description: Library name: AT1G12630_B_oleracea_TO1000DH3_DAPi710B04-ORGi5021-96P151


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: AT2G02820_B_oleracea_TO1000DH3_DAPi710B09-ORGi5021-96P151

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: 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

molecule: genomic DNA

organism: Brassica oleracea

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: tf family

value: MYB

tag: multidap sample_id

tag: 96 well_plate_id

tag: tf source_species


title: DGM-10475_M0_am

type: RNA

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

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

molecule: total RNA

organism: Homo sapiens

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.

tag: smoking status

value: nonsmoker

tag: cell type

value: alveolar macrophages


description: Library name: AT5G60850_C_rubella_Monte_Gargano_DAPi711F05-ORGi5037-96P166

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

organism: Capsella rubella


title: DGM-10707_M0_am


title: DGM-10447_M0_am


description: Library name: AT3G20310_C_rubella_Monte_Gargano_DAPi711F06-ORGi5037-96P166


title: DGM-11634_sm

source_name: small airway epithelium brushing

value: waterpipe smoker

value: small airway epithelium brushing


description: Library name: AT1G14687_C_rubella_Monte_Gargano_DAPi711F04-ORGi5037-96P166

value: ZFHD


description: Library name: AT2G45410_B_oleracea_TO1000DH3_DAPi710B02-ORGi5021-96P151


description: Library name: AT3G50410_B_oleracea_TO1000DH3_DAPi710B03-ORGi5021-96P151


description: Library name: AT1G18330_C_rubella_Monte_Gargano_DAPi711F03-ORGi5037-96P166

value: MYBRELATED


title: DGM-10500_M0_am


description: Library name: AT1G12610_B_oleracea_TO1000DH3_DAPi710A11-ORGi5021-96P151


description: Library name: AT1G27730_C_rubella_Monte_Gargano_DAPi711F01-ORGi5037-96P166


description: Library name: AT4G16750_C_rubella_Monte_Gargano_DAPi711E12-ORGi5037-96P166


description: Library name: AT3G03200_B_oleracea_TO1000DH3_DAPi710A10-ORGi5021-96P151

value: NAC


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712H01-ORGi5019-96P247

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: Sorghum bicolor RTx430: Phytozome v2.1
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: Sorghum bicolor


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712H12-ORGi5019-96P247


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712A12-ORGi5019-96P247


title: DGM-10343_M0_am


title: DGM-10254_M0_am


description: Library name: AT5G62470_B_oleracea_TO1000DH3_DAPi710A08-ORGi5021-96P151


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712A01-ORGi5019-96P247


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712H12-ORGi5019-96P220


description: Library name: AT1G25340_B_oleracea_TO1000DH3_DAPi710B01-ORGi5021-96P151


title: DGM-10383_M0_am


description: Library name: AT2G46680_C_rubella_Monte_Gargano_DAPi711E11-ORGi5037-96P166

value: HOMEOBOX


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712H01-ORGi5019-96P220


description: Library name: AT5G19790_B_oleracea_TO1000DH3_DAPi710A07-ORGi5021-96P151


description: Library name: AT2G23340_C_rubella_Monte_Gargano_DAPi711E08-ORGi5037-96P166


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712A12-ORGi5019-96P220


title: DGM-10270_M0_am


title: DGM-10380_M0_am


description: Library name: AT2G28810_B_oleracea_TO1000DH3_DAPi710A06-ORGi5021-96P151


title: DGM-10288_M0_am


description: Library name: Control_TF_DNA_S_bicolor_RTx430_DAPi712A01-ORGi5019-96P220


title: DGM-01774_M0_am


title: DGM-00342_M0_am


description: Library name: AT5G08330_C_rubella_Monte_Gargano_DAPi711E05-ORGi5037-96P166

value: TCP


description: Library name: AL2G28980.t1_S_bicolor_RTx430_DAPi712H11-ORGi5019-96P247


title: DGM-10226_M0_am


description: Library name: Carub.0002s1959.1_S_bicolor_RTx430_DAPi712H10-ORGi5019-96P247


description: Library name: AT2G46270_S_bicolor_RTx430_DAPi712H11-ORGi5019-96P220

value: BZIP


description: Library name: AT5G60130_B_oleracea_TO1000DH3_DAPi710A04-ORGi5021-96P151


description: Library name: AT1G30210_C_rubella_Monte_Gargano_DAPi711E03-ORGi5037-96P166


description: Library name: AT2G47070_S_bicolor_RTx430_DAPi712H10-ORGi5019-96P220

value: SBP


title: DGM-10159_M0_am


title: DGM-10123_M0_am


description: Library name: XP_013634112.1_S_bicolor_RTx430_DAPi712H08-ORGi5019-96P247


description: Library name: AT5G62320_B_oleracea_TO1000DH3_DAPi710A03-ORGi5021-96P151


description: Library name: AT5G08520_C_rubella_Monte_Gargano_DAPi711E02-ORGi5037-96P166


description: Library name: Solyc08g078340.3.1_S_bicolor_RTx430_DAPi712H09-ORGi5019-96P247


description: Library name: AT1G68320_B_oleracea_TO1000DH3_DAPi709H11-ORGi5021-96P169


description: Library name: AT2G23320_C_rubella_Monte_Gargano_DAPi711E01-ORGi5037-96P166

value: WRKY


description: Library name: LOC_Os01g17260.2_S_bicolor_RTx430_DAPi712H07-ORGi5019-96P247


description: Library name: AT5G18560_S_bicolor_RTx430_DAPi712H07-ORGi5019-96P220


description: Library name: AT5G17300_S_bicolor_RTx430_DAPi712H08-ORGi5019-96P220


description: Library name: AT1G19000_C_rubella_Monte_Gargano_DAPi711D11-ORGi5037-96P166


description: Library name: AT1G49480_C_rubella_Monte_Gargano_DAPi711D12-ORGi5037-96P166

value: REM


description: Library name: AL4G45550.t1_S_bicolor_RTx430_DAPi712H06-ORGi5019-96P247


title: DGM-10261_M0_am


description: Library name: AT5G58850_B_oleracea_TO1000DH3_DAPi710A05-ORGi5021-96P151


description: Library name: AT3G50410_S_bicolor_RTx430_DAPi712H06-ORGi5019-96P220


description: Library name: AT3G24050_B_oleracea_TO1000DH3_DAPi709H10-ORGi5021-96P169


description: Library name: AT3G60490_B_oleracea_TO1000DH3_DAPi710A02-ORGi5021-96P151


description: Library name: AT1G01060_S_bicolor_RTx430_DAPi712H05-ORGi5019-96P220


description: Library name: Solyc01g102340.3.1_S_bicolor_RTx430_DAPi712H04-ORGi5019-96P247


description: Library name: AT1G79180_B_oleracea_TO1000DH3_DAPi709H09-ORGi5021-96P169


description: Library name: AT5G65410_C_rubella_Monte_Gargano_DAPi711D09-ORGi5037-96P166


description: Library name: AT3G02940_S_bicolor_RTx430_DAPi712H04-ORGi5019-96P220


description: Library name: AT3G15210_C_rubella_Monte_Gargano_DAPi711D10-ORGi5037-96P166


description: Library name: XP_013629448.1_S_bicolor_RTx430_DAPi712H03-ORGi5019-96P247


description: Library name: AT2G30250_S_bicolor_RTx430_DAPi712H03-ORGi5019-96P220


description: Library name: XP_013609718.1_S_bicolor_RTx430_DAPi712G12-ORGi5019-96P247


description: Library name: AT2G22430_S_bicolor_RTx430_DAPi712H02-ORGi5019-96P220


description: Library name: AT5G09410_S_bicolor_RTx430_DAPi712G11-ORGi5019-96P220

value: CAMTA


description: Library name: AT5G62000_C_rubella_Monte_Gargano_DAPi711D08-ORGi5037-96P166

value: ARF


description: Library name: AT5G08130_B_oleracea_TO1000DH3_DAPi709H05-ORGi5021-96P169

value: plant

value: BHLH


description: Library name: AT1G51220_B_oleracea_TO1000DH3_DAPi709G12-ORGi5021-96P169


description: Library name: AT1G19210_B_oleracea_TO1000DH3_DAPi709H02-ORGi5021-96P169


description: Library name: AT3G50260_C_rubella_Monte_Gargano_DAPi711D06-ORGi5037-96P166


description: Library name: XP_013589913.1_S_bicolor_RTx430_DAPi712G10-ORGi5019-96P247


description: Library name: AT3G14180_C_rubella_Monte_Gargano_DAPi711D03-ORGi5037-96P166

value: TRIHELIX


description: Library name: LOC_Os10g41200.1_S_bicolor_RTx430_DAPi712G09-ORGi5019-96P247


description: Library name: AT1G72740_S_bicolor_RTx430_DAPi712G09-ORGi5019-96P220


description: Library name: AT5G45300_S_bicolor_RTx430_DAPi712G10-ORGi5019-96P220


description: Library name: AT1G71450_B_oleracea_TO1000DH3_DAPi709G11-ORGi5021-96P169


description: Library name: AT3G50060_C_rubella_Monte_Gargano_DAPi711D07-ORGi5037-96P166

value: MYB


description: Library name: AT5G67580_C_rubella_Monte_Gargano_DAPi711D05-ORGi5037-96P166


description: Library name: AT1G69180_B_oleracea_TO1000DH3_DAPi709G09-ORGi5021-96P169


description: Library name: AT2G01940_S_bicolor_RTx430_DAPi712G08-ORGi5019-96P220


description: Library name: AT1G33240_C_rubella_Monte_Gargano_DAPi711C10-ORGi5037-96P166


description: Library name: Carub.0003s1161.1.p_S_bicolor_RTx430_DAPi712G07-ORGi5019-96P247


description: Library name: AT1G46768_B_oleracea_TO1000DH3_DAPi709H03-ORGi5021-96P169


description: Library name: AT5G19790_S_bicolor_RTx430_DAPi712G07-ORGi5019-96P220


description: Library name: AT5G51190_B_oleracea_TO1000DH3_DAPi709G07-ORGi5021-96P169


description: Library name: AL4G38490.t1_S_bicolor_RTx430_DAPi712G08-ORGi5019-96P247


description: Library name: AT1G69180_S_bicolor_RTx430_DAPi712G05-ORGi5019-96P220


description: Library name: AT5G47230_B_oleracea_TO1000DH3_DAPi709G06-ORGi5021-96P169


description: Library name: AT4G31800_C_rubella_Monte_Gargano_DAPi711C07-ORGi5037-96P166


description: Library name: AT5G25190_C_rubella_Monte_Gargano_DAPi711C05-ORGi5037-96P166


description: Library name: LOC_Os01g18240.1_S_bicolor_RTx430_DAPi712G04-ORGi5019-96P247


description: Library name: AT3G50060_S_bicolor_RTx430_DAPi712G02-ORGi5019-96P220


description: Library name: AT1G46768_S_bicolor_RTx430_DAPi712G04-ORGi5019-96P220


description: Library name: AT5G62020_B_oleracea_TO1000DH3_DAPi709G02-ORGi5021-96P169

value: HSF


description: Library name: AT5G13080_C_rubella_Monte_Gargano_DAPi711B12-ORGi5037-96P166


description: Library name: AT1G18330_S_bicolor_RTx430_DAPi712G01-ORGi5019-96P220


description: Library name: Solyc03g116890.3.1_S_bicolor_RTx430_DAPi712G11-ORGi5019-96P247


description: Library name: AT1G50640_B_oleracea_TO1000DH3_DAPi709G04-ORGi5021-96P169


description: Library name: LOC_Os09g25060.1_S_bicolor_RTx430_DAPi712F11-ORGi5019-96P247


description: Library name: AT1G80840_S_bicolor_RTx430_DAPi712G03-ORGi5019-96P220


description: Library name: AT5G02320_S_bicolor_RTx430_DAPi712G06-ORGi5019-96P220


description: Library name: AT2G32460_B_oleracea_TO1000DH3_DAPi709G05-ORGi5021-96P169


description: Library name: AT5G56110_B_oleracea_TO1000DH3_DAPi709F12-ORGi5021-96P169


description: Library name: AT1G76880_S_bicolor_RTx430_DAPi712F11-ORGi5019-96P220


description: Library name: AT1G25550_C_rubella_Monte_Gargano_DAPi711C01-ORGi5037-96P166


description: Library name: AT2G30250_C_rubella_Monte_Gargano_DAPi711B11-ORGi5037-96P166


description: Library name: AT4G14770_S_bicolor_RTx430_DAPi712F10-ORGi5019-96P220

value: CPP


description: Library name: AT2G46590_C_rubella_Monte_Gargano_DAPi711B10-ORGi5037-96P166


description: Library name: Carub.0008s0039.1_S_bicolor_RTx430_DAPi712F09-ORGi5019-96P247


description: Library name: AT2G45480_S_bicolor_RTx430_DAPi712F09-ORGi5019-96P220

value: GRF


description: Library name: AT5G64060_B_oleracea_TO1000DH3_DAPi709F10-ORGi5021-96P169


description: Library name: AT2G02820_S_bicolor_RTx430_DAPi712F08-ORGi5019-96P220


description: Library name: AT5G24110_C_rubella_Monte_Gargano_DAPi711B09-ORGi5037-96P166


description: Library name: XP_013586407.1_S_bicolor_RTx430_DAPi712F07-ORGi5019-96P247


description: Library name: AT1G64620_C_rubella_Monte_Gargano_DAPi711C04-ORGi5037-96P166


description: Library name: AT1G01720_B_oleracea_TO1000DH3_DAPi709F09-ORGi5021-96P169


description: Library name: AT3G12730_C_rubella_Monte_Gargano_DAPi711B08-ORGi5037-96P166


description: Library name: AT5G52830_S_bicolor_RTx430_DAPi712F07-ORGi5019-96P220


description: Library name: AL2G32420.t2_S_bicolor_RTx430_DAPi712F10-ORGi5019-96P247

value: MYBRELATED


description: Library name: AT1G29160_B_oleracea_TO1000DH3_DAPi709G01-ORGi5021-96P169


description: Library name: AT3G24120_C_rubella_Monte_Gargano_DAPi711B06-ORGi5037-96P166


description: Library name: AT4G25480_S_bicolor_RTx430_DAPi712F04-ORGi5019-96P220


description: Library name: AT1G49010_B_oleracea_TO1000DH3_DAPi709F03-ORGi5021-96P169


description: Library name: AT3G08500_B_oleracea_TO1000DH3_DAPi709F05-ORGi5021-96P169


description: Library name: AT5G47370_C_rubella_Monte_Gargano_DAPi711B05-ORGi5037-96P166


description: Library name: AT2G01060_S_bicolor_RTx430_DAPi712F05-ORGi5019-96P220


description: Library name: AT2G45420_S_bicolor_RTx430_DAPi712F06-ORGi5019-96P220


description: Library name: Solyc08g079120.3.1_S_bicolor_RTx430_DAPi712F03-ORGi5019-96P247

value: NAC


description: Library name: AT2G44940_B_oleracea_TO1000DH3_DAPi709F02-ORGi5021-96P169


description: Library name: AT4G31800_S_bicolor_RTx430_DAPi712F02-ORGi5019-96P220


description: Library name: AT5G47390_S_bicolor_RTx430_DAPi712F01-ORGi5019-96P220


description: Library name: AT1G33240_S_bicolor_RTx430_DAPi712F03-ORGi5019-96P220


description: Library name: Solyc04g078640.3.1_S_bicolor_RTx430_DAPi712F01-ORGi5019-96P247


description: Library name: AT5G67300_C_rubella_Monte_Gargano_DAPi711B01-ORGi5037-96P166


description: Library name: AT1G52880_S_bicolor_RTx430_DAPi712E12-ORGi5019-96P220


description: Library name: AT3G57920_B_oleracea_TO1000DH3_DAPi709E12-ORGi5021-96P169


description: Library name: Solyc05g007180.3.1_S_bicolor_RTx430_DAPi712E12-ORGi5019-96P247

value: HOMEOBOX


description: Library name: AT1G80840_C_rubella_Monte_Gargano_DAPi711A11-ORGi5037-96P166


description: Library name: AT3G04030_C_rubella_Monte_Gargano_DAPi711A08-ORGi5037-96P166


description: Library name: AT1G20980_S_bicolor_RTx430_DAPi712E11-ORGi5019-96P220


description: Library name: Carub.0002s2670.1_S_bicolor_RTx430_DAPi712E11-ORGi5019-96P247


description: Library name: Solyc10g005080.3.1_S_bicolor_RTx430_DAPi712E10-ORGi5019-96P247


description: Library name: AT4G06746_B_oleracea_TO1000DH3_DAPi709E10-ORGi5021-96P169


description: Library name: AT3G01530_C_rubella_Monte_Gargano_DAPi711A05-ORGi5037-96P166


description: Library name: AT4G17980_S_bicolor_RTx430_DAPi712E10-ORGi5019-96P220


description: Library name: AT3G16280_B_oleracea_TO1000DH3_DAPi709E11-ORGi5021-96P169


description: Library name: AT3G56400_C_rubella_Monte_Gargano_DAPi711A04-ORGi5037-96P166


description: Library name: XP_013615900.1_S_bicolor_RTx430_DAPi712E09-ORGi5019-96P247


description: Library name: AT3G01220_B_oleracea_TO1000DH3_DAPi709F01-ORGi5021-96P169


description: Library name: AT5G02840_B_oleracea_TO1000DH3_DAPi709E07-ORGi5021-96P169


description: Library name: AT2G20400_B_oleracea_TO1000DH3_DAPi709E09-ORGi5021-96P169


description: Library name: AL3G23910.t2_S_bicolor_RTx430_DAPi712E07-ORGi5019-96P247


description: Library name: AT5G56110_S_bicolor_RTx430_DAPi712E06-ORGi5019-96P220


description: Library name: AT5G14960_S_bicolor_RTx430_DAPi712E08-ORGi5019-96P220


description: Library name: AT4G01250_C_rubella_Monte_Gargano_DAPi711A02-ORGi5037-96P166


description: Library name: AT4G23550_B_oleracea_TO1000DH3_DAPi709E05-ORGi5021-96P169


description: Library name: AT1G72740_C_rubella_Monte_Gargano_DAPi710H11-ORGi5037-96P151


description: Library name: AT5G62020_S_bicolor_RTx430_DAPi712E04-ORGi5019-96P220


description: Library name: AT3G60530_S_bicolor_RTx430_DAPi712E05-ORGi5019-96P220


description: Library name: AT3G55370_C_rubella_Monte_Gargano_DAPi710H10-ORGi5037-96P151


description: Library name: AT5G25810_B_oleracea_TO1000DH3_DAPi709E04-ORGi5021-96P169


description: Library name: LOC_Os02g42970.1_S_bicolor_RTx430_DAPi712E03-ORGi5019-96P247


description: Library name: AT4G01280_B_oleracea_TO1000DH3_DAPi709E03-ORGi5021-96P169


description: Library name: AT1G79580_C_rubella_Monte_Gargano_DAPi710H09-ORGi5037-96P151


description: Library name: LOC_Os06g07030.1_S_bicolor_RTx430_DAPi712E01-ORGi5019-96P247


description: Library name: AT1G13260_S_bicolor_RTx430_DAPi712E01-ORGi5019-96P220

value: RAV


description: Library name: AT5G64750_S_bicolor_RTx430_DAPi712E03-ORGi5019-96P220


description: Library name: AT1G74650_C_rubella_Monte_Gargano_DAPi710H08-ORGi5037-96P151


description: Library name: AT5G11260_S_bicolor_RTx430_DAPi712D12-ORGi5019-96P220

value: BZIP


description: Library name: AT4G25470_B_oleracea_TO1000DH3_DAPi709D11-ORGi5021-96P169


description: Library name: LOC_Os10g26500.1_S_bicolor_RTx430_DAPi712D12-ORGi5019-96P247


description: Library name: AT4G24240_C_rubella_Monte_Gargano_DAPi711A03-ORGi5037-96P166


description: Library name: AT1G01060_B_oleracea_TO1000DH3_DAPi709D10-ORGi5021-96P169


description: Library name: AT2G18550_S_bicolor_RTx430_DAPi712E07-ORGi5019-96P220


description: Library name: XP_013587997.1_S_bicolor_RTx430_DAPi712D11-ORGi5019-96P247


description: Library name: AT3G18990_S_bicolor_RTx430_DAPi712D11-ORGi5019-96P220


description: Library name: AT5G54230_B_oleracea_TO1000DH3_DAPi709D07-ORGi5021-96P169


description: Library name: AT2G18380_C_rubella_Monte_Gargano_DAPi710H06-ORGi5037-96P151


description: Library name: LOC_Os08g06110.3_S_bicolor_RTx430_DAPi712D10-ORGi5019-96P247


description: Library name: AL8G10650.t1_S_bicolor_RTx430_DAPi712D09-ORGi5019-96P247


description: Library name: AT1G74480_C_rubella_Monte_Gargano_DAPi710H04-ORGi5037-96P151

value: RWPRK


description: Library name: AT5G03150_S_bicolor_RTx430_DAPi712D08-ORGi5019-96P220


description: Library name: AT5G62940_B_oleracea_TO1000DH3_DAPi709D05-ORGi5021-96P169


description: Library name: Carub.0008s0285.1_S_bicolor_RTx430_DAPi712D08-ORGi5019-96P247


description: Library name: AT1G74480_S_bicolor_RTx430_DAPi712D07-ORGi5019-96P220


description: Library name: AT2G30340_C_rubella_Monte_Gargano_DAPi710H03-ORGi5037-96P151


description: Library name: AT3G57920_S_bicolor_RTx430_DAPi712D06-ORGi5019-96P220

value: SBP


description: Library name: AT4G25480_B_oleracea_TO1000DH3_DAPi709D03-ORGi5021-96P169


description: Library name: AT1G06280_C_rubella_Monte_Gargano_DAPi710H02-ORGi5037-96P151


description: Library name: LOC_Os02g33430.1_S_bicolor_RTx430_DAPi712D05-ORGi5019-96P247


description: Library name: AT1G36060_B_oleracea_TO1000DH3_DAPi709D02-ORGi5021-96P169


description: Library name: Carub.0001s1194.1_S_bicolor_RTx430_DAPi712D03-ORGi5019-96P247


description: Library name: AT5G05550_C_rubella_Monte_Gargano_DAPi710G12-ORGi5037-96P151


description: Library name: AT3G25990_C_rubella_Monte_Gargano_DAPi710H05-ORGi5037-96P151


description: Library name: AT2G45480_C_rubella_Monte_Gargano_DAPi710G11-ORGi5037-96P151


description: Library name: AT5G65410_S_bicolor_RTx430_DAPi712D03-ORGi5019-96P220

value: ZFHD


description: Library name: AT3G50260_S_bicolor_RTx430_DAPi712D02-ORGi5019-96P220


description: Library name: AT2G40260_B_oleracea_TO1000DH3_DAPi709C12-ORGi5021-96P169


description: Library name: Solyc01g095460.3.1_S_bicolor_RTx430_DAPi712D07-ORGi5019-96P247


description: Library name: Carub.0002s1646.1_S_bicolor_RTx430_DAPi712C12-ORGi5019-96P247


description: Library name: AT5G10030_B_oleracea_TO1000DH3_DAPi709C11-ORGi5021-96P169


description: Library name: AT1G12260_S_bicolor_RTx430_DAPi712C12-ORGi5019-96P220


description: Library name: AT5G65310_C_rubella_Monte_Gargano_DAPi710G10-ORGi5037-96P151


description: Library name: AT3G18400_B_oleracea_TO1000DH3_DAPi709C10-ORGi5021-96P169


description: Library name: AL2G40550.t1_S_bicolor_RTx430_DAPi712C11-ORGi5019-96P247

value: WRKY


description: Library name: AT1G34670_C_rubella_Monte_Gargano_DAPi710G09-ORGi5037-96P151


description: Library name: AT1G53230_B_oleracea_TO1000DH3_DAPi709C08-ORGi5021-96P169

value: TCP


description: Library name: AT5G14960_C_rubella_Monte_Gargano_DAPi710G08-ORGi5037-96P151

value: plant


description: Library name: Carub.0001s0116.1_S_bicolor_RTx430_DAPi712C10-ORGi5019-96P247


description: Library name: AT4G00730_S_bicolor_RTx430_DAPi712C11-ORGi5019-96P220


description: Library name: AT3G11280_B_oleracea_TO1000DH3_DAPi709C06-ORGi5021-96P169


description: Library name: Solyc06g048630.3.1_S_bicolor_RTx430_DAPi712C09-ORGi5019-96P247


description: Library name: AT3G02940_B_oleracea_TO1000DH3_DAPi709C05-ORGi5021-96P169


description: Library name: XP_013613838.1_S_bicolor_RTx430_DAPi712C08-ORGi5019-96P247


description: Library name: AT2G01930_S_bicolor_RTx430_DAPi712D05-ORGi5019-96P220

value: BBRBPC


description: Library name: Carub.0001s3581.1.p_S_bicolor_RTx430_DAPi712D01-ORGi5019-96P247


description: Library name: AT5G62470_S_bicolor_RTx430_DAPi712C08-ORGi5019-96P220


description: Library name: AT5G52830_C_rubella_Monte_Gargano_DAPi710G06-ORGi5037-96P151


description: Library name: AT3G10030_C_rubella_Monte_Gargano_DAPi710G03-ORGi5037-96P151

value: TRIHELIX


description: Library name: Solyc08g068320.3.1_S_bicolor_RTx430_DAPi712C04-ORGi5019-96P247

value: MYB


description: Library name: AT5G60130_S_bicolor_RTx430_DAPi712C07-ORGi5019-96P220


description: Library name: AT5G03790_S_bicolor_RTx430_DAPi712C06-ORGi5019-96P220


description: Library name: AT3G27010_B_oleracea_TO1000DH3_DAPi709C02-ORGi5021-96P169


description: Library name: AT5G02320_C_rubella_Monte_Gargano_DAPi710G02-ORGi5037-96P151


description: Library name: AT3G27010_S_bicolor_RTx430_DAPi712C04-ORGi5019-96P220


description: Library name: AT4G21080_C_rubella_Monte_Gargano_DAPi710G07-ORGi5037-96P151


description: Library name: XP_013602769.1_S_bicolor_RTx430_DAPi712C03-ORGi5019-96P247


description: Library name: LOC_Os01g46970.1_S_bicolor_RTx430_DAPi712C07-ORGi5019-96P247


description: Library name: AT1G76420_S_bicolor_RTx430_DAPi712C09-ORGi5019-96P220


description: Library name: AT1G69690_S_bicolor_RTx430_DAPi712C02-ORGi5019-96P220


description: Library name: AT5G03790_B_oleracea_TO1000DH3_DAPi709B12-ORGi5021-96P169


description: Library name: AT1G69570_C_rubella_Monte_Gargano_DAPi710F11-ORGi5037-96P151


description: Library name: AT2G40620_S_bicolor_RTx430_DAPi712B12-ORGi5019-96P220


description: Library name: AT1G27730_S_bicolor_RTx430_DAPi712C01-ORGi5019-96P220


description: Library name: Solyc07g040920.2.1_S_bicolor_RTx430_DAPi712B11-ORGi5019-96P247


description: Library name: AT3G01970_B_oleracea_TO1000DH3_DAPi709C04-ORGi5021-96P169


description: Library name: AT1G09540_C_rubella_Monte_Gargano_DAPi710F07-ORGi5037-96P151


description: Library name: XP_013589953.1_S_bicolor_RTx430_DAPi712B12-ORGi5019-96P247


description: Library name: AT3G52440_B_oleracea_TO1000DH3_DAPi709B11-ORGi5021-96P169


description: Library name: AT1G22810_B_oleracea_TO1000DH3_DAPi709B04-ORGi5021-96P169


description: Library name: AT1G20910_S_bicolor_RTx430_DAPi712B10-ORGi5019-96P220

value: ARID


description: Library name: AT5G22990_C_rubella_Monte_Gargano_DAPi710F02-ORGi5037-96P151


description: Library name: XP_013587350.1_S_bicolor_RTx430_DAPi712B10-ORGi5019-96P247


description: Library name: AT5G17300_C_rubella_Monte_Gargano_DAPi710F09-ORGi5037-96P151


description: Library name: LOC_Os03g21800.1_S_bicolor_RTx430_DAPi712B09-ORGi5019-96P247


description: Library name: AT1G03800_B_oleracea_TO1000DH3_DAPi709C01-ORGi5021-96P169


description: Library name: AT2G15740_C_rubella_Monte_Gargano_DAPi710F08-ORGi5037-96P151


description: Library name: AT4G38000_B_oleracea_TO1000DH3_DAPi709B02-ORGi5021-96P169


description: Library name: AT4G25470_S_bicolor_RTx430_DAPi712B06-ORGi5019-96P220


description: Library name: AT1G79580_S_bicolor_RTx430_DAPi712B09-ORGi5019-96P220


description: Library name: AT2G33550_C_rubella_Monte_Gargano_DAPi710F01-ORGi5037-96P151


description: Library name: AT2G24430_B_oleracea_TO1000DH3_DAPi709B10-ORGi5021-96P169


description: Library name: AT5G45580_B_oleracea_TO1000DH3_DAPi709A11-ORGi5021-96P169


description: Library name: Carub.0004s2898.1.p_S_bicolor_RTx430_DAPi712B07-ORGi5019-96P247


description: Library name: AT1G28470_C_rubella_Monte_Gargano_DAPi710E12-ORGi5037-96P151


description: Library name: AL8G13510.t2_S_bicolor_RTx430_DAPi712B08-ORGi5019-96P247


description: Library name: AT5G52020_B_oleracea_TO1000DH3_DAPi709A10-ORGi5021-96P169


description: Library name: AT5G65130_B_oleracea_TO1000DH3_DAPi709B01-ORGi5021-96P169


description: Library name: XP_013631649.1_S_bicolor_RTx430_DAPi712B05-ORGi5019-96P247


description: Library name: AT2G37590_C_rubella_Monte_Gargano_DAPi710E09-ORGi5037-96P151


description: Library name: AT3G08500_S_bicolor_RTx430_DAPi712B05-ORGi5019-96P220


description: Library name: AT1G29160_S_bicolor_RTx430_DAPi712B04-ORGi5019-96P220


description: Library name: AT5G03150_C_rubella_Monte_Gargano_DAPi710E08-ORGi5037-96P151


description: Library name: AT3G28920_B_oleracea_TO1000DH3_DAPi709A08-ORGi5021-96P169


description: Library name: AT3G56400_S_bicolor_RTx430_DAPi712B02-ORGi5019-96P220


description: Library name: AT4G25490_C_rubella_Monte_Gargano_DAPi710E07-ORGi5037-96P151


description: Library name: AT1G28370_B_oleracea_TO1000DH3_DAPi709A07-ORGi5021-96P169


description: Library name: AT5G67300_S_bicolor_RTx430_DAPi712B01-ORGi5019-96P220


description: Library name: AT2G18550_C_rubella_Monte_Gargano_DAPi710E06-ORGi5037-96P151


description: Library name: LOC_Os01g51154.1_S_bicolor_RTx430_DAPi712A11-ORGi5019-96P247


description: Library name: AT5G52660_B_oleracea_TO1000DH3_DAPi709A06-ORGi5021-96P169


description: Library name: AL1G11460.t1_S_bicolor_RTx430_DAPi712A10-ORGi5019-96P247


description: Library name: AT4G28500_C_rubella_Monte_Gargano_DAPi710E05-ORGi5037-96P151


description: Library name: AT5G07310_B_oleracea_TO1000DH3_DAPi709A05-ORGi5021-96P169


description: Library name: AT5G05550_S_bicolor_RTx430_DAPi712A10-ORGi5019-96P220


description: Library name: AT5G13910_B_oleracea_TO1000DH3_DAPi709A04-ORGi5021-96P169


description: Library name: AT1G28160_C_rubella_Monte_Gargano_DAPi710E04-ORGi5037-96P151


description: Library name: AL1G53260.t1_S_bicolor_RTx430_DAPi712B01-ORGi5019-96P247


description: Library name: AT2G42430_C_rubella_Monte_Gargano_DAPi710E01-ORGi5037-96P151


description: Library name: AT3G09600_B_oleracea_TO1000DH3_DAPi709A02-ORGi5021-96P169


description: Library name: AT4G25490_S_bicolor_RTx430_DAPi712A08-ORGi5019-96P220


description: Library name: AT3G12250_C_rubella_Monte_Gargano_DAPi710E03-ORGi5037-96P151


description: Library name: AT5G10030_S_bicolor_RTx430_DAPi712A06-ORGi5019-96P220


description: Library name: AT4G31060_B_oleracea_TO1000DH3_DAPi709A03-ORGi5021-96P169


description: Library name: LOC_Os08g37970.1_S_bicolor_RTx430_DAPi712A06-ORGi5019-96P247


description: Library name: XP_013631386.1_S_bicolor_RTx430_DAPi712A07-ORGi5019-96P247


description: Library name: AL1G23550.t1_S_bicolor_RTx430_DAPi712B03-ORGi5019-96P247


description: Library name: AT5G62940_S_bicolor_RTx430_DAPi712A05-ORGi5019-96P220


title: Boleracea,seedling,rep4

description: Library name: NOTCX

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: whole seedling

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: whole seedling

tag: tissue condition

value: frozen

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


description: Library name: AT3G12250_S_bicolor_RTx430_DAPi712A07-ORGi5019-96P220


description: Library name: AT2G26960_C_rubella_Monte_Gargano_DAPi710D11-ORGi5037-96P151


description: Library name: AT1G69780_S_bicolor_RTx430_DAPi712A03-ORGi5019-96P220


title: Boleracea,seedling,rep3

description: Library name: NOTCW


description: Library name: AT1G02250_C_rubella_Monte_Gargano_DAPi710D09-ORGi5037-96P151

value: NAC


description: Library name: Solyc11g064950.3.1_S_bicolor_RTx430_DAPi712A08-ORGi5019-96P247


title: XY Kdm6b-null sample 2

city: Durham

first: Blanche

last: Capel

state: North Carolina

address: 307 Research Dr Nanaline Duke Bldg Room 456

department: Cell Biology

institute: Duke University

description: Library name: XY Null 2

library_source: transcriptomic

data_processing:
Sequencing results were trimmed with CutAdapt v4.9
Reads were mapped to the mouse mm10 genome using RNA STAR v2.7.11
Read counts were calculated using featureCounts v2.0.8
Differentially expressed genes were identified with DESeq2 v2.11.40.8
Significance cutoff of p-adj 0.1 and log2FC 1
Assembly: GRCm38
Supplementary files format and content: tab-dellimited text file contains normalized counts for each sample
Supplementary files format and content: csv files include log2FC, p-values, p-adj for each sample

organism: Mus musculus

source_name: gonad

growth_protocol: Embryos at E11.5 were sexed and genotyped for Kdm6b. Two pairs of gonads per sex were pooled for each replicate, resulting in four samples for sequencing.

extract_protocol:
Tissue was disrupted using the QiaShredder spin column (QIAGEN), and total RNA was extracted using the RNeasy kit (QIAGEN). Genomic DNA was removed with on-column DNase treatment
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit. A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then first-strand cDNA is generated using random hexamer-primed reverse transcription with the fragmented RNA as template. To synthesize the second-strand cDNA, the synthesis reaction system is prepared and dUTP is used to replace dTTP. After obtaining the double strand cDNA product, it is converted to blunt end with end repair reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the library adapters are ligated to the two ends of the cDNA with ligation reaction. Finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded circularized DNA products. Any single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and sequencing reads with PE100 bases length are generated on DNBseq-G400 platform.

treatment_protocol: Tissue was not treated prior to RNA extraction

value: gonad

value: pre-Sertoli

value: Kdm6b knockout


title: Boleracea,seedling,rep1

description: Library name: NNAWN


title: XY Kdm6b-null sample 1

description: Library name: XY Null 1


title: XY Wildtype control sample 2

description: Library name: XY Wildtype 2

value: WT


title: FH_99_SP8

type: genomic

city: Berlin

first: Julia

middle: K

last: Polansky

address: Augustenburger Platz 1

country: Germany

institute: Berlin Institute of Health @ Charité Universitätsmedizin Berlin

hyb_protocol: After bisulfite conversion, the gDNA, was fragmented, hybridized, and stained as per the guidelines of the Infinium HD protocol.

scan_protocol: Bead arrays were scanned using the iScan.

data_processing:
The raw intensity data files (IDAT) were preprocessed using minfi version 1.42.0 by quantile normalization. Probes were filtered based on not meeting the detection p-value threshold against the background (p<0.01), being reported as cross-reactive, revisions of Illumina's manifest (Infinium MethylationEPIC v1.0 13.03.2020), or being at a SNP, using the minfi function dropLociWithSnps.
*processed value definition: Quantile normalized, filtered based on p-value and croos-reactivity, batch-corrected beta values. Beta values, between 0-1.

label: other

label_protocol: Infinium HD Methylation Assay Reference Guide.

growth_protocol: Mouse Model (FH37-FH52): Cord blood samples were obtained from the DKMS Cord Blood Bank, Dresden and were used in accordance with the guidelines approved by the ethics committees of Dresden University of Technology, and University Clinics Jena. All animal experiments were performed in accordance with German animal welfare legislation and were approved by the relevant authorities: Landesdirektion Dresden and the Thüringer Landesamt für Verbraucherschutz (TLV). CD34+ HSCs were isolated using dual magnetic beads enrichment according to the manufacturer’s instructions (Miltenyi Biotech). Purities >95% were considered acceptable. 5*10^4 CD34+HSCs were transplanted intravenously into non‐irradiated NSGW41hIL7 mice. 29 weeks post transplantation, the thymus of humanized NSGW41hIL7 mice were sampled, processed as described before (Coppin et al., 2021) and single cell suspensions were incubated with the antibody panel listed in Suppl. Table 4. The following thymocyte populations were sorted using a FACS ARIA Fusion SORP (Becton Dickinson): DN: hCD45+hCD56‐ hCD19‐hCD4‐hCD8‐hCD7+. DPE: hCD45+hCD56‐hCD19‐hCD3+hCD4+hCD8+TCRab‐hCD5‐. DPL: hCD45+hCD56‐hCD19‐hCD3+hCD4+hCD8+TCRab+hCD5hi. SP4: hCD45+hCD56‐hCD19‐hCD3+hCD4+. The sorted thymocytes populations were washed in PBS and the dry pellet was snap frozen on dry ice and stores at ‐80°C until further processing. For ex-vivo human samples (FH57-FH99): Human neonatal thymus samples were obtained during routine pediatric corrective cardiac surgery from female and male patients aged 2 - 466 days. Legal guardians of the donors gave their written and informed consent prior to participating in the study (Ethics committee of the Charite Universitaetsmedizin Berlin, application numbers EA2/138/22). Thymus samples were dissociated by being filtered through a 100 µm mesh filter (Miltenyi 130-098-463) and washed in PBS with 1% BSA and 2mM/0.4% EDTA. Samples were subjected to erythrocyte lysis (Qiagen 79217) and after a washing step, were filtered again through a fresh 100 µm mesh filter. Prior to FACS-based purification, thymocytes were partially depleted of CD8+ cells using CD8 MicroBeads (Miltenyi, 130-045-201) and the Miltenyi autoMACS Pro Separator. For FACS of neonatal human thymic T cell progenitor subsets, thymocytes were stained using the fluorescently conjugated monoclonal antibodies listed in Table 3 of the publication. CD4-CD8- DN cells were characterized based on their surface expression of CD7, CD1a, CD161, CD38, CD3 and TCRab into DN1 (CD7+CD1a-CD161-CD38-), DN2 (CD7+CD1a-CD161-CD38+CD3-TCRab-) and DN3 (CD7+CD1a+) subsets. CD4+CD8+ DP cells were further separated based on CD69 and TCRab expression into DPE cells (CD69-TCRab-) and more mature DPL cells (CD69+TCRab+). Cells expressing CD4 exclusively (CD4+CD8-) were divided based on expression of CD3, TCRab and CD1a into ISP (CD3-TCRab-CD1ahigh) and mature SP4 (CD3+TCRab+). SP8 (CD4-CD8+) were also isolated and represent, together with SP4 cells, the final stage of thymocyte maturation prior to thymic egress and emigration into the peripheral blood as mature naïve CD4+ and CD8+ T cell populations.

extract_protocol: genomic DNA was extracted using Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) following instructions provided by the manufacturer. Samples with cell counts <25,000 cells were not subjected to DNA extraction. Instead, the cell pellets were directly taken up in a mix of 40 µl lysate buffer from the Zymo’s Quick-DNA MicroPREP Kit (Zymo Research) with 1.25 mg/ml Proteinase K (Sigma-Aldrich 3115828001) and incubated for 3 hours at room temperature. Isolated genomic DNA and cell lysates from Proteinase K digestion were subjected to bisulfite conversion using Zymo’s EZ DNA Methylation-Gold Kit (Zymo Research) according to manufacturer's instructions.

tag: donor

tag: Sex

value: Female

tag: age (days)


description: Library name: AT2G01930_B_oleracea_TO1000DH3_DAPi709D06-ORGi5021-96P169


description: Library name: AT1G08320_C_rubella_Monte_Gargano_DAPi710D12-ORGi5037-96P151

value: BZIP


description: Library name: AT1G49480_S_bicolor_RTx430_DAPi712A04-ORGi5019-96P220

value: REM


title: FH_98_SP4


title: XX Wildtype control sample 1

description: Library name: XX Wildtype 1

value: pre-granulosa


description: Library name: AT5G18560_C_rubella_Monte_Gargano_DAPi710D07-ORGi5037-96P151

value: plant


description: Library name: AT1G47655_C_rubella_Monte_Gargano_DAPi710D05-ORGi5037-96P151


description: Library name: Carub.0004s2291.1_S_bicolor_RTx430_DAPi712A09-ORGi5019-96P247


description: Library name: AT3G46590_C_rubella_Monte_Gargano_DAPi710D06-ORGi5037-96P151

value: MYBRELATED


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H12-ORGi5033-96P247

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: Populus trichocarpa Nisqually-1: Phytozome v4.1
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: Populus trichocarpa


title: XX Kdm6b-null sample 1

description: Library name: XX Null 1


title: FH_96_DPE

source_name: DPE

value: DPE


title: XX Kdm6b-null sample 2

description: Library name: XX Null 2


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H01-ORGi5033-96P247


description: Library name: AT5G56840_C_rubella_Monte_Gargano_DAPi710D01-ORGi5037-96P151


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A12-ORGi5033-96P247


title: FH_95_ISP

source_name: ISP

value: ISP


description: Library name: AT5G39760_S_bicolor_RTx430_DAPi712A02-ORGi5019-96P220

value: ZFHD


description: Library name: AT1G75240_C_rubella_Monte_Gargano_DAPi710C12-ORGi5037-96P151


title: FH_94_DN3


description: Library name: AT4G01550_C_rubella_Monte_Gargano_DAPi710D08-ORGi5037-96P151


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H12-ORGi5033-96P220


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712H01-ORGi5033-96P220


title: XY Wildtype control sample 1

description: Library name: XY Wildtype 1


title: XX Wildtype control sample 2

description: Library name: XX Wildtype 2


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A12-ORGi5033-96P220


description: Library name: AT2G40740_C_rubella_Monte_Gargano_DAPi710C11-ORGi5037-96P151

value: WRKY


title: FH_93_DN1


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A01-ORGi5033-96P220


title: FH_97_DPL

source_name: DPL

value: DPL


description: Library name: AL2G28980.t1_P_trichocarpa_Nisqually-1_DAPi712H11-ORGi5033-96P247

value: HOMEOBOX


title: FH_92_DN2


description: Library name: AT2G01940_C_rubella_Monte_Gargano_DAPi710C09-ORGi5037-96P151


description: Library name: Solyc08g078340.3.1_P_trichocarpa_Nisqually-1_DAPi712H09-ORGi5033-96P247


description: Library name: Carub.0002s1959.1_P_trichocarpa_Nisqually-1_DAPi712H10-ORGi5033-96P247


title: FH_90_SP4


description: Library name: AT2G47070_P_trichocarpa_Nisqually-1_DAPi712H10-ORGi5033-96P220

value: SBP


description: Library name: AT1G63030_C_rubella_Monte_Gargano_DAPi710C07-ORGi5037-96P151


description: Library name: AT3G17730_C_rubella_Monte_Gargano_DAPi710C06-ORGi5037-96P151

value: NAC


description: Library name: XP_013634112.1_P_trichocarpa_Nisqually-1_DAPi712H08-ORGi5033-96P247


description: Library name: AT2G46270_P_trichocarpa_Nisqually-1_DAPi712H11-ORGi5033-96P220


description: Library name: AT1G76420_C_rubella_Monte_Gargano_DAPi710C10-ORGi5037-96P151


title: FH_91_SP8


title: FH_89_DPL


description: Library name: AT5G17300_P_trichocarpa_Nisqually-1_DAPi712H08-ORGi5033-96P220


description: Library name: AT1G77200_C_rubella_Monte_Gargano_DAPi710C05-ORGi5037-96P151


title: FH_88_DPE


description: Library name: LOC_Os01g17260.2_P_trichocarpa_Nisqually-1_DAPi712H07-ORGi5033-96P247


description: Library name: AT5G18560_P_trichocarpa_Nisqually-1_DAPi712H07-ORGi5033-96P220


description: Library name: AT5G51990_C_rubella_Monte_Gargano_DAPi710C04-ORGi5037-96P151


description: Library name: AL4G45550.t1_P_trichocarpa_Nisqually-1_DAPi712H06-ORGi5033-96P247


title: FH_87_ISP


description: Library name: AT3G50410_P_trichocarpa_Nisqually-1_DAPi712H06-ORGi5033-96P220


title: FH_86_DN3


description: Library name: AT3G02940_P_trichocarpa_Nisqually-1_DAPi712H04-ORGi5033-96P220

value: MYB


description: Library name: AT1G01060_P_trichocarpa_Nisqually-1_DAPi712H05-ORGi5033-96P220


description: Library name: Control_TF_DNA_P_trichocarpa_Nisqually-1_DAPi712A01-ORGi5033-96P247


title: FH_85_DN1


description: Library name: Solyc01g102340.3.1_P_trichocarpa_Nisqually-1_DAPi712H04-ORGi5033-96P247


description: Library name: XP_013629448.1_P_trichocarpa_Nisqually-1_DAPi712H03-ORGi5033-96P247


title: FH_84_DN2


title: FH_82_SP8

value: Male


description: Library name: AT3G10580_C_rubella_Monte_Gargano_DAPi710C01-ORGi5037-96P151


description: Library name: AT5G66940_C_rubella_Monte_Gargano_DAPi710B10-ORGi5037-96P151


description: Library name: XP_013589913.1_P_trichocarpa_Nisqually-1_DAPi712G10-ORGi5033-96P247


description: Library name: AT5G26170_C_rubella_Monte_Gargano_DAPi710B11-ORGi5037-96P151


description: Library name: AT2G30250_P_trichocarpa_Nisqually-1_DAPi712H03-ORGi5033-96P220


description: Library name: Solyc03g116890.3.1_P_trichocarpa_Nisqually-1_DAPi712G11-ORGi5033-96P247


description: Library name: AT5G09410_P_trichocarpa_Nisqually-1_DAPi712G11-ORGi5033-96P220

value: CAMTA


title: FH_81_SP4


description: Library name: AT3G30210_C_rubella_Monte_Gargano_DAPi710C02-ORGi5037-96P151


description: Library name: AT2G22430_P_trichocarpa_Nisqually-1_DAPi712H02-ORGi5033-96P220


description: Library name: AT1G01250_C_rubella_Monte_Gargano_DAPi710B07-ORGi5037-96P151


description: Library name: XP_013609718.1_P_trichocarpa_Nisqually-1_DAPi712G12-ORGi5033-96P247


title: FH_80_DPL


description: Library name: LOC_Os10g41200.1_P_trichocarpa_Nisqually-1_DAPi712G09-ORGi5033-96P247


description: Library name: AT1G72740_P_trichocarpa_Nisqually-1_DAPi712G09-ORGi5033-96P220


description: Library name: AT5G45300_P_trichocarpa_Nisqually-1_DAPi712G10-ORGi5033-96P220


title: FH_79_DPE


description: Library name: AL4G38490.t1_P_trichocarpa_Nisqually-1_DAPi712G08-ORGi5033-96P247


description: Library name: AT5G47660_C_rubella_Monte_Gargano_DAPi710B06-ORGi5037-96P151

value: TRIHELIX


description: Library name: AT2G01940_P_trichocarpa_Nisqually-1_DAPi712G08-ORGi5033-96P220


description: Library name: AT1G12630_C_rubella_Monte_Gargano_DAPi710B04-ORGi5037-96P151


title: FH_78_ISP


description: Library name: AT2G02820_C_rubella_Monte_Gargano_DAPi710B09-ORGi5037-96P151


description: Library name: AT5G19790_P_trichocarpa_Nisqually-1_DAPi712G07-ORGi5033-96P220


description: Library name: AT1G69180_P_trichocarpa_Nisqually-1_DAPi712G05-ORGi5033-96P220


title: FH_76_DN1


title: FH_77_DN3


description: Library name: AT5G02320_P_trichocarpa_Nisqually-1_DAPi712G06-ORGi5033-96P220


description: Library name: LOC_Os01g18240.1_P_trichocarpa_Nisqually-1_DAPi712G04-ORGi5033-96P247


title: FH_75_DN2


description: Library name: Carub.0003s1161.1.p_P_trichocarpa_Nisqually-1_DAPi712G07-ORGi5033-96P247

value: BZIP


description: Library name: AT3G50410_C_rubella_Monte_Gargano_DAPi710B03-ORGi5037-96P151


description: Library name: AT1G46768_P_trichocarpa_Nisqually-1_DAPi712G04-ORGi5033-96P220


description: Library name: AT3G50060_P_trichocarpa_Nisqually-1_DAPi712G02-ORGi5033-96P220


description: Library name: AT1G18330_P_trichocarpa_Nisqually-1_DAPi712G01-ORGi5033-96P220


title: FH_73_SP8


description: Library name: AT1G80840_P_trichocarpa_Nisqually-1_DAPi712G03-ORGi5033-96P220


description: Library name: AT2G45410_C_rubella_Monte_Gargano_DAPi710B02-ORGi5037-96P151


description: Library name: LOC_Os09g25060.1_P_trichocarpa_Nisqually-1_DAPi712F11-ORGi5033-96P247


description: Library name: AT1G76880_P_trichocarpa_Nisqually-1_DAPi712F11-ORGi5033-96P220


description: Library name: AT3G03200_C_rubella_Monte_Gargano_DAPi710A10-ORGi5037-96P151


title: FH_72_SP4


description: Library name: AL2G32420.t2_P_trichocarpa_Nisqually-1_DAPi712F10-ORGi5033-96P247


title: FH_71_DPL


description: Library name: AT5G62470_C_rubella_Monte_Gargano_DAPi710A08-ORGi5037-96P151


description: Library name: AT4G14770_P_trichocarpa_Nisqually-1_DAPi712F10-ORGi5033-96P220

value: CPP


description: Library name: AT5G19790_C_rubella_Monte_Gargano_DAPi710A07-ORGi5037-96P151


description: Library name: Carub.0008s0039.1_P_trichocarpa_Nisqually-1_DAPi712F09-ORGi5033-96P247


description: Library name: AT1G25340_C_rubella_Monte_Gargano_DAPi710B01-ORGi5037-96P151


description: Library name: AT2G45480_P_trichocarpa_Nisqually-1_DAPi712F09-ORGi5033-96P220

value: GRF


title: FH_70_DPE


title: FH_69_ISP


description: Library name: AT2G02820_P_trichocarpa_Nisqually-1_DAPi712F08-ORGi5033-96P220

value: plant


description: Library name: AT1G12610_C_rubella_Monte_Gargano_DAPi710A11-ORGi5037-96P151


description: Library name: AT2G45420_P_trichocarpa_Nisqually-1_DAPi712F06-ORGi5033-96P220


title: FH_68_DN3


description: Library name: AT5G58850_C_rubella_Monte_Gargano_DAPi710A05-ORGi5037-96P151


description: Library name: AT5G52830_P_trichocarpa_Nisqually-1_DAPi712F07-ORGi5033-96P220


title: FH_67_DN1


description: Library name: AT2G28810_C_rubella_Monte_Gargano_DAPi710A06-ORGi5037-96P151


description: Library name: AT2G01060_P_trichocarpa_Nisqually-1_DAPi712F05-ORGi5033-96P220


description: Library name: Solyc08g079120.3.1_P_trichocarpa_Nisqually-1_DAPi712F03-ORGi5033-96P247


description: Library name: AT4G25480_P_trichocarpa_Nisqually-1_DAPi712F04-ORGi5033-96P220


description: Library name: AT1G33240_P_trichocarpa_Nisqually-1_DAPi712F03-ORGi5033-96P220


description: Library name: AT5G62320_C_rubella_Monte_Gargano_DAPi710A03-ORGi5037-96P151


description: Library name: AT5G60130_C_rubella_Monte_Gargano_DAPi710A04-ORGi5037-96P151


title: FH_64_SP8


description: Library name: AT3G60490_C_rubella_Monte_Gargano_DAPi710A02-ORGi5037-96P151


description: Library name: Solyc04g078640.3.1_P_trichocarpa_Nisqually-1_DAPi712F01-ORGi5033-96P247


description: Library name: AT5G47390_P_trichocarpa_Nisqually-1_DAPi712F01-ORGi5033-96P220

value: MYBRELATED


description: Library name: AT4G31800_P_trichocarpa_Nisqually-1_DAPi712F02-ORGi5033-96P220


title: FH_63_SP4


description: Library name: AT1G68320_C_rubella_Monte_Gargano_DAPi709H11-ORGi5037-96P169


description: Library name: XP_013586407.1_P_trichocarpa_Nisqually-1_DAPi712F07-ORGi5033-96P247


description: Library name: AT1G52880_P_trichocarpa_Nisqually-1_DAPi712E12-ORGi5033-96P220


title: FH_62_DPL


description: Library name: AT3G24050_C_rubella_Monte_Gargano_DAPi709H10-ORGi5037-96P169


description: Library name: Carub.0002s2670.1_P_trichocarpa_Nisqually-1_DAPi712E11-ORGi5033-96P247


description: Library name: AT1G20980_P_trichocarpa_Nisqually-1_DAPi712E11-ORGi5033-96P220


title: FH_66_DN2


title: FH_61_DPE

value: DPE


title: FH_60_ISP

value: ISP


description: Library name: AT4G17980_P_trichocarpa_Nisqually-1_DAPi712E10-ORGi5033-96P220


description: Library name: Solyc10g005080.3.1_P_trichocarpa_Nisqually-1_DAPi712E10-ORGi5033-96P247


description: Library name: AT5G08130_C_rubella_Monte_Gargano_DAPi709H05-ORGi5037-96P169

value: BHLH


description: Library name: AT1G79180_C_rubella_Monte_Gargano_DAPi709H09-ORGi5037-96P169


description: Library name: XP_013615900.1_P_trichocarpa_Nisqually-1_DAPi712E09-ORGi5033-96P247


description: Library name: AT1G46768_C_rubella_Monte_Gargano_DAPi709H03-ORGi5037-96P169


title: FH_59_DN3


description: Library name: AT5G56110_P_trichocarpa_Nisqually-1_DAPi712E06-ORGi5033-96P220


description: Library name: AT5G14960_P_trichocarpa_Nisqually-1_DAPi712E08-ORGi5033-96P220


description: Library name: AT2G18550_P_trichocarpa_Nisqually-1_DAPi712E07-ORGi5033-96P220


description: Library name: AT3G60530_P_trichocarpa_Nisqually-1_DAPi712E05-ORGi5033-96P220


description: Library name: AT1G19210_C_rubella_Monte_Gargano_DAPi709H02-ORGi5037-96P169


description: Library name: Solyc05g007180.3.1_P_trichocarpa_Nisqually-1_DAPi712E12-ORGi5033-96P247


title: FH_57_DN2


description: Library name: AT5G62020_P_trichocarpa_Nisqually-1_DAPi712E04-ORGi5033-96P220

value: HSF


description: Library name: AT1G71450_C_rubella_Monte_Gargano_DAPi709G11-ORGi5037-96P169


description: Library name: AT1G51220_C_rubella_Monte_Gargano_DAPi709G12-ORGi5037-96P169


description: Library name: AT5G64750_P_trichocarpa_Nisqually-1_DAPi712E03-ORGi5033-96P220


description: Library name: LOC_Os02g42970.1_P_trichocarpa_Nisqually-1_DAPi712E03-ORGi5033-96P247


title: FH_52_SP4

tag: strain

value: Female


description: Library name: LOC_Os06g07030.1_P_trichocarpa_Nisqually-1_DAPi712E01-ORGi5033-96P247


title: FH_51_DPL

value: DPL


description: Library name: AT1G13260_P_trichocarpa_Nisqually-1_DAPi712E01-ORGi5033-96P220

value: RAV


description: Library name: AT1G69180_C_rubella_Monte_Gargano_DAPi709G09-ORGi5037-96P169


description: Library name: AL3G23910.t2_P_trichocarpa_Nisqually-1_DAPi712E07-ORGi5033-96P247


title: FH_58_DN1


description: Library name: AT5G11260_P_trichocarpa_Nisqually-1_DAPi712D12-ORGi5033-96P220


description: Library name: LOC_Os10g26500.1_P_trichocarpa_Nisqually-1_DAPi712D12-ORGi5033-96P247

value: HOMEOBOX


title: FH_50_DPE


description: Library name: AT3G18990_P_trichocarpa_Nisqually-1_DAPi712D11-ORGi5033-96P220


description: Library name: AT5G51190_C_rubella_Monte_Gargano_DAPi709G07-ORGi5037-96P169


title: FH_48_SP4


title: FH_49_DN

source_name: DN

value: DN


description: Library name: AT5G47230_C_rubella_Monte_Gargano_DAPi709G06-ORGi5037-96P169


description: Library name: XP_013587997.1_P_trichocarpa_Nisqually-1_DAPi712D11-ORGi5033-96P247

value: WRKY


description: Library name: LOC_Os08g06110.3_P_trichocarpa_Nisqually-1_DAPi712D10-ORGi5033-96P247


title: FH_47_DPL


description: Library name: AT1G50640_C_rubella_Monte_Gargano_DAPi709G04-ORGi5037-96P169


description: Library name: AT2G32460_C_rubella_Monte_Gargano_DAPi709G05-ORGi5037-96P169

value: MYB


title: FH_46_DPE


description: Library name: Carub.0008s0285.1_P_trichocarpa_Nisqually-1_DAPi712D08-ORGi5033-96P247


description: Library name: AT5G62020_C_rubella_Monte_Gargano_DAPi709G02-ORGi5037-96P169


description: Library name: Solyc01g095460.3.1_P_trichocarpa_Nisqually-1_DAPi712D07-ORGi5033-96P247


description: Library name: AT5G03150_P_trichocarpa_Nisqually-1_DAPi712D08-ORGi5033-96P220


description: Library name: AT1G29160_C_rubella_Monte_Gargano_DAPi709G01-ORGi5037-96P169


description: Library name: AL8G10650.t1_P_trichocarpa_Nisqually-1_DAPi712D09-ORGi5033-96P247


description: Library name: AT3G57920_P_trichocarpa_Nisqually-1_DAPi712D06-ORGi5033-96P220

value: SBP


title: FH_45_DN


description: Library name: AT5G56110_C_rubella_Monte_Gargano_DAPi709F12-ORGi5037-96P169


description: Library name: Carub.0001s1194.1_P_trichocarpa_Nisqually-1_DAPi712D03-ORGi5033-96P247

value: NAC


title: FH_44_SP4


description: Library name: AT5G65410_P_trichocarpa_Nisqually-1_DAPi712D03-ORGi5033-96P220

value: ZFHD


description: Library name: AT3G50260_P_trichocarpa_Nisqually-1_DAPi712D02-ORGi5033-96P220


title: FH_43_DPL


description: Library name: Carub.0001s3581.1.p_P_trichocarpa_Nisqually-1_DAPi712D01-ORGi5033-96P247


title: FH_42_DPE


title: FH_41_DN


description: Library name: AT1G74480_P_trichocarpa_Nisqually-1_DAPi712D07-ORGi5033-96P220

value: RWPRK


description: Library name: AT1G01720_C_rubella_Monte_Gargano_DAPi709F09-ORGi5037-96P169

value: plant


description: Library name: AT3G08500_C_rubella_Monte_Gargano_DAPi709F05-ORGi5037-96P169


description: Library name: Carub.0002s1646.1_P_trichocarpa_Nisqually-1_DAPi712C12-ORGi5033-96P247


description: Library name: AL2G40550.t1_P_trichocarpa_Nisqually-1_DAPi712C11-ORGi5033-96P247


description: Library name: AT1G12260_P_trichocarpa_Nisqually-1_DAPi712C12-ORGi5033-96P220


title: FH_40_SP4


description: Library name: AT3G01220_C_rubella_Monte_Gargano_DAPi709F01-ORGi5037-96P169


description: Library name: Solyc06g048630.3.1_P_trichocarpa_Nisqually-1_DAPi712C09-ORGi5033-96P247

value: BZIP


description: Library name: AT1G76420_P_trichocarpa_Nisqually-1_DAPi712C09-ORGi5033-96P220


description: Library name: Carub.0001s0116.1_P_trichocarpa_Nisqually-1_DAPi712C10-ORGi5033-96P247

value: MYBRELATED


description: Library name: AT4G00730_P_trichocarpa_Nisqually-1_DAPi712C11-ORGi5033-96P220


title: FH_38_DPE

value: DPE


description: Library name: AT5G64060_C_rubella_Monte_Gargano_DAPi709F10-ORGi5037-96P169


description: Library name: XP_013613838.1_P_trichocarpa_Nisqually-1_DAPi712C08-ORGi5033-96P247


title: FH_39_DPL


description: Library name: LOC_Os01g46970.1_P_trichocarpa_Nisqually-1_DAPi712C07-ORGi5033-96P247


title: FH_37_DN


description: Library name: AT2G01930_P_trichocarpa_Nisqually-1_DAPi712D05-ORGi5033-96P220

value: BBRBPC


description: Library name: LOC_Os02g33430.1_P_trichocarpa_Nisqually-1_DAPi712D05-ORGi5033-96P247


description: Library name: AT5G60130_P_trichocarpa_Nisqually-1_DAPi712C07-ORGi5033-96P220


description: Library name: AT3G57920_C_rubella_Monte_Gargano_DAPi709E12-ORGi5037-96P169


description: Library name: AT5G03790_P_trichocarpa_Nisqually-1_DAPi712C06-ORGi5033-96P220


description: Library name: AT3G16280_C_rubella_Monte_Gargano_DAPi709E11-ORGi5037-96P169


description: Library name: Solyc08g068320.3.1_P_trichocarpa_Nisqually-1_DAPi712C04-ORGi5033-96P247


description: Library name: AT1G49010_C_rubella_Monte_Gargano_DAPi709F03-ORGi5037-96P169


title: 6spec-mix,root,rep1

description: Library name: OWGSB

organism:
Arabidopsis thaliana
Sorghum bicolor
Thlaspi arvense
Brachypodium distachyon
Capsella rubella
Panicum hallii

source_name: root

value: root

value: frozen

value: BD Rhapsody


description: Library name: AT3G27010_P_trichocarpa_Nisqually-1_DAPi712C04-ORGi5033-96P220

value: TCP


description: Library name: AT4G06746_C_rubella_Monte_Gargano_DAPi709E10-ORGi5037-96P169


title: monocot-mix,leaf,rep2

description: Library name: OWGSA

organism:
Sorghum bicolor
Brachypodium distachyon
Panicum hallii

source_name: leaf

value: leaf


description: Library name: AT2G20400_C_rubella_Monte_Gargano_DAPi709E09-ORGi5037-96P169


description: Library name: AT2G44940_C_rubella_Monte_Gargano_DAPi709F02-ORGi5037-96P169


description: Library name: AT1G27730_P_trichocarpa_Nisqually-1_DAPi712C01-ORGi5033-96P220


description: Library name: AT1G69690_P_trichocarpa_Nisqually-1_DAPi712C02-ORGi5033-96P220


description: Library name: XP_013589953.1_P_trichocarpa_Nisqually-1_DAPi712B12-ORGi5033-96P247

value: HOMEOBOX


description: Library name: AT5G62470_P_trichocarpa_Nisqually-1_DAPi712C08-ORGi5033-96P220


description: Library name: Solyc07g040920.2.1_P_trichocarpa_Nisqually-1_DAPi712B11-ORGi5033-96P247


title: monocot-mix,root,rep2

description: Library name: OUGHX


description: Library name: AT2G40620_P_trichocarpa_Nisqually-1_DAPi712B12-ORGi5033-96P220


title: monocot-mix,leaf,rep1

description: Library name: OWGPZ


description: Library name: AT4G23550_C_rubella_Monte_Gargano_DAPi709E05-ORGi5037-96P169

value: WRKY


description: Library name: AT5G25810_C_rubella_Monte_Gargano_DAPi709E04-ORGi5037-96P169


description: Library name: XP_013587350.1_P_trichocarpa_Nisqually-1_DAPi712B10-ORGi5033-96P247


description: Library name: AT1G79580_P_trichocarpa_Nisqually-1_DAPi712B09-ORGi5033-96P220


title: 6spec-mix,root,rep2

description: Library name: OWGSC


title: monocot-mix,root,rep1

description: Library name: OUGHW


description: Library name: XP_013602769.1_P_trichocarpa_Nisqually-1_DAPi712C03-ORGi5033-96P247


description: Library name: AL8G13510.t2_P_trichocarpa_Nisqually-1_DAPi712B08-ORGi5033-96P247


description: Library name: LOC_Os03g21800.1_P_trichocarpa_Nisqually-1_DAPi712B09-ORGi5033-96P247


title: fakA mutant, 6 h, TSB + 14 mM glucose, rep 3

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

description: Library name: fakA mutant sample C

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench (v11) software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Replicate data sets were grouped and normalized using "quantile normalization"
Normalized expression values were exported into excel files
Assembly: The reference genome used for the analysis was based on NC_007793
Supplementary files format and content: Expression values for each gene were initially calculated as RPKM values. The RPKM values were then normalized and the "Normalized expression values" are presented in the excel files

organism: Staphylococcus aureus

source_name: bacterial

growth_protocol: Strains were grown in TSB medium + 14 mM glucose at 37°C with shaking for 6 hours

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion turbo DNA-free
Library construction was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

value: bacterial

value: fakA mutant

tag: growth medium

value: TSB + 14 mM glucose

tag: growth conditions


description: Library name: AT4G25470_C_rubella_Monte_Gargano_DAPi709D11-ORGi5037-96P169

tag: tissue

tag: genotype


description: Library name: AT5G02840_C_rubella_Monte_Gargano_DAPi709E07-ORGi5037-96P169

tag: tf id

tag: tf family


title: fakA mutant, 6 h, TSB + 14 mM glucose, rep 2

description: Library name: fakA mutant sample B


description: Library name: AT1G29160_P_trichocarpa_Nisqually-1_DAPi712B04-ORGi5033-96P220

tag: multidap sample_id

tag: 96 well_plate_id


description: Library name: Carub.0004s2898.1.p_P_trichocarpa_Nisqually-1_DAPi712B07-ORGi5033-96P247

tag: tf source_species


description: Library name: AT4G25470_P_trichocarpa_Nisqually-1_DAPi712B06-ORGi5033-96P220


title: fakA mutant, 6 h, TSB + 14 mM glucose, rep 1

description: Library name: fakA mutant sample A

tag: cell type


description: Library name: AL1G23550.t1_P_trichocarpa_Nisqually-1_DAPi712B03-ORGi5033-96P247

value: NAC


description: Library name: AT5G54230_C_rubella_Monte_Gargano_DAPi709D07-ORGi5037-96P169

value: MYB


description: Library name: AT3G08500_P_trichocarpa_Nisqually-1_DAPi712B05-ORGi5033-96P220

value: plant


description: Library name: AT3G56400_P_trichocarpa_Nisqually-1_DAPi712B02-ORGi5033-96P220


title: Wild type, 6 h, TSB + 14 mM glucose, rep 2

description: Library name: Wild type sample B

value: wild type


description: Library name: AT5G67300_P_trichocarpa_Nisqually-1_DAPi712B01-ORGi5033-96P220


description: Library name: AT1G20910_P_trichocarpa_Nisqually-1_DAPi712B10-ORGi5033-96P220

value: ARID


description: Library name: AT1G01060_C_rubella_Monte_Gargano_DAPi709D10-ORGi5037-96P169

value: MYBRELATED


description: Library name: AT4G01280_C_rubella_Monte_Gargano_DAPi709E03-ORGi5037-96P169


description: Library name: AT2G01930_C_rubella_Monte_Gargano_DAPi709D06-ORGi5037-96P169

value: BBRBPC


title: Wild type, 6 h, TSB + 14 mM glucose, rep 1

description: Library name: Wild type sample A


description: Library name: AT5G62940_C_rubella_Monte_Gargano_DAPi709D05-ORGi5037-96P169


description: Library name: AL1G53260.t1_P_trichocarpa_Nisqually-1_DAPi712B01-ORGi5033-96P247


description: Library name: LOC_Os01g51154.1_P_trichocarpa_Nisqually-1_DAPi712A11-ORGi5033-96P247


description: Library name: AT4G25480_C_rubella_Monte_Gargano_DAPi709D03-ORGi5037-96P169


description: Library name: AL1G11460.t1_P_trichocarpa_Nisqually-1_DAPi712A10-ORGi5033-96P247


description: Library name: AT5G05550_P_trichocarpa_Nisqually-1_DAPi712A10-ORGi5033-96P220

value: TRIHELIX


title: Glycine max, Melatonin, 72hr, rep3

city: Taipei

first: Ying-Chung Jimmy

last: Lin

address: No.1, Sec. 4, Roosevelt Rd., Da'an Dist.

department: Department of Life Sciences

country: Taiwan

institute: National Taiwan University

data_processing:
Quality check by fastp.
Transcript abundance estimation by RSEM.
FDR calculation by DESeq2 based on RSEM read counts.
Determine up- or down-regulation by TPM > 1.5 fold or < 2/3 fold, and FDR < 0.05.
Assembly: Glycine max Lee v1.1 (Phytozome)
Supplementary files format and content: Matrix of raw read count for each sample
Supplementary files format and content: Matrix of TPM value for each sample

organism: Glycine max

source_name: stem

extract_protocol:
We applied the CTAB (cetyltrimethylammonium bromide) RNA extraction method and RNA kit (NEBNext® Ultra™ II Directional RNA Library Prep Kit) to purify high quality mRNA.
We used the NEBNext® Ultra™ II Directional RNA Library Prep Kit for the cDNA library construction.

tag: treatment

value: Melatonin

tag: time

value: stem


description: Library name: Carub.0004s2291.1_P_trichocarpa_Nisqually-1_DAPi712A09-ORGi5033-96P247

value: BZIP


description: Library name: XP_013631649.1_P_trichocarpa_Nisqually-1_DAPi712B05-ORGi5033-96P247


description: Library name: AT1G36060_C_rubella_Monte_Gargano_DAPi709D02-ORGi5037-96P169


description: Library name: Solyc11g064950.3.1_P_trichocarpa_Nisqually-1_DAPi712A08-ORGi5033-96P247


title: Wild type, 6 h, TSB + 14 mM glucose, rep 3

description: Library name: Wild type sample C


description: Library name: AT4G25490_P_trichocarpa_Nisqually-1_DAPi712A08-ORGi5033-96P220


title: Glycine max, Melatonin, 72hr, rep2


description: Library name: AT3G12250_P_trichocarpa_Nisqually-1_DAPi712A07-ORGi5033-96P220


description: Library name: AT2G40260_C_rubella_Monte_Gargano_DAPi709C12-ORGi5037-96P169


description: Library name: XP_013631386.1_P_trichocarpa_Nisqually-1_DAPi712A07-ORGi5033-96P247


title: Glycine max, Melatonin, 72hr, rep1


description: Library name: AT5G10030_C_rubella_Monte_Gargano_DAPi709C11-ORGi5037-96P169


description: Library name: AT3G18400_C_rubella_Monte_Gargano_DAPi709C10-ORGi5037-96P169


title: Glycine max, Melatonin, 48hr, rep2


description: Library name: AT5G10030_P_trichocarpa_Nisqually-1_DAPi712A06-ORGi5033-96P220


description: Library name: AT5G62940_P_trichocarpa_Nisqually-1_DAPi712A05-ORGi5033-96P220


description: Library name: AT1G49480_P_trichocarpa_Nisqually-1_DAPi712A04-ORGi5033-96P220

value: REM


description: Library name: AT1G69780_P_trichocarpa_Nisqually-1_DAPi712A03-ORGi5033-96P220

value: HOMEOBOX


description: Library name: LOC_Os08g37970.1_P_trichocarpa_Nisqually-1_DAPi712A06-ORGi5033-96P247


description: Library name: AT1G53230_C_rubella_Monte_Gargano_DAPi709C08-ORGi5037-96P169

value: TCP


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H12-ORGi5034-96P247

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: Fragaria vesca Hawaii-4-F7: UCD/HAU via Phytozome v4.0.a2
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: Fragaria vesca


description: Library name: AT3G11280_C_rubella_Monte_Gargano_DAPi709C06-ORGi5037-96P169


description: Library name: AT5G39760_P_trichocarpa_Nisqually-1_DAPi712A02-ORGi5033-96P220

value: ZFHD


title: Glycine max, Melatonin, 24hr, rep3


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H01-ORGi5034-96P247


description: Library name: AT3G02940_C_rubella_Monte_Gargano_DAPi709C05-ORGi5037-96P169


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A12-ORGi5034-96P247


title: Glycine max, Melatonin, 24hr, rep2


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H12-ORGi5034-96P220


description: Library name: AT3G01970_C_rubella_Monte_Gargano_DAPi709C04-ORGi5037-96P169

value: WRKY


description: Library name: AT3G27010_C_rubella_Monte_Gargano_DAPi709C02-ORGi5037-96P169


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712H01-ORGi5034-96P220


title: Glycine max, Melatonin, 24hr, rep1


description: Library name: AL2G28980.t1_F_vesca_Hawaii-4-F7_DAPi712H11-ORGi5034-96P247


description: Library name: AT1G03800_C_rubella_Monte_Gargano_DAPi709C01-ORGi5037-96P169


title: Glycine max, Melatonin, 6hr, rep3


title: Glycine max, Melatonin, 48hr, rep3


title: Glycine max, Melatonin, 6hr, rep2


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A01-ORGi5034-96P220


description: Library name: AT2G46270_F_vesca_Hawaii-4-F7_DAPi712H11-ORGi5034-96P220


description: Library name: AT5G03790_C_rubella_Monte_Gargano_DAPi709B12-ORGi5037-96P169


title: Glycine max, Melatonin, 48hr, rep1


description: Library name: Solyc08g078340.3.1_F_vesca_Hawaii-4-F7_DAPi712H09-ORGi5034-96P247


description: Library name: AT2G47070_F_vesca_Hawaii-4-F7_DAPi712H10-ORGi5034-96P220

value: SBP


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A01-ORGi5034-96P247


title: Glycine max, Control, 72hr, rep3

value: Control


title: Glycine max, Melatonin, 6hr, rep1


description: Library name: AT2G24430_C_rubella_Monte_Gargano_DAPi709B10-ORGi5037-96P169

value: NAC


description: Library name: AT5G17300_F_vesca_Hawaii-4-F7_DAPi712H08-ORGi5034-96P220

value: plant


description: Library name: LOC_Os01g17260.2_F_vesca_Hawaii-4-F7_DAPi712H07-ORGi5034-96P247


description: Library name: AT5G18560_F_vesca_Hawaii-4-F7_DAPi712H07-ORGi5034-96P220


description: Library name: AT1G22810_C_rubella_Monte_Gargano_DAPi709B04-ORGi5037-96P169


title: Glycine max, Control, 72hr, rep2


description: Library name: AT3G52440_C_rubella_Monte_Gargano_DAPi709B11-ORGi5037-96P169


description: Library name: AL4G45550.t1_F_vesca_Hawaii-4-F7_DAPi712H06-ORGi5034-96P247


title: Glycine max, Control, 72hr, rep1


description: Library name: Control_TF_DNA_F_vesca_Hawaii-4-F7_DAPi712A12-ORGi5034-96P220


description: Library name: AT4G38000_C_rubella_Monte_Gargano_DAPi709B02-ORGi5037-96P169


description: Library name: AT1G01060_F_vesca_Hawaii-4-F7_DAPi712H05-ORGi5034-96P220


description: Library name: AT3G50410_F_vesca_Hawaii-4-F7_DAPi712H06-ORGi5034-96P220


title: Glycine max, Control, 48hr, rep3


description: Library name: AT3G02940_F_vesca_Hawaii-4-F7_DAPi712H04-ORGi5034-96P220

value: MYB


description: Library name: Solyc01g102340.3.1_F_vesca_Hawaii-4-F7_DAPi712H04-ORGi5034-96P247


description: Library name: Carub.0002s1959.1_F_vesca_Hawaii-4-F7_DAPi712H10-ORGi5034-96P247


title: Glycine max, Control, 48hr, rep2


description: Library name: XP_013629448.1_F_vesca_Hawaii-4-F7_DAPi712H03-ORGi5034-96P247


title: Glycine max, Control, 48hr, rep1


description: Library name: AT2G30250_F_vesca_Hawaii-4-F7_DAPi712H03-ORGi5034-96P220


description: Library name: AT2G22430_F_vesca_Hawaii-4-F7_DAPi712H02-ORGi5034-96P220


description: Library name: AT5G52020_C_rubella_Monte_Gargano_DAPi709A10-ORGi5037-96P169


description: Library name: XP_013634112.1_F_vesca_Hawaii-4-F7_DAPi712H08-ORGi5034-96P247


description: Library name: AT3G28920_C_rubella_Monte_Gargano_DAPi709A08-ORGi5037-96P169


description: Library name: XP_013609718.1_F_vesca_Hawaii-4-F7_DAPi712G12-ORGi5034-96P247


title: Glycine max, Control, 24hr, rep2


title: Glycine max, Control, 24hr, rep3


description: Library name: Solyc03g116890.3.1_F_vesca_Hawaii-4-F7_DAPi712G11-ORGi5034-96P247


description: Library name: AT1G28370_C_rubella_Monte_Gargano_DAPi709A07-ORGi5037-96P169


title: LubriShield_catheter_biofilm_2Bioreps_pooled

city: Solna

first: Ana

middle: I

last: Romero

address: Maria Aspmans Gata 44A

country: Sweden

institute: CytaCoat AB

description: Library name: Sample_3

data_processing:
Data filtering was performed with SOAPnuke.2.2.1 (Parameters: -l 15 -q 0.5 -n 0.05 -i).
Assembly was performed with HISAT2 v2.2.1 (Parameters: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF), StringTie v2.2.1 (Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8), Cufflinks v2.2.1 (Parameters: Default parameters).
Coding ability prediction was performed with CPC2 (Parameters: Default parameters), CNCI (Parameters: Default parameters) and LGC, v. LGC-1.0 (Parameters: Default parameters).
Quantitative analysis was performed using Bowtie2 v. 2.4.5 (Parameters: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 8 -k 20 -N 1) and RSEM v. 1.3.1 (Parameters: --forward-prob 0).
Assembly: Reference genome used is GCF_000006765.1 (Pseudomonas aeruginosa PA01)
Supplementary files format and content: Excel tables including raw counts and FPKM values for each sample

organism: Pseudomonas aeruginosa PAO1

source_name: Adherent cells

growth_protocol: Pseudomonas aeruginosa were grown on the surface of 2cm silicon catheter pieces, either uncoated or coateld with Lubrishield TM, in the artificial urine medium for 7 days at 37°C with low intensity shaking with daily growth medium change.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen, USA), following to the manufacturer's protocol, and resuspensed in RNase - free water. Ribosomal RNA was removed using TIANSeq rRNA Depletion Kit (G-bacteria) (TIANGEN, China), following to the manufacturer's protocol.
The libraray was consturcted using Optimal Dual-mode mRNA Library Prep Kit (MGI, China), following to the manufacturer's protocol.

treatment_protocol: Silicon pieces were briefly rinsed, 2mm ends cut off and fast frozen prior the total RNA extraction.

value: Adherent cells

value: WT

value: 7 days


description: Library name: AT5G09410_F_vesca_Hawaii-4-F7_DAPi712G11-ORGi5034-96P220

value: CAMTA


title: Uncoated_catheter_biofilm_BioRep3

description: Library name: Control_3


description: Library name: AT5G45580_C_rubella_Monte_Gargano_DAPi709A11-ORGi5037-96P169


description: Library name: AT5G65130_C_rubella_Monte_Gargano_DAPi709B01-ORGi5037-96P169


description: Library name: XP_013589913.1_F_vesca_Hawaii-4-F7_DAPi712G10-ORGi5034-96P247

value: MYBRELATED


title: Glycine max, Control, 6hr, rep2

value: stem


description: Library name: AT5G45300_F_vesca_Hawaii-4-F7_DAPi712G10-ORGi5034-96P220


description: Library name: AT5G07310_C_rubella_Monte_Gargano_DAPi709A05-ORGi5037-96P169


title: Uncoated_catheter_biofilm_BioRep2

description: Library name: Control_2


description: Library name: AT5G13910_C_rubella_Monte_Gargano_DAPi709A04-ORGi5037-96P169


description: Library name: AT5G52660_C_rubella_Monte_Gargano_DAPi709A06-ORGi5037-96P169


title: Uncoated_catheter_biofilm_BioRep1

description: Library name: Control_1


description: Library name: LOC_Os10g41200.1_F_vesca_Hawaii-4-F7_DAPi712G09-ORGi5034-96P247


title: Glycine max, Control, 6hr, rep3


description: Library name: AT4G31060_C_rubella_Monte_Gargano_DAPi709A03-ORGi5037-96P169


title: THP-1 cells, M1+HA4-3, Day1

city: Kizugawa

first: Eiko

last: Uno

state: Kyoto

address: 6-5-4 Kunimidai

country: Japan

institute: Rohto Pharmaceutical Co., Ltd.

description: Library name: Sample 9

data_processing:
The resulting reads were analyzed using CLC Genomics Workbench software (ver. 8.01, Qiagen, Venlo, The Netherlands).
Using the RNA-Seq Analysis tool in CLC Genomics Workbench, read counts were obtained for each gene ID and transcript ID. The counts were then normalized by gene length and read depth to calculate TPM (Transcripts Per Million) values. In the processed data file, the expression values represent TPM values.
Statistical differences were analyzed by multiple unpaired t-tests using Prism (version 10.0; GraphPad Software, Boston, MA, USA).
Gene pathway analysis was performed using Ingenuity Pathway Analysis (Qiagen, Venlo, The Netherlands).
The heat map displayed log2(TPM+1) values for each gene from the RNA-seq data created with Prism.
A volcano plot was produced with log2(fold change) on the x-axis and -log10(p-value) on the y-axis using Origin Pro 2023 (Northampton, MA).
Principal component analysis (PCA) was conducted using JMP Pro 18 (SAS Institute Cary, CA) to validate intragroup variance.
Assembly: Homo sapience GRCh37 (hg19) release-75
Supplementary files format and content: xlsx file include TPM values for each sample

source_name: skin

growth_protocol: The human acute monocytic leukemia cell line, THP-1, was obtained from the American Type Culture Collection (Manassas, VA, USA). THP-1 cells were maintained in RPMI-1640 medium fortified with 10% FBS, penicillin (100 IU/mL), streptomycin (100 μg/mL), and β-mercaptoethanol (50μM), and they were also grown in an incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from macrophages and NHDF utilizing the Maxwell® RSC Instrument (Promega, Madison, WI, USA).
The mRNA was then purified using oligo dT beads (NEBNext Poly (A) mRNA Magnet Isolation Module, New England Biolabs, NEB, Ipswich, MA). Complementary DNA (cDNA) library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit (NEB) along with NEBNextplex Oligos for Illumina according to a previously established method (9). Index sequences were incorporated into the fragments through PCR amplification. The cDNA libraries were combined in equal molecular amounts and sequenced on an Illumina Next-seq DNA sequencer, employing a 75-bp single-end cycle sequencing kit (Illumina, San Diego, CA).

treatment_protocol: THP-1 cells were differentiated into M0 macrophages by treating them with 5 ng/mL phorbol 12-myristate 13-acetate (PMA) for 72 hours. For M1 polarization, M0 macrophages received treatment with 10 ng/mL lipopolysaccharide (LPS) and 20 ng/mL interferon-γ (IFN-γ) for 24 hours. The impact of HA4 was evaluated during M1 polarization, conducted with and without 0.1% (w/v) or 1% (w/v) HA4 added for 24 h at initiation. RNA extraction was performed 24 hours after the last stimulation for M1  group macrophages.

value: skin

tag: cell line

value: Macrophages

value: Macrophage differentiation


title: Glycine max, Control, 6hr, rep1


title: THP-1 cells, M1+HA4-2, Day1

description: Library name: Sample 8


description: Library name: AL4G38490.t1_F_vesca_Hawaii-4-F7_DAPi712G08-ORGi5034-96P247

value: BZIP


description: Library name: AT3G09600_C_rubella_Monte_Gargano_DAPi709A02-ORGi5037-96P169


title: Glycine max, Control, 0hr, rep1


description: Library name: AT1G72740_F_vesca_Hawaii-4-F7_DAPi712G09-ORGi5034-96P220


description: Library name: AT2G01940_F_vesca_Hawaii-4-F7_DAPi712G08-ORGi5034-96P220


title: Glycine max, Control, 0hr, rep2


title: 58187_549WO

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: P549WO

data_processing:
RNA-Seq reads were trimmed to remove sequencing adapters using Trimmomatic and polyA tails using FASTP.
The processed reads were mapped to the human genome hg38 using STAR (v. 2.6.0.a), and gene expression levels were summarized by HTSeq-count v.0.11.1.
Gene expression raw counts were normalized using TMM normalization method and differential expression analysis was conducted using log likelihood ratio test implemented in “edgeR”.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Peripheral blood

extract_protocol:
RNA extraction, sequencing, and analysis RNA from 100,000 cells from each CAR T cell product was extracted with the miRNeasy Mini Kit (QIAGEN, 217004), and RNA quality was assessed using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions.
The libraries were prepared with SMART-Seq® Ultra Low Input RNA Kit for Sequencing – v4 (TaKaRa, Cat. 634888) according to the manufacturer's protocol. The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit. Sequencing was performed on Illumina HiSeq 2500 with the single read mode of 51cycle.

value: Peripheral blood

value: T cells

value: Wild type

value: Without Rapamycin


title: Glycine max, Control, 24hr, rep1

value: Control


title: THP-1 cells, M1-3, Day1

description: Library name: Sample 6


title: 58186_549W

description: Library name: P549W

value: With Rapamycin


title: con_rep3

city: Hangzhou

first: Qinyu

last: Luo

state: Zhejiang

address: Yuhangtang road #866

country: China

institute: zhejiang university

description: Library name: con_rep3

data_processing:
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05. To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS(http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05.
Assembly: Briefly, WGCNA constructs networks using the absolute value of the Pearson’s correlation coefficient as the gene co-expression measure, which is raised to a power to create the adjacency matrix. The topological overlap distance calculated from the adjacency matrix is then clustered with the average linkage hierarchical clustering.Our modules were defined using the cutreeDynamic function with a minimum module size of 30 genes. A module eigengene distance threshold of 0.25 was used to merge highly similar modules use mergeCloseModules function.We empirically set the cut-off of the weight value as 0.10 to determine biologically significant edges for each module. Correlation analyses between module eigengenes and measured agronomic traits were applied to explore the biological significances for each module. A gene with top 15% number of edges in a module was determined as the hub gene
Supplementary files format and content: genes.read.txt

organism: Escherichia coli

source_name: whole cell

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed usingDNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0,>10μg) is used to construct sequencing library.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5μg of total RNA. Shortly, rRNA removal by RiboZero rRNA removal kit(Epicenter) , fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, Paired-end libraries were sequenced by Illumina NovaSeq 6000 sequencing (150bp*2, Shanghai BIOZERON Co., Ltd ).

value: whole cell


description: Library name: Carub.0003s1161.1.p_F_vesca_Hawaii-4-F7_DAPi712G07-ORGi5034-96P247

source_name: plant

value: plant


title: 58185_543WO

description: Library name: P543WO


title: THP-1 cells, M1-2, Day1

description: Library name: Sample 5

value: WT


title: Glycine max, Control, 0hr, rep3


description: Library name: AT5G19790_F_vesca_Hawaii-4-F7_DAPi712G07-ORGi5034-96P220


title: 58184_543W

description: Library name: P543W


title: 58183_466WO

description: Library name: P466WO


title: con_rep2

description: Library name: con_rep2


description: Library name: AT1G69180_F_vesca_Hawaii-4-F7_DAPi712G05-ORGi5034-96P220


title: con_rep1

description: Library name: con_rep1


description: Library name: AT5G02320_F_vesca_Hawaii-4-F7_DAPi712G06-ORGi5034-96P220

value: MYB


title: dsf_rep3

description: Library name: dsf_rep3


title: THP-1 cells, M0-3, Day1

description: Library name: Sample 3


title: THP-1 cells, M1-1, Day1

description: Library name: Sample 4


description: Library name: LOC_Os01g18240.1_F_vesca_Hawaii-4-F7_DAPi712G04-ORGi5034-96P247


title: 58182_466W

description: Library name: P466W


title: dsf_rep2

description: Library name: dsf_rep2


title: THP-1 cells, M0-1, Day1

description: Library name: Sample 1


title: 58180_397W

description: Library name: P397W


title: 58181_397WO

description: Library name: P397WO


title: dsf_rep1

description: Library name: dsf_rep1


description: Library name: AT1G46768_F_vesca_Hawaii-4-F7_DAPi712G04-ORGi5034-96P220


title: HCT116 p53-/- ORC1 deletion, rep2 [ATACseq]

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

institute: University of Alabama

description: Library name: Sample4

data_processing:
Raw sequence data in fastq format were processed as follows: FastQC (v0.11.5) (Andrews, 2010) was used for quality control and sequence data were then mapped to human genome (hg38) using bowtie2 (v2.2.9) (Langdon, 2015). Sam files were converted into bam files using samtools (v1.12) (Li et al., 2009) and only high-quality reads (q-score ≥30) were retained for subsequent analyses. Bam files were then converted to bed files using samtools. Reads no longer than 150 bp were selected and used for ATAC-seq peak calling. Peak calling for ATAC-seq data was performed with MACS2 callpeak function (callpeak -g hs -B --SPMR -q 0.05 --keep-dup 1 -f BEDPE) (v2.1.4) (Zhang et al., 2008).
Assembly: hg38
Supplementary files format and content: BigWig files with pileup signals are generated by bdg2bw.

growth_protocol: HCT116 p53-/- cell (referred to as wild-type, RRID: CVCL_S744) was a generous gift from Fred Bunz (Johns Hopkins) (Bunz et al., 1998). ORC2B2 (referred to as ORC2-/-) was a clonal cell line that was established by CRISPR/Cas9 technology in the HCT116 p53-/- background (Shibata et al., 2016). ORC2 rescue cells were established by pLHCXORC2 cloning ORC2 with 3’UTR and 5’UTR and clonal selection. ORC1 or ORC5KO clones were established in HCT116 p53-/- cells using CRISPR/Cas9 technology (Shibata and Dutta, 2020; Shibata et al., 2016). All cell lines were maintained in McCoy’s 5A-modified medium (Corning, no. 10-050-CV) supplemented with 10% fetal bovine serum.

extract_protocol: ATAC-seq for cell lines was performed based on Omni-ATAC-seq protocol (Corces et al., 2017) with 50,000 cells. Nuclear pellet was subjected to transposition with Nextera DNA Sample Preparation Kit (Illumina, no. FC-121-1030) in the presence of 0.01% digitonin and 0.1% Tween-20 at 37 degree for 30 minutes.  The reaction was then cleaned up by DNA Clean and Concentrator-5 Kit (Zymo, no. D4014) and PCR amplified with NEBNext High-Fidelity 2X PCR Master Mix (NEB, no. M0541L) and Nextera Index kit (Illumina, no. 15055289). The resulting libraries were pooled and sequenced on Illumina NextSeq500, according to validated standard operating procedures established by the University of Virginia Genome And Technology Core, RRID: SCR_018883.

value: ORC1 deletion


title: KD_PA 2

city: Changsha

first: Zhang

middle: xiu

last: mei

address: tian ma road

institute: Haijun Tu

data_processing:
The image data measured by the high-throughput sequencer is converted into sequence data (reads) by Casava base recognition.
It mainly includes the removal of reads with adapter, the removal of reads containing n (n indicates that the base information cannot be determined), and the removal of low-quality reads (the base number with qphred < =20 accounts for more than 50% of the whole read length).
The raw gene expression matrix was imported into the R environment for further processing and analysis. Genes with low read counts (less than 50 reads in all eight libraries) were filtered out.
Reads were mapped to the worm reference genome (Wbcel235) using HISAT2. Uniquely mapped reads were summarised to Worm Base annotated genes using feature Counts.
Assembly: Wbcel235
Supplementary files format and content: CT_OP_1_1.fq and CT_OP_1_2.fq files include complete reads for each sample.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Transferring L4 stage worms, which were maintained in NGM plate at 20C, to new plate  at  25C.

extract_protocol:
RNA was harvested using TransZol  Up Plus RNA Kit(Thermo Fisher).
>=1ug total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Using pathogenic bacterial PA14 to infect worms.

value: whole body

value: DCL569 + inx-14 RNAi

value: PA14 infection


description: Library name: AT1G80840_F_vesca_Hawaii-4-F7_DAPi712G03-ORGi5034-96P220

value: WRKY


title: HCT116 p53-/- ORC1 deletion, rep1 [ATACseq]

description: Library name: Sample3


title: 58179_293WO

description: Library name: P293WO


title: KD_PA 1


title: THP-1 cells, M0-2, Day1

description: Library name: Sample 2

value: skin

value: Macrophages

value: Macrophage differentiation


title: 58178_293W

description: Library name: P293W

value: Peripheral blood

value: T cells


title: HCT116 p53-/- WT, rep2 [ATACseq]-2

description: Library name: Sample2

value: wild-type


title: CT_PA 2