAI7246A1_221
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_F05_N720_S515, Adult

description:
CAI7246A1_218
genes.fpkm_table
genes.attr_table
samples.table

value: Tnaive


title: 696378 Control

tag: Sex

tag: case control_definition


title: Exp1_KK42_Plate3_A2P3_E05_N720_S513, Adult

description:
CAI7246A1_217
genes.fpkm_table
genes.attr_table
samples.table

tag: age

value: Tcm


title: 695499 Control

tag: full pc2


title: Exp1_KK42_Plate3_A2P3_D05_N719_S522, Adult

description:
CAI7246A1_216
genes.fpkm_table
genes.attr_table
samples.table

tag: phenotype


title: 556731 Control

tag: rnaseq inclusion

tag: site


title: GBMpat_t0_D3

type: RNA

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

description: RNA extracted from peripheral blood monocytes obtained from GBM patients

hyb_protocol: 5.2 µg of fragmented and labeled sscDNA target was hybridized to Clariom™ D Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific). Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific).

data_processing: Processing of gene array was performed with R statistical language within Rstudio environment. Using oligo (v1.62.2; RRID:SCR_015729) package, raw CEL files were input into R (oligo::read.celfiles), and Robust Multichip Average (RMA)-based background correction and quantile normalization were performed with rma function, using pd.clariom.d.human (v3.14.1) for Affymetrix Clariom D Human platform design specification. Annotation of probe IDs was performed with affycoretools (v1.70.0) package (annotateEset function), using clariomdhumantranscriptcluster.db (c8.8.0) as reference ChipDb package. Analysis of differentially expressed genes was performed with limma package in R,

label: biotin

source_name: GBM patient monocyte

label_protocol: Fragmentation and labeling were performed with the GeneChip® WT Pico Labeling Kit according to the manufacturer’s instructions. The sample volume was 15ul at 30ng/ul out of which 200 ng of total RNA was used to generate amplified sense strand cDNA targets using GeneChip® WT Pico Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling of 5.5 ug sscDNA.

growth_protocol: Differentiated, primary Macrophages from healthy donors were exposed to SF medium in hypoxia with or without GBM-EVs (50 µg/mL). After 24 h, cells were extensively washed with 1M NaCl in PBS.

extract_protocol: TAF, no TAF areas (N = 8 patients with a total area of approximately 20 mm2), and PBMC samples were dissolved in 50 μl lysis solution provided by the AllPrep DNA/RNA Micro Kit for RNA isolation according to the manufacturer’s instructions. Total RNA quality was assessed by Agilent Technologies 2200 Tapestation and concentrations were measured by NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Human GBM tumor cryosections (10 μm) were mounted on DNase and RNase-free membranes (FrameSlidePET), rapidly stained for nuclei with cresyl violet and dehydrated in ice-cold ethanol. Adjacent sections were mounted on poly-lysine coated slides and stained for nuclei (Hoechst), CD68, and LipidTox to identify areas of interest. TAF (CD68+LD+) and no TAF (CD68+LD-) areas were isolated by LCM using the Zeiss PALM system. For PBMCs: PBMCs were collected from three patients with GBM before surgery and from three healthy donors by density-gradient centrifugation. BMDMs were isolated by positive selection for CD14+ with antibody-coated microbeads according to the manufacturer's instructions. After washing, cells were directly re-suspended in 350 μL lysis buffer.

value: Peripheral blood mononuclear cells (PBMCs)


title: GBMpat_t0_D2


title: Exp1_KK42_Plate3_A2P3_F06_N720_S521, Adult

description:
CAI7246A1_223
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_A05_N719_S520, Adult

description:
CAI7246A1_214
genes.fpkm_table
genes.attr_table
samples.table

tag: cell line

value: Bulk C1R

value: Bulk C1R cell line


title: Exp1_KK42_Plate3_A2P3_C05_N719_S521, Adult

description:
CAI7246A1_215
genes.fpkm_table
genes.attr_table
samples.table


title: GBMpat_t0_D1


title: HC_M0_D2

description: RNA extracted from peripheral blood monocytes differentiated into macrophages obtained from healthy donors

source_name: Macrophages, no treatment


title: HC_M0_EV_D2

description: RNA extracted from peripheral blood monocytes differentiated into macrophages obtained from healthy donors and cultured with extracellular vesicles

source_name: Macrophages, EV-treated


title: HC_t0_D2

description: RNA extracted from peripheral blood monocytes obtained from healthy donors

source_name: Healthy Donor monocyte


title: Exp1_KK42_Plate3_A2P3_F04_N719_S517, Adult

description:
CAI7246A1_212
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_G04_N719_S518, Adult

description:
CAI7246A1_213
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_E04_N719_S516, Adult

description:
CAI7246A1_211
genes.fpkm_table
genes.attr_table
samples.table


title: 293993 Control

tag: asthma

tag: active asthma

tag: rin nasalepithelium


title: Exp1_KK42_Plate3_A2P3_D04_N719_S515, Adult

description:
CAI7246A1_210
genes.fpkm_table
genes.attr_table
samples.table


title: 702288 Control

value: Male

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: Exp1_KK42_Plate3_A2P3_C04_N719_S513, Adult

description:
CAI7246A1_209
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue


title: Exp1_KK42_Plate3_A2P3_B04_N718_S522, Adult

description:
CAI7246A1_208
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type


title: 666259 Control

value: Denver

tag: denver pc1

tag: denver pc2


title: Exp1_KK42_Plate3_A2P3_A04_N718_S521, Adult

description:
CAI7246A1_207
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope


title: HC_M0_D1


title: 680250 Control

value: Nasal Epithelium

tag: Sex

tag: case control_definition

tag: age


title: HC_M0_EV_D1


title: 966333 Control

value: Female

tag: rnaseq inclusion

tag: full pc2


title: Exp1_KK42_Plate3_A2P3_E03_N718_S517, Adult

description:
CAI7246A1_204
genes.fpkm_table
genes.attr_table
samples.table

tag: phenotype


title: 536350 Control

value: Control

tag: site

tag: asthma


title: Exp1_KK42_Plate3_A2P3_D03_N718_S516, Adult

description:
CAI7246A1_203
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_B03_N718_S515, Adult

description:
CAI7246A1_202
genes.fpkm_table
genes.attr_table
samples.table


title: 251593 Control

tag: active asthma

tag: rin nasalepithelium


title: Exp1_KK42_Plate3_A2P3_A03_N718_S513, Adult

description:
CAI7246A1_201
genes.fpkm_table
genes.attr_table
samples.table

tag: cell line


title: Exp1_KK42_Plate3_A2P3_G02_N716_S522, Adult

description:
CAI7246A1_200
genes.fpkm_table
genes.attr_table
samples.table


title: 460697 Control

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: Exp1_KK42_Plate3_A2P3_F02_N716_S521, Adult

description:
CAI7246A1_199
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type


title: M0_noLD_C2

description: RNA extracted from brain tissue areas low in lipid droplets, batch 2.

source_name: Cohort 2, microdissected GBM regions, high macrophage, no lipid droplets

value: Brain


title: Exp1_KK42_Plate3_A2P3_D02_N716_S520, Adult

description:
CAI7246A1_198
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope


title: M0_LD_C1

description: RNA extracted from brain tissue areas high in lipid droplets, batch 1.

source_name: Cohort 1, microdissected GBM regions, high macrophage, with lipid droplets


title: 255440 Control

tag: Sex

tag: denver pc1

tag: denver pc2


title: Exp1_KK42_Plate3_A2P3_C02_N716_S518, Adult

description:
CAI7246A1_197
genes.fpkm_table
genes.attr_table
samples.table

tag: age


title: M0_noLD_C1

description: RNA extracted from brain tissue areas low in lipid droplets, batch 1.

source_name: Cohort 1, microdissected GBM regions, high macrophage, no lipid droplets


title: Exp1_KK42_Plate3_A2P3_B02_N716_S517, Adult

description:
CAI7246A1_196
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate3_A2P3_G03_N718_S520, Adult

description:
CAI7246A1_206
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: HBMEC_CM_EV_D2

description: RNA extracted from HBMEC cells treated with EV conditioned media, donor 2

hyb_protocol: 5.2 µg of fragmented and labelled sscDNA target was hybridized to Clariom™ D Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific). Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol.

data_processing: Processing of gene array was performed with method SST_RMA, with annotation done with Clariom_D_Human.r1.na36.hg38.a1.transcript.csv and statistics with limma's moderated t.

source_name: HBMEC+CM M0EV D2

label_protocol: Fragmentation and labeling were performed with the GeneChip® WT Plus Labeling Kit according to the manufacturer’s instructions. 200 ng of total RNA was used to generate amplified sense strand cDNA targets using GeneChip® WT Plus Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling of 5.5 ug sscDNA.

growth_protocol: Cells were seeded in 24-well plates in full medium, followed by 24 h starvation in SF EC medium.

extract_protocol: HBMEC samples were dissolved in 50 μl lysis solution provided by the AllPrep DNA/RNA Micro Kit for RNA isolation according to the manufacturer’s instructions. Total RNA quality was assessed by Agilent Technologies 2200 Tapestation and concentrations were measured by NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Serum-free or EV-conditioned media, collected from macrophages pre-conditioned were added to HBMECs for 6 h at 37°C in hypoxia.

value: HBMEC


title: M0_LD_C2

source_name: Cohort 2, microdissected GBM regions, high macrophage, with lipid droplets


title: Exp1_KK42_Plate3_A2P3_G01_N716_S516, Adult

description:
CAI7246A1_195
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: Exp1_KK42_Plate3_A2P3_F03_N718_S518, Adult

description:
CAI7246A1_205
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell


title: HBMEC_CM_EV_LDDD_D2

description: RNA extracted from HBMEC cells treated with EV conditioned media with LDDD, donor 2

source_name: HBMEC+CM M0EV+LDDD D2


title: 668166 Control

tag: case control_definition

tag: rnaseq inclusion

value: Washington DC

value: Not Asthmatic

tag: full pc2

tag: washington dc_pc1

tag: washington dc_pc2


title: HBMEC_CM_EV_LDDD_D1

description: RNA extracted from HBMEC cells treated with EV conditioned media with LDDD, donor 1

source_name: HBMEC+CM M0EV+LDDD D1


title: 574555 Control

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium


title: 595900 Control

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: Exp1_KK42_Plate3_A2P3_F01_N716_S515, Adult

description:
CAI7246A1_194
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

tag: epitope

value: Adult

tag: phenotype

value: Tnaive


title: 656722 Control

tag: Sex

tag: age

tag: denver pc1

tag: denver pc2


title: Exp1_KK42_Plate3_A2P3_C01_N715_S522, Adult

description:
CAI7246A1_192
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: Exp1_KK42_Plate3_A2P3_E01_N716_S513, Adult

description:
CAI7246A1_193
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate1_A2P1_F10_N715_S521, Adult

description:
CAI7246A1_191
genes.fpkm_table
genes.attr_table
samples.table


title: HBMEC_CM_EV_D1

description: RNA extracted from HBMEC cells treated with EV conditioned media, donor 1

source_name: HBMEC+CM M0EV D1


title: HBMEC_CM_SF_LDDD_D2

description: RNA extracted from HBMEC cells treated with serum-free conditioned media with LDDD, donor 2

source_name: HBMEC+CM M0SF+LDDD D2


title: HBMEC_CM_SF_LDDD_D1

description: RNA extracted from HBMEC cells treated with serum-free conditioned media with LDDD, donor 1

source_name: HBMEC+CM M0SF+LDDD D1


title: HBMEC_CM_SF_D1

description: RNA extracted from HBMEC cells treated with serum-free conditioned media, donor 1

source_name: HBMEC+CM M0SF D1


title: HC_t0_D1

description: RNA extracted from peripheral blood monocytes obtained from healthy donors

value: Peripheral blood mononuclear cells (PBMCs)


title: HBMEC_CM_SF_D2

description: RNA extracted from HBMEC cells treated with serum-free conditioned media, donor 2

source_name: HBMEC+CM M0SF D2


title: Exp1_KK42_Plate1_A2P1_E10_N715_S520, Adult

description:
CAI7246A1_190
genes.fpkm_table
genes.attr_table
samples.table

source_name: PBMCs


title: Exp1_KK42_Plate1_A2P1_B10_N715_S517, Adult

description:
CAI7246A1_188
genes.fpkm_table
genes.attr_table
samples.table


title: 114480 Control

source_name: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

tag: full pc2


title: 573327 Control

tag: site

tag: asthma


title: SON_M125_1

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

department: Biomedical Sciences

institute: University of North Dakota

library_source: genomic

data_processing:
Fastq reads were indexed using Nanopolish (v0.14.0).
Reads were aligned to rn7 assembly using minimap2 (v2.24) and indexed with Samtools (v1.6).
CpG methylation calling was performed using Nanopolish.
Methylation frequency was determined by the "calculate_methylation_frequency.py" script provided by Nanopolish.
Assembly: rn7
Supplementary files format and content: Text file of tab-separated values (.tsv) of called methylation values.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Supraoptic Nucleus

extract_protocol:
Rats were anesthetized with isoflurane and euthanized via transcardial perfusion with PBS. Brains were serial sectioned via vibratome and a tissue puncher was used to collected the supraoptic nucleus, which were immediately flash frozen by liquid nitrogen.
Genomic DNA was collected by ethanol precipitation. In brief, frozen tissue was ground under liquid nitrogen, and lysed with buffer ATL (Qiagen). DNA was isolated via phenol:chloroform: isoamyl alcohol and cintrifuged. DNA was washed and precipitated with 70% ethanol and the resuting DNA pellet was resuspended in buffer EB (Qiagen).
DNA was fragmented using a Covaris g-TUBE (Covaris). Libraries were prepared using the Oxford Nanopore Ligation Sequencing Kit (Oxford).
Other - long-read DNA sequencing nanopore

treatment_protocol: Rats were grown to the ages of 35 days old or 125 days old prior to tissue collection.

value: Supraoptic Nucleus

tag: strain

value: Sprague Dawley

tag: treatment

value: Age - 125 days old


title: SON_M125_3

value: Male


title: 385813 Control

value: Nasal Epithelium

value: Female

value: Denver

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: Exp1_KK42_Plate1_A2P1_B09_N715_S513, Adult

description:
CAI7246A1_185
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type


title: Exp1_KK42_Plate1_A2P1_C09_N715_S515, Adult

description:
CAI7246A1_186
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype


title: SON_M35_3

tag: Sex

value: Age - 35 days old (Control)


title: Exp1_KK42_Plate1_A2P1_F09_N715_S516, Adult

description:
CAI7246A1_187
genes.fpkm_table
genes.attr_table
samples.table

tag: age


title: SON_M125_2


title: Exp1_KK42_Plate1_A2P1_G07_N714_S517, Adult

description:
CAI7246A1_180
genes.fpkm_table
genes.attr_table
samples.table

value: Tscm


title: 549731 Case

value: Case

value: Brazil

value: Asthmatic

value: Active Asthma

tag: rin nasalepithelium

tag: full pc1

tag: brazil pc1

tag: brazil pc2


title: Exp1_KK42_Plate1_A2P1_E08_N714_S522, Adult

description:
CAI7246A1_184
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: CD8+ T cell

value: Adult


title: 136972 Case

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Barbados

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: Exp1_KK42_Plate1_A2P1_D07_N714_S515, Adult

description:
CAI7246A1_178
genes.fpkm_table
genes.attr_table
samples.table


title: Exp1_KK42_Plate1_A2P1_F07_N714_S516, Adult

description:
CAI7246A1_179
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: 351346 Case

value: Nigeria

tag: asthma

tag: active asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: nigeria pc1

tag: nigeria pc2


title: 397600 Control

tag: tissue

tag: Sex

value: Control

tag: age

value: Not Asthmatic

tag: denver pc1

tag: denver pc2


title: Exp1_KK42_Plate1_A2P1_F06_N712_S521, Adult

description:
CAI7246A1_175
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: phenotype


title: Exp1_KK42_Plate1_A2P1_C08_N714_S521, Adult

description:
CAI7246A1_183
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: neural stem cells were infected with ZIKV SV0127/14, replicate 2

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

data_processing:
Transcriptome analysis was carried out using the BGISEQ-500 platform by BGI Shenzhen Company (China), and data was filtered using SOAP Nuke software.
Transcript alignment of filtered reads was performed using HISAT (Kim et al. 2019) against the reference genome of Sus scrofa (NCBI Reference Genome Version: GCF_000003025.6_Sscrofa11.1).
Assembly: Sus scrofa (GCF_000003025.6_Sscrofa11.1)
Supplementary files format and content: normalizedReadCount.csv

organism: Sus scrofa

source_name: pig induce neural stem cells (piNSCs)

growth_protocol: Zika virus were infected Vero cells. The CPE was detected two to three days after infection. ZIKV-infected supernatant was collected.

extract_protocol:
RNA was extracted following the miRNeasy Mini Kit (217004, Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA-seq library preparation and sequencing were performed through service by  BGI (China)

treatment_protocol: The porcine induced neural stem cells (piNSCs) were infected with a mock and two strain of Zika virus. After two days of infection, the piNSCs were collected for transcriptome analysis

value: pig induce neural stem cells (piNSCs)

tag: treatment

value: infected with ZIKV SV0127/14

tag: biological replicate


title: 702340 Case

value: Nasal Epithelium

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Chicago

tag: full pc1

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: Exp1_KK42_Plate1_A2P1_B08_N714_S520, Adult

description:
CAI7246A1_182
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue


title: Exp1_KK42_Plate1_A2P1_A08_N714_S518, Adult

description:
CAI7246A1_181
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells


title: Exp1_KK42_Plate1_A2P1_D10_N715_S518, Adult

description:
CAI7246A1_189
genes.fpkm_table
genes.attr_table
samples.table

value: Tem


title: neural stem cells were infected with ZIKV SV0127/14, replicate 3


title: Exp1_KK42_Plate1_A2P1_E06_N712_S520, Adult

description:
CAI7246A1_174
genes.fpkm_table
genes.attr_table
samples.table


title: SON_M35_2

value: Supraoptic Nucleus

tag: Sex

tag: strain

value: Sprague Dawley

value: Age - 35 days old (Control)


title: neural stem cells were infected with ZIKV SV0127/14, replicate 1


title: SON_M35_1


title: Exp1_KK42_Plate1_A2P1_A06_N712_S516, Adult

description:
CAI7246A1_171
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: age

value: Adult


title: Exp1_KK42_Plate1_A2P1_C06_N712_S517, Adult

description:
CAI7246A1_172
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Tcm


title: Exp1_KK42_Plate1_A2P1_G05_N712_S515, Adult

description:
CAI7246A1_170
genes.fpkm_table
genes.attr_table
samples.table


title: neural stem cells were infected with ZIKV strain SV0010/15, replicate 3

value: infected with ZIKV strain SV0010/15


title: Exp1_KK42_Plate1_A2P1_E05_N711_S522, Adult

description:
CAI7246A1_168
genes.fpkm_table
genes.attr_table
samples.table

value: Tscm


title: 208243 Case

value: Female

value: Case

value: Nigeria

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: nigeria pc1

tag: nigeria pc2


title: 373780 Case

value: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

value: Brazil

tag: brazil pc1

tag: brazil pc2


title: neural stem cells were infected with ZIKV strain SV0010/15, replicate 2

tag: cell type

value: pig induce neural stem cells (piNSCs)

tag: treatment

tag: biological replicate


title: 409849 Case

tag: tissue

tag: Sex

tag: site

value: Barbados

tag: full pc1

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: Exp1_KK42_Plate1_A2P1_D05_N711_S521, Adult

description:
CAI7246A1_167
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: age

tag: phenotype


title: Exp1_KK42_Plate1_A2P1_A07_N714_S513, Adult

description:
CAI7246A1_177
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells


title: 466852 Case

tag: case control_definition

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: neural stem cells were infected with ZIKV strain SV0010/15, replicate 1

tag: cell type

tag: treatment

tag: biological replicate


title: 809888 Case

tag: tissue

tag: Sex

tag: rnaseq inclusion

tag: site

tag: brazil pc1

tag: brazil pc2


title: Exp1_KK42_Plate1_A2P1_A05_N711_S520, Adult

description:
CAI7246A1_166
genes.fpkm_table
genes.attr_table
samples.table

tag: cell line

value: Bulk C1R

value: Bulk C1R cell line

tag: epitope

tag: age


title: Exp1_KK42_Plate1_A2P1_H06_N712_S522, Adult

description:
CAI7246A1_176
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Adult

tag: phenotype


title: Exp1_KK42_Plate1_A2P1_F04_N711_S517, Adult

description:
CAI7246A1_164
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Tcm


title: Exp1_KK42_Plate1_A2P1_D06_N712_S518, Adult

description:
CAI7246A1_173
genes.fpkm_table
genes.attr_table
samples.table


title: neural stem cells, replicate 3

value: control


title: Exp1_KK42_Plate1_A2P1_H04_N711_S518, Adult

description:
CAI7246A1_165
genes.fpkm_table
genes.attr_table
samples.table


title: neural stem cells, replicate 2


title: 220887 Case

value: Female

tag: case control_definition

value: Chicago

tag: asthma

tag: active asthma

tag: full pc1

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: 638550 Case

tag: tissue

value: Case

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: barbados pc1

tag: barbados pc2


title: Exp1_KK42_Plate1_A2P1_F05_N712_S513, Adult

description:
CAI7246A1_169
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type


title: biventricular heart, WT, biol rep 5

city: Birmingham

first: Lamario

middle: J

last: Williams

state: AL

address: 1825 University Boulevard, Room 121

department: Medicine

institute: University of Alabama at Birmingham

description:
MHC33
rawCounts.xlsx

data_processing:
Basecalls were performed using Illumina's bcl2fastq version 2.18.0.12
Raw sequence reads were aligned with STAR (version 2.7.9a) using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment BAM files using HTSeq-count (version 0.11.1) using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm39 Release M26
Supplementary files format and content: Excel file containing Ensembl ID# and raw counts for each gene in each sample

organism: Mus musculus

source_name: biventricular heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: strain

tag: Sex

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: WT


title: 412366 Case

value: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: age

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: full pc1


title: Exp1_KK42_Plate1_A2P1_E04_N711_S516, Adult

description:
CAI7246A1_163
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: epitope

tag: phenotype


title: biventricular heart, Cre CON, biol rep 4

description:
MHC34
rawCounts.xlsx

value: Cre CON


title: biventricular heart, Cre CON, biol rep 3

description:
MHC29
rawCounts.xlsx


title: GSC, chromatin input control, rep1

first: Allan

middle: C

last: Spradling

state: Maryland

address: 3520 San Martin Drive

department: HHMI Lab at Embryology

institute: Carnegie Institution for Science

description: H3K9me3 ChIP-seq of FACS-purified Drosophila melanogaster germ cells

data_processing:
Reads were mapped with Bowtie2 (2.4.4). SAM output was filtered for MAPQ (>= 20), sorted, converted to BAM, and indexed with SAMtools (1.6). A genome-wide coverage bedGraph was computed with BEDtools (2.30.0). A BigWig file was generated using wigToBigWig from Kent Utils 420 (-clip). BEDtools was used to obtain coverage counts in 250 kb bins across the genome.
Assembly: Genome and Gene Annotation Set: BDGP6.22.Ensembl.98 (dm6, Ensembl release 98, NCBI: GCA_000001215.4). For samples with mouse cell spike-ins, a "hybrid genome assembly" was constructed by combining the BDGP6.22.Ensembl.98 dm6 Drosophila genome assembly with the mm10 mouse genome assembly from which 'hybrid genome' bowtie2 indexes were constructed.
Supplementary files format and content: RNAseq: STAR-RSEM output of estimated expression ; ChIPseq: bigWig ; HMM state paths: bedGraph with states 1 (depleted), 2 (no-change), and 3 (enriched). HMM gene annotations: BED-like tab-sepatated file with description in column names ;
Supplementary files format and content: AllDataTable.csv: aggregated data table of processed data of ATACseq, H3K27ac ChIPseq, H3K27me3 ChIPseq, and RNAseq from GSC to stage 9 nurse cells (NCs)

organism: Drosophila melanogaster

source_name: FACS purified germ cell

growth_protocol: flies were grown on standard food plus wet yeast paste for 3-6 days

extract_protocol:
Chip-seq was carried out as described in Deluca et al (2020). Since we worked with cells with various ploidy levels spanning from 2C to 512C, we standardized input to the number of genomes rather than the number of cells. Specifically, for each IP, the equivalent of 500,000 2C sorted nuclei (i.e. 1 million genomes) were mixed with a specific amount of fixed mouse 3T3 cells as a spike-in (the same amount across samples). Mixed samples were then sonicated to acquire mono-nucleosome fragments: nuclei were resuspended in 100 µl of Nuclei Resuspension Buffer (all recipes at end), and were sonicated in a Bioruptor Pico instrument with 22 cycles of 30 s on, 30 s off. Fragment sizes were confirmed with the Bioanalyzer (Agilent). Subsequently, 900 µl of Dilution Buffer was added to the 100 ul of mononucleosome fragments, then 1% of each sample was set aside to be used for input controls. To prepare antibody-conjugated beads, 10 µl of antibody (either H3K27ac, H3K27me3, or H3K9me3) was preincubated with 25 µl of a 1:1 mix of proteinA:proteinG dynabeads, then washed twice with PBS + 0.02% Tween 20 (PBST). To bind mononucleosome fragments that harbored the target antigen, we combined antibody-conjugated beads with the chromatin extract(s) on a rocker at 4°C overnight. The next day, the beads were washed twice for 15 min each with Wash buffer A, Wash buffer B, Wash buffer C, and TE buffer. Chromatin was eluted and reverse-crosslinked by incubating at 65°C overnight with Direct Elution Buffer (DEB). For input samples (set aside earlier), cross links were reversed by adding NaCl to 300 mM, then adding DEB to equalize the volume between inputs and IPs, then incubating at 65°C overnight. All samples were then incubated for 30 min at 37°C with 0.3 mg/ml RNAse A, and subsequently for 2 hr at 55°C with 0.6 mg/ml proteinase K. DNA was then extracted with phenol:chloroform, precipitated with NaAc/ethanol, washed with 70% ethanol wash, and resuspended samples in 10 µl water and of which all 10 µl was used for library preps.   Recipes: Nuclei Resuspension Buffer (50 mM TrisHCl pH 8.0, 10 mM EDTA, 1% SDS, and proteinase inhibitor cocktail (Roche)). Dilution Buffer (15 mM TrisHCl pH 8.0, 1 mM EDTA, 1% Triton X-100, 150 mM NaCl). Wash buffer A (20 mM TrisHCl pH8.0, 2 mM EDTA, 0.1% SDS, 1% Triton X100, 150 mM NaCl), Wash buffer B (20 mM TrisHCl pH8.0, 2 mM EDTA, 0.1% SDS, 1% Triton X100, 500 mM NaCl), Wash buffer C (10 mM TrisHCl pH8.0, 1 mM EDTA, 1% NP40, 1% Sodium deoxycholate, 0.25M LiCl), TE buffer (10 mM TrisHCl pH8.0, 1 mM EDTA). Direct Elution Buffer (DEB) (10 mM TrisHCl pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS).
The Illumina sequencing library was prepared with Takara Bio / Rubicon ThruPLEX DNA-seq kit and sequenced on an Illumina NextSeq 500 to yield 75 bp, single-end reads.

value: FACS purified germ cell

value: female

tag: developmental stage

value: GSC

value: C587-Gal4, UAS-GFP, bam{delta}86


title: neural stem cells, replicate 1

tag: cell type

value: pig induce neural stem cells (piNSCs)

tag: treatment

tag: biological replicate


title: Exp1_KK42_Plate1_A2P1_D04_N711_S515, Adult

description:
CAI7246A1_162
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: CD8+ T cell

value: Adult

value: Tcm


title: 569544 Case

tag: Sex

value: Female

value: Case

value: Brazil

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: biventricular heart, WT, biol rep 4

description:
MHC32
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: WT


title: biventricular heart, Cre CON, biol rep 2

description:
MHC21
rawCounts.xlsx

tag: tissue


title: biventricular heart, WT, biol rep 2

description:
MHC28
rawCounts.xlsx


title: 913594 Case

value: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Barbados

tag: age

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: full pc1

tag: barbados pc1

tag: barbados pc2


title: Exp1_KK42_Plate1_A2P1_A04_N710_S522, Adult

description:
CAI7246A1_160
genes.fpkm_table
genes.attr_table
samples.table

tag: cell line

value: Bulk C1R

tag: cell type

value: Bulk C1R cell line

tag: epitope

tag: phenotype


title: NC, 4C, chromatin input control, rep1

value: FACS purified germ cell

tag: Sex

value: female

tag: developmental stage

value: 4C NC

value: MTD-Gal4, UASz-tdTomato


title: 561010 Case

value: Baltimore

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: biventricular heart, Cre CON, biol rep 1

description:
MHC20
rawCounts.xlsx

tag: strain

tag: tissue

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: Cre CON


title: NC, 8C, chromatin input control, rep1

value: 8C NC


title: NC, 8C, H3K9me3 ChIP-seq, rep1


title: Exp1_KK42_Plate1_A2P1_G03_N710_S521, Adult

description:
CAI7246A1_159
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: age

value: Adult

value: Tcm


title: 961485 Case

value: Nasal Epithelium

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: full pc1


title: Exp1_KK42_Plate1_A2P1_D03_N710_S520, Adult

description:
CAI7246A1_158
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope

tag: phenotype


title: biventricular heart, WT, biol rep 6

description:
MHC6
rawCounts.xlsx

tag: Sex

value: male

value: biventricular heart

value: WT


title: NC, 4C, H3K9me3 ChIP-seq, rep1

value: FACS purified germ cell

tag: developmental stage


title: Exp1_KK42_Plate1_A2P1_C04_N711_S513, Adult

description:
CAI7246A1_161
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue


title: Exp1_KK42_Plate1_A2P1_C03_N710_S518, Adult

description:
CAI7246A1_157
genes.fpkm_table
genes.attr_table
samples.table


title: GSC, H3K9me3 ChIP-seq, rep1

value: female

value: GSC

value: C587-Gal4, UAS-GFP, bam{delta}86


title: 178316 Case

value: Barbados

value: Asthmatic

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: biventricular heart, WT, biol rep 3

description:
MHC3
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype


title: 858660 Case

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Chicago

tag: age

tag: asthma

tag: active asthma

tag: full pc1

tag: chicago pc1

tag: chicago pc2


title: 524654 Case

tag: tissue

tag: Sex

value: Male

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2


title: NC, 256C, H3K27ac ChIP-seq, rep1

description: H3K27ac ChIP-seq of FACS-purified Drosophila melanogaster germ cells

data_processing:
Reads were mapped with Bowtie2 (2.3.2). SAM output was filtered for MAPQ (>= 30) and to retain only reads on the major chromosome scaffolds (2L, 2R, 3L, 3R, 4, X and Y), sorted, converted to BAM, and indexed with SAMtools (1.6). A BigWig file was generated from the sorted filtered BAM using DeepTools (3.1.3; -p max -bs 1 --effectiveGenomeSize 127324632 --normalizeUsing CPM).
Assembly: Genome and Gene Annotation Set: BDGP6.22.Ensembl.98 (dm6, Ensembl release 98, NCBI: GCA_000001215.4). For samples with mouse cell spike-ins, a "hybrid genome assembly" was constructed by combining the BDGP6.22.Ensembl.98 dm6 Drosophila genome assembly with the mm10 mouse genome assembly from which 'hybrid genome' bowtie2 indexes were constructed.
Supplementary files format and content: RNAseq: STAR-RSEM output of estimated expression ; ChIPseq: bigWig ; HMM state paths: bedGraph with states 1 (depleted), 2 (no-change), and 3 (enriched). HMM gene annotations: BED-like tab-sepatated file with description in column names ;
Supplementary files format and content: AllDataTable.csv: aggregated data table of processed data of ATACseq, H3K27ac ChIPseq, H3K27me3 ChIPseq, and RNAseq from GSC to stage 9 nurse cells (NCs)

tag: developmental stage

value: 256C NC

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato


title: biventricular heart, Cre CON, biol rep 5

description:
MHC4
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: Cre CON


title: NC, 256C, chromatin input control, rep1


title: biventricular heart, E4BP4 FLOX, biol rep 4

description:
CEK181
rawCounts.xlsx

value: E4BP4 FLOX


title: NC, 32C, chromatin input control, rep1

value: 32C NC


title: Exp1_KK42_Plate1_A2P1_E02_N710_S515, Adult

description:
CAI7246A1_154
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

value: Adult

tag: phenotype

value: Tcm


title: Exp1_KK42_Plate1_A2P1_C02_N710_S513, Adult

description:
CAI7246A1_153
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: biventricular heart, WT, biol rep 1

description:
MHC1
rawCounts.xlsx

value: male

value: biventricular heart

value: WT


title: Exp1_KK42_Plate1_A2P1_F02_N710_S516, Adult

description:
CAI7246A1_155
genes.fpkm_table
genes.attr_table
samples.table

value: Tnaive


title: 648829 Case

value: Nasal Epithelium

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: full pc1

tag: chicago pc1

tag: chicago pc2


title: 712783 Case

tag: tissue

tag: Sex

value: Nigeria

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: 147046 Case

value: Male

tag: age


title: Exp1_KK42_Plate1_A2P1_H01_N707_S522, Adult

description:
CAI7246A1_152
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: phenotype


title: biventricular heart, E4BP4 FLOX, biol rep 3

description:
CEK180
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: E4BP4 FLOX


title: biventricular heart, CEK, biol rep 5

description:
CEK174
rawCounts.xlsx

tag: tissue

value: CEK


title: NC, 32C, H3K27ac ChIP-seq, rep1

value: FACS purified germ cell

tag: Sex

value: female

tag: developmental stage

value: 32C NC

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato


title: NC, 512C, ATAC-seq, rep3

description: ATAC-seq of FACS-purified Drosophila melanogaster germ cells

extract_protocol:
ATAC-seq libraries were prepared with either the Illumina Nextera™ DNA Sample Preparation Kits or using the Illumina DNA Prep kit with a modified protocol. Briefly, sorted nuclei were resuspended in the Tagmentation Buffer 1 (TB1), then incubated with DNA Tagment DNA Enzyme (TDE1) for 30 min at 37℃ before stopping the reaction by incubating overnight at 65˚C with Tagment Stop Buffer (TSB). The reaction was then digested with RNAase for 1 hour, then  Proteinase K for 2 hours.
Tagmented DNA was extracted with phenol/chloroform and amplified with Enhanced PCR Mix (EPM) and i7/i5 index primers for 10 PCR cycles. Amplified DNA was cleaned up with the Sample Purification Beads (SPB) from the Illumina Kit or AMPure XP beads (Beckman Coulter). Libraries were assessed for quantity and fragment size using an Agilent Bioanalyzer, then sequenced on an Illumina NextSeq 500 to yield 75 bp, single-end reads.

value: 512C NC


title: biventricular heart, Cre CON, biol rep 6

description:
MHC7
rawCounts.xlsx

value: male

value: biventricular heart

value: Cre CON


title: 511352 Case

value: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1


title: 617605 Case

value: Barbados

tag: age

tag: rnaseq cg_content

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: NC, 512C, ATAC-seq, rep2

tag: genotype


title: Exp1_KK42_Plate1_A2P1_A03_N710_S517, Adult

description:
CAI7246A1_156
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

tag: cell line

value: Bulk C1R

tag: cell type

value: Bulk C1R cell line

tag: epitope

value: Adult

tag: phenotype


title: Exp1_KK42_Plate1_A2P1_G01_N707_S521, Adult

description:
CAI7246A1_151
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Tcm


title: biventricular heart, CEK, biol rep 4

description:
CEK173
rawCounts.xlsx

tag: strain

tag: Sex

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

value: CEK


title: 943003 Case

value: Male

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1


title: biventricular heart, E4BP4 FLOX, biol rep 2

description:
CEK172
rawCounts.xlsx

tag: tissue

tag: genotype

value: E4BP4 FLOX


title: NC, 256C, ATAC-seq, rep3

value: FACS purified germ cell

value: female

tag: developmental stage

value: 256C NC

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato


title: 420928 Case

value: Nasal Epithelium

value: Female

value: Barbados

tag: age

tag: rnaseq cg_content

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: Exp1_KK42_Plate1_A2P1_E01_N707_S518, Adult

description:
CAI7246A1_149
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

tag: epitope

tag: phenotype


title: NC, 256C, ATAC-seq, rep2

tag: Sex


title: biventricular heart, CEK, biol rep 3

description:
CEK171
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox


title: Exp1_KK42_Plate1_A2P1_C01_N707_S516, Adult

description:
CAI7246A1_147
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Adult

value: Tcm


title: biventricular heart, CEK, biol rep 2

description:
CEK103
rawCounts.xlsx

value: CEK


title: 397435 Case

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1


title: NC, 128C, ATAC-seq, rep3

tag: tissue

tag: developmental stage

value: 128C NC

tag: genotype


title: NC, 256C, ATAC-seq, rep1

value: FACS purified germ cell


title: Exp1_KK42_Plate1_A2P1_D01_N707_S517, Adult

description:
CAI7246A1_148
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: age

tag: phenotype


title: Exp1_TN024_Plate2_K2P2_B10_N707_S515, Child

description:
CAI7246A1_146
genes.fpkm_table
genes.attr_table
samples.table

value: Child

value: Temra


title: 673217 Case

tag: Sex

value: Brazil

value: Active Asthma

tag: rnaseq cg_content

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: 618407 Case

value: Nasal Epithelium

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma


title: 798170 Case

value: Barbados

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: barbados pc1

tag: barbados pc2


title: NC, 128C, ATAC-seq, rep2

tag: tissue

value: female

tag: developmental stage

tag: genotype

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato


title: Exp1_TN024_Plate2_K2P2_A10_N707_S513, Child

description:
CAI7246A1_145
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

tag: phenotype

value: Tnaive


title: biventricular heart, CEK, biol rep 1

description:
CEK91
rawCounts.xlsx

tag: strain

tag: Sex

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

value: CEK


title: biventricular heart, E4BP4 FLOX, biol rep 1

description:
CEK170
rawCounts.xlsx

value: E4BP4 FLOX


title: NC, 128C, ATAC-seq, rep1

value: FACS purified germ cell

value: 128C NC


title: NC, 512C, ATAC-seq, rep1

value: 512C NC


title: Exp1_TN024_Plate2_K2P2_B09_N706_S522, Child

description:
CAI7246A1_144
genes.fpkm_table
genes.attr_table
samples.table

value: Child

value: Temra


title: biventricular heart, E4BP4 FLOX, biol rep 6

description:
CEK93
rawCounts.xlsx


title: biventricular heart, E4BP4 FLOX, biol rep 5

description:
CEK90
rawCounts.xlsx


title: Exp1_TN024_Plate2_K2P2_A09_N706_S521, Child

description:
CAI7246A1_143
genes.fpkm_table
genes.attr_table
samples.table


title: NC, 64C, ATAC-seq, rep3

value: 64C NC


title: 912560 Case

value: Nasal Epithelium

value: Male

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Brazil

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq cg_content

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: Exp1_KK42_Plate1_A2P1_F01_N707_S520, Adult

description:
CAI7246A1_150
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

value: Adult

value: Tem


title: 900634 Case

tag: Sex

value: Baltimore

tag: rnaseq libraryprep_batch

tag: full pc1

tag: baltimore pc1

tag: baltimore pc2


title: biventricular heart, CEK, biol rep 6

description:
CEK84
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: CEK


title: NC, 64C, ATAC-seq, rep2

value: FACS purified germ cell

value: female

tag: developmental stage

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato


title: Exp1_TN024_Plate2_K2P2_B08_N706_S520, Child

description:
CAI7246A1_142
genes.fpkm_table
genes.attr_table
samples.table

value: Child

tag: phenotype

value: Tnaive


title: 182666 NA

value: Nasal Epithelium

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq cg_content


title: biventricular heart, BMAL1 FLOX, biol rep 4

description:
CBKE208
rawCounts.xlsx

tag: Sex

tag: tissue

value: BMAL1 FLOX


title: NC, 64C, ATAC-seq, rep1

value: 64C NC


title: Exp1_TN024_Plate2_K2P2_A08_N706_S518, Child

description:
CAI7246A1_141
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: Bulk Naive CD8+ T cells

tag: epitope

tag: age


title: 745230 Case

value: Male

value: Case

value: Chicago

value: Asthmatic

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: biventricular heart, CBK, biol rep 4

description:
CBKE200
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: CBK


title: Exp1_TN024_Plate2_K2P2_B07_N706_S517, Child

description:
CAI7246A1_140
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: phenotype


title: NC, 32C, ATAC-seq, rep1

value: FACS purified germ cell

value: female

tag: developmental stage

value: 32C NC

value: otu-Gal4, mata-gal4, nos-gal4, UASz-tdTomato


title: Exp1_TN024_Plate2_K2P2_B06_N706_S516, Child

description:
CAI7246A1_139
genes.fpkm_table
genes.attr_table
samples.table

value: Child

value: Tscm


title: 345849 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq cg_content


title: biventricular heart, BMAL1/E4BP4 FLOX, biol rep 6

description:
CBKE193
rawCounts.xlsx

tag: tissue

value: BMAL1/E4BP4 FLOX


title: NC, 8C, ATAC-seq, rep1

value: 8C NC


title: biventricular heart, BMAL1 FLOX, biol rep 3

description:
CBKE189
rawCounts.xlsx

value: BMAL1 FLOX


title: NC, 16C, ATAC-seq, rep1

value: 16C NC


title: Exp1_TN024_Plate2_K2P2_B05_N706_S513, Child

description:
CAI7246A1_137
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

tag: epitope

tag: age


title: 492250 Case

value: Case

value: Chicago

value: Asthmatic

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: Exp1_TN024_Plate2_K2P2_A06_N706_S515, Child

description:
CAI7246A1_138
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells

tag: phenotype


title: NC, 4C, ATAC-seq, rep1

description: ATAC-seq of FACS-purified Drosophila melanogaster germ cells

value: FACS purified germ cell

tag: Sex

value: female

tag: developmental stage

value: 4C NC

tag: genotype


title: 622911 Case

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma


title: biventricular heart, CBK, biol rep 3

description:
CBKE187
rawCounts.xlsx

tag: strain

value: male

tag: tissue

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

value: CBK


title: GSC, 4C, ATAC-seq, rep1

value: 4C GSC

value: nos-Gal4, UASp-NLS-GFP


title: 997869 Case

value: Nasal Epithelium

value: Female

value: Barbados

tag: age

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: barbados pc1

tag: barbados pc2


title: biventricular heart, CBK, biol rep 2

description:
CBKE185
rawCounts.xlsx

tag: Sex

tag: genotype


title: GSC, 2C, ATAC-seq, rep1

tag: developmental stage

value: 2C GSC


title: Exp1_TN024_Plate1_K2P1_C09_N705_S522, Child

description:
CAI7246A1_136
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

value: CD8+ T cell

tag: epitope

value: Child

tag: phenotype

value: Tscm


title: 727704 Case

tag: tissue

value: Male

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Chicago

tag: asthma

value: Asthmatic

value: Active Asthma

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: Exp1_TN024_Plate2_K2P2_B04_N705_S521, Child

description:
CAI7246A1_135
genes.fpkm_table
genes.attr_table
samples.table

tag: age

value: Tnaive


title: biventricular heart, CBK/CEK, biol rep 3

description:
CBKE181
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

value: CBK/CEK


title: Exp1_TN024_Plate2_K2P2_A04_N705_S520, Child

description:
CAI7246A1_134
genes.fpkm_table
genes.attr_table
samples.table

tag: cell line

value: Bulk C1R

value: Bulk C1R cell line


title: Fig6G_B4006WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC and trimming of reads was carried out using fastx_trimmer
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Assembly: SacCer3 or Candida glabrata (ASM254v2)
Supplementary files format and content: bigwig file (corresponds to sac_cer)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: none (input)

tag: Stage

value: Cycling cells


title: 542171 Case

tag: tissue

value: Nasal Epithelium

tag: Sex

tag: case control_definition

value: Barbados

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: barbados pc1

tag: barbados pc2


title: biventricular heart, BMAL1/E4BP4 FLOX, biol rep 3

description:
CBKE203
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: genotype

value: BMAL1/E4BP4 FLOX


title: 394657 Case

value: Female

tag: rnaseq inclusion

tag: site

tag: age

tag: asthma

tag: full pc2


title: biventricular heart, CBK/CEK, biol rep 2

description:
CBKE180
rawCounts.xlsx

tag: Sex

tag: tissue

tag: e4bp4 flox


title: Fig6G_B4006IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: anti-PK antibody (Bio-Rad)

tag: Stage


title: Fig6G_B4005WCE


title: Exp1_TN024_Plate2_K2P2_A03_N705_S517, Child

description:
CAI7246A1_132
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell line

tag: cell type

tag: epitope

value: Child

tag: phenotype


title: biventricular heart, CBK/CEK, biol rep 1

description:
CBKE159
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: genotype


title: Exp1_TN024_Plate2_K2P2_C02_N705_S516, Child

description:
CAI7246A1_131
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: age

value: Tcm


title: 973374 Case

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: biventricular heart, BMAL1 FLOX, biol rep 2

description:
CBKE127
rawCounts.xlsx

tag: strain

tag: Sex

value: male

tag: tissue

value: biventricular heart

tag: e4bp4 flox

value: BMAL1 FLOX


title: Fig6G_B4005IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

tag: Stage


title: Fig6G_B3945WCE

value: none (input)


title: Exp1_TN024_Plate2_K2P2_B02_N705_S515, Child

description:
CAI7246A1_130
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: age

tag: phenotype


title: 337369 Case

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: biventricular heart, BMAL1/E4BP4 FLOX, biol rep 1

description:
CBKE123
rawCounts.xlsx

tag: strain

tag: Sex

tag: tissue

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype


title: biventricular heart, BMAL1/E4BP4 FLOX, biol rep 2

description:
CBKE124
rawCounts.xlsx


title: Fig6G_B3945IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

tag: Stage

value: Cycling cells


title: Exp1_TN024_Plate2_K2P2_C01_N705_S513, Child

description:
CAI7246A1_129
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: age

tag: phenotype

value: Tnaive


title: 925442 Case

value: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Barbados

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: barbados pc1

tag: barbados pc2


title: biventricular heart, BMAL1 FLOX, biol rep 1

description:
CBKE108
rawCounts.xlsx

tag: strain

tag: Sex

tag: tissue

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype


title: 394904 Case

tag: case control_definition

tag: rnaseq inclusion

tag: age

tag: rnaseq cg_content


title: Fig6G_B4003WCE

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

tag: Stage


title: Exp1_TN024_Plate2_K2P2_B01_N704_S522, Child

description:
CAI7246A1_128
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: phenotype

value: Temra


title: biventricular heart, CBK, biol rep 1

description:
CBKE101
rawCounts.xlsx

tag: strain

tag: Sex

value: CBK


title: Exp1_TN024_Plate1_K2P1_H10_N704_S521, Child

description:
CAI7246A1_127
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

value: Child


title: Fig6G_B4003IP

value: anti-PK antibody (Bio-Rad)


title: 806860 Case

value: Case

tag: site

value: Brazil

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: biventricular heart, CBK/CEK, biol rep 6

description:
CBKE92
rawCounts.xlsx

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: CBK/CEK


title: Exp1_TN024_Plate2_K2P2_B03_N705_S518, Child

description:
CAI7246A1_133
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

tag: phenotype

value: Tscm


title: Exp1_TN024_Plate1_K2P1_G10_N704_S520, Child

description:
CAI7246A1_126
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue


title: 706957 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

value: Active Asthma

tag: rnaseq cg_content


title: biventricular heart, BMAL1/E4BP4 FLOX, biol rep 5

description:
CBKE91
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

value: BMAL1/E4BP4 FLOX


title: 882393 Case

value: Nasal Epithelium

value: Female

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: biventricular heart, CBK/CEK, biol rep 5

description:
CBKE90
rawCounts.xlsx

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype


title: Exp1_TN024_Plate1_K2P1_E10_N704_S517, Child

description:
CAI7246A1_124
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

tag: epitope

tag: age

tag: phenotype

value: Tnaive


title: 406533 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: rnaseq cg_content


title: biventricular heart, CBK/CEK, biol rep 4

description:
CBKE89
rawCounts.xlsx

tag: strain


title: Exp1_TN024_Plate1_K2P1_D10_N704_S516, Child

description:
CAI7246A1_123
genes.fpkm_table
genes.attr_table
samples.table


title: Fig1F_B2851IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

tag: Stage

value: Cycling cells


title: 307021 Case

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: 903836 Case

tag: tissue

tag: Sex

value: Male

tag: case control_definition

value: Barbados

tag: age

tag: barbados pc1

tag: barbados pc2


title: biventricular heart, BMAL1/E4BP4 FLOX, biol rep 4

description:
CBKE87
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype


title: Fig6G_B4002IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: anti-PK antibody (Bio-Rad)

tag: Stage


title: Fig1F_B2269WCE

value: none (input)


title: Exp1_TN024_Plate1_K2P1_C10_N704_S515, Child

description:
CAI7246A1_122
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

tag: epitope

value: Child

tag: phenotype


title: Fig6G_B4002WCE


title: biventricular heart, BMAL1 FLOX, biol rep 6

description:
CBKE79
rawCounts.xlsx

tag: Sex

tag: tissue

value: BMAL1 FLOX


title: Exp1_TN024_Plate1_K2P1_B10_N704_S513, Child

description:
CAI7246A1_121
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: age

value: Tscm


title: 742413 Case

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Washington DC

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: washington dc_pc1

tag: washington dc_pc2


title: Fig1F_B2851WCE

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

tag: Stage


title: Fig1F_B910WCE


title: 757298 Case

tag: tissue

value: Nasal Epithelium

tag: Sex

value: Brazil

tag: age

tag: brazil pc1

tag: brazil pc2


title: Exp1_TN024_Plate1_K2P1_A10_N703_S522, Child

description:
CAI7246A1_120
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: phenotype

value: Tnaive


title: 548925 Case

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content


title: Fig1F_B22697IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

tag: Stage

value: Cycling cells


title: biventricular heart, CBK, biol rep 5

description:
CBKE76
rawCounts.xlsx

tag: strain

tag: Sex

value: male

tag: tissue

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: CBK


title: Exp1_TN024_Plate1_K2P1_F10_N704_S518, Child

description:
CAI7246A1_125
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

tag: epitope

tag: age

tag: phenotype


title: Exp1_TN024_Plate1_K2P1_H09_N703_S521, Child

description:
CAI7246A1_119
genes.fpkm_table
genes.attr_table
samples.table

value: Child

value: Tcm


title: 283400 Case

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Baltimore

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: Fig1C_K22705WCE

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: none (input)

tag: Stage


title: 840310 Case

tag: tissue

tag: Sex

value: Case

tag: age

tag: rnaseq cg_content

tag: brazil pc1

tag: brazil pc2


title: biventricular heart, BMAL1 FLOX, biol rep 5

description:
CBKE75
rawCounts.xlsx

tag: strain

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: BMAL1 FLOX


title: Exp1_TN024_Plate1_K2P1_G09_N703_S520, Child

description:
CAI7246A1_118
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: CD8+ T cell

tag: epitope

tag: phenotype


title: hippocampus, ko_female_input_rep3

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

country: Germany

institute: Deutsches Krebsforschungszentrum

description:
10RNA
Qtrt1_RiboSeq_counts.csv

data_processing:
Footprint data analysis was performed using the RiboView pipeline (Legrand & Tuorto, 2020). After adapter removal using cutadapt (v1.8.1), the sequencing reads (26 to 77 million reads per sample) were trimmed with a minimum length of 25 nt and a maximum length of 36 nt, and a quality score at least 30, using Trimmomatic (v0.39). The remaining reads were depleted of rRNA and other non-nuclear mRNAs by aligning to a depletion reference using Bowtie (v1.0.0). Non-aligned reads in the previous step were finally aligned to the transcriptome (2 to 6 million reads per sample). Both the depletion and the transcriptome reference were downloaded from Ensembl release 101 for Mus Musculus and processed with custom scripts and gtf2table from RiboVIEW.
For determining ribosome densities, adapters were removed with the FASTX-toolkit v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/), retaining only sequences that are at least 28 nt long. The four random nucleotides at the beginning and the end of the reads were trimmed with an in-house developed perl script. Alignment was performed with bowtie v1.2.2 (Langmead et al, 2009) allowing a maximum of two mismatches and reporting all alignments in the best stratum (settings: -a --best --stratum -v 2). Reads that did not map to tRNA or rRNA sequences (as downloaded from the UCSC Genome Browser) were aligned to a mouse transcriptome. Afterwards, reads were summarised at the gene level using samtools v0.1.19 (Li et al, 2009) and an in-house developed perl script to count only reads that are between 27 and 30 nt long and map to ORFs of isoforms arising from one specific gene (as defined by a common gene symbol). An offset of 12 nt upstream of the start and stop codon with respect to the 5’ end of the reads was assumed. RNA-seq reads were processed in an analogous way, omitting adapter removal and size selection. Finally, 5.4 to 15.5 million reads could be uniquely assigned to genes in each sample.
Codon occupancies were determined from the single codon occupany (SCO) files, which are output files of RiboVIEW https://doi.org/10.1093/nar/gkz1074 (produced by custom script "enrichment.py", included in RiboVIEW package).
Genome_build: Ensembl release 101 for Mus Musculus
Supplementary_files_format_and_content: The .csv file Qtrt1_RiboSeq_counts.csv contains the read counts per sample, summarized at the gene level. The codon enrichment files associated with all Ribo-seq samples are tab-separated files with the codon occupancy as determined with the RiboView tool. The columns designated -90 to +90 correspond to the distance in codons from the position where the codon of interest (first column) is in the A-site (position 0). Mean and standard deviation (sd) are given in separate files.
Supplementary_files_format_and_content: SCO files are tab-separated files with the following columns : mRNA identifier (ID), codon position (or codon number, 0 corresponding to AUG, 1 corresponding to the first codon after AUG, and so on), codon sequence, coverage of this codon in A-site, the single codon occupancy (SCO) calculated as the coverage in A-site divided by the expected coverage in the mRNA considered (where expected coverage is the number of reads divided by the number of codons in the coding sequence), and the percentage of the coding sequence of the mRNA considered which is covered by at least one read.

molecule: cytoplasmic RNA

source_name: 559 input RNA

extract_protocol:
For the library preparation, hippocampi were isolated at 4°C according to Ingolia (Ingolia et al., 2011) and Biever (Biever et al., 2020) and directly resuspended in 300 µl polysome lysis buffer containing 20 mM Tris (pH 7.5), 5 mM MgCl2, 150 mM NaCl, 1% Triton X-100, 1 mM DTT, 100 µg/ml cycloheximide, and complete protease inhibitor (Roche). Tissues were dounced ten times with a plastic pestle before being pushed through a 25G syringe ten times. The lysates were cooled on ice for 10 min before being centrifuged at high speed at 4°C for 6 min. After transferring the supernatant to a fresh tube, the centrifugation procedure was repeated. After determining the RNA concentration, 15% of the lysate (≤ 20 µg) was utilised as input (see RNA-seq library preparation section), 50% for ribosome profiling, and 20-25% for polysome profiling.
Ribosome profiling libraries were prepared using 50% (150 µl) of lysate as described previously (Tuorto et al., 2018). Sequencing libraries were prepared according to protocol of the NEB NEXT Small RNA Library Prep Set for Illumina (Multiplex Compatible) E7330. 15% of polysome lysate was used for RNA-seq library preparation. RNA extraction was performed as described previously (Tuorto et al., 2018). After rRNA depletion using Ribo Zero Kit (Illumina), libraries were prepared using NEBNext Ultra II RNA Library Prep Kit (Illumina) according to manufacturer’s instructions. In brief, rRNA-depleted RNAs were fragmented, yielding an insert size of ~200 nt. Following the hybridisation of random primers, first and second strand cDNA syntheses were carried out. The NEBNext adaptors were ligated after the samples were end-repaired. Uracils were eliminated from the adaptor loops and the library yield was enhanced using PCR. Briefly, rRNA depleted RNAs were fragmented and resulted in an insert size of ~200 nt. After hybridisation of random primers, first and second strand cDNA syntheses were performed. Samples were end-repaired, and the NEBNext adaptors were ligated. Uracils were removed from the adaptor loops, and the library yield was increased by PCR. Finally, barcodes/indices were included in the samples to multiplex the libraries. Sequencing was performed on a NextSeq 550 platform. Chemistry used: NextSeq 500/550 highoutput V2 Kit (75cycles), FC-404-2005, loaded on FC 1,8 pM.
ncRNA-Seq

tag: gender

value: female

value: 6 months 21 days

value: hippocampus


title: 975840 Case

value: Nasal Epithelium

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: full pc1

tag: full pc2

tag: baltimore pc1

tag: baltimore pc2


title: 889980 Case

tag: tissue

tag: Sex

value: Female

value: Chicago

tag: age

tag: rnaseq cg_content

tag: chicago pc1

tag: chicago pc2


title: Fig1C_K22705IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: anti-PK antibody (Bio-Rad)

tag: Stage

value: Cycling cells


title: Exp1_TN024_Plate1_K2P1_F09_N703_S518, Child

description:
CAI7246A1_117
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

tag: epitope

value: Child

tag: phenotype

value: Tnaive


title: Exp1_TN024_Plate1_K2P1_E09_N703_S517, Child

description:
CAI7246A1_116
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: biventricular heart, CBK, biol rep 6

description:
CBKE78
rawCounts.xlsx

tag: strain

value: male

value: biventricular heart

tag: cre

tag: bmal1 flox

tag: e4bp4 flox

tag: genotype

value: CBK


title: Fig1C_K22703WCE

value: none (input)


title: Exp1_TN024_Plate1_K2P1_D09_N703_S516, Child

description:
CAI7246A1_115
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: CD8+ T cell


title: hippocampus, wt_female_input_rep3

description:
7RNA
Qtrt1_RiboSeq_counts.csv

source_name: 565 input RNA

value: wild type

tag: gender

value: female

tag: age

value: 6 months 21 days

value: hippocampus


title: hippocampus, ko_female_input_rep1

description:
8RNA
Qtrt1_RiboSeq_counts.csv

source_name: 557 input RNA


title: 149025 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Nigeria

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: full pc2

tag: nigeria pc1

tag: nigeria pc2


title: Exp1_TN024_Plate1_K2P1_W09_N703_S515, Child

description:
CAI7246A1_114
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: cell type

tag: epitope

value: Child

tag: phenotype


title: hippocampus, ko_female_input_rep2

description:
9RNA
Qtrt1_RiboSeq_counts.csv

source_name: 558 input RNA

tag: genotype

tag: gender

tag: age

tag: tissue


title: 822485 Case

tag: Sex

value: Male

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Brazil

tag: brazil pc1

tag: brazil pc2


title: 188804 Case

value: Barbados

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1

tag: barbados pc1

tag: barbados pc2


title: hippocampus, wt_female_input_rep2

description:
6RNA
Qtrt1_RiboSeq_counts.csv

source_name: 564 input RNA

tag: genotype

tag: gender


title: Fig1C_K17407WCE

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: none (input)

tag: Stage

value: Cycling cells


title: Exp1_TN024_Plate1_K2P1_B09_N703_S513, Child

description:
CAI7246A1_113
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

tag: phenotype

value: Tscm


title: Fig1F_B910IP

value: anti-PK antibody (Bio-Rad)


title: Fig1C_K17407IP


title: hippocampus, wt_female_input_rep1

description:
5RNA
Qtrt1_RiboSeq_counts.csv

source_name: 551 input RNA

value: wild type

value: female

value: 6 months 22 days

value: hippocampus


title: 871379 Case

value: Nasal Epithelium

tag: Sex

value: Female

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: Exp1_TN024_Plate1_K2P1_H08_N702_S522, Child

description:
CAI7246A1_112
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Temra


title: 202251 Case

value: Asthmatic

value: Active Asthma

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: hippocampus, ko_male_input_rep2

description:
4RNA
Qtrt1_RiboSeq_counts.csv

source_name: 599 input RNA

tag: genotype

tag: gender

value: male

value: 5 months 16 days

tag: tissue


title: Exp1_TN024_Plate1_K2P1_G08_N702_S521, Child

description:
CAI7246A1_111
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope

tag: age

value: Child

tag: phenotype

value: Tnaive


title: Mononuclear cells, WT HFD

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: TSV
Supplementary files format and content: MTX

source_name: Primary

extract_protocol:
Mononuclear cells isolated via collagenase II digestion followed by flow cytometry for exclusion of (DAPI-stained) dead cells
10X Genomics 3' Gene Expression V3.1

tag: cell line

value: Primary

value: Mononuclear cells

tag: treatment

value: High fat diet (x 6 months)


title: Fig1C_K22703IP

tag: sac_cer strain

tag: can_gla strain (used as a calibration genome)

tag: chip antibody

value: anti-PK antibody (Bio-Rad)

tag: Stage

value: Cycling cells


title: 749811 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Brazil

tag: asthma

tag: active asthma

tag: rin nasalepithelium

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: Exp1_TN024_Plate1_K2P1_F08_N702_S520, Child

description:
CAI7246A1_110
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

tag: phenotype

value: Tcm


title: 572239 Case

value: Nasal Epithelium

value: Male

value: Case

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: Mononuclear cells, WT CD

tag: cell line

tag: genotype

tag: treatment

value: Control diet (x 6 months)


title: hippocampus, wt_male_input_rep2

description:
3RNA
Qtrt1_RiboSeq_counts.csv

source_name: 596 input RNA

value: wild type

tag: gender

value: hippocampus


title: Exp1_TN024_Plate1_K2P1_E08_N702_S518, Child

description:
CAI7246A1_109
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: hippocampus, wt_male_input_rep1

description:
2RNA
Qtrt1_RiboSeq_counts.csv

source_name: 585 input RNA

value: male

value: 6 months 18 days


title: 260716 Case

tag: Sex

value: Female

tag: case control_definition

tag: rnaseq inclusion

tag: site

tag: asthma

value: Asthmatic

tag: active asthma

value: Active Asthma


title: Exp1_TN024_Plate1_K2P1_C08_N702_S516, Child

description:
CAI7246A1_107
genes.fpkm_table
genes.attr_table
samples.table

source_name: PBMCs

tag: tissue

tag: cell type

value: Child

value: Tscm


title: H_K3

city: Xining

first: yujie

last: gao

state: Qinghai

address: No.251 Ningda Road

country: China

institute: Qinghai university

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
Assembly: β-actin（参考基因组）
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: kidney

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: strain

value: hypoxia


title: 209678 NA

source_name: Nasal Epithelium

value: Brazil

tag: age

tag: rin nasalepithelium


title: H_K4


title: 161371 Case

value: Nasal Epithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: Exp1_TN024_Plate1_K2P1_D08_N702_S517, Child

description:
CAI7246A1_108
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: epitope

tag: phenotype

value: Tcm


title: hippocampus, ko_female_footprint_rep2

description:
9footprint
Qtrt1_RiboSeq_counts.csv

source_name: 558 footprint

tag: genotype

tag: gender

value: female

value: 6 months 21 days


title: hippocampus, ko_female_footprint_rep1

description:
8footprint
Qtrt1_RiboSeq_counts.csv

source_name: 557 footprint

value: hippocampus


title: H_K5

tag: treatment


title: 669165 Case

tag: Sex

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

tag: asthma

tag: full pc1


title: Mononuclear cells, KO HFD

tag: cell line

value: Primary

tag: cell type

value: Mononuclear cells

value: High fat diet (x 6 months)


title: H_K2

tag: tissue

tag: strain


title: H_K1


title: hippocampus, ko_female_footprint_rep3

description:
footprint
Qtrt1_RiboSeq_counts.csv

source_name: 559 footprint

tag: age


title: 166333 Case

value: Female

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: brazil pc1

tag: brazil pc2


title: Exp1_TN024_Plate1_K2P1_B08_N702_S515, Child

description:
CAI7246A1_106
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

tag: epitope

value: Child

tag: phenotype


title: hippocampus, wt_female_footprint_rep3

description:
7footprint
Qtrt1_RiboSeq_counts.csv

source_name: 565 footprint

tag: genotype

value: wild type

tag: gender


title: P_K5

value: kidney

tag: treatment

value: control


title: 404505 Case

value: Nasal Epithelium

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Brazil

tag: asthma

value: Active Asthma

tag: full pc1


title: hippocampus, ko_male_input_rep1

description:
1RNA
Qtrt1_RiboSeq_counts.csv

source_name: 584 input RNA

value: male

tag: age

value: 6 months 18 days

tag: tissue


title: P_K4

tag: strain


title: hippocampus, wt_female_footprint_rep2

description:
6footprint
Qtrt1_RiboSeq_counts.csv

source_name: 564 footprint

value: female

value: 6 months 21 days

value: hippocampus


title: Exp1_TN024_Plate1_K2P1_F07_N701_S521, Child

description:
CAI7246A1_103
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: CD8+ T cell

value: Tnaive


title: 663753 Case

value: Male

value: Case

value: Chicago

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: P_K3

tag: treatment


title: hippocampus, wt_female_footprint_rep1

description:
5footprint
Qtrt1_RiboSeq_counts.csv

source_name: 551 footprint

tag: genotype

tag: gender

value: 6 months 22 days


title: 426136 Case

tag: Sex

tag: case control_definition

tag: rnaseq inclusion

tag: site

value: Asthmatic


title: Exp1_TN024_Plate1_K2P1_D07_N701_S518, Child

description:
CAI7246A1_101
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue

value: PBMCs

tag: epitope

tag: age

value: Child

tag: phenotype

value: Tscm


title: P_K2

value: kidney

tag: strain

value: control


title: P_K1


title: hippocampus, ko_male_footprint_rep2

description:
4footprint
Qtrt1_RiboSeq_counts.csv

source_name: 599 footprint

value: male

value: 5 months 16 days


title: hippocampus, wt_male_footprint_rep2

description:
3footprint
Qtrt1_RiboSeq_counts.csv

source_name: 596 footprint

value: wild type


title: Exp1_TN024_Plate1_K2P1_H07_N702_S513, Child

description:
CAI7246A1_105
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: Tcm


title: Exp1_TN024_Plate1_K2P1_C07_N701_S517, Child

description:
CAI7246A1_100
genes.fpkm_table
genes.attr_table
samples.table


title: 510286 Case

value: Nasal Epithelium

value: Female

tag: asthma

tag: active asthma

value: Active Asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: rnaseq cg_content

tag: full pc1


title: 835041 Case

tag: full pc2

tag: chicago pc1

tag: chicago pc2


title: hippocampus, ko_male_footprint_rep1

description:
1footprint
Qtrt1_RiboSeq_counts.csv

source_name: 584 footprint

tag: genotype

tag: gender

value: 6 months 18 days

value: hippocampus


title: hippocampus, wt_male_footprint_rep1

description:
2footprint
Qtrt1_RiboSeq_counts.csv

source_name: 585 footprint

tag: tissue


title: 289085 Case

tag: Sex

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Chicago


title: Exp1_TN024_Plate1_K2P1_B07_N701_S516, Child

description:
CAI7246A1_099
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: CD8+ T cell

tag: epitope

tag: age

tag: phenotype

value: Tnaive


title: Exp1_TN024_Plate1_K2P1_H06_N701_S515, Child

description:
CAI7246A1_098
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Child


title: 419158 Case

value: Denver

tag: asthma

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: denver pc1

tag: denver pc2


title: iBMDM_Untreated_3

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

data_processing:
Base calling was performed with Illumina Real Time Analysis (RTA; Version 3.4.4), and the output of RTA was demultiplexed and converted to the FastQ format with Illumina Bcl2fastq (Version 2.20.0).
Read quality was assessed using FastQC (Version 0.11.7)
Read mapping was performed against the GRCm39 mouse reference genome using Bowtie2 (Version 2.4.1)
Aligned read counts were assessed using feature counts from the Subread package (Version 2.0.0)
Differential gene expression analysis was conducted using the DESeq2 package (Version 1.36.0)  in R (Version 4.2.1).
Assembly: Mouse GRCm39
Supplementary files format and content: RawCounts_Compiled.csv - Contains raw read counts produced by Feature Counts for all samples combined into a single data matrix
Supplementary files format and content: Normalized_Counts.csv - Contains normalized read counts produced by DESeq2 for all samples combined into a single data matrix

source_name: L3 iBMDM

extract_protocol:
A Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) was used to extract RNA according to the manufacturer’s protocol.
Libraries were prepared using an Illumina Stranded mRNA Library Prep kit (Illumina, Cat no. 20040534) with IDT for Illumina RNA Unique Dual Index adapters following the manufacturer’s recommendations, except that half-volume reactions were performed. Generated libraries were quantified and assessed for quality using a combination of Qubit™ dsDNA HS (ThermoFischer Scientific, Cat no. Q32851) and Agilent 4200 TapeStation HS DNA1000 assays (Agilent, Cat no. 5067-5584). The libraries were pooled in equimolar amounts, and the pooled library was quantified using an Invitrogen Collibri Quantification qPCR kit (Invitrogen, Cat no. A38524100).

tag: cell line

value: L3 iBMDM

value: Immortalized BMDM

tag: treatment

value: Untreated


title: iBMDM_Untreated_2


title: iBMDM_Untreated_1


title: 778968 Case

tag: tissue

value: Male

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: cKd_ATc4

city: Wenzhou

first: Ya-Ni

last: Mou

state: China

address: Chashan University Town, Ouhai District, Wenzhou City, Zhejiang Province

institute: Wenzhou Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: MSU_V7.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Toxoplasma gondii

source_name: Tachyzoites

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) 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, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: Tachyzoites

tag: strain

value: TATi-3HA-TgUba1 strains cultured under 0.5 ug/ml ATc (knockout strain)

value: Atc


title: Exp1_TN024_Plate1_K2P1_G06_N701_S513, Child

description:
CAI7246A1_097
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

value: Tcm


title: cKd_ATc3


title: iBMDM_DMSO_IFNg_3

value: DMSO + IFNg


title: Exp1_TN024_Plate1_K2P1_E07_N701_S520, Child

description:
CAI7246A1_102
genes.fpkm_table
genes.attr_table
samples.table

tag: epitope


title: Exp1_TN024_Plate1_K2P1_F06_N715_S511, Child

description:
CAI7246A1_096
genes.fpkm_table
genes.attr_table
samples.table

tag: age


title: cKd_ATc2


title: 208550 Case

value: Nasal Epithelium

tag: Sex

tag: case control_definition

value: Case

tag: rnaseq inclusion

tag: site

value: Active Asthma


title: iBMDM_DMSO_IFNg_2


title: Exp1_TN024_Plate1_K2P1_E06_N715_S510, Child

description:
CAI7246A1_095
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: phenotype


title: cKd_ATc1


title: Exp1_TN024_Plate1_K2P1_D06_N715_S508, Child

description:
CAI7246A1_094
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs

value: Tnaive


title: Exp1_TN024_Plate1_K2P1_C06_N715_S507, Child

description:
CAI7246A1_093
genes.fpkm_table
genes.attr_table
samples.table

value: Child


title: 418474 Case

value: Barbados

tag: asthma

value: Asthmatic

tag: active asthma

tag: rin nasalepithelium

tag: rnaseq libraryprep_batch

tag: barbados pc1

tag: barbados pc2


title: iBMDM_DMSO_3

tag: cell line

value: L3 iBMDM

value: Immortalized BMDM

tag: treatment

value: DMSO


title: iBMDM_DMSO_2


title: cKd_3

tag: tissue

value: Tachyzoites

tag: strain

value: TATi-3HA-TgUba1 strains cultured under DMSO (wild strain)


title: cKd_4


title: Exp1_TN024_Plate1_K2P1_G07_N701_S522, Child

description:
CAI7246A1_104
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type

tag: epitope


title: 233821 Case

tag: Sex

value: Male

tag: age

tag: rnaseq cg_content

tag: full pc1

tag: full pc2


title: iBMDM_DMSO_1


title: Exp1_TN024_Plate1_K2P1_H05_N715_S505, Child

description:
CAI7246A1_091
genes.fpkm_table
genes.attr_table
samples.table

tag: phenotype

value: Tcm