description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi711A12-ORGi5037-96P166


status: Public on Jun 05 2025

type: SRA

city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

country: USA

institute: DOE Joint Genome Institute

description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi711H12-ORGi5037-96P166

library_source: genomic

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Capsella rubella Monte_Gargano: Phytozome v1.1
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

molecule: genomic DNA

organism: Capsella rubella

source_name: plant

growth_protocol: Various growth protocols and tissues were used for gDNA extraction depending on the plant species, however gDNA libraries were PCR amplified upstream of DAP-seq to remove condition/tissue-specific DNA modifications.

extract_protocol:
CTAB protocol for gDNA extraction
Genomic DNA fragment libraries were constructed with an average shearing size at 150 bp. Different species were labeled by unique Illumina i5 index adapters to enable multiplexing following the multiDAP method. Upstream of the DAP-seq assay, fragment libraries were amplified for 10 cycles to remove any DNA modifications. After performing the DAP-seq enrichment in 96-well plates with each well containing a single in vitro expressed transcription factor, the libraries were amplified with i7 index primers to attach a unique i7 adapter corresponding to each well.

tag: tissue

value: plant

tag: genotype

tag: tf id

tag: multidap sample_id

tag: 96 well_plate_id


description: Library name: AT5G64750_A_thaliana_Col-0_DAPi709E03-ORGi5005-96P203

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Arabidopsis thaliana Col-0: TAIR10/Araport11
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

organism: Arabidopsis thaliana

tag: tf family

tag: tf source_species


description: Library name: AT4G01280_A_thaliana_Col-0_DAPi709E03-ORGi5005-96P169

value: MYBRELATED


description: Library name: AT3G60530_A_thaliana_Col-0_DAPi709E05-ORGi5005-96P203


description: Library name: AL3G23910.t2_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P247

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Brassica oleracea TO1000DH3: NCBI RefSeq GCF_000695525.1
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

organism: Brassica oleracea

value: BZIP


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi711A01-ORGi5037-96P166


description: Library name: LOC_Os06g07030.1_A_thaliana_Col-0_DAPi709E01-ORGi5005-96P354


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712H12-ORGi5037-96P155


description: Library name: AT5G56110_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P220

value: MYB


description: Library name: AT2G18550_B_oleracea_TO1000DH3_DAPi712E07-ORGi5021-96P220

value: HOMEOBOX


description: Library name: AT1G13260_A_thaliana_Col-0_DAPi709E01-ORGi5005-96P206

value: RAV


description: Library name: AT5G11260_A_thaliana_Col-0_DAPi709D12-ORGi5005-96P206


description: Library name: AT1G76880_B_oleracea_TO1000DH3_DAPi712E06-ORGi5021-96P155

value: TRIHELIX


description: Library name: AT1G13260_A_thaliana_Col-0_DAPi709E01-ORGi5005-96P203


description: Library name: LOC_Os10g26500.1_A_thaliana_Col-0_DAPi709D12-ORGi5005-96P354


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712A12-ORGi5037-96P155


description: Library name: AT3G60530_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P220


description: Library name: XP_013587997.1_A_thaliana_Col-0_DAPi709D11-ORGi5005-96P354

value: WRKY


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712A01-ORGi5037-96P155


description: Library name: AT4G25470_A_thaliana_Col-0_DAPi709D11-ORGi5005-96P169


description: Library name: AT3G18990_A_thaliana_Col-0_DAPi709D11-ORGi5005-96P206


description: Library name: AT5G11260_A_thaliana_Col-0_DAPi709D12-ORGi5005-96P203


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi710H12-ORGi5037-96P151


description: Library name: AT3G18990_A_thaliana_Col-0_DAPi709D11-ORGi5005-96P203


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi710A12-ORGi5037-96P151


description: Library name: AT5G13790_A_thaliana_Col-0_DAPi709D10-ORGi5005-96P203

value: MADS


description: Library name: AL8G38770.t1_A_thaliana_Col-0_DAPi709E02-ORGi5005-96P354

value: ARF


description: Library name: LOC_Os02g42970.1_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P247

value: NAC


description: Library name: LOC_Os08g06110.3_A_thaliana_Col-0_DAPi709D10-ORGi5005-96P354


description: Library name: AT5G62020_B_oleracea_TO1000DH3_DAPi712E04-ORGi5021-96P220

value: HSF


description: Library name: AT5G13790_A_thaliana_Col-0_DAPi709D10-ORGi5005-96P206


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi710H01-ORGi5037-96P151


description: Library name: AL8G10650.t1_A_thaliana_Col-0_DAPi709D09-ORGi5005-96P354


description: Library name: AT5G64750_B_oleracea_TO1000DH3_DAPi712E03-ORGi5021-96P220


description: Library name: AT1G01060_A_thaliana_Col-0_DAPi709D10-ORGi5005-96P169


description: Library name: AT5G03150_A_thaliana_Col-0_DAPi709D08-ORGi5005-96P206


description: Library name: AT4G00730_B_oleracea_TO1000DH3_DAPi712E05-ORGi5021-96P155


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712H01-ORGi5037-96P220


description: Library name: AT5G03150_A_thaliana_Col-0_DAPi709D08-ORGi5005-96P203


description: Library name: Carub.0008s0285.1_A_thaliana_Col-0_DAPi709D08-ORGi5005-96P354


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712A12-ORGi5037-96P220


description: Library name: AT4G21030_B_oleracea_TO1000DH3_DAPi712E02-ORGi5021-96P155


description: Library name: AT1G74480_A_thaliana_Col-0_DAPi709D07-ORGi5005-96P206

value: RWPRK


description: Library name: LOC_Os06g07030.1_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P247


description: Library name: AT1G13260_B_oleracea_TO1000DH3_DAPi712E01-ORGi5021-96P220


description: Library name: Solyc01g095460.3.1_A_thaliana_Col-0_DAPi709D07-ORGi5005-96P354


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712A01-ORGi5037-96P220


description: Library name: AL2G28980.t1_C_rubella_Monte_Gargano_DAPi712H11-ORGi5037-96P247


description: Library name: AT1G74480_A_thaliana_Col-0_DAPi709D07-ORGi5005-96P203


description: Library name: LOC_Os10g26500.1_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P247


description: Library name: AT3G57920_A_thaliana_Col-0_DAPi709D06-ORGi5005-96P203

value: SBP


description: Library name: AT5G54230_A_thaliana_Col-0_DAPi709D07-ORGi5005-96P169


description: Library name: AT2G46270_C_rubella_Monte_Gargano_DAPi712H11-ORGi5037-96P220


description: Library name: AT3G57920_A_thaliana_Col-0_DAPi709D06-ORGi5005-96P206


description: Library name: AT2G01930_A_thaliana_Col-0_DAPi709D05-ORGi5005-96P206

value: BBRBPC


description: Library name: AT5G11260_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P220


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712H12-ORGi5037-96P220


description: Library name: Carub.0002s1959.1_C_rubella_Monte_Gargano_DAPi712H10-ORGi5037-96P247


description: Library name: AT2G01930_A_thaliana_Col-0_DAPi709D06-ORGi5005-96P169


description: Library name: AT2G01930_A_thaliana_Col-0_DAPi709D05-ORGi5005-96P203


description: Library name: AT3G56850_B_oleracea_TO1000DH3_DAPi712D12-ORGi5021-96P155


description: Library name: AT2G47070_C_rubella_Monte_Gargano_DAPi712H10-ORGi5037-96P220


description: Library name: XP_013587997.1_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P247


description: Library name: AT3G18990_B_oleracea_TO1000DH3_DAPi712D11-ORGi5021-96P220


description: Library name: AT5G62940_A_thaliana_Col-0_DAPi709D05-ORGi5005-96P169


description: Library name: Carub.0001s1194.1_A_thaliana_Col-0_DAPi709D03-ORGi5005-96P354


description: Library name: AT5G65410_A_thaliana_Col-0_DAPi709D03-ORGi5005-96P206

value: ZFHD


description: Library name: Solyc08g078340.3.1_C_rubella_Monte_Gargano_DAPi712H09-ORGi5037-96P247


description: Library name: LOC_Os08g06110.3_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P247


description: Library name: XP_013634112.1_C_rubella_Monte_Gargano_DAPi712H08-ORGi5037-96P247


description: Library name: AT4G25480_A_thaliana_Col-0_DAPi709D03-ORGi5005-96P169


description: Library name: AT3G50260_A_thaliana_Col-0_DAPi709D02-ORGi5005-96P203


description: Library name: AT3G50260_A_thaliana_Col-0_DAPi709D02-ORGi5005-96P206


description: Library name: LOC_Os02g33430.1_A_thaliana_Col-0_DAPi709D05-ORGi5005-96P354


description: Library name: AT1G36060_A_thaliana_Col-0_DAPi709D02-ORGi5005-96P169


description: Library name: LOC_Os01g17260.2_C_rubella_Monte_Gargano_DAPi712H07-ORGi5037-96P247


description: Library name: AT3G22830_A_thaliana_Col-0_DAPi709D01-ORGi5005-96P206


description: Library name: AT5G17300_C_rubella_Monte_Gargano_DAPi712H08-ORGi5037-96P220


description: Library name: AT5G18560_C_rubella_Monte_Gargano_DAPi712H07-ORGi5037-96P220


description: Library name: Carub.0001s3581.1.p_A_thaliana_Col-0_DAPi709D01-ORGi5005-96P354


description: Library name: AT3G22830_A_thaliana_Col-0_DAPi709D01-ORGi5005-96P203


description: Library name: AL8G10650.t1_B_oleracea_TO1000DH3_DAPi712D09-ORGi5021-96P247


description: Library name: Carub.0008s0285.1_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P247


description: Library name: AT3G49530_C_rubella_Monte_Gargano_DAPi712H07-ORGi5037-96P155


description: Library name: AT2G46770_B_oleracea_TO1000DH3_DAPi712D10-ORGi5021-96P155


description: Library name: AT5G65410_A_thaliana_Col-0_DAPi709D03-ORGi5005-96P203


description: Library name: AT1G12260_A_thaliana_Col-0_DAPi709C12-ORGi5005-96P203


description: Library name: AL4G45550.t1_C_rubella_Monte_Gargano_DAPi712H06-ORGi5037-96P247


description: Library name: AT1G12260_A_thaliana_Col-0_DAPi709C12-ORGi5005-96P206


description: Library name: Solyc01g095460.3.1_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P247


description: Library name: AL2G40550.t1_A_thaliana_Col-0_DAPi709C11-ORGi5005-96P354


description: Library name: AT4G00730_A_thaliana_Col-0_DAPi709C11-ORGi5005-96P203


description: Library name: AT2G40260_A_thaliana_Col-0_DAPi709C12-ORGi5005-96P169


description: Library name: AT5G10030_A_thaliana_Col-0_DAPi709C11-ORGi5005-96P169


description: Library name: AT4G00730_A_thaliana_Col-0_DAPi709C11-ORGi5005-96P206


description: Library name: AT5G11510_C_rubella_Monte_Gargano_DAPi712H06-ORGi5037-96P155


description: Library name: AT5G39610_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P155


description: Library name: AT3G57920_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P220


description: Library name: AT1G01060_C_rubella_Monte_Gargano_DAPi712H05-ORGi5037-96P220


description: Library name: AT5G61620_C_rubella_Monte_Gargano_DAPi712H05-ORGi5037-96P155


description: Library name: AT3G18400_A_thaliana_Col-0_DAPi709C10-ORGi5005-96P169


description: Library name: AT4G36620_A_thaliana_Col-0_DAPi709C10-ORGi5005-96P206


description: Library name: AT5G03150_B_oleracea_TO1000DH3_DAPi712D08-ORGi5021-96P220


description: Library name: AT4G36620_A_thaliana_Col-0_DAPi709C10-ORGi5005-96P203


description: Library name: AT1G20980_B_oleracea_TO1000DH3_DAPi712D06-ORGi5021-96P155


description: Library name: Solyc01g102340.3.1_C_rubella_Monte_Gargano_DAPi712H04-ORGi5037-96P247


description: Library name: LOC_Os02g33430.1_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P247


description: Library name: Carub.0002s1646.1_A_thaliana_Col-0_DAPi709C12-ORGi5005-96P354


description: Library name: Carub.0001s0116.1_A_thaliana_Col-0_DAPi709C10-ORGi5005-96P354


description: Library name: AT3G02940_C_rubella_Monte_Gargano_DAPi712H04-ORGi5037-96P220


description: Library name: XP_013613838.1_A_thaliana_Col-0_DAPi709C08-ORGi5005-96P354


description: Library name: AT5G62470_A_thaliana_Col-0_DAPi709C08-ORGi5005-96P206


description: Library name: AT3G50410_C_rubella_Monte_Gargano_DAPi712H06-ORGi5037-96P220


description: Library name: AT5G62470_A_thaliana_Col-0_DAPi709C08-ORGi5005-96P203


description: Library name: AT1G76420_A_thaliana_Col-0_DAPi709C09-ORGi5005-96P206


description: Library name: AT1G53230_A_thaliana_Col-0_DAPi709C08-ORGi5005-96P169

value: TCP


description: Library name: AT1G74480_B_oleracea_TO1000DH3_DAPi712D07-ORGi5021-96P220

value: plant


description: Library name: AT2G47070_C_rubella_Monte_Gargano_DAPi712H04-ORGi5037-96P155


description: Library name: LOC_Os01g46970.1_A_thaliana_Col-0_DAPi709C07-ORGi5005-96P354


description: Library name: AT2G01930_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P220


description: Library name: XP_013629448.1_C_rubella_Monte_Gargano_DAPi712H03-ORGi5037-96P247


description: Library name: AT5G45300_B_oleracea_TO1000DH3_DAPi712D04-ORGi5021-96P155


description: Library name: AT2G30250_C_rubella_Monte_Gargano_DAPi712H03-ORGi5037-96P220


description: Library name: AT1G76420_A_thaliana_Col-0_DAPi709C09-ORGi5005-96P203


description: Library name: AT5G60130_A_thaliana_Col-0_DAPi709C07-ORGi5005-96P206


description: Library name: AT5G60130_A_thaliana_Col-0_DAPi709C07-ORGi5005-96P203


description: Library name: Carub.0001s1194.1_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P247


description: Library name: AT5G65410_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P220


description: Library name: AT5G08130_A_thaliana_Col-0_DAPi709C05-ORGi5005-96P203

value: BHLH


description: Library name: AT3G11280_A_thaliana_Col-0_DAPi709C06-ORGi5005-96P169

value: MYBRELATED


description: Library name: AT5G08130_A_thaliana_Col-0_DAPi709C05-ORGi5005-96P206


description: Library name: AT2G22430_C_rubella_Monte_Gargano_DAPi712H02-ORGi5037-96P220


description: Library name: AT4G17980_B_oleracea_TO1000DH3_DAPi712D03-ORGi5021-96P155


description: Library name: AT5G06100_C_rubella_Monte_Gargano_DAPi712H02-ORGi5037-96P155

value: MYB


description: Library name: AT3G02940_A_thaliana_Col-0_DAPi709C05-ORGi5005-96P169


description: Library name: AT3G27010_A_thaliana_Col-0_DAPi709C04-ORGi5005-96P206


description: Library name: Solyc08g068320.3.1_A_thaliana_Col-0_DAPi709C04-ORGi5005-96P354


description: Library name: XP_013609718.1_C_rubella_Monte_Gargano_DAPi712G12-ORGi5037-96P247

value: HOMEOBOX


description: Library name: AT3G27010_A_thaliana_Col-0_DAPi709C04-ORGi5005-96P203


description: Library name: AT4G36620_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P155


description: Library name: AT3G20770_B_oleracea_TO1000DH3_DAPi712D05-ORGi5021-96P155

value: EIL


description: Library name: AT5G57620_C_rubella_Monte_Gargano_DAPi712G12-ORGi5037-96P155


description: Library name: Carub.0001s3581.1.p_B_oleracea_TO1000DH3_DAPi712D01-ORGi5021-96P247


description: Library name: AT5G03790_A_thaliana_Col-0_DAPi709C06-ORGi5005-96P203


description: Library name: AT3G50260_B_oleracea_TO1000DH3_DAPi712D02-ORGi5021-96P220


description: Library name: AT2G02080_A_thaliana_Col-0_DAPi709C03-ORGi5005-96P203


description: Library name: AT4G36740_C_rubella_Monte_Gargano_DAPi712H03-ORGi5037-96P155


description: Library name: Carub.0002s1646.1_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P247


description: Library name: AT5G09410_C_rubella_Monte_Gargano_DAPi712G11-ORGi5037-96P220

value: CAMTA


description: Library name: AT1G69690_A_thaliana_Col-0_DAPi709C02-ORGi5005-96P206


description: Library name: AT2G02080_A_thaliana_Col-0_DAPi709C03-ORGi5005-96P206


description: Library name: AT1G69690_A_thaliana_Col-0_DAPi709C02-ORGi5005-96P203


description: Library name: AT1G12260_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P220


description: Library name: AT5G03790_A_thaliana_Col-0_DAPi709C06-ORGi5005-96P206


description: Library name: AT3G01970_A_thaliana_Col-0_DAPi709C04-ORGi5005-96P169

value: WRKY


description: Library name: AT3G27010_A_thaliana_Col-0_DAPi709C02-ORGi5005-96P169


description: Library name: AT5G65210_C_rubella_Monte_Gargano_DAPi712G11-ORGi5037-96P155

value: BZIP


description: Library name: AT1G27730_A_thaliana_Col-0_DAPi709C01-ORGi5005-96P206


description: Library name: AT1G27730_A_thaliana_Col-0_DAPi709C01-ORGi5005-96P203


description: Library name: XP_013589913.1_C_rubella_Monte_Gargano_DAPi712G10-ORGi5037-96P247


description: Library name: AT1G06850_B_oleracea_TO1000DH3_DAPi712C12-ORGi5021-96P155


description: Library name: AT2G40620_A_thaliana_Col-0_DAPi709B12-ORGi5005-96P206


description: Library name: AT5G45300_C_rubella_Monte_Gargano_DAPi712G10-ORGi5037-96P220


description: Library name: AL2G40550.t1_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P247


description: Library name: XP_013602769.1_A_thaliana_Col-0_DAPi709C03-ORGi5005-96P354


description: Library name: AT2G40620_A_thaliana_Col-0_DAPi709B12-ORGi5005-96P203


description: Library name: Solyc03g116890.3.1_C_rubella_Monte_Gargano_DAPi712G11-ORGi5037-96P247


description: Library name: Solyc07g040920.2.1_A_thaliana_Col-0_DAPi709B11-ORGi5005-96P354


description: Library name: LOC_Os10g41200.1_C_rubella_Monte_Gargano_DAPi712G09-ORGi5037-96P247


description: Library name: AT5G03790_A_thaliana_Col-0_DAPi709B12-ORGi5005-96P169


description: Library name: AT3G20770_A_thaliana_Col-0_DAPi709B11-ORGi5005-96P206


description: Library name: AT1G72740_C_rubella_Monte_Gargano_DAPi712G09-ORGi5037-96P220


description: Library name: AT1G43700_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P155


description: Library name: AT3G20770_A_thaliana_Col-0_DAPi709B11-ORGi5005-96P203


description: Library name: Carub.0001s0116.1_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P247


description: Library name: AT2G35530_C_rubella_Monte_Gargano_DAPi712G09-ORGi5037-96P155


description: Library name: XP_013587350.1_A_thaliana_Col-0_DAPi709B10-ORGi5005-96P354


description: Library name: AT5G18270_B_oleracea_TO1000DH3_DAPi712C10-ORGi5021-96P155


description: Library name: AT3G52440_A_thaliana_Col-0_DAPi709B11-ORGi5005-96P169


description: Library name: AT1G20910_A_thaliana_Col-0_DAPi709B10-ORGi5005-96P206

value: ARID


description: Library name: AL4G38490.t1_C_rubella_Monte_Gargano_DAPi712G08-ORGi5037-96P247


description: Library name: AT1G03800_A_thaliana_Col-0_DAPi709C01-ORGi5005-96P169


description: Library name: AT1G20910_A_thaliana_Col-0_DAPi709B10-ORGi5005-96P203


description: Library name: Solyc06g048630.3.1_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P247


description: Library name: AT2G24430_A_thaliana_Col-0_DAPi709B10-ORGi5005-96P169

value: NAC


description: Library name: AT2G01940_C_rubella_Monte_Gargano_DAPi712G08-ORGi5037-96P220


description: Library name: AT4G00730_B_oleracea_TO1000DH3_DAPi712C11-ORGi5021-96P220


description: Library name: AT1G76420_B_oleracea_TO1000DH3_DAPi712C09-ORGi5021-96P220


description: Library name: AT1G79580_A_thaliana_Col-0_DAPi709B09-ORGi5005-96P206


description: Library name: AT1G79580_A_thaliana_Col-0_DAPi709B09-ORGi5005-96P203


description: Library name: Carub.0003s1161.1.p_C_rubella_Monte_Gargano_DAPi712G07-ORGi5037-96P247


description: Library name: AT5G19790_C_rubella_Monte_Gargano_DAPi712G07-ORGi5037-96P220


description: Library name: AL8G13510.t2_A_thaliana_Col-0_DAPi709B08-ORGi5005-96P354


description: Library name: Carub.0004s2898.1.p_A_thaliana_Col-0_DAPi709B07-ORGi5005-96P354


description: Library name: AT1G09540_A_thaliana_Col-0_DAPi709B08-ORGi5005-96P206


description: Library name: AT4G34590_C_rubella_Monte_Gargano_DAPi712G07-ORGi5037-96P155


description: Library name: AT5G62470_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P220


description: Library name: AT1G09540_A_thaliana_Col-0_DAPi709B08-ORGi5005-96P203


description: Library name: AT2G30340_A_thaliana_Col-0_DAPi709B07-ORGi5005-96P206


description: Library name: AT5G02320_C_rubella_Monte_Gargano_DAPi712G06-ORGi5037-96P220


description: Library name: LOC_Os01g46970.1_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P247


description: Library name: AT5G60130_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P220


description: Library name: AT5G09410_C_rubella_Monte_Gargano_DAPi712G06-ORGi5037-96P155


description: Library name: AT4G25470_A_thaliana_Col-0_DAPi709B06-ORGi5005-96P206


description: Library name: AT5G03790_B_oleracea_TO1000DH3_DAPi712C06-ORGi5021-96P220


description: Library name: AT4G25470_A_thaliana_Col-0_DAPi709B06-ORGi5005-96P203


description: Library name: AT1G69180_C_rubella_Monte_Gargano_DAPi712G05-ORGi5037-96P220


description: Library name: AT3G08500_A_thaliana_Col-0_DAPi709B05-ORGi5005-96P203


description: Library name: AT1G29160_A_thaliana_Col-0_DAPi709B04-ORGi5005-96P206


description: Library name: XP_013613838.1_B_oleracea_TO1000DH3_DAPi712C08-ORGi5021-96P247


description: Library name: AT5G16820_C_rubella_Monte_Gargano_DAPi712G05-ORGi5037-96P155

value: HSF


description: Library name: AT4G32730_B_oleracea_TO1000DH3_DAPi712C05-ORGi5021-96P155


description: Library name: AT1G22810_A_thaliana_Col-0_DAPi709B04-ORGi5005-96P169


description: Library name: AL1G23550.t1_A_thaliana_Col-0_DAPi709B03-ORGi5005-96P354


description: Library name: Solyc08g068320.3.1_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P247


description: Library name: AT3G56400_A_thaliana_Col-0_DAPi709B02-ORGi5005-96P206


description: Library name: AT2G30340_A_thaliana_Col-0_DAPi709B07-ORGi5005-96P203


description: Library name: LOC_Os01g18240.1_C_rubella_Monte_Gargano_DAPi712G04-ORGi5037-96P247


description: Library name: AT3G56400_A_thaliana_Col-0_DAPi709B02-ORGi5005-96P203


description: Library name: AT1G46768_C_rubella_Monte_Gargano_DAPi712G04-ORGi5037-96P220


description: Library name: AT3G62420_B_oleracea_TO1000DH3_DAPi712C07-ORGi5021-96P155


description: Library name: AT3G08500_A_thaliana_Col-0_DAPi709B05-ORGi5005-96P206


description: Library name: AT3G27010_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P220


description: Library name: AT4G38000_A_thaliana_Col-0_DAPi709B02-ORGi5005-96P169


description: Library name: AL1G53260.t1_A_thaliana_Col-0_DAPi709B01-ORGi5005-96P354


description: Library name: AT5G67300_A_thaliana_Col-0_DAPi709B01-ORGi5005-96P206


description: Library name: LOC_Os03g21800.1_A_thaliana_Col-0_DAPi709B09-ORGi5005-96P354


description: Library name: AT5G67300_A_thaliana_Col-0_DAPi709B01-ORGi5005-96P203


description: Library name: AT1G32150_C_rubella_Monte_Gargano_DAPi712G03-ORGi5037-96P155


description: Library name: XP_013602769.1_B_oleracea_TO1000DH3_DAPi712C03-ORGi5021-96P247


description: Library name: AT1G29160_A_thaliana_Col-0_DAPi709B04-ORGi5005-96P203


description: Library name: LOC_Os01g51154.1_A_thaliana_Col-0_DAPi709A11-ORGi5005-96P354


description: Library name: AT3G50060_C_rubella_Monte_Gargano_DAPi712G02-ORGi5037-96P220


description: Library name: AT1G69690_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P220


description: Library name: AT4G32730_A_thaliana_Col-0_DAPi709A11-ORGi5005-96P206


description: Library name: AT4G01500_C_rubella_Monte_Gargano_DAPi712G02-ORGi5037-96P155


description: Library name: AT4G32730_A_thaliana_Col-0_DAPi709A11-ORGi5005-96P203


description: Library name: AT5G17800_B_oleracea_TO1000DH3_DAPi712C02-ORGi5021-96P155


description: Library name: AT5G45580_A_thaliana_Col-0_DAPi709A11-ORGi5005-96P169


description: Library name: AT1G18330_C_rubella_Monte_Gargano_DAPi712G01-ORGi5037-96P220


description: Library name: AL1G11460.t1_A_thaliana_Col-0_DAPi709A10-ORGi5005-96P354


description: Library name: AT4G14770_B_oleracea_TO1000DH3_DAPi712C04-ORGi5021-96P155

value: CPP


description: Library name: AT1G27730_B_oleracea_TO1000DH3_DAPi712C01-ORGi5021-96P220


description: Library name: AT1G80840_C_rubella_Monte_Gargano_DAPi712G03-ORGi5037-96P220


description: Library name: AT5G05550_A_thaliana_Col-0_DAPi709A10-ORGi5005-96P206

value: TRIHELIX


description: Library name: AT5G52020_A_thaliana_Col-0_DAPi709A10-ORGi5005-96P169


description: Library name: AT4G18450_C_rubella_Monte_Gargano_DAPi712G01-ORGi5037-96P155


description: Library name: Carub.0004s2291.1_A_thaliana_Col-0_DAPi709A09-ORGi5005-96P354


description: Library name: AT1G13600_C_rubella_Monte_Gargano_DAPi712F12-ORGi5037-96P155


description: Library name: LOC_Os09g25060.1_C_rubella_Monte_Gargano_DAPi712F11-ORGi5037-96P247


description: Library name: Solyc11g064950.3.1_A_thaliana_Col-0_DAPi709A08-ORGi5005-96P354


description: Library name: AT5G65130_A_thaliana_Col-0_DAPi709B01-ORGi5005-96P169


description: Library name: AT4G25490_A_thaliana_Col-0_DAPi709A08-ORGi5005-96P206


description: Library name: AT2G40620_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P220


description: Library name: AT4G25490_A_thaliana_Col-0_DAPi709A08-ORGi5005-96P203


description: Library name: AT1G76880_C_rubella_Monte_Gargano_DAPi712F11-ORGi5037-96P220


description: Library name: AT3G28920_A_thaliana_Col-0_DAPi709A08-ORGi5005-96P169


description: Library name: AT1G52880_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P155


description: Library name: Solyc07g040920.2.1_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P247


description: Library name: AT5G11260_C_rubella_Monte_Gargano_DAPi712F11-ORGi5037-96P155


description: Library name: AT1G22070_B_oleracea_TO1000DH3_DAPi712B11-ORGi5021-96P155


description: Library name: AL2G32420.t2_C_rubella_Monte_Gargano_DAPi712F10-ORGi5037-96P247


description: Library name: AT3G12250_A_thaliana_Col-0_DAPi709A07-ORGi5005-96P203


description: Library name: AT5G05550_A_thaliana_Col-0_DAPi709A10-ORGi5005-96P203


description: Library name: XP_013587350.1_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P247


description: Library name: XP_013589953.1_B_oleracea_TO1000DH3_DAPi712B12-ORGi5021-96P247


description: Library name: AT4G14770_C_rubella_Monte_Gargano_DAPi712F10-ORGi5037-96P220


description: Library name: AT1G20910_B_oleracea_TO1000DH3_DAPi712B10-ORGi5021-96P220


description: Library name: AT5G10030_A_thaliana_Col-0_DAPi709A06-ORGi5005-96P203


description: Library name: AT3G15170_C_rubella_Monte_Gargano_DAPi712F10-ORGi5037-96P155


description: Library name: AT5G52660_A_thaliana_Col-0_DAPi709A06-ORGi5005-96P169


description: Library name: AT5G62940_A_thaliana_Col-0_DAPi709A05-ORGi5005-96P206


description: Library name: AT5G62940_A_thaliana_Col-0_DAPi709A05-ORGi5005-96P203


description: Library name: AT5G07310_A_thaliana_Col-0_DAPi709A05-ORGi5005-96P169


description: Library name: XP_013631386.1_A_thaliana_Col-0_DAPi709A07-ORGi5005-96P354


description: Library name: LOC_Os03g21800.1_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P247


description: Library name: Carub.0008s0039.1_C_rubella_Monte_Gargano_DAPi712F09-ORGi5037-96P247


description: Library name: AT1G49480_A_thaliana_Col-0_DAPi709A04-ORGi5005-96P206

value: REM


description: Library name: AT3G12250_A_thaliana_Col-0_DAPi709A07-ORGi5005-96P206


description: Library name: AT2G02820_C_rubella_Monte_Gargano_DAPi712F08-ORGi5037-96P220


description: Library name: AT2G45480_C_rubella_Monte_Gargano_DAPi712F09-ORGi5037-96P220

value: GRF


description: Library name: Carub.0007s0775.1_A_thaliana_Col-0_DAPi709A04-ORGi5005-96P354


description: Library name: AT1G49480_A_thaliana_Col-0_DAPi709A04-ORGi5005-96P203


description: Library name: AT5G07680_C_rubella_Monte_Gargano_DAPi712F08-ORGi5037-96P155


description: Library name: AT1G69780_A_thaliana_Col-0_DAPi709A03-ORGi5005-96P206


description: Library name: AT4G31060_A_thaliana_Col-0_DAPi709A03-ORGi5005-96P169


description: Library name: AT3G04070_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P155


description: Library name: AT1G79580_B_oleracea_TO1000DH3_DAPi712B09-ORGi5021-96P220


description: Library name: Carub.0004s2898.1.p_B_oleracea_TO1000DH3_DAPi712B07-ORGi5021-96P247


description: Library name: XP_013586407.1_C_rubella_Monte_Gargano_DAPi712F07-ORGi5037-96P247


description: Library name: AT5G13910_A_thaliana_Col-0_DAPi709A04-ORGi5005-96P169


description: Library name: AT1G69780_A_thaliana_Col-0_DAPi709A03-ORGi5005-96P203


description: Library name: AT3G09600_A_thaliana_Col-0_DAPi709A02-ORGi5005-96P169


description: Library name: AT5G10030_A_thaliana_Col-0_DAPi709A06-ORGi5005-96P206


description: Library name: AT5G39760_A_thaliana_Col-0_DAPi709A02-ORGi5005-96P206

value: ZFHD


description: Library name: AT3G18990_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P155

value: plant


description: Library name: AT5G52830_C_rubella_Monte_Gargano_DAPi712F07-ORGi5037-96P220


title: Athaliana,shoot,rep2

description: Library name: NYSTG

library_source: transcriptomic single cell

data_processing:
Raw fastq files for each library were filtered using BBTools v38.96 bbduk.sh to remove read pairs with 31-mers in read 2 matching common ribosomal 31-mers. Filtered fastq files from 10X Chromium libraries were processed with Cellranger count v7.0.1, and filtered fastqs from BD Rhapsody libraries were processed with BD Rhapsody CWL pipeline (v2.2, available at bitbucket.org/CRSwDev/cwl) with default parameters. For libraries containing multiplexed species, combined-species reference genome and gene annotation files with species name preprended to the chromosome name were provided. Both processing workflows performed barcode identification, alignment, UMI de-duplication, gene aggregation, and final DGE matrix construction. Custom scripts were used to differentiate cell barcodes containing nuclei from each species (or multiple species in the case of doublets), as well as putatively empty droplets/wells and perform QC filtering. Demultiplexed libraries from the same species and tissue were integrated and clustered using Seurat v5.0 to create final atlases for a subset of species (available here as 14 Supplementary .RDS files).
Assembly: Arabidopsis thaliana Col-0 TAIR/Araport via Phytozome
Assembly: Arabidopsis lyrata MN47 Phytozome v2.1
Assembly: Brassica oleracea TO1000DH3 NCBI RefSeq GCF_000695525.1
Assembly: Capsella rubella Monte_Gargano Phytozome v1.1
Assembly: Sorghum bicolor RTx430 Phytozome v2.1
Assembly: Camelina sativa DH55 (via cruciferseq)
Assembly: Panicum hallii var. FIL2 Phytozome v3.2
Assembly: Brachypodium distachyon Bd21 Phytozome v3.2
Assembly: Thlaspi arvense MN106 NCBI GCA_911865555.2
Supplementary files format and content: Tab-separated values files and matrix files summarising transcript counts of each gene associated with each cell barcode (raw counts before any barcode filtering)

molecule: polyA RNA

source_name: seedling shoot

growth_protocol: Seeds from each species were surface sterilized before planting vertically on agar plates containing 3 mM Ca(NO3)2, 1.5 mM MgSO4, 1.25 mM NH4H2PO4, 1 mM KCl, 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seedling root and shoot tissues from A. thaliana, A. lyrata, C. rubella, and B. oleracea were harvested at the 5-7 day old growth stage, and  root and shoot samples from S. bicolor were harvested from 3 day old seedlings. For mature leaves, we sampled the youngest fully expanded rosette leaf from plants grown in soil in a plant grow room or cold room. For floral buds, we sampled young buds on the main stem from plants grown in soil, where the petal was just emerging (~1 mm visible). Plant tissue samples were either processed immediately after harvest or flash frozen in liquid nitrogen.

extract_protocol:
Nuclei were isolated by chopping 20-100 mg fresh or frozen tissue for 3 minutes using a razor blade on a glass plate with 100-200 μl buffer in a cold room at 4°C. For multiplexed samples, tissues from different species were weighed separately before being combined and chopped together. The samples were then transferred to a 48-well filter plate. The filtered nuclei solution was centrifuged at 500x g for 10 minutes at 4°C to pellet the nuclei, after which the supernatant was discarded.
For profiling with 10X Chromium, the nuclei suspension was diluted to a concentration of 700-1000 nuclei/μl, then single nuclei were partitioned and barcoded using a Chromium system (10x Genomics) with the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index). Approximately 20,000 nuclei in total were loaded for single species samples, and up to 60,000 nuclei for multiplexed species samples. Library creation was carried out following the manufacturer’s protocol. For profiling with BD Rhapsody, the pooled nuclei suspension was diluted to a concentration of 600-900 total nuclei/μl, then single nuclei were partitioned and barcoded on a BD Rhapsody system (BD Rhapsody HT Xpress, BD Rhapsody Scanner), using the BD Rhapsody WTA V3 kit and cartridge, loading 50,000-150,000 total nuclei per lane. Library creation was carried out following the manufacturer’s protocol.

value: seedling shoot

tag: tissue condition

value: frozen

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


title: Athaliana,root,rep1

description: Library name: NYSTO

source_name: seedling root

value: seedling root


description: Library name: AT2G45420_C_rubella_Monte_Gargano_DAPi712F06-ORGi5037-96P220


description: Library name: XP_013631649.1_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P247


description: Library name: AL8G13510.t2_B_oleracea_TO1000DH3_DAPi712B08-ORGi5021-96P247


title: Athaliana,shoot,rep1

description: Library name: NYSTC


description: Library name: AT2G01060_C_rubella_Monte_Gargano_DAPi712F05-ORGi5037-96P220


title: Athaliana,seedling,rep4

description: Library name: NOTCT

source_name: whole seedling

value: whole seedling


title: Athaliana,seedling,rep3

description: Library name: NNAWP


description: Library name: AT3G08500_B_oleracea_TO1000DH3_DAPi712B05-ORGi5021-96P220

value: MYB


description: Library name: AT4G25480_C_rubella_Monte_Gargano_DAPi712F04-ORGi5037-96P220


title: Athaliana,seedling,rep1

description: Library name: HWZAB


description: Library name: AT1G28370_A_thaliana_Col-0_DAPi709A07-ORGi5005-96P169


description: Library name: AT4G25470_B_oleracea_TO1000DH3_DAPi712B06-ORGi5021-96P220


description: Library name: AT1G29160_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P220


description: Library name: Solyc08g079120.3.1_C_rubella_Monte_Gargano_DAPi712F03-ORGi5037-96P247


title: Arabidopsis thaliana, htr14-1, 4 h 140 mM NaCl, Biol Rep 3

city: Madrid

first: Crisanto

last: Gutierrez

address: Nicolas Cabrera 1

department: Genome Dynamics and Function

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

library_source: transcriptomic

data_processing:
RNA-Seq raw reads were trimmed with Trimmomatic (v 0.39) to remove adapters and small sequences.
Quality control of the raw (151 bp, paired-end) and trimmed reads was assessed with FastQC (v.0.11.9)
Trimmed reads were aligned to the A. thaliana reference genome with HISAT2
Unmapped reads and secondary alignments were filtered out with SAMtools
Gene abundances (TPMs and FPKMs) were counted by StringTie (v 2.2.1) using the Araport 11 GFF annotation file
Assembly: TAIR10
Supplementary files format and content: Text files include FPKM and gene count values for each sample

molecule: total RNA

source_name: Root tips

growth_protocol: Arabidopsis thaliana seedlings were grown in Murashige and Skoog (MS) with 1% sucrose and 1% agar medium. Seedlings were grown in long days (16h light 8h dark) at 22ºC.

extract_protocol:
RNA was isolated with miRNeasy Mini Kit® (Qiagen) following the manufacturer´s instructions.
RNA libraries for RNA-seq were generated using TruSeq Stranded Total RNA kit with Ribo-Zero Plant (Illumina)

treatment_protocol: Wild type and htr14-1 seedlings were treated with 140 mM NaCl during 4 hours 5 days after sowing. Control plants grown in MSS were transfered to new MSS plates for 4 h as a control treatment.

value: Root tips

tag: treatment

value: 4 h 140 mM NaCl


title: Arabidopsis thaliana, htr14-1, 4 h 140 mM NaCl, Biol Rep 2


description: Library name: AT5G02460_B_oleracea_TO1000DH3_DAPi712B04-ORGi5021-96P155


description: Library name: AT5G39760_A_thaliana_Col-0_DAPi709A02-ORGi5005-96P203


title: Arabidopsis thaliana, Col0, 4 h 140 mM NaCl, Biol Rep 3


title: Arabidopsis thaliana, htr14-1, 4 h 140 mM NaCl, Biol Rep 1


description: Library name: AL1G23550.t1_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P247


description: Library name: AT4G31800_C_rubella_Monte_Gargano_DAPi712F02-ORGi5037-96P220

value: WRKY


title: Arabidopsis thaliana, Col0, 4 h 140 mM NaCl, Biol Rep 1


title: Arabidopsis thaliana, Col0, 4 h 140 mM NaCl, Biol Rep 2


description: Library name: AT1G02230_B_oleracea_TO1000DH3_DAPi712B03-ORGi5021-96P155

value: NAC


description: Library name: AT3G56400_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P220


description: Library name: AT5G13790_C_rubella_Monte_Gargano_DAPi712F02-ORGi5037-96P155

value: MADS


title: Arabidopsis thaliana, Col0, No stress, Biol Rep 3

value: No stress


title: Arabidopsis thaliana, Col0, No stress, Biol Rep 2


title: Arabidopsis thaliana, Col0, No stress, Biol Rep 1


title: BBX29OE_bio3

city: Beijing

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

country: China

institute: insitute of botany, chinese academy of sciences

data_processing:
150 nt paired-end high throughput sequencing was performed on an Illumina NovaSeq 6000.
Low quality sequencing reads were removed. Clean reads were mapped to the Arabidopsis reference genome (TAIR10, www.arabidopsis.org) with Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software, and differential expressed genes (DEGs) was identified using edgeR in the R package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) if FoldChange > 1.5 and FDR < 0.05 between case group sample and control group sample. GO and KEGG pathway enrichment analysis was performed using TopGO in the R package (http://bioconductor.org/).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Arabidopsis whole seedling

growth_protocol: Plants were grown under LD conditions at 22ºC for 10 days and harvest at ZT0.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
Sequencing libraries were prepared following the protocol of the Directional RNA library Prep Kit (NEB).

value: whole plant

tag: time point

tag: medium

value: MS+3% sucrose

tag: age


description: Library name: Solyc04g078640.3.1_C_rubella_Monte_Gargano_DAPi712F01-ORGi5037-96P247


description: Library name: AT1G16490_B_oleracea_TO1000DH3_DAPi712B02-ORGi5021-96P155


title: BBX29OE_bio2


description: Library name: AT5G47390_C_rubella_Monte_Gargano_DAPi712F01-ORGi5037-96P220

value: MYBRELATED


description: Library name: AL1G53260.t1_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P247


title: BBX29OE_bio1


title: BBX28OE_bio1


description: Library name: AT1G33240_C_rubella_Monte_Gargano_DAPi712F03-ORGi5037-96P220

value: TRIHELIX


description: Library name: AT1G20910_C_rubella_Monte_Gargano_DAPi712F01-ORGi5037-96P155

value: plant

value: ARID


title: BBX28OE_bio2


description: Library name: AT5G67300_B_oleracea_TO1000DH3_DAPi712B01-ORGi5021-96P220


description: Library name: Solyc05g007180.3.1_C_rubella_Monte_Gargano_DAPi712E12-ORGi5037-96P247

value: HOMEOBOX


title: Col_0_bio3

value: Wild type


title: Col_0_bio2


description: Library name: LOC_Os01g51154.1_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P247


description: Library name: AT1G52880_C_rubella_Monte_Gargano_DAPi712E12-ORGi5037-96P220


description: Library name: AT1G12260_B_oleracea_TO1000DH3_DAPi712A11-ORGi5021-96P155


title: GBM, Patient 7

city: Ann Arbor

first: Wajd

middle: N.

last: Al-Holou

state: MI

address: 1500 E Medical Center Dr

department: Neurosurgery

institute: University of Michigan

description: Library name: P7

data_processing:
For each sample, single-end sequencing generated 150 nucleobase reads for 39-85 million sequences. The quality of raw reads was checked using FastQC (version 0.12.1). Bam files were sorted by query name using samtools (version 1.13). Sequencing reads were aligned to human reference genome from Ensembl (Homo_sapiens.GRCh38.113.gtf.gz) using htseq-count (version 2.0.9) with the following command line options: --format=bam --order=name --type=exon --stranded=no.
Assembly: human reference genome from Ensembl (Homo_sapiens.GRCh38.113.gtf.gz)
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

organism: Homo sapiens

source_name: Brain tumor

extract_protocol:
Total RNA was extracted from tumor samples obtained from three patients (P1, P3, and P7) using standard protocols.
RNA library construction was performed by Tempus (Chicago, IL) to generate raw sequencing data.

value: Brain tumor

tag: diagnosis

value: GBM

value: IDH WT

tag: mgmt promoter_methylation

value: Negative

tag: Sex

value: Male


description: Library name: Carub.0002s2670.1_C_rubella_Monte_Gargano_DAPi712E11-ORGi5037-96P247

tag: tissue

value: WRKY


title: GBM, Patient 3

description: Library name: P3

tag: genotype


description: Library name: AL1G11460.t1_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P247

tag: tf id


title: GBM, Patient 1

description: Library name: P1

value: Equivocal (PCR)


description: Library name: AT5G05550_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P220

tag: multidap sample_id


description: Library name: AT5G53950_B_oleracea_TO1000DH3_DAPi712A10-ORGi5021-96P155

value: NAC

tag: 96 well_plate_id


description: Library name: AT4G10350_C_rubella_Monte_Gargano_DAPi712E11-ORGi5037-96P155

tag: tf family


title: BBX28OE_bio3


description: Library name: Solyc10g005080.3.1_C_rubella_Monte_Gargano_DAPi712E10-ORGi5037-96P247

tag: tf source_species


description: Library name: Carub.0004s2291.1_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P247

value: BZIP


description: Library name: AT4G17980_C_rubella_Monte_Gargano_DAPi712E10-ORGi5037-96P220


description: Library name: AT5G66300_C_rubella_Monte_Gargano_DAPi712E10-ORGi5037-96P155


title: MP96B, Monkeypox virus infected intestinal organoids: samples harvested at 96 hour-post infection

city: Chengdu

first: Pengfei

last: Li

address: Chengdu, Sichuan

institute: Sichuan University

description: Library name: Sample17

data_processing:
Format conversion and sorting were performed with SAMtools (version 0.1.19). Read coverage across the genome was assessed using Bedtools (version 2.31.0).
Assembly: accession NC_063383.1, assembly GCF_014621545.1
Supplementary files format and content: MP_24HvsMP_1H.all_KEGGenrich_significant.xls: Significantly regulated pathways by KEGG enrichment analysis, MPXV infected intestinal organoids at 24 hours compared to MPXV infected intestinal organoids at 1 hours
Supplementary files format and content: MP_24HvsMP_1H_deg_all.xls: Differentially expressed genes in MPXV infected intestinal organoids for 24 hours compared to infection for 1 hour.
Supplementary files format and content: MP_48HvsMP_1H.all_KEGGenrich_significant.xls: Significantly regulated pathways by KEGG enrichment analysis, MPXV infected intestinal organoids at 48 hours compared to MPXV infected intestinal organoids at 1 hours.
Supplementary files format and content: MP_48HvsMP_1H_deg_all.xls: Differentially expressed genes in MPXV infected intestinal organoids for 48 hours compared to infection for 1 hour.
Supplementary files format and content: MP_96HvsCTR.all_KEGGenrich_significant.xls: Significantly regulated pathways by KEGG enrichment analysis, MPXV infected intestinal organoids at 96 hours compared to healthy non-infected organoids.
Supplementary files format and content: MP_96HvsCTR_deg_all.xls: Differentially expressed genes in MPXV infected intestinal organoids for 48 hours compared to non-infected intestinal organoids.
Supplementary files format and content: MP_96HvsMP_1H.all_KEGGenrich_significant.xls: Significantly regulated pathways by KEGG enrichment analysis, MPXV infected intestinal organoids at 96 hours compared to infected intestinal organoids at 1 hour.
Supplementary files format and content: MP_96HvsMP_1H_deg_all.xls: Differentially expressed genes in MPXV infected intestinal organoids for 96 hours compared to infection for 1hour.
Supplementary files format and content: TREATvsMP_96H.all_KEGGenrich_significant.xls: Significantly regulated pathways by KEGG enrichment analysis, MPXV infected intestinal organoids with 1 uM clofarabine treatment for 96 hours compared to MPXV infected intestinal organoids for 96 hours without treatment.
Supplementary files format and content: TREATvsMP_96H_deg_all.xls: Differentially expressed genes in MPXV infected intestinal organoids with 1 uM clofarabine treatment for 96 hours compared to MPXV infected intestinal organoids for 96 hours without treatment.

source_name: human intestine

extract_protocol:
Total RNA was isolated using the MachereyNagel NucleoSpin RNA II Kit (Bioke, Netherlands) and quantied with the Bioanalyzer RNA 6000 Picochip.
RNA sequencing was performed by Novogene with paired-end 150 bp (PE 150) sequencing strategy

value: human intestine

tag: cell type

value: Human intestinal organoids


title: MP48A, Monkeypox virus infected intestinal organoids: samples harvested at 48 hour-post infection

description: Library name: Sample13


title: MP96C, Monkeypox virus infected intestinal organoids: samples harvested at 96 hour-post infection

description: Library name: Sample18


title: MP24C, Monkeypox virus infected intestinal organoids: samples harvested at 24 hour-post infection

description: Library name: Sample12


title: MP96A, Monkeypox virus infected intestinal organoids: samples harvested at 96 hour-post infection

description: Library name: Sample16


title: MP24A, Monkeypox virus infected intestinal organoids: samples harvested at 24 hour-post infection

description: Library name: Sample10


description: Library name: AT1G69490_B_oleracea_TO1000DH3_DAPi712A09-ORGi5021-96P155


title: MP48C, Monkeypox virus infected intestinal organoids: samples harvested at 48 hour-post infection

description: Library name: Sample15


title: MP48B, Monkeypox virus infected intestinal organoids: samples harvested at 48 hour-post infection

description: Library name: Sample14


title: MP24B, Monkeypox virus infected intestinal organoids: samples harvested at 24 hour-post infection

description: Library name: Sample11


title: MP1C, Monkeypox virus infected intestinal organoids: samples harvested at 1 hour-post infection

description: Library name: Sample9


title: MP1B, Monkeypox virus infected intestinal organoids: samples harvested at 1 hour-post infection

description: Library name: Sample8


description: Library name: XP_013615900.1_C_rubella_Monte_Gargano_DAPi712E09-ORGi5037-96P247

value: MYBRELATED


description: Library name: Solyc11g064950.3.1_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P247


description: Library name: AT4G25490_B_oleracea_TO1000DH3_DAPi712A08-ORGi5021-96P220


title: CLO3, Human intestinal organoids infected with monkeypox virus, and treated with 1uM clofarabine for 96 hours

description: Library name: Sample6


description: Library name: AT3G15500_C_rubella_Monte_Gargano_DAPi712E09-ORGi5037-96P155


title: MP1A, Monkeypox virus infected intestinal organoids: samples harvested at 1 hour-post infection

description: Library name: Sample7


description: Library name: AT1G20980_C_rubella_Monte_Gargano_DAPi712E11-ORGi5037-96P220

value: SBP


description: Library name: XP_013631386.1_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P247

value: plant


title: CLO2, Human intestinal organoids infected with monkeypox virus, and treated with 1uM clofarabine for 96 hours

description: Library name: Sample5


title: CLO1, Human intestinal organoids infected with monkeypox virus, and treated with 1uM clofarabine for 96 hours

description: Library name: Sample4


description: Library name: AT3G12250_B_oleracea_TO1000DH3_DAPi712A07-ORGi5021-96P220


title: CTR3, Human intestinal organoids (healthy control, without infection)

description: Library name: Sample3


description: Library name: AT1G75390_C_rubella_Monte_Gargano_DAPi712E08-ORGi5037-96P155


description: Library name: AT5G14960_C_rubella_Monte_Gargano_DAPi712E08-ORGi5037-96P220


title: CTR2, Human intestinal organoids (healthy control, without infection)

description: Library name: Sample2


description: Library name: AT5G10030_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P220


description: Library name: LOC_Os08g37970.1_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P247

value: MYB


title: IgG-1

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
*library strategy: LACE-seq
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to rRNA and tRNA of human and unmapped reads were saved
unmapped reads were aligned to hg38 genome by hisat2
Assembly: hg38
Supplementary files format and content: bw, containing the peaks

source_name: clear cell Renal Carcinoma

growth_protocol: 786-O cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
library was construted according to the protocol in 'Global profiling of RNA-binding protein target sites by LACE-seq'

value: clear cell Renal Carcinoma

tag: cell line

value: Human renal cell adenocarcinoma cell


title: IgG-2


title: IGF2BP2-2


description: Library name: AL3G23910.t2_C_rubella_Monte_Gargano_DAPi712E07-ORGi5037-96P247


title: IgG-3


description: Library name: AT2G18550_C_rubella_Monte_Gargano_DAPi712E07-ORGi5037-96P220

value: HOMEOBOX


title: IGF2BP2-3.Input

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
Gene counts were counted by featureCounts
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: xlsx format, containing the raw counts and FPKM values

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RIP-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols


description: Library name: AT5G56110_C_rubella_Monte_Gargano_DAPi712E06-ORGi5037-96P220


title: IGF2BP2-1


title: IGF2BP2-3


description: Library name: AT5G62940_B_oleracea_TO1000DH3_DAPi712A05-ORGi5021-96P220


description: Library name: AT1G76880_C_rubella_Monte_Gargano_DAPi712E06-ORGi5037-96P155

value: TRIHELIX


description: Library name: AT5G66700_B_oleracea_TO1000DH3_DAPi712A06-ORGi5021-96P155


description: Library name: AT1G49480_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P220

value: REM


description: Library name: AT3G60530_C_rubella_Monte_Gargano_DAPi712E05-ORGi5037-96P220


description: Library name: AT3G10113_B_oleracea_TO1000DH3_DAPi712A04-ORGi5021-96P155


title: IGF2BP2-3 RIP-seq


title: IGF2BP2-1.Input


description: Library name: AT4G00730_C_rubella_Monte_Gargano_DAPi712E05-ORGi5037-96P155


title: IGF2BP2-2 RIP-seq


title: IGF2BP2-1 RIP-seq


description: Library name: AT1G69780_B_oleracea_TO1000DH3_DAPi712A03-ORGi5021-96P220


title: shIGF2BP2-3 RNA-seq

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols


description: Library name: AT5G62020_C_rubella_Monte_Gargano_DAPi712E04-ORGi5037-96P220

value: HSF


title: CTR1, Human intestinal organoids (healthy control, without infection)

description: Library name: Sample1


title: shIGF2BP2-2 RNA-seq


description: Library name: AT2G23290_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P155


description: Library name: LOC_Os02g42970.1_C_rubella_Monte_Gargano_DAPi712E03-ORGi5037-96P247


description: Library name: AT1G53170_B_oleracea_TO1000DH3_DAPi711H11-ORGi5021-96P166


description: Library name: AT5G39760_B_oleracea_TO1000DH3_DAPi712A02-ORGi5021-96P220

value: ZFHD


title: shIGF2BP2-1 RNA-seq


title: puro-1 RNA-seq

value: puro


title: puro-3 RNA-seq


title: AML3: scATACseq from CD34+ sorted bone marrow cells from AML patient

city: New York

first: Joy

last: Fan

address: 520 West 120th Street

institute: Columbia University

description:
Library name: AML3_scATAC
10x Genomics

library_source: other

data_processing:
scRNA-seq raw reads were processed using 10X Genomics CellRanger and SEQC pipelines. Filtered count matrices were loaded into AnnData objects using Scanpy v1.7.2. Cells were filtered based on library size using a histogram knee-point threshold. Normalization was performed using sc.pp.normalize_per_cell, and doublet detection was done with DoubletDetection (25 iterations). For scATAC-seq, FASTQ files were processed into cell-by-peak matrices using the CellRanger ATAC pipeline with modifications described in [158]. A median of 10,504 cells/sample and 5,165 molecules/cell were retained after filtering.
Assembly: Human Hg38
Supplementary files format and content: fragments files for each ATAC sample

molecule: other

source_name: Bone Marrow

extract_protocol:
Cryopreserved bone marrow mononuclear cells were thawed in prewarmed FACS buffer (PBS + fetal bovine serum). Cells were pelleted and washed, then blocked with Human TruStain FcX™ (Biolegend #422301) for 15 minutes at 4°C. Antibodies against CD34 (Clone 561; FITC Biolegend 343603) and CD133 (Clone 7; PE Biolegend 372803) were added and incubated for 15 minutes at 4°C. Cells were washed, stained with DAPI, and sorted on a Sony SH800 cell sorter to enrich for immature populations (e.g., CD34+ or PROM+). Unsorted mononuclear cells were also used for sequencing.
All samples and sorted populations were profiled using 10X Genomics Chromium Single Cell 3’ v3 (for scRNA-seq) and the 10X Genomics Single Cell ATAC Reagent Kits v1.1 (for scATAC-seq). For scATAC-seq, nuclei were isolated and subjected to a transposition reaction at 37°C for 60 minutes before encapsulation with the 10X Chromium Controller targeting ~5,000 nuclei. Libraries were constructed per manufacturer instructions (10X Genomics; CG000168 RevA), assessed via Bioanalyzer High-Sensitivity DNA Kit (Agilent), and sequenced on Illumina HiSeq 2500 and NovaSeq platforms.

value: Bone Marrow

value: Bone marrow mononuclear cells


title: AML2: scATACseq from CD34+ sorted bone marrow cells from AML patient

description:
Library name: AML2_scATAC
10x Genomics


title: BM_control: scATACseq from a healthy bone marrow reference sample

description:
Library name: BM_control_scATAC
10x Genomics


description: Library name: AT4G36780_B_oleracea_TO1000DH3_DAPi711H06-ORGi5021-96P166

value: BZR


title: AML1: scATACseq from CD34+ sorted bone marrow cells from AML patient

description:
Library name: AML1_scATAC
10x Genomics


title: IGF2BP2-2.Input


description: Library name: LOC_Os06g07030.1_C_rubella_Monte_Gargano_DAPi712E01-ORGi5037-96P247


description: Library name: AT1G13260_C_rubella_Monte_Gargano_DAPi712E01-ORGi5037-96P220

value: RAV


description: Library name: AT2G03500_B_oleracea_TO1000DH3_DAPi711H07-ORGi5021-96P166


title: SCS_VEH_WS_LA

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

description:
Library name: SCS_VEH_WS_LA
Single-cell wells, low adherance, with serum

data_processing:
Reads were aligned to the transcriptome (GRCh38 Gencode v26) supplemented with ERCC spike in sequences utilizing STAR v2.5.0 with the following non-default parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
Cells were pre-filtered for total detected features (>4k) and fraction of reads aligned to control features (ERCC + mitochondrial) (<0.7). Batch correction and normalization performed with RUVseq RUVs19, with number of unwanted variance factors k=10 as estimated by PCA analysis.
Assembly: hg38
Supplementary files format and content: RDS file of pre-process counts in single cell experiment format

growth_protocol: HCT-116 cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
The C1 integrated fluidics circuits (IFCs) for mRNA seq (small-cell, 5–10 μm) was primed according to the standard Fluidigm mRNA-seq protocol using C1 harvest reagent, C1 preloading reagent, C1 blocking reagent, and Fluidigm cell wash buffer. Priming was performed immediately prior to sample preparation. HCT-116 cells were trypsinised and resuspended in serum-free media at a concentration of 333,000 cells/mL. The standard suspension ratio of 3:2 was used (60 µL of cell suspension was added to 40 µL of Fluidigm suspension reagent) to achieve the final cell mix for IFC loading. After mixing several time the cell preparation, 6 µL of the cell mix was loaded. Following cell loading, light microscopy using EVOS microscope, was used in order to assess each of the 96 capture sites individually and the outcome of loading was recorded in terms of the number of cells present in each capture site and whether debris were present. This information was used as a quality control step to ensure that only confirmed single cell samples were taken forward. Finally, the IFC was placed into the C1 the script “mRNA Seq: Cell Load (1771x/1772x/1773x)” was run. Following the loading, buffer mixes for lysis, reverse transcription and PCR were pipetted into the IFC. The IFC was then placed into the C1 system and the script “mRNA Seq: RT & Amp (1771x/1772x/1773x)” was run overnight. Samples were harvested from the IFC by transferring 3.5 µL of product to a 96 well plate and diluted with 10 µL C1 DNA dilution reagent. The samples corresponding to the confirmed single cell captures were highlighted according to the arrangement on the harvest plate described by Fluidigm. Samples were stored at 4ºC short term and -20ºC long term prior to subsequent quantification and library preparation.
Library preparation was performed using the modified Illumina Nextera XT DNA library preparation protocol provided by Fluidigm. The cDNA concentration was quantified using the PicoGreen Assay (Quant-IT PicoGreen dsDNA Assay Kit, Thermo Fisher Scientific, P11496) using 2 µL per 96 samples processed into 2 replicates in a 384-well plate giving a final well volume of 60 µL for reading in a fluorometer. The data was then processed using the Microsoft Excel worksheet, Single-Cell mRNA Seq PicoGreen Template (Fluidigm, PN 100-6260), to quantify the library. Samples were transferred to a new 96-well plate in order to obtain a sample within the range 0.1-0.3 ng/µL by diluting with C1 Harvest Reagent. Only samples with at least 0.1 ng/µL were taken forward for library preparation. Sequencing libraries were prepared using Nextera XT DNA Library (Illumina) with a modified protocol provided by Fluidigm.

treatment_protocol: Cells were treated with dox at a concentration of 0.2 μg/ml or equivalent volume of vehicle (ddh20) for the indicated time.

value: Vehicle


title: SCS_DOX_WS_LA

description:
Library name: SCS_DOX_WS_LA
Single-cell wells, low adherance, with serum

value: Doxorubicin 0.2 µg/ml 4 hours


title: Col_0_bio1

value: whole plant

value: MS+3% sucrose

value: Wild type


title: SCS_VEH_NS_LA

description:
Library name: SCS_VEH_NS_LA
Single-cell wells, low adherance, no serum


title: SCS_DOX_NS_LA

description:
Library name: SCS_DOX_NS_LA
Single-cell wells, low adherance, no serum


description: Library name: LOC_Os10g26500.1_C_rubella_Monte_Gargano_DAPi712D12-ORGi5037-96P247

value: plant


description: Library name: AT5G11260_C_rubella_Monte_Gargano_DAPi712D12-ORGi5037-96P220

value: BZIP


title: puro-2 RNA-seq

value: clear cell Renal Carcinoma

value: Human renal cell adenocarcinoma cell


description: Library name: AT5G64750_C_rubella_Monte_Gargano_DAPi712E03-ORGi5037-96P220


description: Library name: AT1G72010_B_oleracea_TO1000DH3_DAPi711H03-ORGi5021-96P166

value: TCP


title: DGM-11111_M6_lg_RNA-Seq

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include the RefSeq unique ID with gene ID and location, gene ID  and the FPKM values for all samples

source_name: large airway epithelial cells

extract_protocol:
Pure populations of nonsmoker and smoker small airway samples were obtained by bronchoscopy.  Smoking status was confirmed by tobacco urine metabolites. Active smokers had consistently high cotinine levels (≥104 ng/ml) and nonsmokers had undetectable urine cotinine and urine nicotine levels.  Total RNA was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIA-quick PCR purification kit (Qiagen, Valencia, CA)
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.  HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images.

value: large airway epithelial cells

tag: phenotype

value: smoker

tag: gender

value: M

tag: ethnicity

value: African


description: Library name: AT5G47390_B_oleracea_TO1000DH3_DAPi711H02-ORGi5021-96P166

value: MYBRELATED


description: Library name: AT4G21030_C_rubella_Monte_Gargano_DAPi712E02-ORGi5037-96P155


title: DGM-11066_M0_lg_RNA-Seq


description: Library name: AT5G05790_B_oleracea_TO1000DH3_DAPi711G12-ORGi5021-96P166


description: Library name: XP_013587997.1_C_rubella_Monte_Gargano_DAPi712D11-ORGi5037-96P247

value: WRKY


title: DGM-11016_M0_lg_RNA-Seq

value: F


description: Library name: AT5G58900_B_oleracea_TO1000DH3_DAPi711H04-ORGi5021-96P166


title: DGM-10907_M0_lg_RNA-Seq

value: Hispanic


description: Library name: AT3G18990_C_rubella_Monte_Gargano_DAPi712D11-ORGi5037-96P220


title: DGM-10869_M0_lg_RNA-Seq

value: Caucasian


description: Library name: AT1G69780_B_oleracea_TO1000DH3_DAPi711G07-ORGi5021-96P166

value: HOMEOBOX


description: Library name: LOC_Os08g06110.3_C_rubella_Monte_Gargano_DAPi712D10-ORGi5037-96P247


title: DGM-10522_M0_lg_RNA-Seq


title: DGM-10170_M0_lg_RNA-Seq


description: Library name: AT2G46770_C_rubella_Monte_Gargano_DAPi712D10-ORGi5037-96P155

value: NAC


title: DGM-11852_110825_lg_RNA-Seq

value: nonsmoker

value: Egyptian


description: Library name: AT1G69690_B_oleracea_TO1000DH3_DAPi711G05-ORGi5021-96P166

value: plant


description: Library name: AT5G39760_B_oleracea_TO1000DH3_DAPi711G03-ORGi5021-96P166

value: ZFHD


title: DGM-11374_lg_RNA-Seq


description: Library name: Carub.0008s0285.1_C_rubella_Monte_Gargano_DAPi712D08-ORGi5037-96P247


description: Library name: AL8G10650.t1_C_rubella_Monte_Gargano_DAPi712D09-ORGi5037-96P247


title: DGM-10500_M0_lg_RNA-Seq


title: DGM-10565_M6_lg_RNA-Seq


description: Library name: AT3G56850_C_rubella_Monte_Gargano_DAPi712D12-ORGi5037-96P155

value: BZIP


title: DGM-11008_M0_lg_RNA-Seq


title: DGM-10906_M12_lg_RNA-Seq


title: DGM-10503_M6_lg_RNA-Seq


title: DGM-10922_M0_lg_RNA-Seq


description: Library name: Solyc01g095460.3.1_C_rubella_Monte_Gargano_DAPi712D07-ORGi5037-96P247


description: Library name: AT5G03150_C_rubella_Monte_Gargano_DAPi712D08-ORGi5037-96P220


description: Library name: AT5G64750_B_oleracea_TO1000DH3_DAPi711G09-ORGi5021-96P166


title: DGM-10194_M3_lg_RNA-Seq


description: Library name: AT2G31230_B_oleracea_TO1000DH3_DAPi711G02-ORGi5021-96P166


description: Library name: AT5G41570_B_oleracea_TO1000DH3_DAPi711G08-ORGi5021-96P166


title: DGM-10284_M6_lg_RNA-Seq


title: DGM-10123_M0_lg_RNA-Seq


title: DGM-01774_090416_lg_RNA-Seq


title: DGM-01620_110531_lg_RNA-Seq


description: Library name: AT1G74480_C_rubella_Monte_Gargano_DAPi712D07-ORGi5037-96P220

value: RWPRK


title: DGM-11525_Baseline_sm_RNA-Seq

source_name: small airway epithelial cells

value: small airway epithelial cells


description: Library name: AT1G29280_B_oleracea_TO1000DH3_DAPi711F12-ORGi5021-96P166


title: DGM-11964_sm_RNA-Seq


description: Library name: AT4G34410_B_oleracea_TO1000DH3_DAPi711F11-ORGi5021-96P166


description: Library name: AT5G39610_C_rubella_Monte_Gargano_DAPi712D07-ORGi5037-96P155


description: Library name: AT3G15270_B_oleracea_TO1000DH3_DAPi711F08-ORGi5021-96P166

value: SBP


title: DGM-10369_M47_sm_RNA-Seq

value: smoker

value: M

value: Other


title: DGM-10757_M0_sm_RNA-Seq

value: African


description: Library name: AT3G57920_C_rubella_Monte_Gargano_DAPi712D06-ORGi5037-96P220


title: DGM-10851_M0_sm_RNA-Seq


description: Library name: AT2G22430_B_oleracea_TO1000DH3_DAPi711F07-ORGi5021-96P166


description: Library name: AT3G22830_B_oleracea_TO1000DH3_DAPi711G01-ORGi5021-96P166

value: HSF


description: Library name: AT1G20980_C_rubella_Monte_Gargano_DAPi712D06-ORGi5037-96P155


title: DGM-10685_M0_sm_RNA-Seq

value: F


title: DGM-10571_M0_sm_RNA-Seq

value: Hispanic


description: Library name: AT3G20310_B_oleracea_TO1000DH3_DAPi711F06-ORGi5021-96P166


description: Library name: LOC_Os02g33430.1_C_rubella_Monte_Gargano_DAPi712D05-ORGi5037-96P247


title: DGM-10358_M0_sm_RNA-Seq


title: DGM-10625_M12_sm_RNA-Seq

value: Caucasian


description: Library name: AT1G14687_B_oleracea_TO1000DH3_DAPi711F04-ORGi5021-96P166


title: DGM-11111_M12_sm_RNA-Seq


description: Library name: AT5G60850_B_oleracea_TO1000DH3_DAPi711F05-ORGi5021-96P166


title: DGM-11066_M12_sm_RNA-Seq


title: DGM-00221_M12_sm_RNA-Seq


description: Library name: AT5G45300_C_rubella_Monte_Gargano_DAPi712D04-ORGi5037-96P155


title: DGM-11038_M12_sm_RNA-Seq


description: Library name: AT1G18330_B_oleracea_TO1000DH3_DAPi711F03-ORGi5021-96P166

value: MYBRELATED


title: DGM-11016_M12_sm_RNA-Seq


description: Library name: AT3G20770_C_rubella_Monte_Gargano_DAPi712D05-ORGi5037-96P155

value: EIL


description: Library name: AT1G27730_B_oleracea_TO1000DH3_DAPi711F01-ORGi5021-96P166


title: DGM-10922_M12_sm_RNA-Seq


description: Library name: AT2G01930_C_rubella_Monte_Gargano_DAPi712D05-ORGi5037-96P220

value: BBRBPC


description: Library name: Carub.0001s1194.1_C_rubella_Monte_Gargano_DAPi712D03-ORGi5037-96P247

value: plant

value: NAC


title: DGM-10906_M12_sm_RNA-Seq


title: DGM-10886_M12_sm_RNA-Seq


description: Library name: AT4G16750_B_oleracea_TO1000DH3_DAPi711E12-ORGi5021-96P166


description: Library name: AT2G46680_B_oleracea_TO1000DH3_DAPi711E11-ORGi5021-96P166

value: HOMEOBOX


title: DGM-10869_M12_sm_RNA-Seq


description: Library name: AT4G17980_C_rubella_Monte_Gargano_DAPi712D03-ORGi5037-96P155


description: Library name: AT3G50260_C_rubella_Monte_Gargano_DAPi712D02-ORGi5037-96P220


title: DGM-10731_M12_sm_RNA-Seq


title: DGM-10986_M12_sm_RNA-Seq


title: DGM-10768_M6_sm_RNA-Seq


description: Library name: AT4G36620_C_rubella_Monte_Gargano_DAPi712D02-ORGi5037-96P155


description: Library name: AT1G30210_B_oleracea_TO1000DH3_DAPi711E03-ORGi5021-96P166

value: TCP


description: Library name: AT5G08330_B_oleracea_TO1000DH3_DAPi711E05-ORGi5021-96P166


title: DGM-10732_M12_sm_RNA-Seq

value: small airway epithelial cells


description: Library name: Carub.0001s3581.1.p_C_rubella_Monte_Gargano_DAPi712D01-ORGi5037-96P247


title: DGM-10707_M0_sm_RNA-Seq

value: nonsmoker


title: DGM-10159_M12_sm_RNA-Seq


title: DGM-10704_M12_sm_RNA-Seq

value: smoker


description: Library name: Carub.0002s1646.1_C_rubella_Monte_Gargano_DAPi712C12-ORGi5037-96P247


title: DGM-10573_M6_sm_RNA-Seq

value: M


description: Library name: AT5G65410_C_rubella_Monte_Gargano_DAPi712D03-ORGi5037-96P220

value: ZFHD


description: Library name: AT5G08520_B_oleracea_TO1000DH3_DAPi711E02-ORGi5021-96P166


title: DGM-10568_M0_sm_RNA-Seq


description: Library name: AT1G12260_C_rubella_Monte_Gargano_DAPi712C12-ORGi5037-96P220


title: DGM-10261_M0_sm_RNA-Seq

value: African


description: Library name: AT1G49480_B_oleracea_TO1000DH3_DAPi711D12-ORGi5021-96P166

value: REM


description: Library name: AT1G06850_C_rubella_Monte_Gargano_DAPi712C12-ORGi5037-96P155

value: BZIP


title: DGM-01774_M3_sm_RNA-Seq


title: DGM-10808_M12_sm_RNA-Seq


description: Library name: AT1G19000_B_oleracea_TO1000DH3_DAPi711D11-ORGi5021-96P166


title: DGM-10901_M3_sm_RNA-Seq

value: Hispanic


description: Library name: AT2G23340_B_oleracea_TO1000DH3_DAPi711E08-ORGi5021-96P166


description: Library name: AT3G15210_B_oleracea_TO1000DH3_DAPi711D10-ORGi5021-96P166


description: Library name: AL2G40550.t1_C_rubella_Monte_Gargano_DAPi712C11-ORGi5037-96P247

value: WRKY


title: DGM-10503_M12_sm_RNA-Seq


title: DGM-10500_M6_sm_RNA-Seq

value: F


title: DGM-10475_M3_sm_RNA-Seq


title: DGM-10284_M12_sm_RNA-Seq


title: DGM-10194_M12_sm_RNA-Seq

value: Caucasian


description: Library name: AT5G65410_B_oleracea_TO1000DH3_DAPi711D09-ORGi5021-96P166


description: Library name: AT1G43700_C_rubella_Monte_Gargano_DAPi712C11-ORGi5037-96P155


title: DGM-10270_M12_sm_RNA-Seq


title: DGM-10343_M12_sm_RNA-Seq


title: DGM-10565_M12_sm_RNA-Seq


title: DGM-00342_M12_sm_RNA-Seq


description: Library name: Carub.0001s0116.1_C_rubella_Monte_Gargano_DAPi712C10-ORGi5037-96P247

value: MYBRELATED


title: DGM-10380_M12_sm_RNA-Seq


description: Library name: AT3G50060_B_oleracea_TO1000DH3_DAPi711D07-ORGi5021-96P166

value: plant

value: MYB


title: DGM-10288_M12_sm_RNA-Seq


description: Library name: Solyc06g048630.3.1_C_rubella_Monte_Gargano_DAPi712C09-ORGi5037-96P247


title: DGM-10254_M12_sm_RNA-Seq


description: Library name: AT3G50260_B_oleracea_TO1000DH3_DAPi711D06-ORGi5021-96P166


description: Library name: AT5G67580_B_oleracea_TO1000DH3_DAPi711D05-ORGi5021-96P166


description: Library name: AT4G00730_C_rubella_Monte_Gargano_DAPi712C11-ORGi5037-96P220

value: HOMEOBOX


description: Library name: AT5G62000_B_oleracea_TO1000DH3_DAPi711D08-ORGi5021-96P166

value: ARF


title: SAECs, smoker, DGM-10369_M47_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10369_M47

value: Other

value: small airway epithelial cells


title: SAECs, smoker, DGM-10851_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10851_M0

value: smoker


description: Library name: AT1G76420_C_rubella_Monte_Gargano_DAPi712C09-ORGi5037-96P220

value: NAC


description: Library name: AT5G62470_C_rubella_Monte_Gargano_DAPi712C08-ORGi5037-96P220


description: Library name: AT3G14180_B_oleracea_TO1000DH3_DAPi711D03-ORGi5021-96P166

value: TRIHELIX


title: SAECs, smoker, DGM-10685_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10685_M0


description: Library name: AT5G18270_C_rubella_Monte_Gargano_DAPi712C10-ORGi5037-96P155


title: SAECs, smoker, DGM-10757_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10757_M0

value: M

value: African


title: SAECs, smoker, DGM-10625_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10625_M12


description: Library name: AT1G33240_B_oleracea_TO1000DH3_DAPi711C10-ORGi5021-96P166


title: DGM-10383_M12_sm_RNA-Seq

value: nonsmoker


title: SAECs, smoker, DGM-10571_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10571_M0

value: Hispanic


description: Library name: AT5G25190_B_oleracea_TO1000DH3_DAPi711C05-ORGi5021-96P166


description: Library name: AT5G60130_C_rubella_Monte_Gargano_DAPi712C07-ORGi5037-96P220


title: SAECs, smoker, DGM-00221_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-00221_M12


title: DGM-10123_M12_sm_RNA-Seq


title: SAECs, smoker, DGM-10358_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10358_M0


title: SAECs, smoker, DGM-11066_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-11066_M12


description: Library name: AT3G62420_C_rubella_Monte_Gargano_DAPi712C07-ORGi5037-96P155

value: BZIP


description: Library name: AT1G25550_B_oleracea_TO1000DH3_DAPi711C01-ORGi5021-96P166


title: SAECs, smoker, DGM-11111_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-11111_M12


description: Library name: XP_013613838.1_C_rubella_Monte_Gargano_DAPi712C08-ORGi5037-96P247


title: SAECs, smoker, DGM-11038_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-11038_M12


title: SAECs, smoker, DGM-11016_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-11016_M12

value: F


description: Library name: AT5G13080_B_oleracea_TO1000DH3_DAPi711B12-ORGi5021-96P166

value: WRKY


description: Library name: LOC_Os01g46970.1_C_rubella_Monte_Gargano_DAPi712C07-ORGi5037-96P247


title: SAECs, smoker, DGM-10986_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10986_M12


title: SAECs, smoker, DGM-10906_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10906_M12


description: Library name: AT2G30250_B_oleracea_TO1000DH3_DAPi711B11-ORGi5021-96P166


description: Library name: AT4G32730_C_rubella_Monte_Gargano_DAPi712C05-ORGi5037-96P155


description: Library name: AT5G03790_C_rubella_Monte_Gargano_DAPi712C06-ORGi5037-96P220


description: Library name: AT2G46590_B_oleracea_TO1000DH3_DAPi711B10-ORGi5021-96P166


title: SAECs, smoker, DGM-10901_M3_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10901_M3


title: SAECs, smoker, DGM-10886_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10886_M12


description: Library name: Solyc08g068320.3.1_C_rubella_Monte_Gargano_DAPi712C04-ORGi5037-96P247


title: SAECs, smoker, DGM-10869_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10869_M12

value: Caucasian


description: Library name: AT3G27010_C_rubella_Monte_Gargano_DAPi712C04-ORGi5037-96P220

value: plant

value: TCP


description: Library name: AT5G24110_B_oleracea_TO1000DH3_DAPi711B09-ORGi5021-96P166


title: SAECs, smoker, DGM-10808_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10808_M12


description: Library name: AT4G14770_C_rubella_Monte_Gargano_DAPi712C04-ORGi5037-96P155

value: CPP


description: Library name: AT3G12730_B_oleracea_TO1000DH3_DAPi711B08-ORGi5021-96P166


title: SAECs, smoker, DGM-10732_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10732_M12


description: Library name: XP_013602769.1_C_rubella_Monte_Gargano_DAPi712C03-ORGi5037-96P247


title: SAECs, smoker, DGM-10573_M6_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10573_M6


title: SAECs, smoker, DGM-10922_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10922_M12


title: SAECs, smoker, DGM-10704_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10704_M12


title: SAECs, smoker, DGM-10731_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10731_M12


description: Library name: AT3G24120_B_oleracea_TO1000DH3_DAPi711B06-ORGi5021-96P166


description: Library name: AT1G69690_C_rubella_Monte_Gargano_DAPi712C02-ORGi5037-96P220


description: Library name: AT4G31800_B_oleracea_TO1000DH3_DAPi711C07-ORGi5021-96P166


description: Library name: AT5G17800_C_rubella_Monte_Gargano_DAPi712C02-ORGi5037-96P155

value: MYB


title: SAECs, nonsmoker, DGM-10284_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10284_M12


description: Library name: AT5G47370_B_oleracea_TO1000DH3_DAPi711B05-ORGi5021-96P166

value: HOMEOBOX


title: SAECs, smoker, DGM-10768_M6_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10768_M6

value: small airway epithelial cells


description: Library name: AT1G27730_C_rubella_Monte_Gargano_DAPi712C01-ORGi5037-96P220


title: SAECs, nonsmoker, DGM-10159_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10159_M12


description: Library name: AT5G67300_B_oleracea_TO1000DH3_DAPi711B01-ORGi5021-96P166


title: SAECs, nonsmoker, DGM-10261_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10261_M0


title: SAECs, nonsmoker, DGM-10707_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10707_M0


title: SAECs, nonsmoker, DGM-10568_M0_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10568_M0


description: Library name: AT1G80840_B_oleracea_TO1000DH3_DAPi711A11-ORGi5021-96P166


title: SAECs, nonsmoker, DGM-00342_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-00342_M12


description: Library name: AT3G04030_B_oleracea_TO1000DH3_DAPi711A08-ORGi5021-96P166


description: Library name: XP_013589953.1_C_rubella_Monte_Gargano_DAPi712B12-ORGi5037-96P247


title: SAECs, nonsmoker, DGM-01774_M3_sm_RNA-Seq

description:
small airway epithelium samples
DGM-01774_M3


title: SAECs, nonsmoker, DGM-10475_M3_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10475_M3


description: Library name: AT3G01530_B_oleracea_TO1000DH3_DAPi711A05-ORGi5021-96P166


description: Library name: AT2G40620_C_rubella_Monte_Gargano_DAPi712B12-ORGi5037-96P220


description: Library name: AT1G52880_C_rubella_Monte_Gargano_DAPi712B12-ORGi5037-96P155


title: SAECs, nonsmoker, DGM-10500_M6_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10500_M6


title: SAECs, nonsmoker, DGM-10565_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10565_M12


description: Library name: AT3G56400_B_oleracea_TO1000DH3_DAPi711A04-ORGi5021-96P166


title: SAECs, nonsmoker, DGM-10194_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10194_M12


description: Library name: AT1G64620_B_oleracea_TO1000DH3_DAPi711C04-ORGi5021-96P166


description: Library name: Solyc07g040920.2.1_C_rubella_Monte_Gargano_DAPi712B11-ORGi5037-96P247

value: MYBRELATED


title: SAECs, nonsmoker, DGM-10270_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10270_M12


title: SAECs, nonsmoker, DGM-10343_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10343_M12


title: SAECs, nonsmoker, DGM-10380_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10380_M12


description: Library name: XP_013587350.1_C_rubella_Monte_Gargano_DAPi712B10-ORGi5037-96P247


description: Library name: AT4G01250_B_oleracea_TO1000DH3_DAPi711A02-ORGi5021-96P166


description: Library name: AT1G22070_C_rubella_Monte_Gargano_DAPi712B11-ORGi5037-96P155


title: SAECs, nonsmoker, DGM-10503_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10503_M12


title: SAECs, nonsmoker, DGM-10383_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10383_M12


description: Library name: AT1G72740_B_oleracea_TO1000DH3_DAPi710H11-ORGi5021-96P151


description: Library name: AT4G24240_B_oleracea_TO1000DH3_DAPi711A03-ORGi5021-96P166


title: SAECs, nonsmoker, DGM-10288_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10288_M12


description: Library name: AT2G23320_B_oleracea_TO1000DH3_DAPi711E01-ORGi5021-96P166


title: SAECs, nonsmoker, DGM-10161_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10161_M12


description: Library name: AT1G20910_C_rubella_Monte_Gargano_DAPi712B10-ORGi5037-96P220

value: ARID


title: DGM-00167

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using the human reference genome build GRCh37/hg19, STAR (2.3.1z13_r470) for aligning reads, RefSeq gene definitions (2014-06-02) and Cufflinks (v2.2, http://cufflinks.cbcb.umd.edu)
To correct for transcript length and depth of coverage raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM).
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent STAR results into one file. This file contains all the aligned reads for each read pair. Finally Cufflinks was run on the merged STAR output to produce a file with FPKM values for each sample
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM text files include UniqueID with geneID and location, GeneID, and the FPKM values for all samples

source_name: small airway epithelium brushing

extract_protocol:
Total RNA was extracted with TRIzol with subsequent RNA clean-up using the RNeasy  RNA purification kit to remove residual DNA
The TruSeq RNA v2 Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA
Samples were loaded onto an Illumina flowcell for paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500.

tag: smoking status

value: smoker

tag: batch

value: small airway epithelium


description: Library name: LOC_Os03g21800.1_C_rubella_Monte_Gargano_DAPi712B09-ORGi5037-96P247


description: Library name: AT3G55370_B_oleracea_TO1000DH3_DAPi710H10-ORGi5021-96P151


title: DGM-11738

value: M


title: SAECs, nonsmoker, DGM-10254_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10254_M12

value: nonsmoker

tag: age


description: Library name: AT1G79580_C_rubella_Monte_Gargano_DAPi712B09-ORGi5037-96P220

value: NAC


title: DGM-01961


title: SAECs, nonsmoker, DGM-10123_M12_sm_RNA-Seq

description:
small airway epithelium samples
DGM-10123_M12

value: Hispanic


title: DGM-00127


description: Library name: AT2G18380_B_oleracea_TO1000DH3_DAPi710H06-ORGi5021-96P151


description: Library name: AT1G74650_B_oleracea_TO1000DH3_DAPi710H08-ORGi5021-96P151


title: DGM-10161_M12_sm_RNA-Seq

value: F

value: African


description: Library name: AT1G79580_B_oleracea_TO1000DH3_DAPi710H09-ORGi5021-96P151


title: DGM-11379


description: Library name: AL8G13510.t2_C_rubella_Monte_Gargano_DAPi712B08-ORGi5037-96P247


description: Library name: AT3G04070_C_rubella_Monte_Gargano_DAPi712B09-ORGi5037-96P155


title: DGM-00342


description: Library name: Carub.0004s2898.1.p_C_rubella_Monte_Gargano_DAPi712B07-ORGi5037-96P247

value: BZIP


description: Library name: AT4G25470_C_rubella_Monte_Gargano_DAPi712B06-ORGi5037-96P220

value: plant


title: DGM-11270


description: Library name: AT1G74480_B_oleracea_TO1000DH3_DAPi710H04-ORGi5021-96P151

value: RWPRK


title: DGM-11276


title: DGM-01774


description: Library name: AT3G18990_C_rubella_Monte_Gargano_DAPi712B06-ORGi5037-96P155


title: DGM-10800


title: DGM-10922


description: Library name: AT3G25990_B_oleracea_TO1000DH3_DAPi710H05-ORGi5021-96P151

value: TRIHELIX


title: DGM-10984


description: Library name: AT2G30340_B_oleracea_TO1000DH3_DAPi710H03-ORGi5021-96P151


description: Library name: XP_013631649.1_C_rubella_Monte_Gargano_DAPi712B05-ORGi5037-96P247


description: Library name: AT1G06280_B_oleracea_TO1000DH3_DAPi710H02-ORGi5021-96P151


title: DGM-10986


title: DGM-11047


description: Library name: AT1G29160_C_rubella_Monte_Gargano_DAPi712B04-ORGi5037-96P220


title: DGM-11613


description: Library name: AT3G08500_C_rubella_Monte_Gargano_DAPi712B05-ORGi5037-96P220

value: MYB


title: DGM-11038


description: Library name: AT5G65310_B_oleracea_TO1000DH3_DAPi710G10-ORGi5021-96P151

value: HOMEOBOX


title: DGM-11068


title: DGM-11077


description: Library name: AT2G45480_B_oleracea_TO1000DH3_DAPi710G11-ORGi5021-96P151

value: GRF


title: DGM-11061


description: Library name: AT5G02460_C_rubella_Monte_Gargano_DAPi712B04-ORGi5037-96P155


title: DGM-11111


title: DGM-11066


description: Library name: AL1G23550.t1_C_rubella_Monte_Gargano_DAPi712B03-ORGi5037-96P247


description: Library name: AT1G34670_B_oleracea_TO1000DH3_DAPi710G09-ORGi5021-96P151


description: Library name: AT5G14960_B_oleracea_TO1000DH3_DAPi710G08-ORGi5021-96P151


title: DGM-11060


title: DGM-10361


title: DGM-10808


description: Library name: AT1G02230_C_rubella_Monte_Gargano_DAPi712B03-ORGi5037-96P155


description: Library name: AT3G56400_C_rubella_Monte_Gargano_DAPi712B02-ORGi5037-96P220

value: WRKY


title: DGM-10919


description: Library name: AT4G21080_B_oleracea_TO1000DH3_DAPi710G07-ORGi5021-96P151


title: DGM-11016


title: DGM-11008


description: Library name: AT1G16490_C_rubella_Monte_Gargano_DAPi712B02-ORGi5037-96P155


description: Library name: AT5G52830_B_oleracea_TO1000DH3_DAPi710G06-ORGi5021-96P151


title: DGM-10262


description: Library name: AT3G10030_B_oleracea_TO1000DH3_DAPi710G03-ORGi5021-96P151


title: DGM-10946


title: DGM-01753


title: DGM-10704


title: DGM-10906


description: Library name: AL1G53260.t1_C_rubella_Monte_Gargano_DAPi712B01-ORGi5037-96P247


title: DGM-10732


description: Library name: AT1G69570_B_oleracea_TO1000DH3_DAPi710F11-ORGi5021-96P151


title: DGM-10731


description: Library name: AT5G67300_C_rubella_Monte_Gargano_DAPi712B01-ORGi5037-96P220


description: Library name: LOC_Os01g51154.1_C_rubella_Monte_Gargano_DAPi712A11-ORGi5037-96P247

value: MYBRELATED


title: DGM-10475


description: Library name: AT5G17300_B_oleracea_TO1000DH3_DAPi710F09-ORGi5021-96P151


title: DGM-10869

value: smoker


title: DGM-10901

value: small airway epithelium


description: Library name: AT5G05550_B_oleracea_TO1000DH3_DAPi710G12-ORGi5021-96P151


description: Library name: AT1G12260_C_rubella_Monte_Gargano_DAPi712A11-ORGi5037-96P155


title: DGM-01275

value: M


description: Library name: AL1G11460.t1_C_rubella_Monte_Gargano_DAPi712A10-ORGi5037-96P247


description: Library name: AT1G09540_B_oleracea_TO1000DH3_DAPi710F07-ORGi5021-96P151


title: DGM-10774


title: DGM-10886


description: Library name: AT2G33550_B_oleracea_TO1000DH3_DAPi710F01-ORGi5021-96P151


title: DGM-10573


description: Library name: AT5G22990_B_oleracea_TO1000DH3_DAPi710F02-ORGi5021-96P151


title: DGM-10500

value: nonsmoker


description: Library name: AT5G02320_B_oleracea_TO1000DH3_DAPi710G02-ORGi5021-96P151


description: Library name: Carub.0004s2291.1_C_rubella_Monte_Gargano_DAPi712A09-ORGi5037-96P247


title: DGM-10435


title: DGM-10503


description: Library name: AT1G28470_B_oleracea_TO1000DH3_DAPi710E12-ORGi5021-96P151

value: NAC


title: DGM-10565


description: Library name: AT2G37590_B_oleracea_TO1000DH3_DAPi710E09-ORGi5021-96P151


title: DGM-10194


description: Library name: AT1G69490_C_rubella_Monte_Gargano_DAPi712A09-ORGi5037-96P155


title: DGM-10549


description: Library name: Solyc11g064950.3.1_C_rubella_Monte_Gargano_DAPi712A08-ORGi5037-96P247


description: Library name: AT2G15740_B_oleracea_TO1000DH3_DAPi710F08-ORGi5021-96P151


description: Library name: AT5G05550_C_rubella_Monte_Gargano_DAPi712A10-ORGi5037-96P220


description: Library name: AT5G03150_B_oleracea_TO1000DH3_DAPi710E08-ORGi5021-96P151


title: DGM-10672


title: DGM-10768


title: DGM-10270


description: Library name: AT4G25490_C_rubella_Monte_Gargano_DAPi712A08-ORGi5037-96P220


description: Library name: AT5G53950_C_rubella_Monte_Gargano_DAPi712A10-ORGi5037-96P155


title: DGM-10343


description: Library name: XP_013631386.1_C_rubella_Monte_Gargano_DAPi712A07-ORGi5037-96P247


title: DGM-10380


title: DGM-10383


description: Library name: AT2G18550_B_oleracea_TO1000DH3_DAPi710E06-ORGi5021-96P151


title: DGM-10288


description: Library name: AT3G12250_C_rubella_Monte_Gargano_DAPi712A07-ORGi5037-96P220


description: Library name: AT4G28500_B_oleracea_TO1000DH3_DAPi710E05-ORGi5021-96P151


title: DGM-11525


description: Library name: LOC_Os08g37970.1_C_rubella_Monte_Gargano_DAPi712A06-ORGi5037-96P247


description: Library name: AT3G12250_B_oleracea_TO1000DH3_DAPi710E03-ORGi5021-96P151


description: Library name: AT5G10030_C_rubella_Monte_Gargano_DAPi712A06-ORGi5037-96P220


title: DGM-11964


title: DGM-10254


title: DGM-10123


description: Library name: AT5G66700_C_rubella_Monte_Gargano_DAPi712A06-ORGi5037-96P155


description: Library name: AT5G62940_C_rubella_Monte_Gargano_DAPi712A05-ORGi5037-96P220


description: Library name: AT4G25490_B_oleracea_TO1000DH3_DAPi710E07-ORGi5021-96P151


description: Library name: AT2G42430_B_oleracea_TO1000DH3_DAPi710E01-ORGi5021-96P151


description: Library name: AT1G08320_B_oleracea_TO1000DH3_DAPi710D12-ORGi5021-96P151


title: DGM-10161


description: Library name: AT1G49480_C_rubella_Monte_Gargano_DAPi712A04-ORGi5037-96P220

value: REM


description: Library name: AT2G26960_B_oleracea_TO1000DH3_DAPi710D11-ORGi5021-96P151


description: Library name: AT3G10113_C_rubella_Monte_Gargano_DAPi712A04-ORGi5037-96P155


description: Library name: AT1G02250_B_oleracea_TO1000DH3_DAPi710D09-ORGi5021-96P151


description: Library name: AT1G28160_B_oleracea_TO1000DH3_DAPi710E04-ORGi5021-96P151


description: Library name: AT1G69780_C_rubella_Monte_Gargano_DAPi712A03-ORGi5037-96P220


description: Library name: AT5G39760_C_rubella_Monte_Gargano_DAPi712A02-ORGi5037-96P220

value: ZFHD


description: Library name: AT5G18560_B_oleracea_TO1000DH3_DAPi710D07-ORGi5021-96P151


description: Library name: AT2G23290_C_rubella_Monte_Gargano_DAPi712A02-ORGi5037-96P155


description: Library name: AT3G46590_B_oleracea_TO1000DH3_DAPi710D06-ORGi5021-96P151


description: Library name: AT1G53170_C_rubella_Monte_Gargano_DAPi711H11-ORGi5037-96P166


description: Library name: AT1G47655_B_oleracea_TO1000DH3_DAPi710D05-ORGi5021-96P151


description: Library name: AT4G36780_C_rubella_Monte_Gargano_DAPi711H06-ORGi5037-96P166

value: BZR


description: Library name: AT2G03500_C_rubella_Monte_Gargano_DAPi711H07-ORGi5037-96P166


description: Library name: AT1G75240_B_oleracea_TO1000DH3_DAPi710C12-ORGi5021-96P151


title: DGM-12697_am

type: RNA

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: alveolar macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

value: waterpipe smoker

value: alveolar macrophages


title: DGM-12699_am


title: DGM-12715_am


description: Library name: AT2G40740_B_oleracea_TO1000DH3_DAPi710C11-ORGi5021-96P151

value: plant


title: DGM-12706_am


description: Library name: AT5G58900_C_rubella_Monte_Gargano_DAPi711H04-ORGi5037-96P166


title: DGM-12699_sm

value: small airway epithelium brushing


title: DGM-12750_sm


title: DGM-12750_am


title: DGM-12697_sm


title: DGM-12707_sm


title: DGM-12715_sm


title: DGM-12708_am


title: DGM-12682_sm


title: DGM-12682_am


description: Library name: AT5G56840_B_oleracea_TO1000DH3_DAPi710D01-ORGi5021-96P151


title: DGM-12708_sm


description: Library name: AT1G72010_C_rubella_Monte_Gargano_DAPi711H03-ORGi5037-96P166

value: TCP


title: DGM-12490_am


title: DGM-12706_sm


title: DGM-12685_am


title: DGM-12685_sm


title: DGM-12490_sm


title: DGM-12614_sm


description: Library name: AT1G76420_B_oleracea_TO1000DH3_DAPi710C10-ORGi5021-96P151


description: Library name: AT4G01550_B_oleracea_TO1000DH3_DAPi710D08-ORGi5021-96P151


description: Library name: AT5G05790_C_rubella_Monte_Gargano_DAPi711G12-ORGi5037-96P166


title: DGM-12707_am


description: Library name: AT2G01940_B_oleracea_TO1000DH3_DAPi710C09-ORGi5021-96P151


description: Library name: AT1G63030_B_oleracea_TO1000DH3_DAPi710C07-ORGi5021-96P151


description: Library name: AT5G64750_C_rubella_Monte_Gargano_DAPi711G09-ORGi5037-96P166


title: DGM-12614_am


description: Library name: AT3G17730_B_oleracea_TO1000DH3_DAPi710C06-ORGi5021-96P151


description: Library name: AT1G77200_B_oleracea_TO1000DH3_DAPi710C05-ORGi5021-96P151


description: Library name: AT1G69780_C_rubella_Monte_Gargano_DAPi711G07-ORGi5037-96P166

value: HOMEOBOX


description: Library name: AT5G47390_C_rubella_Monte_Gargano_DAPi711H02-ORGi5037-96P166


description: Library name: AT5G51990_B_oleracea_TO1000DH3_DAPi710C04-ORGi5021-96P151


title: DGM-12414_sm


title: DGM-12337_am


title: DGM-12414_am


description: Library name: AT3G30210_B_oleracea_TO1000DH3_DAPi710C02-ORGi5021-96P151

value: MYB


description: Library name: AT1G69690_C_rubella_Monte_Gargano_DAPi711G05-ORGi5037-96P166


description: Library name: AT5G39760_C_rubella_Monte_Gargano_DAPi711G03-ORGi5037-96P166


title: DGM-11726_am


description: Library name: AT3G10580_B_oleracea_TO1000DH3_DAPi710C01-ORGi5021-96P151


description: Library name: AT5G26170_B_oleracea_TO1000DH3_DAPi710B11-ORGi5021-96P151

value: WRKY


title: DGM-12337_sm


description: Library name: AT5G66940_B_oleracea_TO1000DH3_DAPi710B10-ORGi5021-96P151


title: DGM-11634_am


title: DGM-11756_sm


title: DGM-11622_am


title: DGM-11726_sm


title: DGM-12277_sm


description: Library name: AT1G29280_C_rubella_Monte_Gargano_DAPi711F12-ORGi5037-96P166


title: DGM-11565_am


description: Library name: AT3G22830_C_rubella_Monte_Gargano_DAPi711G01-ORGi5037-96P166

value: HSF


description: Library name: AT5G41570_C_rubella_Monte_Gargano_DAPi711G08-ORGi5037-96P166


description: Library name: AT2G31230_C_rubella_Monte_Gargano_DAPi711G02-ORGi5037-96P166


title: DGM-01198_am


description: Library name: AT1G01250_B_oleracea_TO1000DH3_DAPi710B07-ORGi5021-96P151


title: DGM-11756_am


title: DGM-10706_M0_am


title: DGM-01198_sm


description: Library name: AT3G15270_C_rubella_Monte_Gargano_DAPi711F08-ORGi5037-96P166

value: SBP


title: DGM-10662_M0_am


title: DGM-12481_sm


title: DGM-11565_sm


title: DGM-11622_sm


title: DGM-10568_M0_am


description: Library name: AT4G34410_C_rubella_Monte_Gargano_DAPi711F11-ORGi5037-96P166


description: Library name: AT2G22430_C_rubella_Monte_Gargano_DAPi711F07-ORGi5037-96P166


description: Library name: AT5G47660_B_oleracea_TO1000DH3_DAPi710B06-ORGi5021-96P151

value: TRIHELIX