title: OPPERA_methylation 204873630131_R06C01

description:
OPPERA_methylation
204873630131_R06C01


title: OPPERA_methylation 204873630131_R01C01

status: Public on Apr 24 2024

type: genomic

city: Montreal

first: Luda

last: Diatchenko

state: Quebec

address: 3775 University Street

department: Faculty of Dental Medicine and Oral Health Sciences

country: Canada

institute: McGill University

description:
OPPERA_methylation
204873630131_R01C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented, precipitate, resuspensed and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing:
Genomestudio v2011
Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: OPPERAI

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from TMD samples using Qiagen Extraction Kit according to standard instructions

tag: gender

value: F

value: current

tag: sampleID

tag: group

value: TMD


title: OPPERA_methylation 204873630131_R02C01

description:
OPPERA_methylation
204873630131_R02C01

value: never


title: OPPERA_methylation 204873630131_R05C01

description:
OPPERA_methylation
204873630131_R05C01


title: OPPERA_methylation 204873630105_R01C01

description:
OPPERA_methylation
204873630105_R01C01

value: M


title: OPPERA_methylation 204873630105_R06C01

description:
OPPERA_methylation
204873630105_R06C01


title: OPPERA_methylation 204873630105_R03C01

description:
OPPERA_methylation
204873630105_R03C01

value: former

value: nonTMD


title: OPPERA_methylation 204873630105_R08C01

description:
OPPERA_methylation
204873630105_R08C01

source_name: OPPERAII


title: OPPERA_methylation 204873630132_R02C01

description:
OPPERA_methylation
204873630132_R02C01


title: OPPERA_methylation 204873630138_R05C01

description:
OPPERA_methylation
204873630138_R05C01


title: OPPERA_methylation 204855010028_R07C01

description:
OPPERA_methylation
204855010028_R07C01

value: sHC


title: OPPERA_methylation 204873630131_R07C01

description:
OPPERA_methylation
204873630131_R07C01


title: OPPERA_methylation 204873630105_R02C01

description:
OPPERA_methylation
204873630105_R02C01


title: OPPERA_methylation 204855010028_R04C01

description:
OPPERA_methylation
204855010028_R04C01


title: OPPERA_methylation 204855010028_R03C01

description:
OPPERA_methylation
204855010028_R03C01


title: OPPERA_methylation 204873630138_R06C01

description:
OPPERA_methylation
204873630138_R06C01


title: OPPERA_methylation 204873630105_R07C01

description:
OPPERA_methylation
204873630105_R07C01


title: OPPERA_methylation 204855010028_R06C01

description:
OPPERA_methylation
204855010028_R06C01


title: OPPERA_methylation 204873630105_R04C01

description:
OPPERA_methylation
204873630105_R04C01


title: OPPERA_methylation 204855010028_R02C01

description:
OPPERA_methylation
204855010028_R02C01


title: OPPERA_methylation 204855010028_R01C01

description:
OPPERA_methylation
204855010028_R01C01


title: OPPERA_methylation 204855010042_R07C01

description:
OPPERA_methylation
204855010042_R07C01


title: OPPERA_methylation 204855010042_R08C01

description:
OPPERA_methylation
204855010042_R08C01


title: OPPERA_methylation 204855010042_R03C01

description:
OPPERA_methylation
204855010042_R03C01


title: OPPERA_methylation 204873630105_R05C01

description:
OPPERA_methylation
204873630105_R05C01


title: OPPERA_methylation 204855010042_R04C01

description:
OPPERA_methylation
204855010042_R04C01


title: OPPERA_methylation 204855010042_R05C01

description:
OPPERA_methylation
204855010042_R05C01


title: OPPERA_methylation 204855010042_R06C01

description:
OPPERA_methylation
204855010042_R06C01


title: OPPERA_methylation 204855010042_R02C01

description:
OPPERA_methylation
204855010042_R02C01


title: OPPERA_methylation 204855010036_R07C01

description:
OPPERA_methylation
204855010036_R07C01


title: OPPERA_methylation 204855010042_R01C01

description:
OPPERA_methylation
204855010042_R01C01


title: OPPERA_methylation 204855010036_R04C01

description:
OPPERA_methylation
204855010036_R04C01


title: OPPERA_methylation 204855010036_R03C01

description:
OPPERA_methylation
204855010036_R03C01


title: OPPERA_methylation 204855010036_R08C01

description:
OPPERA_methylation
204855010036_R08C01


title: OPPERA_methylation 204855010036_R05C01

description:
OPPERA_methylation
204855010036_R05C01


title: OPPERA_methylation 204855010025_R08C01

description:
OPPERA_methylation
204855010025_R08C01


title: OPPERA_methylation 204855010036_R02C01

description:
OPPERA_methylation
204855010036_R02C01


title: OPPERA_methylation 204855010028_R05C01

description:
OPPERA_methylation
204855010028_R05C01


title: OPPERA_methylation 204855010036_R06C01

description:
OPPERA_methylation
204855010036_R06C01


title: OPPERA_methylation 204855010036_R01C01

description:
OPPERA_methylation
204855010036_R01C01


title: OPPERA_methylation 204855010025_R03C01

description:
OPPERA_methylation
204855010025_R03C01


title: OPPERA_methylation 204855010025_R07C01

description:
OPPERA_methylation
204855010025_R07C01


title: OPPERA_methylation 204855010025_R06C01

description:
OPPERA_methylation
204855010025_R06C01


title: OPPERA_methylation 204855010025_R04C01

description:
OPPERA_methylation
204855010025_R04C01


title: OPPERA_methylation 204855010025_R02C01

description:
OPPERA_methylation
204855010025_R02C01


title: OPPERA_methylation 204855010002_R04C01

description:
OPPERA_methylation
204855010002_R04C01


title: OPPERA_methylation 204855010025_R01C01

description:
OPPERA_methylation
204855010025_R01C01


title: OPPERA_methylation 204855010002_R07C01

description:
OPPERA_methylation
204855010002_R07C01


title: OPPERA_methylation 204855010002_R08C01

description:
OPPERA_methylation
204855010002_R08C01


title: OPPERA_methylation 204855010002_R03C01

description:
OPPERA_methylation
204855010002_R03C01


title: OPPERA_methylation 204855010002_R02C01

description:
OPPERA_methylation
204855010002_R02C01


title: OPPERA_methylation 204855010002_R06C01

description:
OPPERA_methylation
204855010002_R06C01


title: OPPERA_methylation 204855010002_R05C01

description:
OPPERA_methylation
204855010002_R05C01


title: OPPERA_methylation 204855010002_R01C01

description:
OPPERA_methylation
204855010002_R01C01


title: OPPERA_methylation 204855010003_R08C01

description:
OPPERA_methylation
204855010003_R08C01


title: OPPERA_methylation 204855010003_R07C01

description:
OPPERA_methylation
204855010003_R07C01


title: OPPERA_methylation 204855010003_R04C01

description:
OPPERA_methylation
204855010003_R04C01


title: OPPERA_methylation 204855010003_R06C01

description:
OPPERA_methylation
204855010003_R06C01


title: OPPERA_methylation 204855010003_R03C01

description:
OPPERA_methylation
204855010003_R03C01


title: OPPERA_methylation 204855010025_R05C01

description:
OPPERA_methylation
204855010025_R05C01


title: OPPERA_methylation 204855010003_R02C01

description:
OPPERA_methylation
204855010003_R02C01


title: OPPERA_methylation 204855010003_R05C01

description:
OPPERA_methylation
204855010003_R05C01


title: OPPERA_methylation 204855010072_R04C01

description:
OPPERA_methylation
204855010072_R04C01


title: OPPERA_methylation 204855010072_R03C01

description:
OPPERA_methylation
204855010072_R03C01


title: OPPERA_methylation 204855010003_R01C01

description:
OPPERA_methylation
204855010003_R01C01


title: OPPERA_methylation 204855010072_R07C01

description:
OPPERA_methylation
204855010072_R07C01


title: OPPERA_methylation 204855010072_R06C01

description:
OPPERA_methylation
204855010072_R06C01


title: OPPERA_methylation 204855010072_R08C01

description:
OPPERA_methylation
204855010072_R08C01


title: OPPERA_methylation 204855010072_R05C01

description:
OPPERA_methylation
204855010072_R05C01


title: OPPERA_methylation 204855010045_R07C01

description:
OPPERA_methylation
204855010045_R07C01


title: OPPERA_methylation 204855010072_R02C01

description:
OPPERA_methylation
204855010072_R02C01


title: OPPERA_methylation 204855010072_R01C01

description:
OPPERA_methylation
204855010072_R01C01


title: OPPERA_methylation 204855010045_R03C01

description:
OPPERA_methylation
204855010045_R03C01


title: OPPERA_methylation 204855010045_R05C01

description:
OPPERA_methylation
204855010045_R05C01


title: OPPERA_methylation 204855010045_R04C01

description:
OPPERA_methylation
204855010045_R04C01


title: OPPERA_methylation 204855010045_R02C01

description:
OPPERA_methylation
204855010045_R02C01


title: OPPERA_methylation 204855010045_R08C01

description:
OPPERA_methylation
204855010045_R08C01


title: OPPERA_methylation 204873630123_R07C01

description:
OPPERA_methylation
204873630123_R07C01


title: OPPERA_methylation 204873630123_R03C01

description:
OPPERA_methylation
204873630123_R03C01


title: OPPERA_methylation 204873630123_R04C01

description:
OPPERA_methylation
204873630123_R04C01


title: OPPERA_methylation 204873630123_R08C01

description:
OPPERA_methylation
204873630123_R08C01


title: OPPERA_methylation 204855010045_R01C01

description:
OPPERA_methylation
204855010045_R01C01


title: OPPERA_methylation 204873630123_R06C01

description:
OPPERA_methylation
204873630123_R06C01


title: OPPERA_methylation 204873630123_R05C01

description:
OPPERA_methylation
204873630123_R05C01


title: OPPERA_methylation 204873630123_R01C01

description:
OPPERA_methylation
204873630123_R01C01


title: OPPERA_methylation 204873630094_R07C01

description:
OPPERA_methylation
204873630094_R07C01


title: OPPERA_methylation 204873630094_R04C01

description:
OPPERA_methylation
204873630094_R04C01


title: OPPERA_methylation 204873630094_R08C01

description:
OPPERA_methylation
204873630094_R08C01


title: OPPERA_methylation 204873630094_R06C01

description:
OPPERA_methylation
204873630094_R06C01


title: OPPERA_methylation 204873630094_R03C01

description:
OPPERA_methylation
204873630094_R03C01


title: OPPERA_methylation 204873630094_R01C01

description:
OPPERA_methylation
204873630094_R01C01


title: OPPERA_methylation 204873630094_R05C01

description:
OPPERA_methylation
204873630094_R05C01


title: OPPERA_methylation 204873630111_R08C01

description:
OPPERA_methylation
204873630111_R08C01


title: OPPERA_methylation 204873630094_R02C01

description:
OPPERA_methylation
204873630094_R02C01


title: OPPERA_methylation 204855010045_R06C01

description:
OPPERA_methylation
204855010045_R06C01


title: OPPERA_methylation 204873630111_R06C01

description:
OPPERA_methylation
204873630111_R06C01


title: OPPERA_methylation 204873630111_R05C01

description:
OPPERA_methylation
204873630111_R05C01


title: OPPERA_methylation 204873630111_R04C01

description:
OPPERA_methylation
204873630111_R04C01


title: OPPERA_methylation 204873630111_R07C01

description:
OPPERA_methylation
204873630111_R07C01


title: OPPERA_methylation 204873630111_R01C01

description:
OPPERA_methylation
204873630111_R01C01


title: OPPERA_methylation 204873630111_R02C01

description:
OPPERA_methylation
204873630111_R02C01


title: OPPERA_methylation 204873630126_R07C01

description:
OPPERA_methylation
204873630126_R07C01


title: OPPERA_methylation 204873630126_R05C01

description:
OPPERA_methylation
204873630126_R05C01


title: OPPERA_methylation 204873630126_R06C01

description:
OPPERA_methylation
204873630126_R06C01


title: OPPERA_methylation 204873630123_R02C01

description:
OPPERA_methylation
204873630123_R02C01


title: OPPERA_methylation 204873630126_R08C01

description:
OPPERA_methylation
204873630126_R08C01


title: OPPERA_methylation 204873630126_R04C01

description:
OPPERA_methylation
204873630126_R04C01


title: OPPERA_methylation 204873630126_R03C01

description:
OPPERA_methylation
204873630126_R03C01


title: OPPERA_methylation 204867380144_R04C01

description:
OPPERA_methylation
204867380144_R04C01


title: OPPERA_methylation 204867380144_R07C01

description:
OPPERA_methylation
204867380144_R07C01


title: OPPERA_methylation 204867380144_R03C01

description:
OPPERA_methylation
204867380144_R03C01


title: OPPERA_methylation 204867380144_R06C01

description:
OPPERA_methylation
204867380144_R06C01


title: OPPERA_methylation 204867380144_R01C01

description:
OPPERA_methylation
204867380144_R01C01


title: OPPERA_methylation 204867380144_R02C01

description:
OPPERA_methylation
204867380144_R02C01


title: OPPERA_methylation 204867380144_R05C01

description:
OPPERA_methylation
204867380144_R05C01


title: OPPERA_methylation 204873630111_R03C01

description:
OPPERA_methylation
204873630111_R03C01


title: OPPERA_methylation 204867380180_R07C01

description:
OPPERA_methylation
204867380180_R07C01


title: OPPERA_methylation 204867380180_R08C01

description:
OPPERA_methylation
204867380180_R08C01


title: OPPERA_methylation 204867380180_R06C01

description:
OPPERA_methylation
204867380180_R06C01


title: OPPERA_methylation 204867380180_R04C01

description:
OPPERA_methylation
204867380180_R04C01


title: OPPERA_methylation 204867380180_R05C01

description:
OPPERA_methylation
204867380180_R05C01


title: OPPERA_methylation 204867380180_R02C01

description:
OPPERA_methylation
204867380180_R02C01


title: OPPERA_methylation 204867380171_R08C01

description:
OPPERA_methylation
204867380171_R08C01


title: OPPERA_methylation 204867380180_R01C01

description:
OPPERA_methylation
204867380180_R01C01


title: OPPERA_methylation 204867380171_R07C01

description:
OPPERA_methylation
204867380171_R07C01


title: OPPERA_methylation 204873630126_R02C01

description:
OPPERA_methylation
204873630126_R02C01


title: OPPERA_methylation 204867380171_R04C01

description:
OPPERA_methylation
204867380171_R04C01


title: OPPERA_methylation 204873630126_R01C01

description:
OPPERA_methylation
204873630126_R01C01


title: OPPERA_methylation 204867380171_R03C01

description:
OPPERA_methylation
204867380171_R03C01


title: OPPERA_methylation 204867380171_R06C01

description:
OPPERA_methylation
204867380171_R06C01


title: OPPERA_methylation 204867380171_R02C01

description:
OPPERA_methylation
204867380171_R02C01


title: OPPERA_methylation 204867380171_R01C01

description:
OPPERA_methylation
204867380171_R01C01


title: OPPERA_methylation 204867380139_R07C01

description:
OPPERA_methylation
204867380139_R07C01


title: OPPERA_methylation 204867380139_R03C01

description:
OPPERA_methylation
204867380139_R03C01


title: OPPERA_methylation 204867380139_R05C01

description:
OPPERA_methylation
204867380139_R05C01


title: OPPERA_methylation 204867380139_R06C01

description:
OPPERA_methylation
204867380139_R06C01


title: OPPERA_methylation 204867380139_R08C01

description:
OPPERA_methylation
204867380139_R08C01


title: OPPERA_methylation 204867380139_R04C01

description:
OPPERA_methylation
204867380139_R04C01


title: OPPERA_methylation 204867380139_R02C01

description:
OPPERA_methylation
204867380139_R02C01


title: OPPERA_methylation 204867380139_R01C01

description:
OPPERA_methylation
204867380139_R01C01


title: OPPERA_methylation 204873630049_R03C01

description:
OPPERA_methylation
204873630049_R03C01


title: OPPERA_methylation 204873630049_R06C01

description:
OPPERA_methylation
204873630049_R06C01


title: OPPERA_methylation 204867380180_R03C01

description:
OPPERA_methylation
204867380180_R03C01


title: OPPERA_methylation 204873630049_R08C01

description:
OPPERA_methylation
204873630049_R08C01


title: OPPERA_methylation 204873630049_R01C01

description:
OPPERA_methylation
204873630049_R01C01


title: OPPERA_methylation 204873630069_R07C01

description:
OPPERA_methylation
204873630069_R07C01


title: OPPERA_methylation 204873630049_R02C01

description:
OPPERA_methylation
204873630049_R02C01


title: OPPERA_methylation 204873630049_R05C01

description:
OPPERA_methylation
204873630049_R05C01


title: OPPERA_methylation 204867380171_R05C01

description:
OPPERA_methylation
204867380171_R05C01


title: OPPERA_methylation 204873630069_R04C01

description:
OPPERA_methylation
204873630069_R04C01


title: OPPERA_methylation 204873630069_R06C01

description:
OPPERA_methylation
204873630069_R06C01


title: OPPERA_methylation 204873630069_R02C01

description:
OPPERA_methylation
204873630069_R02C01


title: OPPERA_methylation 204873630069_R03C01

description:
OPPERA_methylation
204873630069_R03C01


title: OPPERA_methylation 204873630069_R01C01

description:
OPPERA_methylation
204873630069_R01C01


title: OPPERA_methylation 204873630069_R05C01

description:
OPPERA_methylation
204873630069_R05C01


title: OPPERA_methylation 204873630062_R08C01

description:
OPPERA_methylation
204873630062_R08C01


title: OPPERA_methylation 204873630062_R07C01

description:
OPPERA_methylation
204873630062_R07C01


title: OPPERA_methylation 204873630062_R04C01

description:
OPPERA_methylation
204873630062_R04C01


title: OPPERA_methylation 204873630062_R05C01

description:
OPPERA_methylation
204873630062_R05C01


title: OPPERA_methylation 204873630062_R01C01

description:
OPPERA_methylation
204873630062_R01C01


title: OPPERA_methylation 204873630008_R08C01

description:
OPPERA_methylation
204873630008_R08C01


title: OPPERA_methylation 204873630008_R07C01

description:
OPPERA_methylation
204873630008_R07C01


title: OPPERA_methylation 204873630062_R02C01

description:
OPPERA_methylation
204873630062_R02C01


title: OPPERA_methylation 204873630062_R06C01

description:
OPPERA_methylation
204873630062_R06C01


title: OPPERA_methylation 204873630008_R04C01

description:
OPPERA_methylation
204873630008_R04C01


title: OPPERA_methylation 204873630008_R03C01

description:
OPPERA_methylation
204873630008_R03C01


title: OPPERA_methylation 204873630069_R08C01

description:
OPPERA_methylation
204873630069_R08C01


title: OPPERA_methylation 204873630008_R06C01

description:
OPPERA_methylation
204873630008_R06C01


title: OPPERA_methylation 204873630008_R01C01

description:
OPPERA_methylation
204873630008_R01C01


title: OPPERA_methylation 204867380158_R08C01

description:
OPPERA_methylation
204867380158_R08C01


title: OPPERA_methylation 204873630008_R05C01

description:
OPPERA_methylation
204873630008_R05C01


title: OPPERA_methylation 204873630049_R07C01

description:
OPPERA_methylation
204873630049_R07C01


title: OPPERA_methylation 204873630008_R02C01

description:
OPPERA_methylation
204873630008_R02C01


title: OPPERA_methylation 204867380158_R07C01

description:
OPPERA_methylation
204867380158_R07C01


title: OPPERA_methylation 204867380158_R04C01

description:
OPPERA_methylation
204867380158_R04C01


title: OPPERA_methylation 204867380158_R06C01

description:
OPPERA_methylation
204867380158_R06C01


title: OPPERA_methylation 204867380153_R08C01

description:
OPPERA_methylation
204867380153_R08C01


title: OPPERA_methylation 204867380158_R05C01

description:
OPPERA_methylation
204867380158_R05C01


title: OPPERA_methylation 204867380158_R01C01

description:
OPPERA_methylation
204867380158_R01C01


title: OPPERA_methylation 204873630062_R03C01

description:
OPPERA_methylation
204873630062_R03C01


title: OPPERA_methylation 204867380153_R07C01

description:
OPPERA_methylation
204867380153_R07C01


title: OPPERA_methylation 204867380153_R04C01

description:
OPPERA_methylation
204867380153_R04C01


title: OPPERA_methylation 204867380153_R05C01

description:
OPPERA_methylation
204867380153_R05C01


title: OPPERA_methylation 204867380153_R03C01

description:
OPPERA_methylation
204867380153_R03C01


title: OPPERA_methylation 204867380153_R02C01

description:
OPPERA_methylation
204867380153_R02C01


title: OPPERA_methylation 204867380159_R07C01

description:
OPPERA_methylation
204867380159_R07C01


title: OPPERA_methylation 204867380159_R03C01

description:
OPPERA_methylation
204867380159_R03C01


title: OPPERA_methylation 204867380159_R04C01

description:
OPPERA_methylation
204867380159_R04C01


title: OPPERA_methylation 204867380159_R06C01

description:
OPPERA_methylation
204867380159_R06C01


title: OPPERA_methylation 204867380159_R08C01

description:
OPPERA_methylation
204867380159_R08C01


title: OPPERA_methylation 204867380153_R01C01

description:
OPPERA_methylation
204867380153_R01C01


title: OPPERA_methylation 204867380159_R02C01

description:
OPPERA_methylation
204867380159_R02C01


title: OPPERA_methylation 204867380159_R05C01

description:
OPPERA_methylation
204867380159_R05C01


title: OPPERA_methylation 204873630127_R08C01

description:
OPPERA_methylation
204873630127_R08C01


title: OPPERA_methylation 204867380159_R01C01

description:
OPPERA_methylation
204867380159_R01C01


title: OPPERA_methylation 204873630127_R07C01

description:
OPPERA_methylation
204873630127_R07C01


title: OPPERA_methylation 204873630127_R04C01

description:
OPPERA_methylation
204873630127_R04C01


title: OPPERA_methylation 204873630127_R03C01

description:
OPPERA_methylation
204873630127_R03C01


title: OPPERA_methylation 204867380158_R02C01

description:
OPPERA_methylation
204867380158_R02C01


title: OPPERA_methylation 204867380158_R03C01

description:
OPPERA_methylation
204867380158_R03C01


title: OPPERA_methylation 204873630127_R06C01

description:
OPPERA_methylation
204873630127_R06C01


title: OPPERA_methylation 204873630127_R02C01

description:
OPPERA_methylation
204873630127_R02C01


title: OPPERA_methylation 204873630127_R05C01

description:
OPPERA_methylation
204873630127_R05C01


title: OPPERA_methylation 204873630127_R01C01

description:
OPPERA_methylation
204873630127_R01C01


title: OPPERA_methylation 204854830135_R05C01

description:
OPPERA_methylation
204854830135_R05C01


title: OPPERA_methylation 204854830135_R06C01

description:
OPPERA_methylation
204854830135_R06C01


title: OPPERA_methylation 204867380153_R06C01

description:
OPPERA_methylation
204867380153_R06C01


title: OPPERA_methylation 204854830135_R04C01

description:
OPPERA_methylation
204854830135_R04C01


title: OPPERA_methylation 204854830135_R07C01

description:
OPPERA_methylation
204854830135_R07C01


title: OPPERA_methylation 204873630049_R04C01

description:
OPPERA_methylation
204873630049_R04C01


title: OPPERA_methylation 204854830135_R02C01

description:
OPPERA_methylation
204854830135_R02C01


title: OPPERA_methylation 204854830135_R03C01

description:
OPPERA_methylation
204854830135_R03C01


title: OPPERA_methylation 204854830135_R01C01

description:
OPPERA_methylation
204854830135_R01C01


title: OPPERA_methylation 204854830044_R08C01

description:
OPPERA_methylation
204854830044_R08C01


title: OPPERA_methylation 204854830044_R07C01

description:
OPPERA_methylation
204854830044_R07C01


title: OPPERA_methylation 204854830044_R02C01

description:
OPPERA_methylation
204854830044_R02C01


title: OPPERA_methylation 204854830044_R06C01

description:
OPPERA_methylation
204854830044_R06C01


title: OPPERA_methylation 204854830132_R08C01

description:
OPPERA_methylation
204854830132_R08C01


title: OPPERA_methylation 204854830044_R01C01

description:
OPPERA_methylation
204854830044_R01C01


title: OPPERA_methylation 204854830044_R03C01

description:
OPPERA_methylation
204854830044_R03C01


title: OPPERA_methylation 204854830132_R07C01

description:
OPPERA_methylation
204854830132_R07C01


title: OPPERA_methylation 204854830132_R03C01

description:
OPPERA_methylation
204854830132_R03C01


title: OPPERA_methylation 204854830132_R06C01

description:
OPPERA_methylation
204854830132_R06C01


title: OPPERA_methylation 204854830132_R05C01

description:
OPPERA_methylation
204854830132_R05C01


title: OPPERA_methylation 204854830086_R08C01

description:
OPPERA_methylation
204854830086_R08C01


title: OPPERA_methylation 204854830132_R02C01

description:
OPPERA_methylation
204854830132_R02C01


title: OPPERA_methylation 204854830132_R01C01

description:
OPPERA_methylation
204854830132_R01C01


title: OPPERA_methylation 204854830086_R07C01

description:
OPPERA_methylation
204854830086_R07C01


title: OPPERA_methylation 204854830086_R03C01

description:
OPPERA_methylation
204854830086_R03C01


title: OPPERA_methylation 204854830086_R04C01

description:
OPPERA_methylation
204854830086_R04C01


title: OPPERA_methylation 204854830086_R02C01

description:
OPPERA_methylation
204854830086_R02C01


title: OPPERA_methylation 204854830086_R01C01

description:
OPPERA_methylation
204854830086_R01C01


title: OPPERA_methylation 204867380124_R08C01

description:
OPPERA_methylation
204867380124_R08C01


title: OPPERA_methylation 204854830086_R06C01

description:
OPPERA_methylation
204854830086_R06C01


title: OPPERA_methylation 204867380124_R07C01

description:
OPPERA_methylation
204867380124_R07C01


title: OPPERA_methylation 204867380124_R04C01

description:
OPPERA_methylation
204867380124_R04C01


title: OPPERA_methylation 204854830086_R05C01

description:
OPPERA_methylation
204854830086_R05C01


title: OPPERA_methylation 204867380124_R03C01

description:
OPPERA_methylation
204867380124_R03C01


title: OPPERA_methylation 204854830044_R04C01

description:
OPPERA_methylation
204854830044_R04C01


title: OPPERA_methylation 204867380124_R05C01

description:
OPPERA_methylation
204867380124_R05C01


title: OPPERA_methylation 204867380124_R06C01

description:
OPPERA_methylation
204867380124_R06C01


title: OPPERA_methylation 204854830044_R05C01

description:
OPPERA_methylation
204854830044_R05C01


title: OPPERA_methylation 204867380124_R01C01

description:
OPPERA_methylation
204867380124_R01C01


title: OPPERA_methylation 204867380124_R02C01

description:
OPPERA_methylation
204867380124_R02C01


title: OPPERA_methylation 204867380114_R08C01

description:
OPPERA_methylation
204867380114_R08C01


title: OPPERA_methylation 204867380114_R03C01

description:
OPPERA_methylation
204867380114_R03C01


title: OPPERA_methylation 204854830132_R04C01

description:
OPPERA_methylation
204854830132_R04C01


title: OPPERA_methylation 204867380114_R04C01

description:
OPPERA_methylation
204867380114_R04C01


title: OPPERA_methylation 204867380114_R06C01

description:
OPPERA_methylation
204867380114_R06C01


title: OPPERA_methylation 204867380114_R02C01

description:
OPPERA_methylation
204867380114_R02C01


title: OPPERA_methylation 204867380131_R08C01

description:
OPPERA_methylation
204867380131_R08C01


title: OPPERA_methylation 204867380131_R07C01

description:
OPPERA_methylation
204867380131_R07C01


title: OPPERA_methylation 204867380131_R06C01

description:
OPPERA_methylation
204867380131_R06C01


title: OPPERA_methylation 204867380131_R03C01

description:
OPPERA_methylation
204867380131_R03C01


title: OPPERA_methylation 204867380131_R05C01

description:
OPPERA_methylation
204867380131_R05C01


title: OPPERA_methylation 204867380131_R01C01

description:
OPPERA_methylation
204867380131_R01C01


title: OPPERA_methylation 204873630005_R08C01

description:
OPPERA_methylation
204873630005_R08C01


title: OPPERA_methylation 204873630005_R07C01

description:
OPPERA_methylation
204873630005_R07C01


title: OPPERA_methylation 204873630005_R04C01

description:
OPPERA_methylation
204873630005_R04C01


title: OPPERA_methylation 204873630005_R05C01

description:
OPPERA_methylation
204873630005_R05C01


title: OPPERA_methylation 204873630005_R02C01

description:
OPPERA_methylation
204873630005_R02C01


title: OPPERA_methylation 204873630005_R01C01

description:
OPPERA_methylation
204873630005_R01C01


title: OPPERA_methylation 204867380114_R07C01

description:
OPPERA_methylation
204867380114_R07C01


title: OPPERA_methylation 204867380161_R07C01

description:
OPPERA_methylation
204867380161_R07C01


title: OPPERA_methylation 204867380161_R04C01

description:
OPPERA_methylation
204867380161_R04C01


title: OPPERA_methylation 204867380161_R03C01

description:
OPPERA_methylation
204867380161_R03C01


title: OPPERA_methylation 204867380114_R05C01

description:
OPPERA_methylation
204867380114_R05C01


title: OPPERA_methylation 204867380161_R06C01

description:
OPPERA_methylation
204867380161_R06C01


title: OPPERA_methylation 204867380161_R05C01

description:
OPPERA_methylation
204867380161_R05C01


title: OPPERA_methylation 204867380163_R08C01

description:
OPPERA_methylation
204867380163_R08C01


title: OPPERA_methylation 204867380161_R01C01

description:
OPPERA_methylation
204867380161_R01C01


title: OPPERA_methylation 204867380114_R01C01

description:
OPPERA_methylation
204867380114_R01C01


title: OPPERA_methylation 204867380161_R02C01

description:
OPPERA_methylation
204867380161_R02C01


title: OPPERA_methylation 204867380163_R04C01

description:
OPPERA_methylation
204867380163_R04C01


title: OPPERA_methylation 204867380163_R06C01

description:
OPPERA_methylation
204867380163_R06C01


title: OPPERA_methylation 204867380131_R02C01

description:
OPPERA_methylation
204867380131_R02C01


title: OPPERA_methylation 204867380131_R04C01

description:
OPPERA_methylation
204867380131_R04C01


title: OPPERA_methylation 204873630005_R03C01

description:
OPPERA_methylation
204873630005_R03C01


title: OPPERA_methylation 204867380163_R05C01

description:
OPPERA_methylation
204867380163_R05C01


title: OPPERA_methylation 204867380163_R02C01

description:
OPPERA_methylation
204867380163_R02C01


title: OPPERA_methylation 204867380163_R01C01

description:
OPPERA_methylation
204867380163_R01C01


title: OPPERA_methylation 204873630005_R06C01

description:
OPPERA_methylation
204873630005_R06C01


title: OPPERA_methylation 204867380142_R07C01

description:
OPPERA_methylation
204867380142_R07C01


title: OPPERA_methylation 204867380142_R08C01

description:
OPPERA_methylation
204867380142_R08C01


title: OPPERA_methylation 204867380142_R04C01

description:
OPPERA_methylation
204867380142_R04C01


title: OPPERA_methylation 204867380161_R08C01

description:
OPPERA_methylation
204867380161_R08C01


title: OPPERA_methylation 204867380142_R05C01

description:
OPPERA_methylation
204867380142_R05C01


title: OPPERA_methylation 204867380142_R06C01

description:
OPPERA_methylation
204867380142_R06C01


title: OPPERA_methylation 204867380142_R03C01

description:
OPPERA_methylation
204867380142_R03C01


title: OPPERA_methylation 204867380142_R02C01

description:
OPPERA_methylation
204867380142_R02C01


title: OPPERA_methylation 204867380142_R01C01

description:
OPPERA_methylation
204867380142_R01C01


title: OPPERA_methylation 204867380169_R08C01

description:
OPPERA_methylation
204867380169_R08C01


title: OPPERA_methylation 204867380169_R03C01

description:
OPPERA_methylation
204867380169_R03C01


title: OPPERA_methylation 204867380169_R07C01

description:
OPPERA_methylation
204867380169_R07C01


title: OPPERA_methylation 204867380163_R07C01

description:
OPPERA_methylation
204867380163_R07C01


title: OPPERA_methylation 204867380169_R06C01

description:
OPPERA_methylation
204867380169_R06C01


title: OPPERA_methylation 204867380169_R05C01

description:
OPPERA_methylation
204867380169_R05C01


title: OPPERA_methylation 205090800026_R07C01

description:
OPPERA_methylation
205090800026_R07C01


title: OPPERA_methylation 204867380169_R02C01

description:
OPPERA_methylation
204867380169_R02C01


title: OPPERA_methylation 204867380163_R03C01

description:
OPPERA_methylation
204867380163_R03C01


title: OPPERA_methylation 204867380169_R01C01

description:
OPPERA_methylation
204867380169_R01C01


title: OPPERA_methylation 205090800026_R04C01

description:
OPPERA_methylation
205090800026_R04C01


title: OPPERA_methylation 205090800026_R03C01

description:
OPPERA_methylation
205090800026_R03C01


title: OPPERA_methylation 205090800026_R05C01

description:
OPPERA_methylation
205090800026_R05C01


title: OPPERA_methylation 205090800026_R02C01

description:
OPPERA_methylation
205090800026_R02C01


title: OPPERA_methylation 205090800032_R04C01

description:
OPPERA_methylation
205090800032_R04C01


title: OPPERA_methylation 205090800032_R08C01

description:
OPPERA_methylation
205090800032_R08C01


title: OPPERA_methylation 205090800032_R07C01

description:
OPPERA_methylation
205090800032_R07C01


title: OPPERA_methylation 205090800032_R05C01

description:
OPPERA_methylation
205090800032_R05C01


title: OPPERA_methylation 205090800032_R03C01

description:
OPPERA_methylation
205090800032_R03C01


title: OPPERA_methylation 205090800032_R01C01

description:
OPPERA_methylation
205090800032_R01C01


title: OPPERA_methylation 205090800032_R06C01

description:
OPPERA_methylation
205090800032_R06C01


title: OPPERA_methylation 205090800026_R01C01

description:
OPPERA_methylation
205090800026_R01C01


title: OPPERA_methylation 205090800061_R08C01

description:
OPPERA_methylation
205090800061_R08C01


title: OPPERA_methylation 205090800061_R04C01

description:
OPPERA_methylation
205090800061_R04C01


title: OPPERA_methylation 205090800026_R06C01

description:
OPPERA_methylation
205090800026_R06C01


title: OPPERA_methylation 205090800061_R03C01

description:
OPPERA_methylation
205090800061_R03C01


title: OPPERA_methylation 205090800061_R06C01

description:
OPPERA_methylation
205090800061_R06C01


title: OPPERA_methylation 205090800061_R07C01

description:
OPPERA_methylation
205090800061_R07C01


title: OPPERA_methylation 204867380169_R04C01

description:
OPPERA_methylation
204867380169_R04C01


title: OPPERA_methylation 205090800061_R05C01

description:
OPPERA_methylation
205090800061_R05C01


title: OPPERA_methylation 205090800061_R02C01

description:
OPPERA_methylation
205090800061_R02C01


title: OPPERA_methylation 205089030104_R08C01

description:
OPPERA_methylation
205089030104_R08C01


title: OPPERA_methylation 205089030104_R04C01

description:
OPPERA_methylation
205089030104_R04C01


title: OPPERA_methylation 205090800061_R01C01

description:
OPPERA_methylation
205090800061_R01C01


title: OPPERA_methylation 205089030104_R03C01

description:
OPPERA_methylation
205089030104_R03C01


title: OPPERA_methylation 205089030104_R06C01

description:
OPPERA_methylation
205089030104_R06C01


title: OPPERA_methylation 205089030104_R02C01

description:
OPPERA_methylation
205089030104_R02C01


title: OPPERA_methylation 205089030104_R05C01

description:
OPPERA_methylation
205089030104_R05C01


title: OPPERA_methylation 205103220153_R08C01

description:
OPPERA_methylation
205103220153_R08C01


title: OPPERA_methylation 205103220153_R07C01

description:
OPPERA_methylation
205103220153_R07C01


title: OPPERA_methylation 205090800032_R02C01

description:
OPPERA_methylation
205090800032_R02C01


title: OPPERA_methylation 205103220153_R03C01

description:
OPPERA_methylation
205103220153_R03C01


title: OPPERA_methylation 205103220105_R08C01

description:
OPPERA_methylation
205103220105_R08C01


title: OPPERA_methylation 205103220153_R01C01

description:
OPPERA_methylation
205103220153_R01C01


title: OPPERA_methylation 205103220161_R07C01

description:
OPPERA_methylation
205103220161_R07C01


title: OPPERA_methylation 205103220153_R06C01

description:
OPPERA_methylation
205103220153_R06C01


title: OPPERA_methylation 205103220105_R02C01

description:
OPPERA_methylation
205103220105_R02C01


title: OPPERA_methylation 205103220153_R04C01

description:
OPPERA_methylation
205103220153_R04C01


title: OPPERA_methylation 205103220105_R04C01

description:
OPPERA_methylation
205103220105_R04C01


title: OPPERA_methylation 205103220153_R05C01

description:
OPPERA_methylation
205103220153_R05C01


title: OPPERA_methylation 205103220105_R06C01

description:
OPPERA_methylation
205103220105_R06C01


title: OPPERA_methylation 205103220105_R03C01

description:
OPPERA_methylation
205103220105_R03C01


title: OPPERA_methylation 205103220153_R02C01

description:
OPPERA_methylation
205103220153_R02C01


title: OPPERA_methylation 205103220161_R08C01

description:
OPPERA_methylation
205103220161_R08C01


title: OPPERA_methylation 205103220105_R01C01

description:
OPPERA_methylation
205103220105_R01C01


title: OPPERA_methylation 205103220161_R06C01

description:
OPPERA_methylation
205103220161_R06C01


title: OPPERA_methylation 205103220105_R05C01

description:
OPPERA_methylation
205103220105_R05C01


title: OPPERA_methylation 205103220105_R07C01

description:
OPPERA_methylation
205103220105_R07C01


title: OPPERA_methylation 205103220161_R01C01

description:
OPPERA_methylation
205103220161_R01C01


title: OPPERA_methylation 205103220161_R05C01

description:
OPPERA_methylation
205103220161_R05C01


title: OPPERA_methylation 205103220135_R04C01

description:
OPPERA_methylation
205103220135_R04C01


title: OPPERA_methylation 205103220161_R03C01

description:
OPPERA_methylation
205103220161_R03C01


title: OPPERA_methylation 205103220161_R02C01

description:
OPPERA_methylation
205103220161_R02C01


title: OPPERA_methylation 205089030104_R01C01

description:
OPPERA_methylation
205089030104_R01C01


title: OPPERA_methylation 205103220135_R03C01

description:
OPPERA_methylation
205103220135_R03C01


title: OPPERA_methylation 205103220135_R08C01

description:
OPPERA_methylation
205103220135_R08C01


title: OPPERA_methylation 205103220135_R06C01

description:
OPPERA_methylation
205103220135_R06C01


title: OPPERA_methylation 205089030104_R07C01

description:
OPPERA_methylation
205089030104_R07C01


title: OPPERA_methylation 205103220135_R07C01

description:
OPPERA_methylation
205103220135_R07C01


title: OPPERA_methylation 205103220161_R04C01

description:
OPPERA_methylation
205103220161_R04C01


title: OPPERA_methylation 204873630108_R08C01

description:
OPPERA_methylation
204873630108_R08C01


title: OPPERA_methylation 205103220135_R01C01

description:
OPPERA_methylation
205103220135_R01C01


title: OPPERA_methylation 205103220135_R05C01

description:
OPPERA_methylation
205103220135_R05C01


title: OPPERA_methylation 204873630108_R03C01

description:
OPPERA_methylation
204873630108_R03C01


title: OPPERA_methylation 204873630108_R06C01

description:
OPPERA_methylation
204873630108_R06C01


title: OPPERA_methylation 204873630108_R07C01

description:
OPPERA_methylation
204873630108_R07C01


title: OPPERA_methylation 204873630074_R05C01

description:
OPPERA_methylation
204873630074_R05C01


title: OPPERA_methylation 204873630108_R01C01

description:
OPPERA_methylation
204873630108_R01C01


title: OPPERA_methylation 205103220135_R02C01

description:
OPPERA_methylation
205103220135_R02C01


title: OPPERA_methylation 204873630108_R05C01

description:
OPPERA_methylation
204873630108_R05C01


title: OPPERA_methylation 204873630108_R04C01

description:
OPPERA_methylation
204873630108_R04C01


title: OPPERA_methylation 204873630074_R04C01

description:
OPPERA_methylation
204873630074_R04C01


title: OPPERA_methylation 204873630107_R08C01

description:
OPPERA_methylation
204873630107_R08C01


title: OPPERA_methylation 204873630074_R02C01

description:
OPPERA_methylation
204873630074_R02C01


title: OPPERA_methylation 204873630074_R03C01

description:
OPPERA_methylation
204873630074_R03C01


title: OPPERA_methylation 204873630074_R07C01

description:
OPPERA_methylation
204873630074_R07C01


title: OPPERA_methylation 204873630108_R02C01

description:
OPPERA_methylation
204873630108_R02C01


title: OPPERA_methylation 204873630074_R08C01

description:
OPPERA_methylation
204873630074_R08C01


title: OPPERA_methylation 204873630107_R07C01

description:
OPPERA_methylation
204873630107_R07C01


title: OPPERA_methylation 204873630107_R02C01

description:
OPPERA_methylation
204873630107_R02C01


title: OPPERA_methylation 204873630107_R05C01

description:
OPPERA_methylation
204873630107_R05C01


title: OPPERA_methylation 204873630100_R08C01

description:
OPPERA_methylation
204873630100_R08C01


title: OPPERA_methylation 204873630107_R03C01

description:
OPPERA_methylation
204873630107_R03C01


title: OPPERA_methylation 204873630107_R06C01

description:
OPPERA_methylation
204873630107_R06C01


title: OPPERA_methylation 204873630074_R06C01

description:
OPPERA_methylation
204873630074_R06C01


title: OPPERA_methylation 204873630074_R01C01

description:
OPPERA_methylation
204873630074_R01C01


title: OPPERA_methylation 204873630107_R04C01

description:
OPPERA_methylation
204873630107_R04C01


title: OPPERA_methylation 204873630107_R01C01

description:
OPPERA_methylation
204873630107_R01C01


title: OPPERA_methylation 204873630100_R07C01

description:
OPPERA_methylation
204873630100_R07C01


title: OPPERA_methylation 204873630100_R04C01

description:
OPPERA_methylation
204873630100_R04C01


title: OPPERA_methylation 204873630100_R03C01

description:
OPPERA_methylation
204873630100_R03C01


title: OPPERA_methylation 204873630100_R05C01

description:
OPPERA_methylation
204873630100_R05C01


title: OPPERA_methylation 204873630100_R02C01

description:
OPPERA_methylation
204873630100_R02C01


title: OPPERA_methylation 204873630100_R01C01

description:
OPPERA_methylation
204873630100_R01C01


title: OPPERA_methylation 204873630100_R06C01

description:
OPPERA_methylation
204873630100_R06C01


title: Arabidopsis, Mock, 8 hours, rep 1

type: SRA

city: Helsinki

first: Xixi

last: Zhang

address: Pläsinpellonkuja 4 B 50

country: Finland

institute: University of Helsinki

library_source: transcriptomic

data_processing:
RNA-seq data analysis was performed using packages available in Chipster
Assembly: TAIR 10.39
Supplementary files format and content: tab-delimited text file (tsv) includes raw counts for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Root

extract_protocol:
Total RNA was isolated using a GeneJET Plant RNA purification kit (ThermoFisher) following the manufacturer’s instructions
RNA-seq libraries were constructed using a TruSeq Stranded Total RNA Library prep kit (Illumina)

tag: tissue

value: Root

tag: genotype

tag: treatment

value: DMSO


title: Arabidopsis, Mock, 24 hours, rep 1


title: Arabidopsis, Mock, 8 hours, rep 2


title: Arabidopsis, Induced, 24 hours, rep 1

value: EST


title: Arabidopsis, Induced, 8 hours, rep 3


title: Sample F3-Ej4 technical replicate d

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ej4, technical replicate d

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.3. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (Rnor_6.0 from Ensembl version 91) using the STAR mapper (version 2.6.1b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, Rattus norvegicus GTF genome annotation version 91 from Ensembl database was used (GTF annotation from Ensembl 106 for the Pecam1 gene, transcripts and exons was merged  in GTF annotation from Ensembl 91). All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3.
Assembly: Rnor_6.0 from Ensembl 91
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample

organism: Rattus norvegicus

source_name: Cerebral cortex

extract_protocol:
Total mRNAs were extracted from purified using the RNeasy Micro kit (Qiagen)
Messenger (polyA+) RNAs were purified from 150 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

value: Cerebral cortex

tag: cell type

value: Endothelial cell

value: 3 days fast


title: Sample F3-Ek4 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ek4, technical replicate d


title: Sample F3-Ej4 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ej4, technical replicate c


title: Sample F3-Ej4 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ej4, technical replicate b


title: Sample F3-Ei4 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ei4, technical replicate c


title: Arabidopsis, Mock, 24 hours, rep 2


title: Sample F3-Ek4 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ek4, technical replicate b


title: Arabidopsis, Induced, 24 hours, rep 3


title: Arabidopsis, Mock, 8 hours, rep 3


title: Sample F3-Ek4 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ek4, technical replicate c


title: Arabidopsis, Induced, 24 hours, rep 2


title: Arabidopsis, Induced, 8 hours, rep 1


title: Sample F3-Ei4 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ei4, technical replicate d


title: Sample F3-Ei4 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ei4, technical replicate b


title: Sample F2-Ek3 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ek3, technical replicate d

value: 2 days fast


title: Sample F3-Ei4 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ei4, technical replicate a


title: Sample F3-Ej4 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ej4, technical replicate a


title: Sample F2-Ek3 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ek3, technical replicate c


title: Arabidopsis, Mock, 24 hours, rep 3


title: Arabidopsis, Induced, 8 hours, rep 2


title: Sample F2-Ek3 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ek3, technical replicate b


title: Sample F2-Ek3 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ek3, technical replicate a


title: Sample F3-Ek4 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 3 days fast rats, sample F3-Ek4, technical replicate a


title: Sample F2-Ej3 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ej3, technical replicate c


title: Sample F2-Ej3 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ej3, technical replicate b


title: Sample F2-Ei3 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ei3, technical replicate c


title: Sample F2-Ei3 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ei3, technical replicate d


title: Sample F2-Ei3 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ei3, technical replicate a


title: Sample F1-Ej2 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ej2, technical replicate d

value: 1 day fast


title: Sample F1-Ek2 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ek2, technical replicate c


title: Sample F1-Ek2 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ek2, technical replicate b


title: CD4 T-cells, Theileria parva infected, day 69, 609232

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

country: United Kingdom

institute: The Roslin Institute, The University of Edinburgh

data_processing:
Quality control using FastQC (v 0.11.9 - default parameters)
Trimming using TrimGalore (v 0.6.4) (--illumina --length 35 --paired)
Pseudoalignment using kallisto (v 0.46.1 - default parameters - 10 bootstraps)
Import of transcript-level abundances into R using tximport (v 1.24.0)
Differential expression analysis using DESeq2 (v 1.36.0)
Assembly: bosTau 9 (ARS-UCD1.2) and PiroplasmDB T. parva Muguga (GCA_000165365.1)
Supplementary files format and content: Comma-separated values files with raw counts of Bos taurus genes for each sample
Supplementary files format and content: Comma-separated values files with raw counts of Theileria parva genes for each sample

organism:
Theileria parva
Bos taurus

source_name: CD4 T-cells

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% FBS, 50mM beta-mercaptoethanol and 1X penicillin-streptomycin, in a humidified incubator at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen). 500ng of total RNA was use for library preparation.
The NEBNEXT Ultra II Directional RNA Library Prep kit was used with the Poly-A mRNA magnetic isolation module for library construction.

treatment_protocol: Cells were infected with saturating levels of fresh T. parva Muguga sporozoites.

value: CD4 T-cells

tag: time

value: day 69

tag: disease state

value: attenuated


title: Sample F2-Ej3 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ej3, technical replicate a


title: CD4 T-cells, Theileria parva infected, day 69, 309236


title: Sample F1-Ek2 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F1-Ek2, technical replicate d


title: CD4 T-cells, Theileria parva infected, day 7, 709247

value: day 7

value: pathogenic


title: Sample F1-Ej2 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ej2, technical replicate b


title: CD4 T-cells, Theileria parva infected, day 7, 509238


title: Sample F1-Ek2 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ek2, technical replicate a


title: CD4 T-cells, Theileria parva infected, day 7, 609232


title: Sample F1-Ej2 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ej2, technical replicate c


title: CD4 T-cells, Theileria parva infected, day 69, 000035


title: Sample F1-Ej2 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ej2, technical replicate a


title: CD4 T-cells, Theileria parva infected, day 7, 000066


title: Sample F1-Ei2 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ei2, technical replicate c


title: Sample F1-Ei2 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ei2, technical replicate d


title: Sample F2-Ej3 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ej3, technical replicate d


title: CD4 T-cells, Theileria parva infected, day 7, 000035


title: CD4 T-cells, Theileria parva infected, day 7, 309236


title: Sample F1-Ei2 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ei2, technical replicate b


title: CD4 T-cells, Theileria parva infected, day 69, 509238


title: Sample F2-Ei3 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from 2 days fast rats, sample F2-Ei3, technical replicate b


title: Sample F1-Ei2 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from 1 day fast rats, sample F1-Ei2, technical replicate a


title: Sample A1-Ek1 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ek1, technical replicate d

value: ad libitum


title: Sample A1-Ek1 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ek1, technical replicate c


title: Sample A1-Ej1 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ej1, technical replicate c


title: Sample A1-Ej1 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ej1, technical replicate b


title: Sample A1-Ej1 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ej1, technical replicate a


title: Sample A1-Ej1 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ej1, technical replicate d


title: Sample A1-Ei1 technical replicate d

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ei1, technical replicate d


title: Sample A1-Ei1 technical replicate c

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ei1, technical replicate c


title: Sample A1-Ei1 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ei1, technical replicate a


title: Hep2 cells infected with d27LacZ (MOI 5) at 3 hpi synchronous infection replicate 2

city: Ithaca

first: Joel

middle: D

last: Baines

state: NY

address: 235 Hungerfordhill Rd

country: USA

institute: Cornell University

description: RNA was generated from a nuclear run on containing biotinylated nucleotides ATP, GTP, and CTP

data_processing:
Pro-seq2 pipeline (https://github.com/Danko-Lab/proseq2.0)
Assembly: hg38, HSV-1 (F), Drosophila S2
Supplementary files format and content: bigwig files of read counts for each nt
Library strategy: PRO-Seq

molecule: nuclear RNA

organism:
Drosophila melanogaster
Homo sapiens
Human alphaherpesvirus 1

source_name: Human, Drosophila, and HSV-1 (KOS)

growth_protocol: Hep2 cells were grown in DMEM supplemented with 10% New Born Calf Serum

extract_protocol:
Nuclei were extracted as previously published (Birkenheuer and Baines, 2018)
PRO-seq libraries were constructed using the protocol (doi: https://doi.org/10.1101/2020.05.18.102277)
Single End NextSeq550

treatment_protocol: Cells were infected at an MOI of 5

tag: cell line

value: Hep2 Cells (human) S2 cells (Drosophila)

value: human epithelial cells arising from a HeLa cell line contaminant and late stage embryo Drosophila melanogaster cells

value: KOS mutant d27LacZ

value: infected at MOI 5 for 3 hours


title: Hep2 cells infected with d27LacZ (MOI 5) at 6 hpi synchronous infection replicate 1

value: infected at MOI 5 for 6 hours


title: Hep2 cells infected with d27LacZ (MOI 5) at 6 hpi synchronous infection replicate2


title: Hep2 cells infected with wt KOS (MOI 5) at 6 hpi synchronous infection replicate 1

value: wt KOS HSV-1


title: Hep2 cells infected with wt KOS (MOI 5) at 6 hpi synchronous infection replicate 2


title: Sample A1-Ei1 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ei1, technical replicate b

value: Cerebral cortex


title: Hep2 cells infected wit h d27LacZ (MOI5) at 3 hpi synchronous infection replicate 1


title: Hep2 cells infected with wt KOS (MOI 5) at 3 hpi synchronous infection replicate 2


title: Sample A1-Ek1 technical replicate a

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ek1, technical replicate a

value: Endothelial cell


title: Sample A1-Ek1 technical replicate b

description: Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ek1, technical replicate b


title: seminal, endometrial biopsy sample 8

type: RNA

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

description: gene expression during implantation window

hyb_protocol: Following fragmentation,  cRNA was hybridized for 16 hr at 45C on Clariom D Array for human samples. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner GCS3000

data_processing: Thermofisher Applied Biosystems Transcriptome Analysis Console version 4.0.14, SST-RMA normalization, limma t-test used for differential gene expression analysis

label: biotin

source_name: endometrium

label_protocol: GeneChip Whole Transcript (WT) PLUS reagent kit was used to obtain the biotinylated cRNA (250 ng of RNA per sample used).  All the procedures were performed following the manufacturer´s instructions.

growth_protocol: not relevant

extract_protocol: Total RNA was purified using the miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: A Curette with Vacu-Lok syringe was used to collect the endometrial biopsy scratching the uterine lining. Cold saline solution was used to extract the endometrial biopsy from the tube. The samples were centrifuged (1000g, 5 min), the supernatant removed and the remaining endometrial sample was snap-frozen in liquid nitrogen and stored at −80°C until further analysis.

value: endometrial biopsy

value: seminal


title: placebo, endometrial biopsy sample 2

value: placebo


title: HeLa_small_RNA_Tris8.8_17h_NaBH4_SSIV.rep1

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
To analyze the small RNA sequencing data from HeLa cells, we initiated the process by aligning the modified reads to the hg19 reference genome assembly. Raw reverse (R1) reads with depleted PCR duplicates and removed adaptors were mapped to the rRNA (NR_003285.3.fa, NR_003286.4.fa and NR_003287.4.fa) download from NCBI Nucleotide data, and tRNA (hg19-mature-tRNAs.fa) genomes downloaded from the GtRNAdb database (http://gtrnadb.ucsc.edu/Hsapi19/Hsapi19-seq.html).
This alignment was performed using bwa mem under its default parameters. Following this, the mapped SAM files were converted to BAM format and sorted using Samtools sort (v1.9). To refine our data further, we filtered the sorted BAM files using Samtools view (-q 10) to obtain uniquely mapped reads. For mutation identification, we employed rnaseqmut utilizing the parameters "-t -s -3 -m 2" to ensure sensitive detection.
Our analysis incorporated several stringent cutoffs to filter the mutation list for downstream analysis: 1) we selected mutations with a reference Adenine (A) and a read coverage of at least 50 and a mutation ratio of 5% or greater in both SSIV and PSII libraries, coupled with a p value of less than 0.05. 2) For two control libraries, we focused on adenine sites with a read coverage of at least 50 and a mutation ratio of less than 5%.
Additionally, we required that mutation ratios in both NaBH4 SSIV and PSII libraries be at least 2-fold higher than those in two control libraries.
Assembly: mm10
Supplementary files format and content: txt, mutation list on mature tRNA
Supplementary files format and content: txt, mutation list on rRNA

source_name: HeLa

growth_protocol: HeLa cells (American Type Culture Collection) were cultured in DMEM medium (Gibco™, catalog no. 11995065) supplemented with 10% (v/v) fetal bovine serum (Gibco™ #16000044), 100 U/mL of penicillin and 100 μg/mL streptomycin (Gibco™ #15140122) at 37 °C with 5% CO2.

extract_protocol:
Total RNA from cultured cells was extracted with TRIzol™ Reagent (Invitrogen™, Catalog no. 15596026) following manufacturer’s instructions. Small RNA fraction was enriched from total RNA using RNA Clean & Concentrator-25 (Zymo, Catalog no. R1017).
500 ng of HepG2 small RNA (<200 nt) was mixed with 0.5 ng of 43-mer m1A RNA oligo and 1 ng of 45-mer m1A RNA oligo. 1x T4 PNK buffer (NEB), 0.4 U/μL SUPERase•In (Invitrogen) and 0.8 U/μL T4 PNK (NEB M0201) were added and mixture was incubated at 37 °C for 45 min. Next, RNA was purified with RNA Clean & Concentrator-5 (Zymo Research) and eluted with 21 μL water. RNA concentration was measured with Qubit (Invitrogen). RNA volume was then adjusted to 36 μL and split to set up four 3’ RNA ligation reactions. ~100 ng RNA of RNA in 9 μL water was mixed with 1 μL of 11.25 μM 3’ RNA adaptor and incubated at 70 °C for 2 min then kept on ice for 2 min. Next, 2 μL water, 2.5 μL of 10X T4 RNA Ligase Reaction Buffer (NEB B0216S), 7.5 μL of 50% PEG8000 (NEB B1004S), 1 μL of SUPERase•In and 2 μL of T4 RNA ligase 2 truncated KQ (NEB 0373) were added and the mixture was incubated ar 25 °C for 1 h followed by incubation at 16 °C for 16 hr. Next day,  to each ligation mixture, 1 μL of 5’ deadenylase (NEB M0331) was added and incubated at 30 °C for 1h. Adaptor excess was digested by adding to each ligation mixture 1 μL of RecJf (NEB M0264) and incubating at 37°C for 1h. After adaptor digestion, all four ligation mixtures were combined and purified with RNA Clean & Concentrator-5. To further remove undigested 3’ adaptor, EtOH volume was adjusted. Briefly, ligation reactions mixture volume was adjusted to 400 μL with water. Then, 400 μL RNA Binding Buffer (Zymo) and 320 μL of 100% EtOH were added to the sample and then loaded onto the column. Further steps were performed according to manufacturer’s instructions. Purified 3’ RNA ligated sample was then divided into three parts: (i) to treat with NaBH4, (ii) to treat with pNTP, (iii) to treat with Tris-HCl pH 8.8. Each part was further subdivided into three parts as technical replicates. Treatment was performed as follows: (i) Store 3’ ligated RNA to treat with NaBH4 at -80 °C until ready to use. (ii) pNTP treatment was performed as described previously (REF). Briefly, to 3’ ligated RNA in 25 μL water, add 25 μL of 2x reaction mixture (2x stock: 50 mM pNTP (Thermo Scientific Chemicals H59240.14), 10 mM THP (Sigma-Aldrich 777854) in 10 %(v/v) DMF (Sigma-Aldrich 270547), pH 6). Incubate at 50 °C for 16 h. (iii) To 3’ ligated RNA in 40.5 μL water, add 4.5 μL of 1.5 M Tris-HCl pH 8.8 and incubate at 95 °C in a lid-heated to 110 °C thermoblock for 16 h. Next, add 5 μL of 1 M NaHCO3 pH 9.2 and incubate for additional 10 min at 95 °C. Put on ice immediately and add 10 μL of 3M NaOAc pH 5.5 buffer to neutralize the sample and prevent from further degradation. Purify pNTP- and Tris-treated samples with RNA Clean & Concentrator-5. Further steps were performed according to manufacturer’s instructions and refer the method session in the manuscript.

value: HeLa

value: Wide type


title: HeLa_small_RNA_Tris8.8_17h_NaBH4_SSIV.rep3


title: HeLa_small_RNA_Tris8.8_17h_NaBH4_SSIV.rep2


title: seminal, endometrial biopsy sample 7


title: Hep2 cells infected with d27LacZ (MOI 5) at 1.5 hpi synchronous infection replicate 2

value: infected at MOI 5 for 1.5 hours


title: seminal, endometrial biopsy sample 9


title: HeLa_small_RNA_4NTP_17h_NaBH4_SSIV.rep3


title: Hep2 cells infected with d27LacZ (MOI 5) at 1.5 hpi synchronous infection replicate 1


title: HeLa_small_RNA_4NTP_17h_NaBH4_SSIV.rep2


title: seminal, endometrial biopsy sample 6


title: seminal, endometrial biopsy sample 3


title: placebo, endometrial biopsy sample 4


title: placebo, endometrial biopsy sample 1


title: HeLa_small_RNA_NaBH4_SSIV.rep3


title: placebo, endometrial biopsy sample 5


title: HeLa_small_RNA_4NTP_17h_NaBH4_SSIV.rep1


title: HeLa_small_RNA_NaBH4_SSIV.rep2


title: Lung, control, scRNA-seq

city: hangzhou

first: kang

last: zhiying

address: 浙江省杭州市西湖区余杭塘路866号

country: China

institute: zhejiang universty

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw gene expression matrix generated from each sample were aggregated using CellRanger(v5.0.1) provided on the 10x genomics website. The merged matrix was transferred into the R statistical environment for further analysis using the Seurat package (v.4.3.0.1). The cells with mitochondrial UMI counts greater than 10%, or below 200 genes were identified as low-quality cells and removed. Batch effects were corrected by the “SCT” function. We used TOP 30 PCs for downstream analysis. The cells were clustered and identified by the “FindNeighbors” and “FindClusters” functions with a resolution of 0.3. The clusters were projected into a two-dimensional plot for visualization using the “RunUMAP” functions.The main reference data for cell marker genes used for cellular annotation were obtained from CellMarker 2.0. GO enrichment of DEGs of cell subgroups was performed using the “compareCluster” function in the “clusterProfiler” packages.We used CellChat(v2.1.1) to infer cell–cell interactions between immune cell subsets, and cells with a total number greater than 200 were left for analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Lung

extract_protocol:
The correct enzymes are selected according to different tissue types. The enzyme solution is then prepared using centrifuge tubes and preheated into 37℃ water bath.
The tissue sample is taken from a 4℃ refrigerator. After centrifuging, tissue preservation solution is removed. Tissue is then cleaned using DMEM and immediately cut into 2-3mm tissue block using a scalpel. The tissue block is transferred into a centrifuge tube filling with enzymatic hydrolysate and placed in a 37 ℃ water bath for digestion.
Repetitive pipetting is done every 15-20 mins. After 30 mins, tissue digestion is examined via trypan blue staining until no obvious tissue block exists and the digestion stops.
40µm cell strainer is used to filter the cell suspension. The residual cells are cleaned using the 2-3mL precooled complete medium in which the cleaning solution is filtered and collected into a centrifuge tube. Centrifuge at 300g and 4℃ for 5 mins and discard the supernatant.
According to different tissue types and colours of cell precipitations, red blood cell lysis buffer at room temperature is added to resuspend cells and lyse the red blood cells for 2-5 mins. Equal amounts of PBS-BSA (0.04%) solution are added to stop the lysis of the red blood cells.
Centrifuge at 300g and 4℃ for 5 mins and discard the supernatant. Cell status is observed via trypan blue staining in which then the Dead Cell Removal Kit can be used to remove dead cells and debris.
PBS-BSA (0.04%) is used to wash cells. Centrifuge at 300g and 4℃ for 5 mins and discard the supernatant. A right amount of PBS-BSA (0.04%) is used to resuspend the precipitation followed by counting the cells using a hemacytometer.
1 Microscope Assessment of the Cell or Nuclei
The cellular or nuclei suspension is stained with 0.4% trypan blue to assess cell viability under microscopic observation. Cells with greater than 80% viability are qualified for library construction process.
2 GEM Generation and Reverse Transcription
Prepared single-cell suspension is then partitioned into GEMs (Gel Beads in Emulsions) in the automated Chromium Controller, and then mRNAs are reverse transcribed into cDNAs.
3 Breaking GEMs
The reaction system is configured for breaking GEMs. After reacting at the suitable temperature for a fixed period of time, the products are purified.
4 cDNA Amplification
The reaction system is configured for PCR. After reacting at the suitable temperature for a fixed period of time, the products are purified.
5 Fragmentation, end Repair & A-tailing
The reaction system is configured. A certain amount of cDNA amplified products is taken. After reacting at the suitable temperature for a fixed period of time, the cDNAs are subjected to fragmentation, end repair and addition of “A” base at the 3'-end of each strand. Finally, the products are purified.
6 Adaptor Ligation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, the cDNAs are subjected to adaptor ligation. Finally, the products are purified.
7 PCR
The PCR reaction system is configured. After reacting at the suitable temperature for a fixed period of time, amplification is processed via PCR. The products are then purified.
8 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
9 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
10 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Lung

value: Mice lung tissue

value: control


title: Hep2 cells infected with wt KOS (MOI 5) at 1.5 hpi synchronous infection replicate 1

description: RNA was generated from a nuclear run on containing biotinylated nucleotides ATP, GTP, and CTP for 3 min

value: Hep2 Cells (human) S2 cells (Drosophila)


title: Lung, extrapulmonary ALI, scRNA-seq

address: 浙江省杭州市西湖区余杭塘路866号

description: 10x Genomics

value: extrapulmonary ALI


title: HeLa_small_RNA_NaBH4_SSIV.rep1


title: Lung, pulmonary ALI, scRNA-seq

address: 浙江省杭州市西湖区余杭塘路866号

description: 10x Genomics

value: pulmonary ALI


title: HeLa_small_RNA_NaBH4_PSII.rep2


title: Hep2 cells infected with wt KOS (MOI 5) at 3 hpi synchronous infection replicate 1

value: human epithelial cells arising from a HeLa cell line contaminant and late stage embryo Drosophila melanogaster cells

value: infected at MOI 5 for 3 hours


title: GEMM derived GSC line PC326-1 bio rep 3

city: Dallas

first: Samuel

last: McBrayer

state: Texas

address: 6000 Harry Hines Blvd

department: Children's Research Institute

institute: UT Southwestern Medical Center

data_processing:
The sequencing reads were filtered to remove adapter contamination and low quality reads and processed reads were aligned by HiSat2 mouse (UCSC mm39) references for quantification.
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited text file including FPKM values for each sample

molecule: polyA RNA

source_name: brain

growth_protocol: Murine GSC cells were cultured in NeuroCult NS-A Basal Medium (Mouse) with Proliferation Supplement (StemCell Technologies 05701) supplemented with EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 1% penicillin/streptomycin, amphotericin B (250 ng/mL), and Plasmocin (2.5 μg/mL). All murine GSC lines were cultured on ultra-low adherence plates (Corning 4615) in the presence of 5% CO2 and 5% oxygen at 37°C.

extract_protocol:
Total RNA was extracted from fresh cell pellets using the RNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s instructions.
mRNA sequencing of mouse GSC lines was performed by Novogene. Brifly, total RNA served as input for polyA-RNA capture and rRNA removal. Strand-specific libraries were prepared and paired-end 150 bp sequencing was performed using an Illumina NovaSeq 6000 machine.

value: brain

value: glioma stem-like cells

value: IDH1 WT


title: Hep2 cells infected with wt KOS (MOI 5) at 1.5 hpi synchronous infection replicate 2

value: wt KOS HSV-1


title: GEMM derived GSC line PC326-1 bio rep 2


title: HeLa_small_RNA_NaBH4_PSII.rep3


title: HeLa_small_RNA_NaBH4_PSII.rep1


title: GEMM derived GSC line PC326-1 bio rep 1


title: GEMM derived GSC line PC308-1 bio rep 2


title: GEMM derived GSC line PC308-1 bio rep 3


title: Trichoderma reesei QM9414 growth on arabinoxylan for 24h replicate 2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

data_processing:
Illumina data analysis pipeline RTA v2.4.11 abd Bcl2dastq v2.17 softwares used for basecalling. Adaptor sequences were removed using Trimmomatic v0.30. Clean reads were mapped to the genome sequence using TopHat mismatch 2%. Reads were map to genes using HTSeq-count. FPKM values were calculated using Cufflinks with default options Genome_build: T. reesei QM6a v.2 (http://genome.jgi.doe.gov/Trire2/Trire2.home.html) Supplementary_files_format_and_content: excel file include gene length, expected count and FPKM for each sample.
Assembly: Trichoderma reesei QM6a v.2 (http://genome.jgi.doe.gov/Trire2/Trire2.home.html)
Supplementary files format and content: text file containing FPKM values

organism: Trichoderma reesei

source_name: mycelium

growth_protocol: A transfer experiment was performed for transcriptomics. 250 mL of complete medium (CM) (de Vries, et al. Appl Environ Microbiol 2004:70, 3954-9) containing 2% D-fructose in 1 L Erlenmeyer flasks was inoculated with 2.5 x 108 fresh spores, harvested from a PDA plate, and incubated in a rotatory shaker at 28°C for 20 h at 250 rpm. The mycelium was harvested by filtration, washed with liquid Mandels Andreotti medium (MA) (Mandels, M. and Andreotti, R.E. Process Biochemistry 1978:13-6:15) (without carbon source) and 2.5 g mycelium (wet weight) was transferred to 250 mL Erlenmeyer flasks containing 50 mL MA with 25 mM D-galactose or L-arabinose or D-xylose or 1% arabinoxylan, and incubated in a rotatory shaker at 28°C and 250 rpm.

extract_protocol:
RNA samples (5-41 μg DNase-treated total RNA) were processed by GenomeScan (Leiden, The Netherlands) according to the company's workflow pipeline.
The sample preparation was performed according to the protocol “NEBNext Ultra Directional RNA Library Prep Kit for Illumina”.

treatment_protocol: After incubation, the mycelium was harvested by vacuum filtration, dried between tissue paper, directly frozen in liquid nitrogen and stored at -45°C

value: mycelium

value: wild-type

value: growth on arabinoxylan for 24h


title: GEMM derived GSC line PC308-1 bio rep 1


title: GEMM derived GSC line PC134-0 bio rep 3


title: Trichoderma reesei QM9414 growth on arabinoxylan for 24h replicate 1


title: Trichoderma reesei QM9414 Δara1 growth on arabinoxylan for 2h replicate 2

value: growth on arabinoxylan for 2h


title: GEMM derived GSC line PC134-0 bio rep 2


title: Trichoderma reesei QM9414 Δara1 growth on arabinoxylan for 2h replicate 1


title: Trichoderma reesei QM9414 growth on arabinoxylan for 2h replicate 1


title: GEMM derived GSC line PIC496-4 bio rep 3

value: IDH1 mutant


title: Trichoderma reesei QM9414 growth on arabinoxylan for 2h replicate 2


title: GEMM derived GSC line PIC496-3 bio rep 3


title: Trichoderma reesei QM9414 Δara1 growth on D-xylose for 2h replicate 2

value: growth on D-xylose for 2h


title: GEMM derived GSC line PIC496-4 bio rep 2


title: GEMM derived GSC line PC134-0 bio rep 1


title: GEMM derived GSC line PIC496-3 bio rep 2


title: GEMM derived GSC line PIC496-4 bio rep 1


title: Trichoderma reesei QM9414 growth on D-xylose for 2h replicate 1


title: GEMM derived GSC line PIC144-3 bio rep 3


title: GEMM derived GSC line PIC144-3 bio rep 2


title: Trichoderma reesei QM9414 Δara1 growth on D-xylose for 2h replicate 1


title: Trichoderma reesei QM9414 Δara1 growth on arabinoxylan for 24h replicate 2


title: GEMM derived GSC line PIC496-3 bio rep 1


title: GEMM derived GSC line PIC144-3 bio rep 1


title: GEMM derived GSC line PIC144-1 bio rep 3


title: Trichoderma reesei QM9414 Δara1 growth on arabinoxylan for 24h replicate 1


title: C-1

city: Simotsuke-si

first: Akihiro

last: Dohi

state: Tochigi

address: 3311-1 Yakushiji

department: Oral, Maxillofacial Surgery

country: Japan

institute: Jichi Medical University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cervical lymph nodes

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Total RNA was extracted from the cervical lymph nodes of the two groups using ISOGEN reagent (Nippon Gene Co. Ltd., Toyama, Japan) according to the manufacturer’s instructions. Total RNA concentration and purity were measured spectrophotometrically using Nanodrop1000 (NanoDrop Technologies, Inc., Wilmington, DE, USA).

tag: strain

value: Sprague-Dawley

value: male

tag: age

value: 10-12 weeks old

value: cervical lymph nodes

tag: stress


title: GEMM derived GSC line PIC144-1 bio rep 2


title: T.96.C8

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Hybridization was performed according to Nanostring manufacturer's protocol, overnight at 65°C, 18h in a thermocycler

scan_protocol: Cartridges were run on a nCounter Nanostring machine

data_processing: NanoStringNorm package for R software 4.1.2 (R Foundation for Statistical Computing, Vienna, Austria) was used to generate data and for quality check; the geometric mean of the counts relative to each sample, the mean plus two standard deviations and the total sum of counts options were used to correct the data for technical, background, and batch-effect issues, respectively.

source_name: CD3+ selected leukapheresis, patient

label_protocol: Probe labeling was performed according to Nanostring manufacturer's protocol

extract_protocol: RNA was extracted from CD3-positive selected cells with miRNeasy Mini kit (Qiagen) and 100 ng of total RNA were used for the transcriptomic analyses

treatment_protocol: Leukapheresis samples and donor lymphocyte infusions were quickly thawed and CD3+ cells were selected using magnetic anti-CD3 microbeads (Miltenyi Biotec) and the autoMACS Pro Separator (Miltenyi Biotec)

value: large B-cell lymphoma

tag: model (1

value: EXP, 2:poor-EXP):1

value: CD3+ selected leukapheresis, patient


title: T.95.C8

value: EXP, 2:poor-EXP):2


title: GEMM derived GSC line PIC144-1 bio rep 1

value: brain

value: glioma stem-like cells


title: SR1

value: restraint stress (RS)


title: T.94.C8


title: T.93.C8


title: Trichoderma reesei QM9414 growth on D-xylose for 2h replicate 2

value: mycelium


title: T.85.C8


title: T.90.C8


title: T.89.C8


title: Lamina propria, CD4 T cell, TCF7-, rep2

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

data_processing:
FASTQ was merged and filtered using fastp (v0.23.3)
Reads were aligned with the STAR aligner (2.7.10b)
Samtools (v1.17) was used to index and sort BAM friles from STAR
QC report was performed with bamCoverage (v3.5.1), and Qualimap (v.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR’s BAM aligned output.
Assembly: mm10
Supplementary files format and content: bulk_counts.txt.gz raw counts for 6 samples in TAB delimited TXT
Supplementary files format and content: bulk_tpm.txt.gz transcripts per million reads (TPM) counts for 6 samples in TAB delimited TXT
Supplementary files format and content: bulk_metadata.txt.gz metadata for 6 samples in TAB delimited TXT

source_name: Colon Lamina propria

extract_protocol:
Total RNA was purified using the miRNeasy Micro Kit (QIAGEN).
cDNA was reversely transcribed from total RNA with oligo-dT primer, random hexamers with SuperScript™ II Reverse Transcriptase (Invitrogen) and then amplified with IS PCR primers and Kapa HiFi Hotstart Ready Mix (Roche). Then the cDNA library was fragmented and tagged with sequencing adapters using Nextera XT DNA Library Preparation Kit (Illumina), and finally ~500 bp amplicons were got. Quality of library was assessed using the High Sensitivity RNA ScreenTape Kit (Agilent Life Sciences). DNA was quantified using Quant-iT PicoGreen dsDNA Assay Kits (Invitrogen) and purified using AMPure XP beads (Beckman Coulter). Libraries were subjected to 2 × 100-bp paired-end sequencing on an Illumina NovaSeq 6000 (Illumina), generating at least 8 million uniquely mapped reads for each sample.

value: Colon Lamina propria

value: CD4 T cell

value: GFP- effector T cell


title: Lamina propria, CD4 T cell, TCF7+, rep3

value: GFP+ stem-like T cell


title: Lamina propria, CD4 T cell, TCF7-, rep1


title: Lamina propria, CD4 T cell, TCF7-, rep3


title: enteric neurons, WNV, 6 dpi - 4

city: St. Louis

first: Hana

last: Janova

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St. Louis

data_processing:
Sequencing data was demultiplexed using Illumina’s DRAGEN and BCLconvert version 4.2.4 software. Reads were then aligned and mapped to the Ensembl release 101 primary assembly with STAR version 2.7.9a. A count matrix containing all expression data was then generated from the number of uniquely aligned unambiguous read using Subread:featureCount version 2.0.3  and isoform expression of known Ensembl transcripts quantified with Salmon version 1.5.2. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
Assembly: Ensembl release 101 primary assembly with STAR version 2.7.9a
Supplementary files format and content: csv table read counts

source_name: distal part of small intestine

extract_protocol:
Samples were homogenized using homogenization buffer (50 mM Tris, pH 8.0; 100 mM KCl; 12 mM MgCl2; 1 % Igepal; 1 mg/mL sodium heparin; 100 µg/mL cycloheximide; 0.2 U/µL SUPERaseIn RNase Inhibitor, 2 mM DTT). After centrifugation (10,000 x g; 10 min; 4oC) 25 µg of primary antibody against GFP (rabbit; # AB290; Abcam) was added, and samples were rotated for 1 h at 4 oC. Subsequently, 200 µl of DynabeadsTM Protein G (# 10004D; Invitrogen) were added, and samples were incubated rotating overnight at 4 C. The beads were washed four times with high-salt buffer (50 mM Tris, pH 8.0; 300 mM KCl; 12 mM MgCl2; 1 % Igepal; 100 µg/mL cycloheximide). RNA was extracted and purified with Arcturus PicoPure RNA Isolation Kit (ThermoFisher: Kit0204 - Applied biosystems; 12204-01) according to the manufacturer’s instructions. To prevent contamination with DNA, RNase-Free DNase Set (Qiagen; # 29254) was used according to the manufacturer's instructions.
Library preparation was performed with 1-50 ng of total RNA.  cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer's protocol and then fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, an A base was added to the 3' ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: distal part of small intestine

value: WNV


title: Lamina propria, CD4 T cell, TCF7+, rep1


title: T.80.C7


title: T.84.C7


title: enteric neurons, WNV, 6 dpi - 3


title: T.78.C7


title: T.82.C7


title: T.77.C7


title: T.79.C7


title: T.75.C7


title: T.76.C7


title: enteric neurons, WNV, 6 dpi - 2


title: enteric neurons, WNV, 6 dpi - 1


title: T.91.C8


title: enteric neurons, sham control - 3

value: sham


title: enteric neurons, sham control - 2


title: T.71.C6


title: T.74.C7


title: Lamina propria, CD4 T cell, TCF7+, rep2


title: T.70.C6


title: enteric neurons, sham control - 1


title: T.68.C6


title: T.67.C6


title: enteric neurons, sham control - 4


title: T.66.C6


title: T.73.C7


title: T.63.C6


title: T.65.C6


title: T.64.C6


title: hUGT1/Atf4△Hep vehicle 2

first: Andre

middle: Alberto

last: Weber

state: CA

address: 9500 Gilman Dr. La Jolla

institute: UCSD

data_processing:
Illumina NovaSeq6000 sequencer in IGM Genomics Center at UCSD, samples were sequenced with Paired End 100 base pair sequecing, with base calling using bcl2fastq (v2.20; Illumina)
STAR (v2.7.9a) was used to align th sequencing reads to the mouse genome. Differentially expressed genes were calculated with DESSeq2 (1.34.0)
Assembly: mm10
Supplementary files format and content: results-2.xlsx

source_name: Liver

extract_protocol:
RNA was isolated using Trizol (ThermoFisher). 1μg of RNA was used for the construction of sequencing libraries.
The sequencing library for each sample was prepared using the Illumina Stranded mRNA Sample Prep Kit.

value: Liver

value: Humanized UGT1/Atf4{delta}Hep

value: Vehicle


title: hUGT1/Atf4F/F vehicle 1

value: Humanized UGT1/Atf4F/F


title: hUGT1/Atf4F/F TCS 1

value: TCS


title: hUGT1/Atf4△Hep TCS 2


title: hUGT1/Atf4△Hep vehicle 1


title: hUGT1/Atf4F/F TCS 2


title: T.61.C6

value: large B-cell lymphoma

value: EXP, 2:poor-EXP):2

value: CD3+ selected leukapheresis, patient


title: T.59.C5

value: EXP, 2:poor-EXP):1


title: spleen, PICS+LPS6h-2

city: Zhanjiang

first: Chaoxiong

last: Liao

address: 57 Renmin Avenue South

institute: Anesthesia

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen

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

value: spleen

value: sepsis secondary infection


title: T.62.C6


title: T.69.C6


title: spleen, PICS-3

value: sepsis immunosuppression


title: spleen, PICS+LPS6h-3


title: T.58.C5


title: spleen, PICS+LPS6h-1


title: hUGT1/Atf4△Hep TCS 1


title: T.57.C5


title: T.56.C5


title: spleen, PICS-2


title: T.55.C5


title: T.60.C5


title: spleen, PICS-1


title: spleen, SHAM-3

value: sham operation


title: spleen, SHAM-1


title: hUGT1/Atf4F/F vehicle 2


title: spleen, SHAM-2


title: 168_KMT2C_KO_P300_rep2

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Fastq data was processed using CoBRA pipeline (https://bitbucket.org/cfce/cobra/src/master/).
Steps include alignment using BWA mem, filtering for uniquely mapped read and sorting bam files.
Peaks were called using macs2 with default settings (-broad mode)
Output bedgraph files were then used to generate bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: breast cancer

growth_protocol: DMEM, 10% FBS, 1x Pen/Strep, 1x Glutamin, 1x Non-essential amino acids, 5% CO2, 37C

extract_protocol:
Cells were fixed with 1% formaldehyd for 10 minutes. Then, cells were collected, nuclei were isolated and lysed and chromatin was sheared with an ultrasonicator (Covaris E220)
ChIPseq libraries were prepared using xGen DNA library prep reagents (IDT) on a Biomek i7 (Beckman Coulter) liquid handling platform from approximately 1ng of DNA with 14 cycles of PCR amplification according to manufacturer’s protocol.

value: breast cancer

tag: chip antibody


title: 168_KMT2C_KO_P300_input


title: 168_KMT2D_KO_P300_rep1


title: T.53.C5


title: 168_WT_P300_input

value: WT


title: 168_KMT2C_KO_P300_rep1


title: T.50.C5


title: 168_WT_P300_rep1


title: T.51.C5


title: T.52.C5


title: 168_WT_P300_rep2


title: N.45.C4

source_name: CD3+ selected donor lymphocyte infusion, healthy control

value: healthy control

value: EXP, 2:poor-EXP):n/a


title: T.49.C5


title: N.47.C4

value: CD3+ selected donor lymphocyte infusion, healthy control


title: BO-112 flank right treated tumor biological replicate 4

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

data_processing:
FastQC for quality control
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm39 using STAR
Quantification using FeatureCounts
Assembly: mm39
Supplementary files format and content: tab-delimited text files include log2CPM values for each Sample

source_name: Tumor

growth_protocol: Mice were subcutaneously injected with 1.5×105 TC-1/A9 cells in the right flank. Seven days later, tumor were treated.

extract_protocol:
On day 8 and day 14, mice were euthanized, and RNA from tumors was subjected to RNAseq analysis
TruSeq Stranded mRNA preparation

treatment_protocol: Seven days later, mice were intravenously treated with 1×105 RCV FFU artLCMV-E7E6 and received intratumoral injections of 50 μg of poly(I:C) or BO-112 in the right-sided tumor lesion on days 7, 10, and 13.

value: Tumor


title: 168_KMT2D_KO_P300_input


title: N.46.C4


title: T.44.C4


title: T.42.C4


title: T.40.C4


title: T.41.C4


title: 168_KMT2D_KO_P300_rep2


title: T.54.C5


title: T.39.C4


title: T.43.C4


title: Poly(I:C) flank right treated tumor biological replicate 3


title: Poly(I:C) flank right treated tumor biological replicate 4


title: BO-112 flank right treated tumor biological replicate 1


title: BO-112 flank right treated tumor biological replicate 2


title: T.37.C4


title: Poly(I:C) flank right treated tumor biological replicate 2


title: Poly(I:C) flank right treated tumor biological replicate 1


title: Vehicle (PBS) flank left control treated tumor biological replicate 3

value: NO


title: Poly(I:C) flank left treated tumor biological replicate 4


title: Vehicle (PBS) flank left control treated tumor biological replicate 4


title: T.33.C3


title: T.35.C3


title: T.34.C3


title: Poly(I:C) flank Ieft treated tumor biological replicate 1


title: N.30.C3


title: Vehicle (PBS) flank left control treated tumor biological replicate 2


title: N.32.C3


title: T.28.C3


title: T.29.C3


title: T.26.C3


title: Vehicle (PBS) flank left control treated tumor biological replicate 1


title: T.25.C3


title: BO-112 flank right treated tumor biological replicate 3


title: T.27.C3


title: Poly(I:C) flank left treated tumor biological replicate 2


title: hCSF1_4

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road

department: Neurobiology and Behavior

institute: University of California, Irvine

description:
hCSF1x1900
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv

data_processing:
FASTQ files were preprocessed using BBDuk to filter out ribosomal RNA and PhiX reads, trim Illumina adapters, quality trim any base pairs below a PHRED score of 28. and filter out reads less than 45bp after processing.
Reads were then aligned to a mixed species genome consisting of the unmasked top level FASTA files for the human GRCh38 (Ensembl release 99) and mouse GRCm39 (Ensembl release 107) DNA assemblies and aligned using HISAT2 using the -q, -1, and -2 options to align paired-end FASTQ files.
The output SAM files were then parsed using a modified version of the “byPrim.py” Python script from Song et al. (2022) which assigned each read to either mouse or human based on the species for which the primary alignment was specified by HISAT2.
Using the species assignments stored in the output of the “byPrim_MBJ.py” script, the “MBJ_FASTQSorter.py” script generated two sets of paired end reads for each original file, one pair consisting of the forward and reverse human reads and one pair consisting of the forward and reverse mouse reads.
Species-specific FASTQ files were then pseudoaligned to the human GRCh38 transcriptome (Ensembl release 107) or the mouse GRCm39 transcriptome (Ensembl release 107) using Kallisto v0.46.1.
Mouse transcripts were then summarized to the gene level via tximport and the dataset was filtered to retain only genes with 1:1 mouse to human gene homologues and then subsequently filtered to only retain genes with greater than 130 cumulative reads (average of 10 reads per sample). Human transcripts were then similarly summarized to the gene level, filtered to only retain genes with 1:1 homologues, and then both the mouse and human datasets were intersected to only retain genes present in both datasets.
Assembly: Ensembl GRCh38 and GCRm39
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for the sorted human FASTQ files
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for the sorted mouse FASTQ files
Supplementary files format and content: Tab-delimited text file containing VST normalized counts for the combined mouse and human samples

source_name: Brain

extract_protocol:
Animals were perfused (20mL per minute) with 1X DPBS (4°C) for 3 min. Brains were surgically excised from each mouse and cut in half along the mid-sagittal plane. The left hemisphere was placed in 4% (wt/vol) paraformaldehyde (PFA) for 36 h at 4°C for subsequent immunohistochemistry (IHC) and the right hemisphere fresh-frozen on dry ice and stored at -80°C for biochemical analysis. Fresh frozen hemispheres were crushed on dry ice using mortar and pestle and total RNA was isolated using the Qiagen RNeasy Plus Micro Kit following manufacturer protocol.
350ng of total RNA was used as input for library construction using the Illumina TruSeq Stranded mRNA kit which utilizes oligo-dT beads to select and amplify mRNA. cDNA was synthesized using nine rounds of PCR and quality and concentrations of the DNA libraries were assayed using the Agilent 2100 bioanalyzer high sensitivity DNA assay and the DNA high sensitivity Qubit. The libraries were quantified by Kapa qPCR, normalized to 1.5nM and then multiplexed at equimolar concentrations for sequencing on the Illumina NovaSeq 6000 platform with paired-end read 100 base chemistry on an S4 flow cell.

value: Brain

tag: mouse strain

tag: injection

value: PBS


title: Poly(I:C) flank left treated tumor biological replicate 3


title: hCSF1_5

description:
hCSF1x1901
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: hCSF1_2

description:
hCSF1x1880
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: T.38.C4

value: large B-cell lymphoma


title: N.24.C2


title: N.23.C2


title: T.21.C2


title: hCSF1_1

description:
hCSF1x3
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: hFIRE_PBS_4

description:
FIREx201
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: hFIRE_PBS_3

description:
FIREx190
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: T.20.C2

value: EXP, 2:poor-EXP):2


title: T.19.C2

value: CD3+ selected leukapheresis, patient


title: N.31.C3


title: hFIRE_PBS_1

description:
FIREx138
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: hFIRE_PBS_2

description:
FIREx185
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: GCB_Cre_Pos, scRNA-seq

city: Iowa City

first: Noah

middle: S

last: Butler

state: IA

address: 4-350 BSB, 51 Newton Road

department: Department of Microbiology and Immunology

institute: University of Iowa

description: scRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1, 10x Genomics Cloud Analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Splenic germinal center B cells were enriched using anti-GL-7-PE and anti-PE microbeads (Miltenyi Biotec), then FACS-sorted (BD FACSAria II) CD19+B220+CD95+GL-7+ cells from day 32 P. yoelii-infected Cre neg (IL21fl/fl, pooled from n = 4) littermate control or CD4CreERT2 x IL21fl/fl (IL21Δ/Δ, pooled from n = 4) mice that were treated with Tamoxifen on days 16-18 p.i. Sorted cells were loaded onto the 10x Chromium X Controller (10x Genomics) with a target cell number of 10,000 cells per sample.
scRNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (dual index) (10x Genomics) according to the manufacturer’s protocols. Barcoded libraries were pooled and sequenced on an Illumina NovaSeq 6000 instrument (IIHG, University of Iowa) using a NovaSeq SP v1.5 Reagent Kit (138 total cycles) (Illumina) with the following cycle counts: 28 (read 1), 10 (i7 Index), 10 (i5 Index), 90 (read 2). Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division.

treatment_protocol: CD4CreERt2 x IL21 fl/fl (Cre negative used as littermate controls) mice were treated with 4 mg Tamoxifen on days 16, 17, and 18 post-infection with Plasmodium yoelii.

value: GC B cells

value: Cre+

value: tamoxifen


title: T.16.C2


title: T.15.C2


title: GCB_Cre_Neg, scRNA-seq

description: scRNA-seq

value: spleen

value: Cre-


title: Mn-N/C-TUMOR-rep3

city: Shanghai

first: Wen

last: Qiao

address: 1630 Dongfang Road, Pudong New Area, Shanghai

institute: 上海交通大学医学院

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: 1) 10% base quality<15 b) 13% base quality<20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: Excel file contain fpkms and counts for each sample

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. MC38 tumor cells were cultured at 37C at 5% CO2, and were orthotopically injected into the right flank of male C57BL/6J mice subcutaneously.

extract_protocol:
The tumor tissues were harvested and snap frozen in the liquid nitrogen. RNA from tumor tissues was extracted using Trizol.  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice with palpable tumors were intratumorally injected with saline (50μl) or Mn-N/C (70mg/kg, 50μl) every 3 days. Mice were euthanized, and the tumor tissues were collected until the tumor volume reached 800-1000 mm3.

value: colon cancer cells

value: Mn-N/C