title: Tibialis anterior, female, Deficient, ZT05, rep3

description:
59_F_4_5H_TA_S23_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Control, ZT17, rep3

status: Public on Aug 07 2024

type: SRA

city: La Jolla

first: Laura

last: van Rosmalen

state: California

address: 10010 N Torrey Pines Rd

department: RBIO-P

country: USA

institute: Salk Institute for Biological Studies

description:
56_F_16_5L_TA_S22_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

library_source: transcriptomic

data_processing:
Sequencing quality was assessed using FastQC, version 0.11.9
Cutadapt v4.1 was used to trim adapter sequences
Sequence reads were aligned to the Mus musculus (house mouse) genome GRCm38 (mm10) and counted per gene using STAR aligner v2.7.10a
Gene counts were filtered for low counts and normalized per tissue using DESeq2 v1.34.0
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Tibialis anterior

extract_protocol:
Total RNA was extracted from neural and peripheral tissues using TRIzol reagent according to the manufacturer’s instructions. 500ng of total RNA was used for the construction of sequencing libraries
Libraries were prepared using Illumina’s TruSeq Stranded mRNA (PolyA+) kit according to the manufacturer’s instructions

tag: strain

value: CBA/CaJ

tag: tissue

value: Tibialis anterior

tag: Sex

value: female

tag: treatment

value: Control

tag: zeitgeber time


title: Tibialis anterior, male, Control, ZT17, rep2

description:
86_M_L_ZT17_TA_S362
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male


title: Tibialis anterior, female, Deficient, ZT05, rep1

description:
35_F_4_5H_TA_S15_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: Tibialis anterior, female, Control, ZT17, rep2

description:
48_F_16_5L_TA_S21_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Deficient, ZT05, rep2

description:
43_F_4_5H_TA_S18_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Control, ZT05, rep1

description:
31_F_4_5L_TA_S13_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Control, ZT05, rep3

description:
47_F_4_5L_TA_S20_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Deficient, ZT17, rep3

description:
90_M_H_ZT17_EDLt_S319
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Extensor digitorum longus tendon

value: Extensor digitorum longus tendon


title: Tibialis anterior, female, Deficient, ZT17, rep1

description:
36_F_16_5H_TA_S16_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Control, ZT05, rep2

description:
39_F_4_5L_TA_S17_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_TA_S363
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_EDLt_S311
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_EDLt_S314
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_EDLt_S315
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Control, ZT17, rep3

description:
94_M_L_ZT17_EDLt_S321
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Control, ZT17, rep2

description:
86_M_L_ZT17_EDLt_S317
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_EDLt_S318
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_EDLt_S310
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Control, ZT17, rep1

description:
78_M_L_ZT17_EDLt_S313
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Deficient, ZT17, rep2

description:
44_F_16_5H_EDLt_S67_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Control, ZT05, rep3

description:
93_M_L_ZT05_EDLt_S320
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Control, ZT05, rep2

description:
85_M_L_ZT05_EDLt_S316
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Deficient, ZT05, rep2

description:
43_F_4_5H_EDLt_S66_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Deficient, ZT17, rep3

description:
60_F_16_5H_EDLt_S72_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Control, ZT17, rep3

description:
56_F_16_5L_EDLt_S70_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Tibialis anterior, female, Control, ZT17, rep1

description:
32_F_16_5L_TA_S14_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, male, Control, ZT05, rep1

description:
77_M_L_ZT05_EDLt_S312
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Deficient, ZT05, rep3

description:
59_F_4_5H_EDLt_S71_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Control, ZT17, rep1

description:
32_F_16_5L_EDLt_S62_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Control, ZT17, rep2

description:
48_F_16_5L_EDLt_S69_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Deficient, ZT05, rep1

description:
35_F_4_5H_EDLt_S63_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_EDL_S303
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Extensor digitorum longus

value: Extensor digitorum longus


title: Extensor digitorum longus, male, Deficient, ZT17, rep3

description:
90_M_H_ZT17_EDL_S307
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_EDL_S306
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Control, ZT05, rep3

description:
47_F_4_5L_EDLt_S68_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_EDL_S302
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Control, ZT17, rep3

description:
94_M_L_ZT17_EDL_S309
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Control, ZT05, rep1

description:
31_F_4_5L_EDLt_S61_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Control, ZT05, rep2

description:
39_F_4_5L_EDLt_S65_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_EDL_S298
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Control, ZT05, rep3

description:
93_M_L_ZT05_EDL_S308
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Control, ZT17, rep1

description:
78_M_L_ZT17_EDL_S301
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Control, ZT05, rep2

description:
85_M_L_ZT05_EDL_S304
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus tendon, female, Deficient, ZT17, rep1

description:
36_F_16_5H_EDLt_S64_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Deficient, ZT17, rep3

description:
60_F_16_5H_EDL_S36_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Deficient, ZT17, rep2

description:
44_F_16_5H_EDL_S31_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Deficient, ZT05, rep3

description:
59_F_4_5H_EDL_S35_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Deficient, ZT17, rep1

description:
36_F_16_5H_EDL_S28_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Deficient, ZT05, rep2

description:
43_F_4_5H_EDL_S30_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_EDL_S299
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Control, ZT17, rep2

description:
48_F_16_5L_EDL_S33_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Control, ZT05, rep3

description:
47_F_4_5L_EDL_S32_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Control, ZT05, rep1

description:
77_M_L_ZT05_EDL_S300
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Control, ZT17, rep3

description:
56_F_16_5L_EDL_S34_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Deficient, ZT05, rep1

description:
35_F_4_5H_EDL_S27_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, male, Control, ZT17, rep2

description:
86_M_L_ZT17_EDL_S305
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Deficient, ZT17, rep2

description:
54_M_16H_GASten_S129
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Gastrocnemius tendon

value: Gastrocnemius tendon


title: Extensor digitorum longus, female, Control, ZT17, rep1

description:
32_F_16_5L_EDL_S26_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Control, ZT05, rep2

description:
39_F_4_5L_EDL_S29_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Deficient, ZT17, rep1

description:
38_M_16H_GASten_S120
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Deficient, ZT05, rep2

description:
45_M_4H_GASten_S124
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Deficient, ZT17, rep3

description:
62_M_16H_GASten_S134
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Deficient, ZT05, rep1

description:
37_M_4H_GASten_S119
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Deficient, ZT05, rep3

description:
53_M_4H_GASten_S128
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Control, ZT17, rep1

description:
34_M_16L_GASten_S116
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Control, ZT05, rep3

description:
77_M_L_ZT05_GASt_S325
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Control, ZT17, rep3

description:
78_M_L_ZT17_GASt_S326
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Control, ZT17, rep2

description:
58_M_16L_GASten_S131
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Control, ZT05, rep1

description:
33_M_4L_GASten_S115
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Deficient, ZT17, rep2

description:
44_F_16H_GASten_S123
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Deficient, ZT17, rep3

description:
60_F_16H_GASten_S133
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: EpCAM POS 02

status: Public on Aug 08 2024

type: RNA

city: New Brunswick

first: Victoria

last: da Silva-Diz

address: 195 Little Albany Street

institute: Rutgers University

description: full epithelial cancer cells biological replicate 2

hyb_protocol: 8 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix MG-430 PM Array were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization using the normqc function of Bioconductor's MDA package

label: Biotin

source_name: epithelial cancer cells from WD-SCC

label_protocol: 10 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using (GeneChip Mapping 250K Nsp Assay Kit, Affymetrix catalog  # 900766), according to manufacturer's instructions.

extract_protocol: RNA was isolated using magnetic beads RNA Clean XP (Beckman Coulter; catalog # A63987) from a cells lysate.

tag: tumor type of origin

value: WD-SCC

tag: cell type

value: FACS-sorted epithelial cancer cells


title: Gastrocnemius tendon, female, Deficient, ZT17, rep1

description:
36_F_16H_GASten_S118
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, male, Control, ZT05, rep2

description:
49_M_4L_GASten_S127
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Deficient, ZT05, rep2

description:
43_F_4H_GASten_S122
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Control, ZT17, rep3

description:
56_F_16L_GASten_S130
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Deficient, ZT05, rep3

description:
59_F_4H_GASten_S132
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Extensor digitorum longus, female, Control, ZT05, rep1

description:
31_F_4_5L_EDL_S25_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Deficient, ZT05, rep1

description:
35_F_4H_GASten_S117
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Control, ZT05, rep2

description:
39_F_4L_GASten_S121
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Control, ZT05, rep1

description:
31_F_4L_GASten_S113
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Control, ZT17, rep1

description:
32_F_16L_GASten_S114
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Control, ZT05, rep3

description:
47_F_4L_GASten_S125
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius tendon, female, Control, ZT17, rep2

description:
48_F_16L_GASten_S126
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Deficient, ZT17, rep1

description:
54_M_16H_GAS_S107
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Gastrocnemius

value: Gastrocnemius


title: Gastrocnemius, male, Deficient, ZT05, rep2

description:
53_M_4H_GAS_S106
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Control, ZT17, rep2

description:
50_M_16L_GAS_S105
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Deficient, ZT17, rep2

description:
62_M_16H_GAS_S112
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Deficient, ZT05, rep3

description:
73_M_H_ZT05_GAS_S322
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Control, ZT17, rep1

description:
34_M_16L_GAS_S95
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Deficient, ZT05, rep1

description:
37_M_4H_GAS_S98
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Control, ZT05, rep2

description:
49_M_4L_GAS_S104
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Control, ZT05, rep3

description:
77_M_L_ZT05_GAS_S324
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Control, ZT17, rep3

description:
58_M_16L_GAS_S109
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Control, ZT05, rep1

description:
33_M_4L_GAS_S94
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Deficient, ZT17, rep3

description:
60_F_16H_GAS_S111
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: KPSC_3

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

country: China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size were calculated using a protocol from Chepeleve et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Tumor

extract_protocol:
Briefly, orthotopic PDAC tumor were generated and collected after about 10-14 days.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: Orthotopic PDAC tumor

tag: genotype

value: Wild type


title: Gastrocnemius, female, Deficient, ZT05, rep2

description:
43_F_4H_GAS_S100
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, male, Deficient, ZT17, rep3

description:
74_M_H_ZT17_GAS_S323
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Deficient, ZT05, rep3

description:
59_F_4H_GAS_S110
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Deficient, ZT17, rep1

description:
36_F_16H_GAS_S97
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: KPSC_2


title: Gastrocnemius, female, Deficient, ZT17, rep2

description:
44_F_16H_GAS_S101
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Deficient, ZT05, rep1

description:
35_F_4H_GAS_S96
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: KPC_3

value: Setd2 knockout


title: KPSC_1


title: Gastrocnemius, female, Control, ZT17, rep2

description:
48_F_16L_GAS_S103
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Control, ZT17, rep3

description:
56_F_16L_GAS_S108
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: KPC_2


title: Gastrocnemius, female, Control, ZT17, rep1

description:
32_F_16L_GAS_S93
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Control, ZT05, rep2

description:
39_F_4L_GAS_S99
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: KPC_1


title: Gastrocnemius, female, Control, ZT05, rep1

description:
31_F_4L_GAS_S92
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Gastrocnemius, female, Control, ZT05, rep3

description:
47_F_4L_GAS_S102
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Promoter_K27Ac_KO_vitro_CUT&Tag

library_source: genomic

data_processing:
library strategy: CUT&Tag
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: genomic DNA

source_name: pancreatic tumor cell

extract_protocol: CUT&Tag libraries were prepared for sequencing using standard illumina protocols.

tag: strain background

value: cultured pancreatic tumor cell

tag: genotype/variation


title: Promoter_K27me3_WT_CUT&Tag


title: Quadriceps, male, Deficient, ZT17, rep2

description:
62_M_16H_QUAD_S91
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Quadriceps

value: Quadriceps


title: Quadriceps, male, Deficient, ZT17, rep1

description:
38_M_16H_QUAD_S76
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Promoter_K27Ac_WT_CUT&Tag


title: GeneBody_K36me3_WT_CUT&Tag


title: GeneBody_K36me3_KO_CUT&Tag


title: Quadriceps, male, Deficient, ZT05, rep2

description:
45_M_4H_QUAD_S81
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, male, Deficient, ZT05, rep3

description:
53_M_4H_QUAD_S86
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, male, Deficient, ZT17, rep3

description:
74_M_H_ZT17_QUA_S339
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, male, Deficient, ZT05, rep1

description:
37_M_4H_QUAD_S75
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, male, Control, ZT17, rep2

description:
78_M_L_ZT17_QUA_S340
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, male, Control, ZT17, rep1

description:
58_M_16L_QUAD_S88
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Promoter_K27Ac_KO_CUT&Tag


title: WT_Treg_NFAT1_rep2

city: Suita

first: Kenji

last: Ichiyama

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
The quality of sequence reads was confirmed using fastQC to confirm that the average of Phred score was over 20.
Raw sequences were trimmed and fastx_trimmer in fastx_tool kit, using following setting; fastx_trimmer -Q33 -f 12 -l 220 -i ${name}.fastq | fastq_quality_trimmer -Q33 -t 20 -l 30 -o ${name}_trimm.fastq.
Sequencing reads were mapped to the mouse genome mm10 using Bowtie2 with default setting; bowtie2 -p 30 -x mm10 -U ${name}_trim.fastq -S ${name}_accept.sam.
For visualization of ChIP peaks, peak call was performed using MACS2 by the following command;macs2 callpeak -t ${name}_accept.sam -c input.sam -g mm -n ${name} -B -q 0.01 –nomodel. Bdg2bw tool used for the conversion of bedgraph to bigwig.
ChIP-Seq peaks were defined using FindPeaks, with their size fixed at 500 base pairs, minimum distance between peaks being 500 base pairs, FDR set as default, and local filtering switched off.
The overlap of among ChIP-Seq peaks was defined by ≥ 1 base pair overlap using Bedtools. To identify common or specific peaks between given conditions, the identified peaks in each condition were merged. Then, the merged peaks were used to define common or specific peaks using HOMER (getDifferentialPeaks) with default parameters.
Normalized density plots of histone modifications peaks as well as binding of transcription factors around Foxp3-binding sites were calculated using annotatePeaks in Homer package.
Assembly: mm10
Supplementary files format and content: bigwig, bed

source_name: Spleen and Lymph nodes

extract_protocol:
Stimulated Treg cells were cross-linked with 1% Formardehyde for 5 min (histone ChIP) or 30 min (transcription factor ChIP) at room temperature. After nuclear extraction, Cross-linked DNA was fragmentated by sonication using Digital Sonifier (Branson).
Library was prepared using Ion Xpress Plus Fragment Library Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.

treatment_protocol: Purified Treg cells were stimulated with Cell Stimulation Cocktail for 1hr  in RPMI 1640  supplemented with 10% fetal calf serum (FCS), 2-mercaptoethanol and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

value: Spleen and Lymph nodes

tag: cell line

value: Primary

value: Treg cells

value: WT

tag: chip antibody

value: NFAT1 (Abcam)


title: IkE5_Treg_NFAT1_rep2


title: Quadriceps, male, Control, ZT17, rep3

description:
86_M_L_ZT17_QUA_S341
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male

value: Control


title: WT_Treg_Ikaros_rep2

value: Ikaros (Sigma-Aldrich)


title: Quadriceps, male, Control, ZT05, rep3

description:
49_M_4L_QUAD_S84
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: WT_Treg_p300_rep2

value: p300 (Abcam)


title: IkE5_Treg_p300_rep2


title: Quadriceps, male, Control, ZT05, rep2

description:
41_M_4L_QUAD_S78
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, male, Control, ZT05, rep1

description:
33_M_4L_QUAD_S72
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Promoter_K27Ac_WT_vitro_CUT&Tag


title: IkE5_Treg_Foxp3_rep2

value: Foxp3 (Abcam)


title: WT_Treg_Foxp3_rep2


title: Promoter_K27me3_KO_CUT&Tag


title: WT_Treg_Ikaros_rep1


title: Quadriceps, female, Deficient, ZT17, rep3

description:
60_F_16H_QUAD_S90
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female

value: Deficient


title: Quadriceps, female, Deficient, ZT17, rep2

description:
44_F_16H_QUAD_S80
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, female, Deficient, ZT05, rep3

description:
59_F_4H_QUAD_S89
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, female, Deficient, ZT17, rep1

description:
36_F_16H_QUAD_S74
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: IkE5_Treg_p300_rep1


title: WT_Treg_NFAT1_rep1


title: Quadriceps, female, Deficient, ZT05, rep2

description:
43_F_4H_QUAD_S79
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, female, Deficient, ZT05, rep1

description:
35_F_4H_QUAD_S73
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: IkE5_Treg_NFAT1_rep1


title: IkE5_Treg_Foxp3_rep1


title: Quadriceps, female, Control, ZT17, rep3

description:
56_F_16L_QUAD_S87
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: WT_Treg_Foxp3_rep1


title: IkE5_Treg_Input


title: Quadriceps, female, Control, ZT17, rep2

description:
48_F_16L_QUAD_S83
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Quadriceps, female, Control, ZT17, rep1

description:
32_F_16L_QUAD_S71
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: WT_Treg_p300_rep1


title: IkE5_Treg_H3K27ac_rep2

value: H3K27ac (GeneTex)


title: Quadriceps, female, Control, ZT05, rep2

description:
39_F_4L_QUAD_S77
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: WT_Treg_Input


title: Testis, male, Deficient, ZT17, rep3

description:
62_M_16H_TESTIS_S200
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Testis

value: Testis


title: IkE5_Treg_H3K27ac_rep1


title: WT_Treg_H3K27ac_rep2


title: Quadriceps, female, Control, ZT05, rep1

description:
31_F_4L_QUAD_S70
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Testis, male, Deficient, ZT17, rep2

description:
54_M_16H_TESTIS_S198
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: WT_Treg_Input_histone


title: Testis, male, Deficient, ZT17, rep1

description:
38_M_16H_TESTIS_S192
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Testis, male, Deficient, ZT05, rep3

description:
53_M_4H_TESTIS_S197
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Testis, male, Deficient, ZT05, rep2

description:
45_M_4H_TESTIS_S194
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: GLUP_TEAD4KO_3

city: shanghai

first: yang

last: tang

address: Yueyang Road 320

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
The size distribution of libraries was examined by Agilent 2100 analysis. Sequencing was performed by the Illumina HiSeq X-ten platform. Sequencing raw reads were preprocessed by filtering out sequencing adapters, short-fragment reads and other low-quality reads. Bowtie was then used to map the clean reads to the human hg19 reference genome. Peak detection was performed by MACS2. The protein-binding motifs were identified using HOMER software.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

organism: Homo sapiens

growth_protocol: 1640, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Briefly, about 1 x 105 cells were suspended in 100 μl of wash buffer and incubated with concanavalin A-coated magnetic beads for 1 hour to tether the cells onto the beads. The bead-bound cells were then resuspended in 50 μl of antibody buffer with 1 μg indicated antibody at 4°C with slow rotation overnight. Subsequently, the bead-bound cells were treated with 50 μl of secondary antibody diluted with the dig wash buffer for another hour at RT. After being washed with the dig wash buffer three times to remove unbound antibodies, the cells were further incubated with the hyperactive Pa-Th5 transposase adaptor complex to digest host genome and obtain the fragmented DNA. The fragmented DNA was purified using the phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation.
The libraries were amplified by mixing 15 μl the DNA with 5 μl of a universal N5XX and uniquely barcoded N701 primer  followed 15 cycles of 98°C for 10 s, 60°C for 5 s; 72°C for 1 min and hold at 4°C. To purify the PCR products, 1.2x volumes of VAHTS DNA Clean Beads  were added and incubated at RT for 10min.

value: gastric cancer cell

value: TEAD4 KO

value: GLUP peptide


title: Testis, male, Control, ZT17, rep2

description:
50_M_16L_TESTIS_S196
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: GLUP_TEAD4KO_1


title: TEAD4KO_3


title: Testis, male, Deficient, ZT05, rep1

description:
37_M_4H_TESTIS_S191
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Testis, male, Control, ZT17, rep1

description:
34_M_16L_TESTIS_S190
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Testis, male, Control, ZT17, rep3

description:
58_M_16L_TESTIS_S199
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: TEAD4KO_1


title: TEAD4KO_2


title: Testis, male, Control, ZT05, rep3

description:
49_M_4L_TESTIS_S195
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: GLUP2


title: GLUP3


title: GLUP1


title: Quadriceps, female, Control, ZT05, rep3

description:
47_F_4L_QUAD_S82
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Quadriceps


title: Uterus, female, Deficient, ZT17, rep3

description:
60_F_16_5H_UT_S260
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Uterus

value: Uterus


title: Ctrl3

value: WT


title: Testis, male, Control, ZT05, rep1

description:
33_M_4L_TESTIS_S189
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Uterus, female, Deficient, ZT17, rep2

description:
44_F_16_5H_UT_S255
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: WT_Treg_H3K27ac_rep1

value: Spleen and Lymph nodes

value: Primary

value: Treg cells


title: IkE5_Treg_Input_histone


title: Myeloma patient 03 (non-B, non-T cells) Bone Marrow scRNAseq -270d post treatment (M4)

city: Seattle

first: Lawrence

last: Fong

state: Washington

address: 1100 Fairview Ave N

department: Immunotherapy Integrated Research Center, Translational Science and Therapeutics Division

institute: Fred Hutch Cancer Center

description: Bone marrow aspirates were diluted 1:1 in FACS buffer (PBS without magnesium or calcium, with 0.1% BSA and 2 mM EDTA). Peripheral blood samples were diluted 1:2 in FACS buffer. Mononuclear cell separation was performed by density centrifugation (Ficollpauqe, GE) with diluted bone marrow cells. Cells were manually aspirated and washed with FACS buffer. Red blood cells were lysed using RBC lysis buffer (Invitrogen) for 5 min at 4C. Within 1 hour of processing, cells were stained and sorted (Aria Fusion, BD) based on forward and side scatter, gated on CD45+ CD19- CD3+ (T cells) and CD45+ CD19- CD3- (nonB nonT cells). Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x 5 Reagent Kits version 1, according to manufacturer instructions. 10X 5 kits for TCR amplification were used to generate libraries per manufacturer instructions. All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR libraries.

library_source: transcriptomic single cell

data_processing:
All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet for gene expression and 5,000 reads for TCR libraries.
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz; VDJ cellranger output: comma separated values files

source_name: Bone Marrow

extract_protocol:
Bone marrow aspirates were diluted 1:1 in FACS buffer (PBS without magnesium or calcium, with 0.1% BSA and 2 mM EDTA). Peripheral blood samples were diluted 1:2 in FACS buffer. Mononuclear cell separation was performed by density centrifugation (Ficollpauqe, GE) with diluted bone marrow cells. Cells were manually aspirated and washed with FACS buffer. Red blood cells were lysed using RBC lysis buffer (Invitrogen) for 5 min at 4C. Within 1 hour of processing, cells were stained and sorted (Aria Fusion, BD) based on forward and side scatter, gated on CD45+ CD19- CD3+ (T cells) and CD45+ CD19- CD3- (nonB nonT cells).
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x 5ʹ Reagent Kits version 1, according to manufacturer instructions. 10X 5’ kits for TCR amplification were used to generate libraries per manufacturer instructions.

value: Bone Marrow

value: Immune and tumor cells


title: Uterus, female, Deficient, ZT17, rep1

description:
36_F_16_5H_UT_S252
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: GLUP_TEAD4KO_2


title: Uterus, female, Deficient, ZT05, rep3

description:
59_F_4_5H_UT_S259
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Myeloma patient 11 (T-cells) PBMC scRNAseq -14d post treatment (T8)

source_name: PBMC

value: PBMC


title: Uterus, female, Deficient, ZT05, rep2

description:
43_F_4_5H_UT_S254
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: Uterus, female, Deficient, ZT05, rep1

description:
35_F_4_5H_UT_S251
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: Myeloma patient 02 (non-B, non-T cells) Bone Marrow scRNAseq -180d post treatment (M3)


title: Testis, male, Control, ZT05, rep2

description:
41_M_4L_TESTIS_S193
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male

value: Control


title: Uterus, female, Control, ZT17, rep3

description:
56_F_16_5L_UT_S258
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Myeloma patient 11 (T-cells) PBMC scRNAseq -14d post treatment (T7)


title: Uterus, female, Control, ZT17, rep2

description:
48_F_16_5L_UT_S257
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Myeloma patient 04 (T-cells) Bone Marrow scRNAseq -30d post treatment (T6)


title: Uterus, female, Control, ZT17, rep1

description:
32_F_16_5L_UT_S250
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Uterus, female, Control, ZT05, rep3

description:
47_F_4_5L_UT_S256
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Uterus, female, Control, ZT05, rep2

description:
39_F_4_5L_UT_S253
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 6hpi, VV, Replicate1

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

data_processing:
For CUT&Tag equencing reads were mapped to the hg19 genome using bowtie2 with k=1 parapeter
bigWig tracks were created by extending reads to 200, collapsing them into pileups, and normalizing to reads per million
Peaks were called using MACS2, cut off q-value<0.05, IgG samples as control files
Filtering peaks using Bedtools to subtract peaks of 2h.p.i timepoint and subsequent filtering for peaks occuring in two or more consecutive timepoints
Read counting was performed using quasR (Gaidatzis et al, 2015)
Assembly: hg19, HSV1

molecule: polyA RNA

growth_protocol: DMEM, 10% fetal bovine serum, 1mM GlutaMAX, 1mM HEPES and 1x penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2

extract_protocol:
For CUT&Tag, we used the CUT&Tag Assay Kit (Active Motif) using 2.5ug Dux4 antibody (E5-5 Abcam) or 2.5ug rabbit IgG antibody (Cell Signalling Technology)
For RNA-seq, cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Infection in PBS, 0.1% Glucose, 1% fetal bovine serum. After 1h remaining virus was washed away with low pH Wash buffer (40mM Citic acid, 10mM KCl, 135 NaCl, ph3)

tag: dux4 genotype

value: wt

value: VACV WR infection

tag: timepoint


title: HFF-1, 12hpi, VV, Replicate1


title: Uterus, female, Control, ZT05, rep1

description:
31_F_4_5L_UT_S249
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 12hpi, VV, Replicate2


title: Ctrl1

value: gastric cancer cell


title: HFF-1, 6hpi, VV, Replicate2


title: Ovary, female, Deficient, ZT17, rep3

description:
60_F_16H_OV_S188
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Ovary

value: CBA/CaJ

value: Ovary


title: HFF-1, 2hpi, VV, Replicate1


title: HFF-1, 12hpi, MVA, Replicate2

value: MVA T7 infection


title: HFF-1, 12hpi, MVA, Replicate1


title: Ovary, female, Deficient, ZT05, rep3

description:
59_F_4H_OV_S187
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 2hpi, VV, Replicate2


title: Ovary, female, Deficient, ZT17, rep1

description:
36_F_16H_OV_S180
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Ovary, female, Deficient, ZT17, rep2

description:
44_F_16H_OV_S183
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Ovary, female, Deficient, ZT05, rep2

description:
43_F_4H_OV_S182
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 6hpi, MVA, Replicate2


title: HFF-1, 6hpi, MVA, Replicate1


title: T. marneffei ∆acuM rep1

city: Sri Phum, Mueang

first: Tanaporn

last: Wangsanut

state: Chiang Mai

address: 110 Inthawarorot Rd

country: Thailand

institute: Chiang Mai University

data_processing:
Sequencing reads were annotated and aligned to the T. marneffei ATCC18224 reference genomes by using Hisat2 v2.0.5.
StringTie (v1.3.3b) was used to assemble the mapped reads and predict novel transcripts in a reference-based approach
The feature-Counts v1.5.0-p3 was used to count the read numbers mapped to each gene
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene was calculated based on the length of the gene and reads count mapped to the gene.
Differential expression analysis of two conditions was performed using the edgeR package (3.22.5).
The P values were adjusted using the Benjamini & Hochberg method.
Assembly: GCA_000001985.1/JCVI-PMFA1-2.0
Supplementary files format and content: Excel file include gene counts for each sample
Supplementary files format and content: Excel file include FPKM values for each sample
Supplementary files format and content: Excel file include diffential expressed gene values for each sample

organism: Talaromyces marneffei

source_name: cell cultures

growth_protocol: Conidia of T. marneffei ATCC18224, ∆acuK and ∆acuM strains were inoculated at a final concentration of 108 cell/mL in 250 mL synthetic dextrose (SD) broth (1%glucose , 7 uM ferrous sulfate) and incubated at 25°C for 36 hours for the generation of mycelium mass. The cultures were harvested by centrifugation at 4500 rpm for 10 min.

extract_protocol:
The cultures were harvested by centrifugation at 4500 rpm for 10 min. Approximately 2 g wet weight was homogenized in a TRIzol reagent (Invitrogen, Life Technologies, Carlsbad, CA, USA) by using a bead beater (Biospec, Bartlesville, OK, USA). Total RNA was isolated following the manufacturer’s protocol. The RNA was digested with 1 U/µL DNase I to eliminate the residual DNA and purified by isopropanol precipitation. RNA concentrations were determined with a spectrophotometer (Nanodrop 2000: Thermo Scientific, Waltham, MA, USA). RNA integrity and purity were tested by agarose gel electrophoresis.
Library preparation and RNA sequencing were performed by a service from Novogene Co., Ltd. (Hong Kong).

tag: strain/genotype

value: {delta}acuM

value: cell cultures


title: T. marneffei ∆acuK rep1

value: {delta}acuK


title: HFF-1, 2hpi, MVA, Replicate2


title: T. marneffei ATCC18224 rep 1


title: Ovary, female, Control, ZT17, rep3

description:
56_F_16L_OV_S186
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Total_RNA_eIF4E_IP_4EBP1_4A_replica2

city: Heidelberg

first: Mykola

last: Roiuk

address: Im Neuenheimer Feld 580

institute: DKFZ

data_processing:
for footprints only: removal of of adaptors and randomized nucleotides.
The reads aligning to tRNA or rRNA were removed using bowtie2.
Remaining reads were mapped to the human transcriptome (Ensemble transcript assembly 94) and genome (hg38) using BBMap software, with multiple mapping allowed.
The reads mapping to the coding sequences were quantified with lab-based software written in C (https://github.com/aurelioteleman/Teleman-Lab).
To enable to comparison between samples reads were normalised to the library depth, and rpkm values were quantified.
Assembly: hg38
Supplementary files format and content: The processed data file contains raw reads for each of the samples. The reads are not normalised to the library depth. Reads mapped to the coding sequence were counted in Ribosome profiling libraries and total RNA for ribosome profiling samples. Reads mapped to the whole transcript were quantified for eIF4E-IPed and total RNA libraries.

source_name: HeLa

growth_protocol: DMEM (Gibco 41965039) +10% fetal bovine serum (FBS) (Sigma, S0615) +100 U/ml Penicillin/Streptomycin (Gibco 15140122).

extract_protocol:
Total RNA was extracted with Qiagene Rneasy Kit. Ribosomal footprints were extracted from the monosomal fraction after RNaseI digestion via the size selection. eIF4E-IPed RNA was extracted by acid phenol extraction with the protocol previously described (PMID:32589966)
Libraries from total and eIF4E-IPed RNA were prepared using the Illumina TruSeq Stranded library preparation kit. Ribosomal footprints were converted into libraries with the use of Next-Flex small RNA v.4 kit protocol

treatment_protocol: overexpression either of empty vector or a constitutively active version of eIF4E-binding protein (4E-BP)

value: HeLa

value: an immortal human epithelial cell line

value: 4E-BP1 constitutively-active (4E-BP1-4A full length) overexpression


title: HFF-1, 2hpi, MVA, Replicate1


title: Total_RNA_eIF4E_IP_4EBP1_4A_replica1


title: Total_RNA_eIF4E_IP_Empty_vector_replica2


title: HFF-1, 12hpi, MPXGA, Replicate2

value: Gabon/1987 infection


title: Total_RNA_eIF4E_IP_Empty_vector_replica3


title: Total_RNA_eIF4E_IP_Empty_vector_replica1


title: HFF-1, 12hpi, MPXGA, Replicate1


title: eIF4E_IPed_RNA_4EBP1_4A_replica3

description: eIF4E-IPed RNA was used to generate this library


title: Ovary, female, Control, ZT05, rep3

description:
47_F_4L_OV_S184
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: eIF4E_IPed_RNA_4EBP1_4A_replica1


title: Ovary, female, Control, ZT17, rep1

description:
32_F_16L_OV_S178
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Ovary, female, Control, ZT05, rep2

description:
39_F_4L_OV_S181
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Ovary, female, Control, ZT05, rep1

description:
31_F_4L_OV_S177
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 6hpi, MPXGA, Replicate2


title: HFF-1, 6hpi, MPXGA, Replicate1


title: eIF4E_IPed_RNA_Empty_vector_replica3

value: empty vector overexpression


title: HFF-1, 2hpi, MPXGA, Replicate2


title: Ovary, female, Deficient, ZT05, rep1

description:
35_F_4H_OV_S179
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: eIF4E_IPed_RNA_Empty_vector_replica1


title: Total_RNA_Riboseq_4EBP1_4A_replica_2


title: eIF4E_IPed_RNA_Empty_vector_replica2


title: Spleen, male, Deficient, ZT17, rep3

description:
62_M_16H_SPLEEN_S69
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Spleen

value: Spleen

value: male


title: HFF-1, 2hpi, MPXGA, Replicate1

value: wt


title: Total_RNA_Riboseq_4EBP1_4A_replica_1


title: Total_RNA_Riboseq_Empty_vector_replica_2


title: Spleen, male, Deficient, ZT17, rep2

description:
54_M_16H_SPLEEN_S64
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Total_RNA_Riboseq_Empty_vector_replica_1


title: Ovary, female, Control, ZT17, rep2

description:
48_F_16L_OV_S185
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: HFF-1, 12hpi, MPXIC, Replicate2

value: TNP/Taї/12 infection


title: Spleen, male, Deficient, ZT17, rep1

description:
38_M_16H_SPLEEN_S54
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: eIF4E_IPed_RNA_4EBP1_4A_replica2


title: Riboseq_4E-BP1_4A_replica1

description: ribosome footprints were used to generate this library


title: Spleen, male, Deficient, ZT05, rep3

description:
53_M_4H_SPLEEN_S63
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 6hpi, MPXIC, Replicate2


title: Riboseq_Empty_vector_replica2


title: HFF-1, 12hpi, MPXIC, Replicate1


title: Pool, YPD, DOX, Set2, BioRep C

city: Toronto

first: Emily

middle: Haochen

last: Xiong

state: Ontario

address: 101 College Street

department: Department of Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Barcode sequence reads were mapped to an artificial genome containing known UPTAG and DNTAG sequences via Bowtie.
Assembly: Barcode sequence reads were mapped to an artificial genome containing known UPTAG and DNTAG sequences of pooled strains via Bowtie. Read frequency for the UPTAG and DNTAG of each strain were compiled for each indexed sample.
Supplementary files format and content: Single merged comma-seperated file with UPTAG and DNTAG barcode counts for all genes using summed values from all raw sequencing files of each sample
Library strategy: Bar-Seq

organism: Candida albicans

source_name: GRACE mutants in CaSS1 background

growth_protocol: Stock pools were thawed, diluted into 24-well plates (Falcon, 353047) in triplicate 1 ml cultures to an OD600 of 0.05 with or without 100 µg/mL DOX. Cultures were incubated for 24 hours in a static manner in the conditions of interest or until OD600 of cultures reached approximately 5.0 (File S1). The cultures were each sub-cultured into triplicate 1 ml cultures with fresh medium at an OD600 of 0.05 with or without 100 µg/mL DO

extract_protocol:
Genomic DNA was purified using the PureLinkTM Genomic DNA Mini Kit as per instructions with minor modifications, as described. Cell pellets were resuspended in 400 µL of lysis buffer (from PureLink Kit) and physically lysed by adding approximately 200 uL of acid-washed glass beads and bead beating six times for 30 seconds. Extracted genomic DNA was quantified with the Quant-iTTM PicoGreen dsDNA Assay Kit.
Barcode amplification by PCR was performed using 105.6 ng of genomic DNA via the Ex-Taq enzyme UPTAG and DNTAG primer sequences are included in File S5 of associated paper. Separate UPTAG and DNTAG multiplexed pools were formed by combining equal amounts of PCR product from each sample. Pooled UPTAG and DNTAG DNA pools were extracted from a 1% agarose gel using the QIAquick® Gel Extraction Kit. Equal quantities of UPTAG and DNTAG pools as determined by PicoGreen assay were combined to form a library, which was sequenced on an Illumina MiSeq v2 Regular or NextSeq v2.5 Mid-Output instrument (single-end flow cell) using specific primers to sequence and index the UPTAG and DNTAGs (File S5).

treatment_protocol: We screened the barcoded GRACE collection in the baseline condition of synthetic defined YNB medium at 30 °C, as well as six additional growth conditions at 30 °C including: nutrient-rich medium (YPD), YNB containing the osmotic stressor sodium chloride (NaCl), YNB supplemented with serum—a key component in human blood, YNB supplemented with the membrane stressor sodium dodecyl sulfate (SDS), YNB containing the osmotic stressor sorbitol, and iron-free YNB; we also screened in YNB at the elevated temperature of 37 °C. Full Protocol can be found in associated paper.

value: GRACE mutants in CaSS1 background

tag: genetic modification

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.

tag: time

value: 24h, subculture into fresh media, then 48h

value: Pooled culture of GRACE library strains

value: 100 µg/mL DOX

tag: condition

value: YPD at 30 C


title: HFF-1, 6hpi, MPXIC, Replicate1


title: Spleen, male, Deficient, ZT05, rep2

description:
45_M_4H_SPLEEN_S59
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

tag: strain

tag: tissue


title: Spleen, male, Deficient, ZT05, rep1

description:
37_M_4H_SPLEEN_S53
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

tag: Sex

tag: treatment


title: Pool, YPD, NO DOX, Set2, BioRep C

value: No DOX


title: HFF-1, 2hpi, MPXIC, Replicate2


title: Pool, YPD, NO DOX, Set2, BioRep B


title: Spleen, male, Control, ZT17, rep3

description:
58_M_16L_SPLEEN_S66
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

tag: zeitgeber time


title: Pool, YPD, NO DOX, Set2, BioRep A

tag: cell type


title: HFF-1, 2hpi, MPXIC, Replicate1


title: Pool, YPD, DOX, Set1, BioRep C


title: HFF-1, 12hpi, MPXRKI, Replicate2

value: MPXV RKI/18/22 del18 infection


title: Spleen, male, Control, ZT17, rep2

description:
50_M_16L_SPLEEN_S62
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, YPD, DOX, Set1, BioRep B


title: Riboseq_4E-BP1_4A_replica2

value: HeLa

value: an immortal human epithelial cell line

value: 4E-BP1 constitutively-active (4E-BP1-4A full length) overexpression


title: Pool, YPD, DOX, Set1, BioRep A


title: Spleen, male, Control, ZT17, rep1

description:
34_M_16L_SPLEEN_S50
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Spleen


title: Pool, YPD, NO DOX, Set1, BioRep C


title: HFF-1, 12hpi, MPXRKI, Replicate1


title: Riboseq_Empty_vector_replica1

value: empty vector overexpression


title: Pool, YPD, NO DOX, Set1, BioRep A


title: HFF-1, 6hpi, MPXRKI, Replicate2

value: wt


title: Pool, YPD, DOX, Set2, BioRep B


title: Pool, YNB30, DOX, Set5, BioRep C

value: YNB at 30 C


title: Pool, YPD, DOX, Set2, BioRep A


title: HFF-1, 6hpi, MPXRKI, Replicate1


title: Pool, YNB30, DOX, Set5, BioRep A


title: Pool, YNB30, NO DOX, Set5, BioRep C


title: HFF-1, 2hpi, MPXRKI, Replicate2


title: Spleen, female, Deficient, ZT17, rep3

description:
60_F_16H_SPLEEN_S68
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female

value: Deficient


title: Pool, YNB30, NO DOX, Set5, BioRep B

value: GRACE mutants in CaSS1 background


title: HFF-1, 2hpi, MPXRKI, Replicate1


title: Spleen, female, Deficient, ZT17, rep1

description:
36_F_16H_SPLEEN_S52
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Pool, YNB30, NO DOX, Set4, BioRep C

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.

value: 24h, subculture into fresh media, then 48h


title: Spleen, female, Deficient, ZT17, rep2

description:
44_F_16H_SPLEEN_S58
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 12hpi, MPXFR, Replicate2

value: MPXV FR/7767/22 infection


title: Pool, YNB30, DOX, Set4, BioRep B

value: Pooled culture of GRACE library strains

value: 100 µg/mL DOX


title: HFF-1, 12hpi, MPXFR, Replicate1


title: Pool, YNB30, NO DOX, Set4, BioRep A

value: No DOX


title: Spleen, male, Control, ZT05, rep3

description:
77_M_L_ZT05_SPL_S354
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male

value: Control


title: Pool, YNB30, NO DOX, Set4, BioRep B


title: Pool, YNB30, DOX, Set3, BioRep C


title: Spleen, male, Control, ZT05, rep2

description:
41_M_4L_SPLEEN_S56
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Spleen, female, Deficient, ZT05, rep3

description:
59_F_4H_SPLEEN_S67
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Spleen, female, Deficient, ZT05, rep2

description:
43_F_4H_SPLEEN_S57
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, YNB30, DOX, Set4, BioRep A


title: Pool, YNB30, DOX, Set3, BioRep A


title: Pool, YPD, NO DOX, Set1, BioRep B

value: YPD at 30 C


title: Spleen, male, Control, ZT05, rep1

description:
33_M_4L_SPLEEN_S49
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Spleen


title: Pool, YNB30, NO DOX, Set5, BioRep A


title: Pool, YNB30, NO DOX, Set3, BioRep C


title: Pool, YNB30, DOX, Set4, BioRep C


title: Spleen, female, Deficient, ZT05, rep1

description:
35_F_4H_SPLEEN_S51
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 6hpi, MPXFR, Replicate2


title: Spleen, female, Control, ZT17, rep3

description:
56_F_16L_SPLEEN_S65
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 2hpi, MPXFR, Replicate2


title: Pool, YNB30, DOX, Set5, BioRep B


title: Pool, YNB30, NO DOX, Set3, BioRep B


title: Pool, YNB30, NO DOX, Set3, BioRep A


title: HFF-1, 2hpi, MPXFR, Replicate1


title: Pool, YNB30, DOX, Set2, BioRep B


title: Pool, YNB30, DOX, Set2, BioRep A


title: HFF-1, 12hpi, KpxV, Replicate2

value: KPXV H.Meyer infection


title: Pool, YNB30, DOX, Set2, BioRep C


title: HFF-1, 6hpi, MPXFR, Replicate1

value: wt


title: Spleen, female, Control, ZT17, rep2

description:
48_F_16L_SPLEEN_S61
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 12hpi, KpxV, Replicate1


title: Pool, YNB30, NO DOX, Set2, BioRep A

value: YNB at 30 C


title: Pool, YNB30, NO DOX, Set2, BioRep B


title: Pool, YNB30, NO DOX, Set2, BioRep C


title: Spleen, female, Control, ZT05, rep2

description:
39_F_4L_SPLEEN_S55
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: Pool, YNB30, DOX, Set1, BioRep C


title: HFF-1, 6hpi, KpxV, Replicate2


title: Spleen, female, Control, ZT05, rep3

description:
47_F_4L_SPLEEN_S60
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Spleen, female, Control, ZT05, rep1

description:
31_F_4L_SPLEEN_S47
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, YNB30, NO DOX, Set1, BioRep C


title: Kidney, male, Deficient, ZT17, rep3

description:
90_M_H_ZT17_KID_S336
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Kidney

value: Kidney

value: Deficient


title: HFF-1, 2hpi, KpxV, Replicate1


title: Pool, YNB30, NO DOX, Set1, BioRep A

value: GRACE mutants in CaSS1 background


title: Pool, YNB30, DOX, Set1, BioRep A

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.


title: Pool, YNB30, DOX, Set1, BioRep B

value: 24h, subculture into fresh media, then 48h


title: Pool, YNB30, NO DOX, Set1, BioRep B


title: HFF-1, 2hpi, KpxV, Replicate2


title: Pool, Sorbitol, DOX, Set2, BioRep C

value: 72h, subculture into fresh media, then 96h

value: YNB with 1M Sorbitol at 30 C


title: Kidney, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_KID_S332
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Pool, Sorbitol, DOX, Set2, BioRep B

value: Pooled culture of GRACE library strains

value: 100 µg/mL DOX


title: HFF-1, 12hpi, CpxV, Replicate2

value: CPXV GuWi infection


title: HFF-1, 6hpi, KpxV, Replicate1


title: Spleen, female, Control, ZT17, rep1

description:
32_F_16L_SPLEEN_S48
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: Pool, Sorbitol, DOX, Set2, BioRep A


title: Pool, Sorbitol, NO DOX, Set2, BioRep C

value: No DOX


title: Pool, Sorbitol, NO DOX, Set2, BioRep B


title: HFF-1, 6hpi, CpxV, Replicate2


title: Kidney, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_KID_S331
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male


title: Pool, Sorbitol, DOX, Set1, BioRep B


title: Pool, Sorbitol, NO DOX, Set2, BioRep A


title: Pool, Sorbitol, DOX, Set1, BioRep A


title: Pool, Sorbitol, DOX, Set1, BioRep C


title: Kidney, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_KID_S335
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, Sorbitol, NO DOX, Set1, BioRep C


title: Kidney, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_KID_S327
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 2hpi, CpxV, Replicate2

value: wt


title: Pool, Sorbitol, NO DOX, Set1, BioRep A


title: HFF-1, 2hpi, CpxV, Replicate1


title: Pool, SDS, DOX, Set2, BioRep C

value: YNB with 0.03% SDS at 30 C


title: Pool, Sorbitol, NO DOX, Set1, BioRep B


title: Kidney, male, Control, ZT17, rep3

description:
94_M_L_ZT17_KID_S338
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 12hpi, Mock, Replicate2

value: mock infection


title: Pool, SDS, NO DOX, Set2, BioRep C


title: Kidney, male, Control, ZT17, rep1

description:
78_M_L_ZT17_KID_S330
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Kidney


title: Pool, SDS, DOX, Set2, BioRep A


title: Pool, SDS, NO DOX, Set2, BioRep B


title: HFF-1, 12hpi, Mock, Replicate1


title: Kidney, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_KID_S328
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: HFF-1, 12hpi, CpxV, Replicate1


title: Pool, SDS, DOX, Set2, BioRep B

value: GRACE mutants in CaSS1 background


title: HFF-1, 6hpi, Mock, Replicate2


title: Pool, SDS, NO DOX, Set2, BioRep A

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.


title: HFF-1, 6hpi, CpxV, Replicate1


title: HFF-1, 6hpi, Mock, Replicate1


title: Kidney, male, Control, ZT05, rep2

description:
85_M_L_ZT05_KID_S333
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, SDS, DOX, Set1, BioRep A

value: 24h, subculture into fresh media, then 48h


title: Kidney, male, Control, ZT05, rep1

description:
77_M_L_ZT05_KID_S329
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, SDS, DOX, Set1, BioRep C


title: Pool, SDS, DOX, Set1, BioRep B


title: HFF-1, 2hpi, Mock, Replicate2


title: Kidney, female, Deficient, ZT17, rep3

description:
60_F_16_5H_KIDNEY_S12_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: Pool, SDS, NO DOX, Set1, BioRep C


title: HFF-1, 2hpi, Mock, Replicate1


title: Pool, NaCl, DOX, Set1, BioRep C

value: 40h, subculture into fresh media, then 72h

value: YNB with 1M NaCl at 30 C


title: Pool, SDS, NO DOX, Set1, BioRep B

value: Pooled culture of GRACE library strains


title: Pool, SDS, NO DOX, Set1, BioRep A


title: HFF-1, 0hpi, Mock, Replicate2


title: Kidney, male, Control, ZT17, rep2

description:
86_M_L_ZT17_KID_S334
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Kidney, male, Control, ZT05, rep3

description:
93_M_L_ZT05_KID_S337
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Kidney, female, Deficient, ZT17, rep2

description:
44_F_16_5H_KIDNEY_S7_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Kidney, female, Deficient, ZT17, rep1

description:
36_F_16_5H_KIDNEY_S4_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: HFF-1, 0hpi, Mock, Replicate1


title: Pool, NaCl, NO DOX, Set1, BioRep C


title: Kidney, female, Deficient, ZT05, rep3

description:
59_F_4_5H_KIDNEY_S11_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, NaCl, DOX, Set1, BioRep A

value: 100 µg/mL DOX


title: Pool, NaCl, NO DOX, Set1, BioRep B


title: Pool, NaCl, NO DOX, Set1, BioRep A


title: Pool, FeFree, DOX, Set2, BioRep C

value: 30h, subculture into fresh media, then 72h

value: Iron-Free YNB at 30 C


title: Pool, FeFree, DOX, Set2, BioRep B


title: Kidney, female, Deficient, ZT05, rep2

description:
43_F_4_5H_KIDNEY_S6_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: P6_CD4only_CD3CD28

city: Baltimore

first: Milica

last: Moskovljevic

state: Maryland

address: 733 N Baltimore St, Miller Research Building

department: School of Medicine

institute: Johns Hopkins University

description:
0477_B11
P6_CD3CD28

data_processing:
Initial QC and STAR aligned
RSEM
DSEQ2
Assembly: hg19 build of the genome (GRCh37)
Supplementary files format and content: tab-deliminated excel master file include raw counts for each sample

source_name: blood

extract_protocol:
RNA isolation was performed as previously described (Janjic et al PMC8969310)
TruSeq Stranded mRNA, illumina

value: blood

value: peripheral blood mononuclear cells (PBMCs)

value: CD4 T cells


title: Pool, FeFree, DOX, Set2, BioRep A


title: Kidney, female, Deficient, ZT05, rep1

description:
35_F_4_5H_KIDNEY_S3_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: P6_CD4fDC_gagpool

description:
0477_B10
P6_Gagpool


title: P6_CD4fDC_gagp55

description:
0477_D10
P6_GagP55


title: Pool, FeFree, NO DOX, Set2, BioRep C

value: No DOX


title: Pool, FeFree, NO DOX, Set2, BioRep A


title: Kidney, female, Control, ZT17, rep3

description:
56_F_16_5L_KIDNEY_S10_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Kidney

value: Control


title: Pool, FeFree, NO DOX, Set2, BioRep B

value: GRACE mutants in CaSS1 background


title: P6_CD4only_PMAI

description:
0477_D11
P6_PMAI


title: Pool, NaCl, DOX, Set1, BioRep B

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.


title: Pool, FeFree, DOX, Set1, BioRep C


title: Kidney, female, Control, ZT17, rep2

description:
48_F_16_5L_KIDNEY_S9_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, FeFree, DOX, Set1, BioRep B


title: Pool, FeFree, DOX, Set1, BioRep A


title: Kidney, female, Control, ZT17, rep1

description:
32_F_16_5L_KIDNEY_S2_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, FeFree, NO DOX, Set1, BioRep C


title: P6_CD4fDC_NoAg

description:
0477_F10
P6_NoAg


title: P6_CD4only_NoTx

description:
0477_H10
P6_NoTx


title: Pool, FeFree, NO DOX, Set1, BioRep B


title: P4_CD4only_PMAI

description:
3217_B4
P4_PMAI


title: Kidney, female, Control, ZT05, rep3

description:
47_F_4_5L_KIDNEY_S8_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, FeFree, NO DOX, Set1, BioRep A


title: Kidney, female, Control, ZT05, rep2

description:
39_F_4_5L_KIDNEY_S5_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, FBS, DOX, Set2, BioRep C

value: YNB with 10% Fetal Bovine Serum at 30 C


title: Pool, FBS, DOX, Set2, BioRep B


title: P4_CD4only_CD3CD28

description:
3217_B5
P4_CD3CD28


title: Pool, FBS, DOX, Set2, BioRep A


title: Pool, FBS, NO DOX, Set2, BioRep C


title: Pool, FBS, NO DOX, Set2, BioRep B


title: Adrenal gland, male, Deficient, ZT17, rep3

description:
90_M_H_ZT17_ADR_S294
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Adrenal gland

value: Adrenal gland

value: male

value: Deficient


title: P4_CD4fDC_CMV

description:
3217_D4
P4_CMV


title: Pool, FBS, NO DOX, Set2, BioRep A

value: Pooled culture of GRACE library strains


title: Pool, FBS, DOX, Set1, BioRep A


title: Adrenal gland, male, Deficient, ZT17, rep2

description:
82_M_H_ZT17_ADR_S290
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: P4_CD4only_NoTx

description:
3217_H4
P4_NoTx


title: Pool, FBS, NO DOX, Set1, BioRep C


title: Pool, FBS, DOX, Set1, BioRep C

value: 100 µg/mL DOX


title: Pool, FBS, DOX, Set1, BioRep B

value: 30h, subculture into fresh media, then 72h


title: Adrenal gland, male, Deficient, ZT17, rep1

description:
74_M_H_ZT17_ADR_S286
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: P10_CD4fDC_gagpoolp55

description:
dl15_B7
P10_GagP55


title: Pool, FBS, NO DOX, Set1, BioRep A


title: P10_CD4only_CD3CD28

description:
dl15_F7
P10_CD3CD28


title: Adrenal gland, male, Deficient, ZT05, rep3

description:
89_M_H_ZT05_ADR_S293
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Adrenal gland, male, Deficient, ZT05, rep2

description:
81_M_H_ZT05_ADR_S289
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Pool, FBS, NO DOX, Set1, BioRep B


title: Pool, YNB37, DOX, Set2, BioRep B

value: 24h, subculture into fresh media, then 48h

value: YNB at 37 C


title: Pool, YNB37, DOX, Set2, BioRep C


title: Pool, YNB37, DOX, Set2, BioRep A


title: Adrenal gland, male, Deficient, ZT05, rep1

description:
73_M_H_ZT05_ADR_S285
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: P10_CD4fDC_gagpool

description:
dl15_F8
P10_Gagpool

value: blood

value: peripheral blood mononuclear cells (PBMCs)


title: Kidney, female, Control, ZT05, rep1

description:
31_F_4_5L_KIDNEY_S1_L003
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: Pool, YNB37, NO DOX, Set2, BioRep C

value: No DOX


title: P10_CD4only_PMAI

description:
dl15_H7
P10_PMAI

value: CD4 T cells


title: Adrenal gland, male, Control, ZT17, rep3

description:
94_M_L_ZT17_ADR_S296
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: Pool, YNB37, NO DOX, Set2, BioRep B

value: GRACE mutants in CaSS1 background

value: For each strain, one allele of the target gene is deleted using a HIS3 cassette and the other is placed under the regulation of a tetracycline-repressible promoter which allows gene expression to be repressed by the addition of a tetracycline analog, doxycycline.


title: P4_CD4fDC_NoAg

description:
3217_F4
P4_NoAg


title: Pool, YNB37, NO DOX, Set2, BioRep A


title: Adrenal gland, male, Control, ZT17, rep2

description:
86_M_L_ZT17_ADR_S292
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Adrenal gland


title: Pool, YNB30, DOX, Set3, BioRep B

value: YNB at 30 C


title: P10_CD4only_NoTx

description:
dl15_H8
P10_NoTx


title: Pool, YNB37, DOX, Set1, BioRep C


title: Pool, YNB37, DOX, Set1, BioRep B


title: Adrenal gland, male, Control, ZT17, rep1

description:
78_M_L_ZT17_ADR_S288
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: male


title: Pool, YNB37, NO DOX, Set1, BioRep C

value: Pooled culture of GRACE library strains


title: Pool, YNB37, DOX, Set1, BioRep A


title: Pool, YNB37, NO DOX, Set1, BioRep B


title: P1_CD4only_PMAI

description:
rs29_B2
P1_PMAI


title: Adrenal gland, male, Control, ZT05, rep3

description:
93_M_L_ZT05_ADR_S295
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: Pool, YNB37, NO DOX, Set1, BioRep A


title: P1_CD4fDC_NoAg

description:
rs29_F2
P1_NoAg


title: P1_CD4fDC_CMV

description:
rs29_D2
P1_CMV


title: Adrenal gland, male, Control, ZT05, rep2

description:
85_M_L_ZT05_ADR_S291
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: P1_CD4only_NoTx

description:
rs29_H2
P1_NoTx


title: Adrenal gland, male, Control, ZT05, rep1

description:
77_M_L_ZT05_ADR_S287
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: P5_CD4only_PMAI

description:
3171_B2
P5_PMAI


title: ΔapaH biol rep 1

city: Rome

first: Francesco

last: Imperi

state: Rome

address: Viale Marconi, 446

department: Department of Scienze

country: Italy

institute: Roma Tre University

data_processing:
sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Pseudomonas_aeruginosa_PAO1 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. BAM files were generated as a result of this step.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within gene regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed
The Wald test was used to generate p- values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: PAO1 GCA_000006765
Supplementary files format and content: tab-delimited text files include hit counts values for each Sample

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa cultures were grown overnight in LB at 37°C with shaking (200 rpm). Following overnight growth, bacteria were diluted to an OD600 of 0.01 into 10 mL of LB . The cultures were incubated at 37°C with shaking. RNA was extracted from 1 mL of each culture at an OD600 of about 1 (mid exponential phase of growth).

extract_protocol:
mRNA was preserved immediately upon cell harvest using Qiagen RNAprotect. Cells were lysed using sonication and RNA was harvested using RNeasy Mini Kit (Qiagen). Eluted RNA was treated for 1 h at 37°C with TURBO DNase (0.2 U per μg of RNA; Ambion) and with SUPERase-In (0.4 U per μg of RNA; Ambion). DNase I was removed with the RNeasy Column Purification Kit (Qiagen). 3 µg of total RNA was used for the construction of sequencing libraries.
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).

tag: genotype

value: [delta]apaH


title: PAO1 biol rep 2

value: wild type


title: Adrenal gland, female, Deficient, ZT17, rep3

description:
60_F_16H_ADR_S152
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: PAO1 biol rep 1


title: P5_CD4fDC_CMV

description:
3171_B3
P5_CMV


title: E4

city: Nanjing

first: Jie

last: Mei

state: Jiangsu

address: No. 101, Longmian Road

institute: Nanjing Medical University

data_processing:
fastx (version:0.0.13)
Assembly: GRCh38
Supplementary files format and content: csv file include TPM values for each sample

source_name: circulating extracellular vesicles

extract_protocol:
Total RNA was extracted usingmirVana™ miRNA Isolation Kit following the manufacturer’s instructions.
RNA library for RNA-seq were perpared using QIAseq miRNA Library Kit following the manufacturer’s instructions.

value: circulating extracellular vesicles

value: NSCLC

value: WT

value: serum from NSCLC patients with exercise habit


title: E2


title: P5_CD4fDC_NoAg

description:
3171_D2
P5_NoAg

value: blood

value: peripheral blood mononuclear cells (PBMCs)


title: Adrenal gland, female, Deficient, ZT17, rep2

description:
44_F_16H_ADR_S145
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: female


title: E3


title: P5_CD4only_NoTx

description:
3171_F2
P5_NoTx

value: CD4 T cells


title: Adrenal gland, female, Deficient, ZT17, rep1

description:
36_F_16H_ADR_S140
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: NE5

value: serum from NSCLC patients without exercise habit


title: P5_CD4only_CD3CD28

description:
3171_H2
P5_CD3CD28


title: Adrenal gland, female, Deficient, ZT05, rep3

description:
59_F_4H_ADR_S151
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Adrenal gland


title: Adrenal gland, female, Deficient, ZT05, rep2

description:
43_F_4H_ADR_S144
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: ΔapaH biol rep 3


title: NE6


title: ΔapaH biol rep 2


title: NE3


title: NE2


title: P7_CD4fDC_gagpool

description:
0111_B5
P7_Gagpool


title: P7_CD4fDC_gagp55

description:
011_B6
P7_GagP55


title: PAO1 biol rep 3


title: NE1


title: Adrenal gland, female, Control, ZT17, rep3

description:
56_F_16L_ADR_S149
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Control


title: P7_CD4fDC_NoAg

description:
0111_D5
P7_NoAg


title: Adrenal gland, female, Control, ZT17, rep2

description:
48_F_16L_ADR_S148
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: MASH 3

city: Shreveport

first: Sandeep

last: Das

state: LA

address: 1501 Kings Highway

department: Pathology

institute: LSU Health Shreveport

description:
s2986
MASH24-2986 Fraction Methylated

data_processing:
Bismark v0.23.0
methylKit 1.28.0
Assembly: mm39
Supplementary files format and content: 02CDLSU_Mouse_RRBS_Control24_vs_MASH24_region.xlsx

source_name: liver

extract_protocol:
Genomic DNA was extracted using the Quick-gDNA MiniPrep kit (Zymo Research, Irvine, CA, USA, D3024) following the manufacturer’s instructions for tissues.
The steps of RRBS analysis involved DNA digestion using the restriction enzyme MspI, which cuts DNA at its recognition site, CCGG, independently of CpG methylation status. Subsequent reactions for DNA end repair, A-tailing and adaptor ligation were followed by Illumina sequencing (NextSeq 500) after size selection. Bisulfite conversion was then performed for total genomic DNA. Bisulfite conversion with sodium bisulfite allows conversion of cytosines to uracils in a single-stranded DNA, whereas 5-methylcytosines (5mCs) are resistant to this conversion and remain as cytosines, allowing 5mCs to be distinguished from unmethylated cytosines. During subsequent PCR amplification, the DNA sequences are amplified with primers specific for one strand of uracil converted from methylated cytosine, and uracil is amplified as thymine. If cytosine in the CpG dinucleotide exists as 5mC, PCR recognizes 5mC as cytosine.

treatment_protocol: Mice were fed with chow or MASH diet for 24 weeks.

value: liver

value: MASH Diet


title: MASH 2

description:
s2979
MASH24-2979 Fraction Methylated


title: MASH 4

description:
s3089
MASH24-3089 Fraction Methylated


title: P7_CD4only_NoTx

description:
0111_D6
P7_NoTx


title: E1


title: Control 4

description:
s3909
Control2-3909 Fraction Methylated

value: Chow Diet


title: Adrenal gland, female, Control, ZT17, rep1

description:
32_F_16L_ADR_S136
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: CBA/CaJ


title: P7_CD4only_CD3CD28

description:
0111_F5
P7_CD3CD28


title: MASH 1

description:
s2974
MASH24-2974 Fraction Methylated


title: Control 3

description:
s3907
Control2-3907 Fraction Methylated


title: Sox10-Cre-RFP_S1_L001

city: Athens

first: Hong-Xiang

last: Liu

state: Georgia

address: 425 River Road

department: Animal & Dairy Science

institute: University of Georgia

description: 10X Genomics

data_processing:
The reads from sequencing were processed using Cell Ranger (v7.0.0) for alignment, filtering, barcode counting, UMI counting and cell counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Epithelium of circumvallate/vEG cells

extract_protocol:
Freshly collected epithelium of circumvallate/von Ebner’s gland (vEG) tissue were washed with sterile Tyrode's solution. Then, the tissues were dissociated with 0.25% trypsin-EDTA. 5% FBS in DMEM/F12 used to stop the reaction and cells were re-suspend in DMEM/F12 containing 10% FBS and 1% BSA.
Library was performed according to the manufacturer's intructions (10x Genomics)

value: Epithelium of circumvallate/vEG cells

value: Epithelial cells


title: Control 2

description:
s3904
Control2-3904 Fraction Methylated


title: Control 1

description:
s3903
Control2-3903 Fraction Methylated


title: NE4

value: circulating extracellular vesicles


title: Adrenal gland, female, Control, ZT05, rep3

description:
47_F_4L_ADR_S147
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Adrenal gland, female, Deficient, ZT05, rep1

description:
35_F_4H_ADR_S139
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

value: Deficient


title: P7_CD4only_PMAI

description:
011_H5
P7_PMAI


title: Adrenal gland, female, Control, ZT05, rep2

description:
39_F_4L_ADR_S142
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Adrenal gland, female, Control, ZT05, rep1

description:
31_F_4L_ADR_S135
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv


title: Liver, male, Deficient, ZT17, rep3

description:
62_M_16H_LIVER_S23
RED-S_mouse_tissue_expression_raw_counts_v1.csv
RED-S_mouse_tissue_expression_normalized_counts_v1.csv

source_name: Liver

value: Liver

value: male


title: WT_Treg_ATAC_rep2

data_processing:
The quality of sequence reads was confirmed using fastQC to confirm that the average of Phred score was over 20.
Raw sequenced reads were processed with fastx_trimmer and cmpfastq_pe.
Processed reads were mapped to mm10 reference using Bowtie2 with default setting.
The peak call was performed using MACS2 by the following command; macs2 callpeak -t ${filename}.bam -g mm -n ${filename} -B –nomodel –shift 100 –extsize 200 –keep-dup all.
ATAC-seq peaks were defined using FindPeaks, with their size fixed at 250 base pairs, FDR set as default, and local filtering switched off.
Normalized density of mapped reads around Foxp3-binding sites was determined using annotatePeaks in Homer package.
Assembly: mm10
Supplementary files format and content: bigwig, bed

source_name: Spleen and Lymph nodes

extract_protocol:
Purified CD4+FYP+ Treg cells (1 x 105) were lysed using 50 ml of lysis buffer for 3 min on ice.
Tn5 tagmentation was performed using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina), following manufacturer’s instruction. Tagmented DNA was amplified using NEBNext High-Fidelity PCR Master Mix. Prepared DNA libraries were size-selected (150-1000 bp) by Ampure XP.

value: Spleen and Lymph nodes

value: Primary

value: Treg cells

value: WT


title: WT_Treg_ATAC_rep1


title: IkE5_Treg_ATAC_rep1


title: Day 5 iPSC IFNg_BS

city: Barcelona

first: Mercedes

last: Barrero

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

data_processing:
Analysis of 5mC and 5hmC percentages was done independently for each CpG contained in the PCR amplicons. A customized pipeline was generated for this analysis. Amplicons which contained the SNP and at least a CpG in the same read were analyzed. First, reads were assigned to their corresponding genes by identification of the primer used for PCR. Then, a 15-20 nucleotides sequence upstream of the SNP was used to classify the reads in Mus or Cas. Then, a 15-20 nucleotides sequence upstream of the CpG was used to determine the presence of CG or TG. Percentages of CG were calculated independently for Mus and Cas, in control or IFNγ-treated samples, in BS or OxBS samples. 5mC percentages were calculated by analyzing the percentage of CG in OxBS samples, while 5hmC were calculated as %CG (BS) - %CG(OxBS). Finally, 5mC and 5hmC percentages for Mus and Cas CpGs were compared between control and IFNγ samples.
Assembly: mm10
Supplementary files format and content: txt: results of number of reads and percentages of CG and TG for X mus and X cas for each CpG. Contains 4 .txt files
Supplementary files format and content: Allele_specific_DNA_methylation_analysis.xlsx: final percentages of 5mC and 5hmC calculated for each CpG in each sample
Library strategy: PCR-amplicon sequencing

source_name: embryonic stem cell

extract_protocol:
DNA was extracted using Wizard® Genomic DNA Purification Kit (Promega, A1120). After measuring DNA quantity by Qubit (ThermoFisher Scientific), 2µg of each sample was evenly splitted for the oxidation reaction (Oxidative Bisulfite -OxBS- treated samples) and the mock-oxidation reaction (Bisulfite -BS- treated samples) where the oxidant solution was replaced by water following the TrueMethyl oxBS Module manufacturer’s instructions (NuGEN-Tecan, 0414). Both aliquots were then processed in parallel for all stages of the protocol. After the oxidation reaction where 5-hydroxymethylcytosine is oxidized to 5-formylcytosine (5fC) and 5-methylcytosine (5mC) stays unchanged, the bisulfite treatment converts 5fC and all non-methylated cytosines to uracil, while 5mC is not altered.
Paired oxidative Bisulfite (OxBS) and the mock-oxidation reaction (Bisulfite BS) treated DNA from day 5 (control and IFNγ) reprogramming samples were used as templates for a two-step PCR amplification with the IMMOLASE™ DNA Polymerase (BIO-21046) with a custom program adapted to each primer pair annealing temperature and resulting amplicon size. In the first PCR, 0.5 ng of DNA were used to amplify the regions of interest to increase the specificity of the second PCR reaction and enrich the region of interest. In the second PCR, 1-3 µl of the first-step products were amplified using staggered primers to provide sequence variability for the sequencing. The sets of staggered forward and reverse primers were designed to contain partial P5 and P7 adaptor sequences, respectively, at the 5’ and 2-5 random nucleotides (N) before the gene-specific sequence. The amplicons from the different regions of interest were gel-purified, quantified, and pooled together for library preparation. 4 libraries corresponding to control and IFNγ samples (BS/BS-OX) at day 5 were prepared for sequencing, and subsequent steps were completed following the MiSeq System protocol (MiSeq Reagent Kit v3, Illumina). Next Generation Sequencing was performed using MiSeq (300bp, single-end).

treatment_protocol: Reprogramming was induced in the presence or absence of IFNγ at 10 ng/ml (from day 0 to 5) (R&D Systems, 485-MI-100). SSEA1+ day 5 iPSCs were sorted with a BD FACSAria II SORP.

value: embryonic stem cell

value: hybrid 129S1/SvImJ, CAST/EiJ


title: Human NK stimulated with IPH6501 (24h), CMO

city: Marseille

first: Eric

last: Vivier

state: PACA

address: 117 Avenue de Luminy BP 30191

country: France

institute: Innate Pharma

description: 10 X Genomics

library_source: other

data_processing:
Droplet-based sequencing data were aligned using Cell Ranger (version 6.0.0) against a combination of the human (GRCh38) and mouse (mm10) reference genomes. Gene expression was quantified as well by Cell Ranger using gene annotations from GENCODE (release 32 for the human genome and M23 for the mouse one).
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files

molecule: other

source_name: NK cell

extract_protocol:
After incubation (4 hours or 24 hours), plates were washed in complete RPMI medium and  centrifuged 400g for 5 minutes at +5 ± 3°C. Cells were washed once with PBS + 1% BSA and centrifuged at 400g for 5 minutes at +5 ± 3°C. Samples from the same conditions of all 4 donors were individually stained with barcoded lipids from 3’ CellPlex kit Set A (10X Genomics, #1000261).
After pooling, samples from the same conditions of all 4 Healthy Donors  were individually stained with barcoded lipids from 3’ CellPlex kit Set A (10X Genomics, #1000261): cells were centrifuged at 400g for 5 minutes at +5 ± 3°C, and resuspended in either 100 µL of individual barcode from 3’ CellPlex kit Set A reagent (10X Genomics, #1000261).
Following recommendations of 10X Genomics, cells were resuspended in 50 µl PBS 1% BSA. Libraries were prepared with Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics). For each condition, 100 ng of Gene Expression Library were mixed with 25 ng of Cell Multiplexing Oligos Library.

treatment_protocol: Purified NK cells from four donors were co-incubated with huCD20B16-F10 cells at an Effector Target (ET) ratio of 10:1, with 100 000 NK cells for 10 000 huCD20B16-F10 cells per well, in a U-bottom 96 wells plate, for 4 or 24 hours at 37°C. Two conditions were tested: 1) Vehicle (US for Unstimulated), containing 100 000 NK cells, 10 000 huCD20B16-F10 cells, no antibody/molecule). 2) ANKET4, containing 100 000 NK cells, 10 000 huCD20B16-F10 cells, and ANKET4 (GA101-T5-3D9H1L1-IL2v) at a concentration of 0.1µg/ml.

value: NK cell

tag: library type

value: CMO

tag: cmo

value: 3’ CellPlex kit Set A  CMO 309 (donor 1), CMO 310 (donor 2), CMO311 (donor 3), CMO 312 (donor 4)


title: Unstimulated human NK (24h), CMO

description: 10 X Genomics

value: Unstimulated (24h)

value: 3’ CellPlex kit Set A CMO 309 (donor 1), CMO 310 (donor 2), CMO311 (donor 3), CMO 312 (donor 4)


title: IkE5_Treg_ATAC_rep2

tag: cell line


title: Human NK stimulated with IPH6501 (4h), CMO

description: 10 X Genomics

value: 3’ CellPlex kit Set A  CMO 305 (donor 1), CMO 306 (donor 2), CMO307 (donor 3), CMO 308 (donor 4)


title: Day 5 iPSC control_BS


title: Unstimulated human NK (4h), CMO

description: 10 X Genomics

value: Unstimulated (4h)

value: 3’ CellPlex kit Set A  CMO 301 (donor 1), CMO 302 (donor 2), CMO303 (donor 3), CMO 304 (donor 4)


title: Day 5 iPSC control_BS_OX