description: Library name: AT5G64750_A_thaliana_Col-0_DAPi712E03-ORGi5005-96P220


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: AL5G10010.t1_A_thaliana_Col-0_DAPi712E01-ORGi5005-96P364

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: Arabidopsis thaliana Col-0: TAIR10/Araport11
Supplementary files format and content: narrowPeak are tab-delimited extended bed format files that contain peak regions identified by MACS3, using the matched negative controls on each 96 well plate to dentify regions that were enriched for by each transcription factor. The identified peaks represent putative transcription factor binding sites.
Supplementary files format and content: bigwig files show the genome coverage of each DAP-seq library. They can be used to compare coverage between different libraries and to view peaks in a genome browser. Note that they should be compared to the matched negative control libraries from the same plate.
Library strategy: DAP-seq

molecule: genomic DNA

organism: Arabidopsis thaliana

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

tag: multidap sample_id

tag: 96 well_plate_id

tag: tf source_species


description: Library name: LOC_Os06g07030.1_A_thaliana_Col-0_DAPi712E01-ORGi5005-96P247


title: Single cell AD6 from distal small intestine

city: Grand Rapids

first: Peter

middle: W

last: Laird

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

data_processing:
Supplementary files format and content: CSV format with columns chr (chromosome), pos (1-based position of C on reference strand), strand (aligned strand), allele (assigned local microhaplotype), beta (beta value), coverage (number of reads covering C), phase_set (local microhaplotype ID), which_all_has_cg (which allele has a CpG, if this CpG is created or destroyed by a SNP used to distinguish between alleles), twosnp_cpg (is this CpG composed of two SNPs which are used to distinguish between alleles?)
Supplementary files format and content: CSV format with columns chr (chromosome), pos (1-based position of C on reference strand), strand (aligned strand), allele (assigned local microhaplotype), beta (beta value), coverage (number of reads covering C), phase_set (local microhaplotype ID), which_all_has_cg (which allele has a CpG, if this CpG is created or destroyed by a SNP used to distinguish between alleles), twosnp_cpg (is this CpG composed of two SNPs which are used to distinguish between alleles?)
Supplementary files format and content: Biscuit BED (no-header TSV with columns chr [chromosome], start [0-based location of C], end [1-based location of G], beta, coverage, and support)
Adapter trimming with Cutadapt; alignment with Biscuit; deduplication with Dupsifter; quality control and filtering with Biscuit and Samtools; methylation calling with Biscuit; allele-resolved methylation analysis with custom tools (see publication methods).
Assembly: mm10

organism: Mus musculus

source_name: distal small intestine

extract_protocol:
Lysis in sodium bisulfite
sc-DEEP-mC

value: distal small intestine


description: Library name: AT1G13260_A_thaliana_Col-0_DAPi712E01-ORGi5005-96P220

value: RAV


title: Single cell AD5 from distal small intestine


title: Single cell AD4 from distal small intestine


description: Library name: AT1G22070_A_lyrata_MN47_DAPi712B11-ORGi5038-96P155

data_processing:
Fastq files were quality filtered and adapters were trimmed using BBTools v38.96 bbduk.sh62 with parameters k=21 mink=11 ktrim=r tbo tpe qtrim=r trimq=6 maq=10, and then aligned to the corresponding reference genome using bowtie2 v2.4.2 and parameters --no-mixed --no-discordant. Bam files from negative control wells were merged using the samtools v1.15.1 merge command, to generate a single background file for each 96-well plate. The MACS3 v3.0.0a6 callpeak command was used to generate narrowPeak files, using the merged background as the control, with the parameters --call-summits --keep-dup 1 and –gsize with the total fasta genome size. Bigwig files were generated using deeptools v3.5.2 bamCoverage with parameters --extendReads --binSize 1 --ignoreDuplicates --maxFragmentLength 600 --normalizeUsing RPGC, and --effectiveGenomeSize with the total fasta genome assembly size of each species.
Assembly: Arabidopsis lyrata MN47: 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: Arabidopsis lyrata

value: BZIP


description: Library name: XP_013587350.1_A_lyrata_MN47_DAPi712B10-ORGi5038-96P247

value: MYBRELATED


description: Library name: AT5G11260_A_thaliana_Col-0_DAPi712D12-ORGi5005-96P220


description: Library name: AT3G56850_A_thaliana_Col-0_DAPi712D12-ORGi5005-96P155


description: Library name: AT2G40620_A_lyrata_MN47_DAPi712B12-ORGi5038-96P220


title: Single cell AD3 from distal small intestine


description: Library name: XP_013587997.1_A_thaliana_Col-0_DAPi712D11-ORGi5005-96P247

value: WRKY


title: Single cell AD12 from distal small intestine


description: Library name: LOC_Os03g21800.1_A_lyrata_MN47_DAPi712B09-ORGi5038-96P247


description: Library name: AT1G20910_A_lyrata_MN47_DAPi712B10-ORGi5038-96P220

value: ARID


description: Library name: Solyc05g009790.1.1_A_thaliana_Col-0_DAPi712D10-ORGi5005-96P364


description: Library name: AT3G18990_A_thaliana_Col-0_DAPi712D11-ORGi5005-96P220


description: Library name: LOC_Os08g06110.3_A_thaliana_Col-0_DAPi712D10-ORGi5005-96P247


description: Library name: AT1G79580_A_lyrata_MN47_DAPi712B09-ORGi5038-96P220

value: NAC


description: Library name: AL8G10650.t1_A_thaliana_Col-0_DAPi712D09-ORGi5005-96P247


description: Library name: Carub.0008s0285.1_A_thaliana_Col-0_DAPi712D08-ORGi5005-96P247


description: Library name: Solyc06g051120.4.1_A_thaliana_Col-0_DAPi712D07-ORGi5005-96P364

value: TRIHELIX


description: Library name: AT2G46770_A_thaliana_Col-0_DAPi712D10-ORGi5005-96P155


description: Library name: Solyc01g095460.3.1_A_thaliana_Col-0_DAPi712D07-ORGi5005-96P247


description: Library name: AT5G03150_A_thaliana_Col-0_DAPi712D08-ORGi5005-96P220


title: Single cell AD10 from distal small intestine


title: Single cell AD1 from distal small intestine


title: Single cell AC9 from distal small intestine


description: Library name: Carub.0004s2898.1.p_A_lyrata_MN47_DAPi712B07-ORGi5038-96P247


title: Single cell AC8 from distal small intestine


description: Library name: LOC_Os10g26500.1_A_thaliana_Col-0_DAPi712D12-ORGi5005-96P247

value: HOMEOBOX


description: Library name: AT5G39610_A_thaliana_Col-0_DAPi712D07-ORGi5005-96P155


description: Library name: AL8G13510.t2_A_lyrata_MN47_DAPi712B08-ORGi5038-96P247


description: Library name: AT3G04070_A_lyrata_MN47_DAPi712B09-ORGi5038-96P155


title: Single cell AD11 from distal small intestine


title: Single cell AC7 from distal small intestine


description: Library name: AT1G20980_A_thaliana_Col-0_DAPi712D06-ORGi5005-96P155

value: SBP


description: Library name: XP_013631649.1_A_lyrata_MN47_DAPi712B05-ORGi5038-96P247


title: Single cell AC5 from distal small intestine


description: Library name: AL5G42830.t1_A_thaliana_Col-0_DAPi712D06-ORGi5005-96P364


description: Library name: LOC_Os02g33430.1_A_thaliana_Col-0_DAPi712D05-ORGi5005-96P247


title: Single cell AC6 from distal small intestine


description: Library name: AT2G01930_A_thaliana_Col-0_DAPi712D05-ORGi5005-96P220

value: BBRBPC


description: Library name: AT3G18990_A_lyrata_MN47_DAPi712B06-ORGi5038-96P155


description: Library name: AT3G57920_A_thaliana_Col-0_DAPi712D06-ORGi5005-96P220


description: Library name: Carub.0004s2803.1_A_thaliana_Col-0_DAPi712D05-ORGi5005-96P364


description: Library name: AT3G08500_A_lyrata_MN47_DAPi712B05-ORGi5038-96P220

value: MYB


description: Library name: Solyc02g094290.1.1_A_thaliana_Col-0_DAPi712D04-ORGi5005-96P364

value: TCP


description: Library name: AT1G29160_A_lyrata_MN47_DAPi712B04-ORGi5038-96P220


title: Single cell AC3 from distal small intestine


description: Library name: AT5G45300_A_thaliana_Col-0_DAPi712D04-ORGi5005-96P155


description: Library name: AT3G20770_A_thaliana_Col-0_DAPi712D05-ORGi5005-96P155

value: EIL


title: Single cell AC4 from distal small intestine


title: Single cell AC2 from distal small intestine


description: Library name: AT5G02460_A_lyrata_MN47_DAPi712B04-ORGi5038-96P155


description: Library name: AL1G23550.t1_A_lyrata_MN47_DAPi712B03-ORGi5038-96P247


description: Library name: AT3G50260_A_thaliana_Col-0_DAPi712D02-ORGi5005-96P220


description: Library name: AT1G02230_A_lyrata_MN47_DAPi712B03-ORGi5038-96P155


title: Single cell AC12 from distal small intestine


description: Library name: AT1G74480_A_thaliana_Col-0_DAPi712D07-ORGi5005-96P220

value: RWPRK


description: Library name: AT4G17980_A_thaliana_Col-0_DAPi712D03-ORGi5005-96P155


description: Library name: Carub.0001s1194.1_A_thaliana_Col-0_DAPi712D03-ORGi5005-96P247


description: Library name: XP_013599228.1_A_thaliana_Col-0_DAPi712D02-ORGi5005-96P364


description: Library name: AT4G36620_A_thaliana_Col-0_DAPi712D02-ORGi5005-96P155


description: Library name: AT3G56400_A_lyrata_MN47_DAPi712B02-ORGi5038-96P220


title: Single cell AC11 from distal small intestine


description: Library name: AT4G25470_A_lyrata_MN47_DAPi712B06-ORGi5038-96P220


title: Single cell AC10 from distal small intestine


description: Library name: Carub.0001s3581.1.p_A_thaliana_Col-0_DAPi712D01-ORGi5005-96P247


description: Library name: AT1G16490_A_lyrata_MN47_DAPi712B02-ORGi5038-96P155


description: Library name: Carub.0002s1646.1_A_thaliana_Col-0_DAPi712C12-ORGi5005-96P247


description: Library name: AT1G12260_A_thaliana_Col-0_DAPi712C12-ORGi5005-96P220


description: Library name: AT5G65410_A_thaliana_Col-0_DAPi712D03-ORGi5005-96P220

value: ZFHD


title: Single cell AC1 from distal small intestine


description: Library name: Solyc02g085630.3.1_A_thaliana_Col-0_DAPi712D01-ORGi5005-96P364

value: plant


description: Library name: AT1G06850_A_thaliana_Col-0_DAPi712C12-ORGi5005-96P155


description: Library name: AT4G00730_A_thaliana_Col-0_DAPi712C11-ORGi5005-96P220


description: Library name: AL2G40550.t1_A_thaliana_Col-0_DAPi712C11-ORGi5005-96P247


description: Library name: AT5G67300_A_lyrata_MN47_DAPi712B01-ORGi5038-96P220


description: Library name: Carub.0001s0116.1_A_thaliana_Col-0_DAPi712C10-ORGi5005-96P247


description: Library name: LOC_Os01g51154.1_A_lyrata_MN47_DAPi712A11-ORGi5038-96P247


title: Single cell AB8 from proximal small intestine

source_name: proximal small intestine

value: proximal small intestine


description: Library name: AT1G43700_A_thaliana_Col-0_DAPi712C11-ORGi5005-96P155


description: Library name: AT1G12260_A_lyrata_MN47_DAPi712A11-ORGi5038-96P155


title: Single cell AB5 from proximal small intestine


description: Library name: LOC_Os01g49830.1_A_thaliana_Col-0_DAPi712C10-ORGi5005-96P364

value: RAV


description: Library name: Solyc06g048630.3.1_A_thaliana_Col-0_DAPi712C09-ORGi5005-96P247

value: BZIP


title: Single cell AB7 from proximal small intestine


description: Library name: AL1G11460.t1_A_lyrata_MN47_DAPi712A10-ORGi5038-96P247

value: MYBRELATED


description: Library name: AT5G18270_A_thaliana_Col-0_DAPi712C10-ORGi5005-96P155


description: Library name: AT1G76420_A_thaliana_Col-0_DAPi712C09-ORGi5005-96P220


description: Library name: AT5G62470_A_thaliana_Col-0_DAPi712C08-ORGi5005-96P220


description: Library name: LOC_Os01g46970.1_A_thaliana_Col-0_DAPi712C07-ORGi5005-96P247


description: Library name: XP_013613838.1_A_thaliana_Col-0_DAPi712C08-ORGi5005-96P247


title: Single cell AB2 from proximal small intestine


description: Library name: AT5G05550_A_lyrata_MN47_DAPi712A10-ORGi5038-96P220


description: Library name: AT5G60130_A_thaliana_Col-0_DAPi712C07-ORGi5005-96P220


description: Library name: AT5G53950_A_lyrata_MN47_DAPi712A10-ORGi5038-96P155


title: Single cell AB11 from proximal small intestine


title: Single cell AB12 from proximal small intestine


description: Library name: Carub.0004s2291.1_A_lyrata_MN47_DAPi712A09-ORGi5038-96P247


title: Single cell AB4 from proximal small intestine


description: Library name: AL1G53260.t1_A_lyrata_MN47_DAPi712B01-ORGi5038-96P247


title: Single cell AB6 from proximal small intestine


title: Single cell AB10 from proximal small intestine


description: Library name: AT3G27010_A_thaliana_Col-0_DAPi712C04-ORGi5005-96P220


title: Single cell AA9 from proximal small intestine


description: Library name: Solyc05g053240.4.1_A_thaliana_Col-0_DAPi712C06-ORGi5005-96P364


description: Library name: LOC_Os01g69980.1_A_thaliana_Col-0_DAPi712C04-ORGi5005-96P364


description: Library name: XP_013602769.1_A_thaliana_Col-0_DAPi712C03-ORGi5005-96P247


description: Library name: AT4G14770_A_thaliana_Col-0_DAPi712C04-ORGi5005-96P155

value: CPP


title: Single cell AB1 from proximal small intestine


description: Library name: AT4G32730_A_thaliana_Col-0_DAPi712C05-ORGi5005-96P155


description: Library name: AT1G69690_A_thaliana_Col-0_DAPi712C02-ORGi5005-96P220


description: Library name: AT4G25490_A_lyrata_MN47_DAPi712A08-ORGi5038-96P220


description: Library name: XP_013631386.1_A_lyrata_MN47_DAPi712A07-ORGi5038-96P247


description: Library name: AT3G12250_A_lyrata_MN47_DAPi712A07-ORGi5038-96P220


description: Library name: AT5G03790_A_thaliana_Col-0_DAPi712C06-ORGi5005-96P220


title: Single cell AA8 from proximal small intestine


description: Library name: AT5G17800_A_thaliana_Col-0_DAPi712C02-ORGi5005-96P155


title: Single cell AA7 from proximal small intestine


description: Library name: LOC_Os03g10210.1_A_thaliana_Col-0_DAPi712C01-ORGi5005-96P364


description: Library name: AT1G27730_A_thaliana_Col-0_DAPi712C01-ORGi5005-96P220


description: Library name: Solyc11g064950.3.1_A_lyrata_MN47_DAPi712A08-ORGi5038-96P247


description: Library name: AT3G62420_A_thaliana_Col-0_DAPi712C07-ORGi5005-96P155


description: Library name: Solyc08g068320.3.1_A_thaliana_Col-0_DAPi712C04-ORGi5005-96P247


description: Library name: AT1G69490_A_lyrata_MN47_DAPi712A09-ORGi5038-96P155


description: Library name: LOC_Os08g37970.1_A_lyrata_MN47_DAPi712A06-ORGi5038-96P247


description: Library name: AT1G52880_A_thaliana_Col-0_DAPi712B12-ORGi5005-96P155


description: Library name: AT5G10030_A_lyrata_MN47_DAPi712A06-ORGi5038-96P220


description: Library name: Solyc07g040920.2.1_A_thaliana_Col-0_DAPi712B11-ORGi5005-96P247


title: Single cell AA5 from proximal small intestine


description: Library name: AT2G40620_A_thaliana_Col-0_DAPi712B12-ORGi5005-96P220


description: Library name: AT1G22070_A_thaliana_Col-0_DAPi712B11-ORGi5005-96P155


description: Library name: Carub.0001s1299.1_A_thaliana_Col-0_DAPi712B10-ORGi5005-96P364


title: Single cell AA4 from proximal small intestine


title: Single cell AA3 from proximal small intestine


description: Library name: AT1G49480_A_lyrata_MN47_DAPi712A04-ORGi5038-96P220

value: REM


description: Library name: AT5G62940_A_lyrata_MN47_DAPi712A05-ORGi5038-96P220


title: Single cell AA2 from proximal small intestine


description: Library name: AT3G10113_A_lyrata_MN47_DAPi712A04-ORGi5038-96P155


description: Library name: AT1G79580_A_thaliana_Col-0_DAPi712B09-ORGi5005-96P220

value: NAC


description: Library name: LOC_Os03g21800.1_A_thaliana_Col-0_DAPi712B09-ORGi5005-96P247


description: Library name: AT1G20910_A_thaliana_Col-0_DAPi712B10-ORGi5005-96P220

value: ARID


description: Library name: AT3G04070_A_thaliana_Col-0_DAPi712B09-ORGi5005-96P155


title: Single cell AA12 from proximal small intestine


description: Library name: XP_013589953.1_A_thaliana_Col-0_DAPi712B12-ORGi5005-96P247

value: HOMEOBOX


description: Library name: AT1G69780_A_lyrata_MN47_DAPi712A03-ORGi5038-96P220


title: Single cell AA6 from proximal small intestine


description: Library name: Carub.0004s2898.1.p_A_thaliana_Col-0_DAPi712B07-ORGi5005-96P247


description: Library name: LOC_Os03g61760.1_A_thaliana_Col-0_DAPi712B06-ORGi5005-96P364

value: SBP


description: Library name: AT5G66700_A_lyrata_MN47_DAPi712A06-ORGi5038-96P155


description: Library name: XP_013587350.1_A_thaliana_Col-0_DAPi712B10-ORGi5005-96P247


description: Library name: AT3G18990_A_thaliana_Col-0_DAPi712B06-ORGi5005-96P155


description: Library name: AL4G44590.t1_A_thaliana_Col-0_DAPi712B05-ORGi5005-96P364


description: Library name: AT4G25470_A_thaliana_Col-0_DAPi712B06-ORGi5005-96P220


description: Library name: AT2G23290_A_lyrata_MN47_DAPi712A02-ORGi5038-96P155


description: Library name: AT5G39760_A_lyrata_MN47_DAPi712A02-ORGi5038-96P220


description: Library name: XP_013631649.1_A_thaliana_Col-0_DAPi712B05-ORGi5005-96P247


description: Library name: AT1G53170_A_lyrata_MN47_DAPi711H11-ORGi5038-96P166


description: Library name: AL8G13510.t2_A_thaliana_Col-0_DAPi712B08-ORGi5005-96P247


title: Single cell AA10 from proximal small intestine


title: Single cell AA1 from proximal small intestine


description: Library name: AT3G08500_A_thaliana_Col-0_DAPi712B05-ORGi5005-96P220


title: Dux KD-Usp17le OE_2

city: Tianjin

first: Pan

middle: Pan

last: Shi

address: No. 38 Tongyan Road

country: China

institute: Nankai University

library_source: transcriptomic

data_processing:
Raw reads were processed using trim-galore and clean reads were mapped to mm10 from UCSC genome by Hisat2 with default parameters .
Uniquely mapped reads annotated in Gencode vM17 were calculated by Featurecounts , with default parameters.
Raw counts were normalized by library size via transcripts per kilobase of exon model per million mapped reads (TPM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols manufacturer's protocols.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

value: Dux KD-Usp17le OE

tag: treatment

value: Usp17le OE was performed by transfecting Usp17le OE plasmid  into Dux knockdown cells


description: Library name: Carub.0006s0445.1_A_thaliana_Col-0_DAPi712B07-ORGi5005-96P364

value: TRIHELIX


description: Library name: Carub.0005s0520.1_A_thaliana_Col-0_DAPi712B04-ORGi5005-96P364

value: TCP


description: Library name: AT2G03500_A_lyrata_MN47_DAPi711H07-ORGi5038-96P166


description: Library name: AT4G36780_A_lyrata_MN47_DAPi711H06-ORGi5038-96P166

value: BZR


title: Dux KD-Usp17le OE_1


title: Single cell AA11 from proximal small intestine


description: Library name: AT1G02230_A_thaliana_Col-0_DAPi712B03-ORGi5005-96P155

value: plant


title: Usp17le OE-Dux KD_2

value: Usp17le OE-Dux KD

value: Dux knockdown was performed by transfecting ShRNA into Usp17le OE cells


description: Library name: Solyc11g022470.2.1_A_thaliana_Col-0_DAPi712B02-ORGi5005-96P364


description: Library name: AL1G23550.t1_A_thaliana_Col-0_DAPi712B03-ORGi5005-96P247


description: Library name: AT5G58900_A_lyrata_MN47_DAPi711H04-ORGi5038-96P166


title: Usp17le OE-Dux KD_1


description: Library name: AT3G56400_A_thaliana_Col-0_DAPi712B02-ORGi5005-96P220

value: WRKY


title: Dux KD_2

value: Dux KD

value: Dux ShRNA was transfected and screened with puro


description: Library name: AT1G72010_A_lyrata_MN47_DAPi711H03-ORGi5038-96P166


description: Library name: AT1G16490_A_thaliana_Col-0_DAPi712B02-ORGi5005-96P155

value: MYB


description: Library name: AT5G47390_A_lyrata_MN47_DAPi711H02-ORGi5038-96P166

value: MYBRELATED


description: Library name: Carub.0003s3279.1_A_thaliana_Col-0_DAPi712B01-ORGi5005-96P364


description: Library name: AT5G05790_A_lyrata_MN47_DAPi711G12-ORGi5038-96P166


description: Library name: AT5G67300_A_thaliana_Col-0_DAPi712B01-ORGi5005-96P220


description: Library name: AT1G29160_A_thaliana_Col-0_DAPi712B04-ORGi5005-96P220


description: Library name: LOC_Os01g51154.1_A_thaliana_Col-0_DAPi712A11-ORGi5005-96P247


title: Dux KD_1


description: Library name: AL1G53260.t1_A_thaliana_Col-0_DAPi712B01-ORGi5005-96P247


description: Library name: Solyc03g116010.3.1_A_thaliana_Col-0_DAPi712A11-ORGi5005-96P364

value: RWPRK


title: Usp17le OE_1

value: Usp17le OE

value: Usp17le OE plasmid was transfected and screened with puro


title: Usp17le OE_2

value: mouse embryonic stem cells


description: Library name: AT5G02460_A_thaliana_Col-0_DAPi712B04-ORGi5005-96P155


description: Library name: XP_013637759.1_A_thaliana_Col-0_DAPi712A10-ORGi5005-96P364

value: RAV


description: Library name: AL1G11460.t1_A_thaliana_Col-0_DAPi712A10-ORGi5005-96P247


description: Library name: AT1G12260_A_thaliana_Col-0_DAPi712A11-ORGi5005-96P155

value: NAC


description: Library name: AT5G41570_A_lyrata_MN47_DAPi711G08-ORGi5038-96P166


title: WT_2

value: WT

value: Cell lines were cultured normally


description: Library name: AT1G69780_A_lyrata_MN47_DAPi711G07-ORGi5038-96P166

value: HOMEOBOX


title: WT_1


title: Ldlr.norm.14.3

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cells with less than 200 detected features were discarded. Genes detected in less than 3 cells were discarded.
Assembly: mm10
Supplementary files format and content: R object containing the raw counts for the cells and genes meeting the criteria described above.

source_name: lung

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
Libraries were prepared according to the manufacter’s instructions (single cell Gene Expression 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

treatment_protocol: Mice were left uninfected (day 0 samples) or infected via aerosol with ~50 of Mycobacterium tuberculosis, strain H37Rv.

value: lung

value: Ldlr-/-

tag: diet

value: normal

tag: day post-infection


description: Library name: AT1G69690_A_lyrata_MN47_DAPi711G05-ORGi5038-96P166

value: plant

value: TCP


description: Library name: Carub.0004s2291.1_A_thaliana_Col-0_DAPi712A09-ORGi5005-96P247

value: BZIP


description: Library name: LOC_Os10g02584.3_A_thaliana_Col-0_DAPi712A09-ORGi5005-96P364

value: BBRBPC


description: Library name: AT1G69490_A_thaliana_Col-0_DAPi712A09-ORGi5005-96P155


title: Ldlr.norm.14.2


description: Library name: Solyc11g064950.3.1_A_thaliana_Col-0_DAPi712A08-ORGi5005-96P247


description: Library name: AT5G39760_A_lyrata_MN47_DAPi711G03-ORGi5038-96P166

value: ZFHD


description: Library name: AT2G31230_A_lyrata_MN47_DAPi711G02-ORGi5038-96P166


description: Library name: AT4G25490_A_thaliana_Col-0_DAPi712A08-ORGi5005-96P220


description: Library name: AT3G12250_A_thaliana_Col-0_DAPi712A07-ORGi5005-96P220


description: Library name: AT5G64750_A_lyrata_MN47_DAPi711G09-ORGi5038-96P166


title: Ldlr.norm.14.1


description: Library name: LOC_Os08g37970.1_A_thaliana_Col-0_DAPi712A06-ORGi5005-96P247

value: MYB


description: Library name: Carub.0004s2981.1_A_thaliana_Col-0_DAPi712A06-ORGi5005-96P364

value: SBP


description: Library name: AT5G05550_A_thaliana_Col-0_DAPi712A10-ORGi5005-96P220

value: TRIHELIX


description: Library name: AT5G62940_A_thaliana_Col-0_DAPi712A05-ORGi5005-96P220


description: Library name: AT5G10030_A_thaliana_Col-0_DAPi712A06-ORGi5005-96P220


title: Ldlr.norm.0.2


description: Library name: AT4G34410_A_lyrata_MN47_DAPi711F11-ORGi5038-96P166


description: Library name: XP_013593496.1_A_thaliana_Col-0_DAPi712A04-ORGi5005-96P364


description: Library name: AT5G53950_A_thaliana_Col-0_DAPi712A10-ORGi5005-96P155


description: Library name: AT3G22830_A_lyrata_MN47_DAPi711G01-ORGi5038-96P166

value: HSF


description: Library name: AT5G66700_A_thaliana_Col-0_DAPi712A06-ORGi5005-96P155


description: Library name: AT1G49480_A_thaliana_Col-0_DAPi712A04-ORGi5005-96P220

value: REM


description: Library name: AT3G15270_A_lyrata_MN47_DAPi711F08-ORGi5038-96P166


description: Library name: AT2G22430_A_lyrata_MN47_DAPi711F07-ORGi5038-96P166


title: Ldlr.HC.14.3

value: high-cholesterol


title: Ldlr.norm.0.1


description: Library name: AT3G10113_A_thaliana_Col-0_DAPi712A04-ORGi5005-96P155

value: MYBRELATED


description: Library name: AT1G69780_A_thaliana_Col-0_DAPi712A03-ORGi5005-96P220


description: Library name: XP_013631386.1_A_thaliana_Col-0_DAPi712A07-ORGi5005-96P247


title: Ldlr.norm.0.3


description: Library name: LOC_Os09g12770.1_A_thaliana_Col-0_DAPi712A02-ORGi5005-96P364


description: Library name: AT1G29280_A_lyrata_MN47_DAPi711F12-ORGi5038-96P166

value: WRKY


title: Ldlr.HC.14.2


description: Library name: AT3G20310_A_lyrata_MN47_DAPi711F06-ORGi5038-96P166


description: Library name: AT2G23290_A_thaliana_Col-0_DAPi712A02-ORGi5005-96P155


description: Library name: AT5G60850_A_lyrata_MN47_DAPi711F05-ORGi5038-96P166


title: Ldlr.HC.14.1


description: Library name: AL2G28980.t1_A_thaliana_Col-0_DAPi711H11-ORGi5005-96P361

value: HOMEOBOX


title: Ldlr.HC.0.3

value: lung


description: Library name: AT5G39760_A_thaliana_Col-0_DAPi712A02-ORGi5005-96P220


description: Library name: AT1G53170_A_thaliana_Col-0_DAPi711H11-ORGi5005-96P166


description: Library name: AT1G14687_A_lyrata_MN47_DAPi711F04-ORGi5038-96P166


description: Library name: Carub.0002s1959.1_A_thaliana_Col-0_DAPi711H10-ORGi5005-96P361


title: Ldlr.HC.0.2

value: Ldlr-/-


title: Ldlr.HC.0.1


description: Library name: Solyc08g078340.3.1_A_thaliana_Col-0_DAPi711H09-ORGi5005-96P361


description: Library name: AT1G27730_A_lyrata_MN47_DAPi711F01-ORGi5038-96P166


description: Library name: LOC_Os01g17260.2_A_thaliana_Col-0_DAPi711H07-ORGi5005-96P361


description: Library name: AT1G18330_A_lyrata_MN47_DAPi711F03-ORGi5038-96P166


description: Library name: AT2G03500_A_thaliana_Col-0_DAPi711H07-ORGi5005-96P166


description: Library name: AL4G45550.t1_A_thaliana_Col-0_DAPi711H06-ORGi5005-96P361


title: B6.norm.14.3

value: normal


description: Library name: XP_013629448.1_A_thaliana_Col-0_DAPi711H03-ORGi5005-96P361

value: plant


description: Library name: AT4G36780_A_thaliana_Col-0_DAPi711H06-ORGi5005-96P166

value: BZR


title: B6.norm.14.2


description: Library name: AT4G16750_A_lyrata_MN47_DAPi711E12-ORGi5038-96P166


description: Library name: AT5G58900_A_thaliana_Col-0_DAPi711H04-ORGi5005-96P166


description: Library name: AT2G46680_A_lyrata_MN47_DAPi711E11-ORGi5038-96P166


title: B6.norm.14.1


title: B6.norm.0.2


description: Library name: AT5G47390_A_thaliana_Col-0_DAPi711H02-ORGi5005-96P166


description: Library name: AT2G23340_A_lyrata_MN47_DAPi711E08-ORGi5038-96P166


description: Library name: AT1G72010_A_thaliana_Col-0_DAPi711H03-ORGi5005-96P166

value: TCP


description: Library name: AT5G05790_A_thaliana_Col-0_DAPi711G12-ORGi5005-96P166


description: Library name: AT5G08330_A_lyrata_MN47_DAPi711E05-ORGi5038-96P166


title: B6.norm.0.1


description: Library name: XP_013634112.1_A_thaliana_Col-0_DAPi711H08-ORGi5005-96P361

value: BZIP


description: Library name: AT1G30210_A_lyrata_MN47_DAPi711E03-ORGi5038-96P166


title: B6.HC.14.3


description: Library name: XP_013589913.1_A_thaliana_Col-0_DAPi711G10-ORGi5005-96P361


description: Library name: LOC_Os10g41200.1_A_thaliana_Col-0_DAPi711G09-ORGi5005-96P361


title: B6.HC.14.2


description: Library name: AT5G08520_A_lyrata_MN47_DAPi711E02-ORGi5038-96P166


description: Library name: AT5G41570_A_thaliana_Col-0_DAPi711G08-ORGi5005-96P166


description: Library name: AT2G23320_A_lyrata_MN47_DAPi711E01-ORGi5038-96P166


description: Library name: AL4G38490.t1_A_thaliana_Col-0_DAPi711G08-ORGi5005-96P361


description: Library name: AT5G64750_A_thaliana_Col-0_DAPi711G09-ORGi5005-96P166


description: Library name: AT1G49480_A_lyrata_MN47_DAPi711D12-ORGi5038-96P166


title: B6.HC.14.1


description: Library name: Carub.0003s1161.1.p_A_thaliana_Col-0_DAPi711G07-ORGi5005-96P361


description: Library name: AT1G69780_A_thaliana_Col-0_DAPi711G07-ORGi5005-96P166


title: B6.HC.0.3


description: Library name: Solyc03g116890.3.1_A_thaliana_Col-0_DAPi711G11-ORGi5005-96P361


description: Library name: XP_013609718.1_A_thaliana_Col-0_DAPi711G12-ORGi5005-96P361


title: B6.HC.0.2


description: Library name: AT1G19000_A_lyrata_MN47_DAPi711D11-ORGi5038-96P166


description: Library name: AT5G39760_A_thaliana_Col-0_DAPi711G03-ORGi5005-96P166

value: ZFHD


title: B6.HC.0.1


description: Library name: AT3G15210_A_lyrata_MN47_DAPi711D10-ORGi5038-96P166


description: Library name: AT3G22830_A_thaliana_Col-0_DAPi711G01-ORGi5005-96P166


description: Library name: AL3G51890.t2_A_thaliana_Col-0_DAPi711F12-ORGi5005-96P361


description: Library name: AT2G31230_A_thaliana_Col-0_DAPi711G02-ORGi5005-96P166


description: Library name: AT1G29280_A_thaliana_Col-0_DAPi711F12-ORGi5005-96P166


description: Library name: AT5G62000_A_lyrata_MN47_DAPi711D08-ORGi5038-96P166

value: ARF


description: Library name: AT5G65410_A_lyrata_MN47_DAPi711D09-ORGi5038-96P166


title: Apoe.norm.14.3

value: Apoe-/-


description: Library name: LOC_Os09g25060.1_A_thaliana_Col-0_DAPi711F11-ORGi5005-96P361


description: Library name: AT4G34410_A_thaliana_Col-0_DAPi711F11-ORGi5005-96P166


description: Library name: Carub.0008s0039.1_A_thaliana_Col-0_DAPi711F09-ORGi5005-96P361


description: Library name: AL2G32420.t2_A_thaliana_Col-0_DAPi711F10-ORGi5005-96P361


title: Apoe.norm.14.2


title: Apoe.norm.14.1


description: Library name: AT3G15270_A_thaliana_Col-0_DAPi711F08-ORGi5005-96P166

value: SBP


description: Library name: XP_013586407.1_A_thaliana_Col-0_DAPi711F07-ORGi5005-96P361


description: Library name: AT1G69690_A_thaliana_Col-0_DAPi711G05-ORGi5005-96P166


description: Library name: AL7G19010.t1_A_thaliana_Col-0_DAPi711G03-ORGi5005-96P361

value: MYB


description: Library name: AT3G50260_A_lyrata_MN47_DAPi711D06-ORGi5038-96P166


description: Library name: AT3G14180_A_lyrata_MN47_DAPi711D03-ORGi5038-96P166

value: TRIHELIX


description: Library name: AT3G20310_A_thaliana_Col-0_DAPi711F06-ORGi5005-96P166


description: Library name: AT3G50060_A_lyrata_MN47_DAPi711D07-ORGi5038-96P166


title: Apoe.norm.0.2


description: Library name: AT1G14687_A_thaliana_Col-0_DAPi711F04-ORGi5005-96P166


description: Library name: AT5G67580_A_lyrata_MN47_DAPi711D05-ORGi5038-96P166


title: Apoe.norm.0.3


description: Library name: AT2G22430_A_thaliana_Col-0_DAPi711F07-ORGi5005-96P166


title: Apoe.HC.14.3

value: high-cholesterol


description: Library name: Solyc08g079120.3.1_A_thaliana_Col-0_DAPi711F03-ORGi5005-96P361

value: NAC


description: Library name: AT5G60850_A_thaliana_Col-0_DAPi711F05-ORGi5005-96P166


description: Library name: AT1G18330_A_thaliana_Col-0_DAPi711F03-ORGi5005-96P166

value: MYBRELATED


description: Library name: AT4G31800_A_lyrata_MN47_DAPi711C07-ORGi5038-96P166

value: WRKY


description: Library name: Solyc04g078640.3.1_A_thaliana_Col-0_DAPi711F01-ORGi5005-96P361


description: Library name: AT1G27730_A_thaliana_Col-0_DAPi711F01-ORGi5005-96P166


description: Library name: AT1G33240_A_lyrata_MN47_DAPi711C10-ORGi5038-96P166


title: Apoe.norm.0.1

value: lung


title: Apoe.HC.14.2


description: Library name: AT5G25190_A_lyrata_MN47_DAPi711C05-ORGi5038-96P166


description: Library name: Solyc05g007180.3.1_A_thaliana_Col-0_DAPi711E12-ORGi5005-96P361

value: HOMEOBOX


description: Library name: AT1G25550_A_lyrata_MN47_DAPi711C01-ORGi5038-96P166


title: Apoe.HC.14.1


description: Library name: Solyc10g005080.3.1_A_thaliana_Col-0_DAPi711E10-ORGi5005-96P361


description: Library name: AT4G16750_A_thaliana_Col-0_DAPi711E12-ORGi5005-96P166


title: Apoe.HC.0.2


description: Library name: AT5G13080_A_lyrata_MN47_DAPi711B12-ORGi5038-96P166


description: Library name: AT2G23340_A_thaliana_Col-0_DAPi711E08-ORGi5005-96P166


title: Neutrophils,C57BL/6,Day28,inf,bio rep 3

data_processing:
Read pairs were aligned to the mouse genome (mm10) using the gsnap aligner.
Concordantly mapping read pairs (∼40 million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Assembly: mm10 + Mtb H37Rv
Supplementary files format and content: allRawCounts.csv contains the raw counts for all samples.

source_name: Alveolar macrophage

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
Libraries were prepared with the SMARTer Stranded Total RNA - Pico Input Mammalian kit, Takara Bio.

treatment_protocol: Mice were infected via aerosol with either ~4000 (Day 10 samples) or ~50 (Day 28 samples) of Mycobacterium tuberculosis, strain H37Rv-mCherry.

value: Alveolar macrophage

value: inf


description: Library name: AT5G08330_A_thaliana_Col-0_DAPi711E05-ORGi5005-96P166

value: plant


description: Library name: LOC_Os02g42970.1_A_thaliana_Col-0_DAPi711E03-ORGi5005-96P361


description: Library name: AT2G30250_A_lyrata_MN47_DAPi711B11-ORGi5038-96P166


description: Library name: XP_013615900.1_A_thaliana_Col-0_DAPi711E09-ORGi5005-96P361


description: Library name: AL3G23910.t2_A_thaliana_Col-0_DAPi711E07-ORGi5005-96P361


title: Apoe.HC.0.1


title: Neutrophils,C57BL/6,Day28,inf,bio rep 1


description: Library name: AT5G08520_A_thaliana_Col-0_DAPi711E02-ORGi5005-96P166


description: Library name: AT1G30210_A_thaliana_Col-0_DAPi711E03-ORGi5005-96P166

value: TCP


title: Neutrophils,C57BL/6,Day28,inf,bio rep 2


title: Neutrophils,C57BL/6,Day28,bys,bio rep 3

value: bys


description: Library name: AT5G24110_A_lyrata_MN47_DAPi711B09-ORGi5038-96P166


description: Library name: AT2G46590_A_lyrata_MN47_DAPi711B10-ORGi5038-96P166


description: Library name: LOC_Os10g26500.1_A_thaliana_Col-0_DAPi711D12-ORGi5005-96P361


description: Library name: LOC_Os06g07030.1_A_thaliana_Col-0_DAPi711E01-ORGi5005-96P361


description: Library name: AT3G12730_A_lyrata_MN47_DAPi711B08-ORGi5038-96P166


description: Library name: AT2G23320_A_thaliana_Col-0_DAPi711E01-ORGi5005-96P166


description: Library name: Carub.0002s2670.1_A_thaliana_Col-0_DAPi711E11-ORGi5005-96P361


description: Library name: AT1G64620_A_lyrata_MN47_DAPi711C04-ORGi5038-96P166


description: Library name: AT1G49480_A_thaliana_Col-0_DAPi711D12-ORGi5005-96P166

value: REM


description: Library name: AT2G46680_A_thaliana_Col-0_DAPi711E11-ORGi5005-96P166


description: Library name: AT5G47370_A_lyrata_MN47_DAPi711B05-ORGi5038-96P166


title: Neutrophils,C57BL/6,Day28,bys,bio rep 1


description: Library name: AT3G24120_A_lyrata_MN47_DAPi711B06-ORGi5038-96P166


description: Library name: XP_013587997.1_A_thaliana_Col-0_DAPi711D11-ORGi5005-96P361


title: Neutrophils,C57BL/6,Day28,bys,bio rep 2


description: Library name: AT1G19000_A_thaliana_Col-0_DAPi711D11-ORGi5005-96P166


description: Library name: LOC_Os08g06110.3_A_thaliana_Col-0_DAPi711D10-ORGi5005-96P361


title: Monocyte-derived macrophages,C57BL/6,Day28,inf,bio rep 3


title: Monocyte-derived macrophages,C57BL/6,Day28,inf,bio rep 2


description: Library name: AT3G15210_A_thaliana_Col-0_DAPi711D10-ORGi5005-96P166


description: Library name: AT1G80840_A_lyrata_MN47_DAPi711A11-ORGi5038-96P166


description: Library name: AL8G10650.t1_A_thaliana_Col-0_DAPi711D09-ORGi5005-96P361


description: Library name: AT5G65410_A_thaliana_Col-0_DAPi711D09-ORGi5005-96P166

value: ZFHD


description: Library name: Carub.0008s0285.1_A_thaliana_Col-0_DAPi711D08-ORGi5005-96P361


description: Library name: AT5G67300_A_lyrata_MN47_DAPi711B01-ORGi5038-96P166


description: Library name: AT3G04030_A_lyrata_MN47_DAPi711A08-ORGi5038-96P166


title: Monocyte-derived macrophages,C57BL/6,Day28,bys,bio rep 3


description: Library name: AT5G62000_A_thaliana_Col-0_DAPi711D08-ORGi5005-96P166

value: ARF


description: Library name: AT3G01530_A_lyrata_MN47_DAPi711A05-ORGi5038-96P166


title: Monocyte-derived macrophages,C57BL/6,Day28,bys,bio rep 2


description: Library name: AT3G50060_A_thaliana_Col-0_DAPi711D07-ORGi5005-96P166


title: Monocyte-derived macrophages,C57BL/6,Day28,bys,bio rep 1


description: Library name: Carub.0001s1194.1_A_thaliana_Col-0_DAPi711D03-ORGi5005-96P361


description: Library name: LOC_Os02g33430.1_A_thaliana_Col-0_DAPi711D05-ORGi5005-96P361


description: Library name: Solyc01g095460.3.1_A_thaliana_Col-0_DAPi711D07-ORGi5005-96P361

value: BZIP


description: Library name: AT4G24240_A_lyrata_MN47_DAPi711A03-ORGi5038-96P166


description: Library name: AT3G56400_A_lyrata_MN47_DAPi711A04-ORGi5038-96P166


description: Library name: AT3G50260_A_thaliana_Col-0_DAPi711D06-ORGi5005-96P166


title: Monocyte-derived macrophages,C57BL/6,Day10,bys,bio rep 3


description: Library name: AT5G67580_A_thaliana_Col-0_DAPi711D05-ORGi5005-96P166


description: Library name: Carub.0001s3581.1.p_A_thaliana_Col-0_DAPi711D01-ORGi5005-96P361


description: Library name: AL2G40550.t1_A_thaliana_Col-0_DAPi711C11-ORGi5005-96P361


description: Library name: AT4G01250_A_lyrata_MN47_DAPi711A02-ORGi5038-96P166


title: Monocyte-derived macrophages,C57BL/6,Day10,bys,bio rep 2


description: Library name: Carub.0002s1646.1_A_thaliana_Col-0_DAPi711C12-ORGi5005-96P361


title: Monocyte-derived macrophages,C57BL/6,Day10,bys,bio rep 1


description: Library name: AT3G14180_A_thaliana_Col-0_DAPi711D03-ORGi5005-96P166


description: Library name: AT1G72740_A_lyrata_MN47_DAPi710H11-ORGi5038-96P151


description: Library name: AT1G33240_A_thaliana_Col-0_DAPi711C10-ORGi5005-96P166


title: Monocyte-derived macrophages,C57BL/6,Day28,inf,bio rep 1


description: Library name: AT3G55370_A_lyrata_MN47_DAPi710H10-ORGi5038-96P151


description: Library name: LOC_Os01g46970.1_A_thaliana_Col-0_DAPi711C07-ORGi5005-96P361


title: Alveolar macrophages,C57BL/6,Day10,inf,bio rep 3


title: Alveolar macrophages,C57BL/6,Day10,inf,bio rep 1


description: Library name: XP_013613838.1_A_thaliana_Col-0_DAPi711C08-ORGi5005-96P361


description: Library name: AT1G74650_A_lyrata_MN47_DAPi710H08-ORGi5038-96P151

value: MYB


description: Library name: AT1G79580_A_lyrata_MN47_DAPi710H09-ORGi5038-96P151


title: Alveolar macrophages,C57BL/6,Day10,bys,bio rep 3


description: Library name: AT5G25190_A_thaliana_Col-0_DAPi711C05-ORGi5005-96P166


description: Library name: Carub.0001s0116.1_A_thaliana_Col-0_DAPi711C10-ORGi5005-96P361


title: Alveolar macrophages,C57BL/6,Day10,bys,bio rep 2


description: Library name: XP_013602769.1_A_thaliana_Col-0_DAPi711C03-ORGi5005-96P361


description: Library name: Solyc08g068320.3.1_A_thaliana_Col-0_DAPi711C04-ORGi5005-96P361


description: Library name: AT1G25550_A_thaliana_Col-0_DAPi711C01-ORGi5005-96P166


description: Library name: AT3G25990_A_lyrata_MN47_DAPi710H05-ORGi5038-96P151

value: TRIHELIX


title: Alveolar macrophages,C57BL/6,Day10,bys,bio rep 1


description: Library name: XP_013589953.1_A_thaliana_Col-0_DAPi711B12-ORGi5005-96P361


description: Library name: AT5G13080_A_thaliana_Col-0_DAPi711B12-ORGi5005-96P166


description: Library name: AT1G74480_A_lyrata_MN47_DAPi710H04-ORGi5038-96P151

value: RWPRK


title: Neutrophils,Apoe,Day28,inf,bio rep 3

value: Apoe


description: Library name: AT2G30340_A_lyrata_MN47_DAPi710H03-ORGi5038-96P151


description: Library name: AT4G31800_A_thaliana_Col-0_DAPi711C07-ORGi5005-96P166


description: Library name: Solyc07g040920.2.1_A_thaliana_Col-0_DAPi711B11-ORGi5005-96P361

value: MYBRELATED


description: Library name: AT2G30250_A_thaliana_Col-0_DAPi711B11-ORGi5005-96P166

value: WRKY


description: Library name: AT2G18380_A_lyrata_MN47_DAPi710H06-ORGi5038-96P151


title: Neutrophils,Apoe,Day28,inf,bio rep 1


title: Neutrophils,Apoe,Day28,inf,bio rep 2


description: Library name: AT2G46590_A_thaliana_Col-0_DAPi711B10-ORGi5005-96P166


description: Library name: XP_013587350.1_A_thaliana_Col-0_DAPi711B10-ORGi5005-96P361


title: Neutrophils,Apoe,Day28,bys,bio rep 1


description: Library name: AT1G06280_A_lyrata_MN47_DAPi710H02-ORGi5038-96P151


description: Library name: LOC_Os03g21800.1_A_thaliana_Col-0_DAPi711B09-ORGi5005-96P361


description: Library name: AT5G05550_A_lyrata_MN47_DAPi710G12-ORGi5038-96P151


description: Library name: AT1G64620_A_thaliana_Col-0_DAPi711C04-ORGi5005-96P166


title: Neutrophils,Apoe,Day28,bys,bio rep 3


description: Library name: AT5G24110_A_thaliana_Col-0_DAPi711B09-ORGi5005-96P166


title: Monocyte-derived macrophages,Apoe,Day28,inf,bio rep 3


description: Library name: AT2G45480_A_lyrata_MN47_DAPi710G11-ORGi5038-96P151

value: GRF


description: Library name: AT1G34670_A_lyrata_MN47_DAPi710G09-ORGi5038-96P151


title: Neutrophils,Apoe,Day28,bys,bio rep 2


description: Library name: AT3G24120_A_thaliana_Col-0_DAPi711B06-ORGi5005-96P166


description: Library name: Carub.0004s2898.1.p_A_thaliana_Col-0_DAPi711B07-ORGi5005-96P361


description: Library name: AT4G21080_A_lyrata_MN47_DAPi710G07-ORGi5038-96P151


description: Library name: AL1G23550.t1_A_thaliana_Col-0_DAPi711B03-ORGi5005-96P361

value: NAC


description: Library name: AT5G14960_A_lyrata_MN47_DAPi710G08-ORGi5038-96P151


description: Library name: AT1G80840_A_thaliana_Col-0_DAPi711A11-ORGi5005-96P166


description: Library name: LOC_Os01g51154.1_A_thaliana_Col-0_DAPi711A11-ORGi5005-96P361


description: Library name: AL1G53260.t1_A_thaliana_Col-0_DAPi711B01-ORGi5005-96P361


description: Library name: Carub.0004s2291.1_A_thaliana_Col-0_DAPi711A09-ORGi5005-96P361


description: Library name: AT3G12730_A_thaliana_Col-0_DAPi711B08-ORGi5005-96P166


title: Monocyte-derived macrophages,Apoe,Day28,inf,bio rep 1

value: Alveolar macrophage


description: Library name: AT5G67300_A_thaliana_Col-0_DAPi711B01-ORGi5005-96P166


title: Monocyte-derived macrophages,Apoe,Day28,inf,bio rep 2

value: inf


description: Library name: AL8G13510.t2_A_thaliana_Col-0_DAPi711B08-ORGi5005-96P361

value: plant


description: Library name: AL1G11460.t1_A_thaliana_Col-0_DAPi711A10-ORGi5005-96P361


description: Library name: AT5G65310_A_lyrata_MN47_DAPi710G10-ORGi5038-96P151

value: HOMEOBOX


description: Library name: AT5G47370_A_thaliana_Col-0_DAPi711B05-ORGi5005-96P166


title: Monocyte-derived macrophages,Apoe,Day28,bys,bio rep 3

value: bys


description: Library name: Solyc11g064950.3.1_A_thaliana_Col-0_DAPi711A08-ORGi5005-96P361


description: Library name: AT3G04030_A_thaliana_Col-0_DAPi711A08-ORGi5005-96P166


description: Library name: LOC_Os08g37970.1_A_thaliana_Col-0_DAPi711A06-ORGi5005-96P361


description: Library name: AT3G10030_A_lyrata_MN47_DAPi710G03-ORGi5038-96P151


description: Library name: XP_013631386.1_A_thaliana_Col-0_DAPi711A07-ORGi5005-96P361


title: Monocyte-derived macrophages,Apoe,Day28,bys,bio rep 2


description: Library name: AT5G02320_A_lyrata_MN47_DAPi710G02-ORGi5038-96P151


title: Monocyte-derived macrophages,Apoe,Day28,bys,bio rep 1


title: Monocyte-derived macrophages,Apoe,Day10,bys,bio rep 2


description: Library name: AT3G55370_A_thaliana_Col-0_DAPi710H10-ORGi5005-96P151


description: Library name: AT3G56400_A_thaliana_Col-0_DAPi711A04-ORGi5005-96P166


description: Library name: Carub.0007s0775.1_A_thaliana_Col-0_DAPi711A04-ORGi5005-96P361


description: Library name: AT2G15740_A_lyrata_MN47_DAPi710F08-ORGi5038-96P151


description: Library name: AT5G52830_A_lyrata_MN47_DAPi710G06-ORGi5038-96P151


description: Library name: AT1G69570_A_lyrata_MN47_DAPi710F11-ORGi5038-96P151


description: Library name: AT4G01250_A_thaliana_Col-0_DAPi711A02-ORGi5005-96P166


title: Monocyte-derived macrophages,Apoe,Day10,bys,bio rep 1


title: Alveolar macrophages,Apoe,Day10,inf,bio rep 3


description: Library name: AT1G79580_A_thaliana_Col-0_DAPi710H09-ORGi5005-96P151


description: Library name: AT1G09540_A_lyrata_MN47_DAPi710F07-ORGi5038-96P151


description: Library name: AT3G01530_A_thaliana_Col-0_DAPi711A05-ORGi5005-96P166


title: Alveolar macrophages,Apoe,Day10,inf,bio rep 2


description: Library name: AT1G74650_A_thaliana_Col-0_DAPi710H08-ORGi5005-96P151


description: Library name: AT5G22990_A_lyrata_MN47_DAPi710F02-ORGi5038-96P151


title: Monocyte-derived macrophages,Apoe,Day10,bys,bio rep 3


description: Library name: AT2G33550_A_lyrata_MN47_DAPi710F01-ORGi5038-96P151


description: Library name: AT5G17300_A_lyrata_MN47_DAPi710F09-ORGi5038-96P151


description: Library name: AT1G72740_A_thaliana_Col-0_DAPi710H11-ORGi5005-96P151


title: Alveolar macrophages,Apoe,Day10,inf,bio rep 1


description: Library name: AT2G18380_A_thaliana_Col-0_DAPi710H06-ORGi5005-96P151


description: Library name: XP_013635977.1_A_thaliana_Col-0_DAPi710H05-ORGi5005-96P358

value: SBP


description: Library name: AT4G24240_A_thaliana_Col-0_DAPi711A03-ORGi5005-96P166


description: Library name: AT1G28470_A_lyrata_MN47_DAPi710E12-ORGi5038-96P151


description: Library name: AL1G24970.t1_A_thaliana_Col-0_DAPi710H09-ORGi5005-96P358

value: RAV


description: Library name: LOC_Os10g28340.1_A_thaliana_Col-0_DAPi710H04-ORGi5005-96P358

value: HSF


title: Alveolar macrophages,Apoe,Day10,bys,bio rep 3


description: Library name: AT1G74480_A_thaliana_Col-0_DAPi710H04-ORGi5005-96P151


title: Alveolar macrophages,Apoe,Day10,bys,bio rep 2


description: Library name: AT1G06280_A_thaliana_Col-0_DAPi710H02-ORGi5005-96P151


description: Library name: AT2G37590_A_lyrata_MN47_DAPi710E09-ORGi5038-96P151


description: Library name: AT2G45480_A_thaliana_Col-0_DAPi710G11-ORGi5005-96P151


description: Library name: AT2G30340_A_thaliana_Col-0_DAPi710H03-ORGi5005-96P151


description: Library name: Carub.0005s0095.1_A_thaliana_Col-0_DAPi710H08-ORGi5005-96P358

value: BBRBPC


description: Library name: AT5G03150_A_lyrata_MN47_DAPi710E08-ORGi5038-96P151


description: Library name: Carub.0002s2128.1_A_thaliana_Col-0_DAPi710G10-ORGi5005-96P358


title: Processed_recipient

city: xian

first: Cangang

last: Zhang

state: State...

address: Yanta district, xi 'an city, shaanxi province

institute: xian jiaotong university

data_processing:
The 10x Genomics Cell Ranger (7.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar contains counts matrix (stored in the Market Exchange Format for sparse matrices).

source_name: Spleen

extract_protocol:
Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer (2% FBS in PBS), then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK (Ammonium-Chloride-Potassium) Lysing Buffer to remove the red blood cells. After washing with 10 ml cold FACS buffer, the remaining cells were stained with 7AAD (Part 76332; Lot B226294 Biolegend) for 30 min at 4 °C, then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter (BD Biosciences). Sorted YFP+7AAD- cells with a viability higher than 90% were used for 10X genomics scRNA-seq. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).
scRNA libraries were performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics) and were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CD45+ immune cells or CD8+ T cells were sorted from the spleens of C57 mice 5 days post-infection.

value: Spleen

value: CD45+ immune cell

value: LM-OVA Infection


title: Alveolar macrophages,Apoe,Day10,bys,bio rep 1

value: Apoe


description: Library name: AT5G05550_A_thaliana_Col-0_DAPi710G12-ORGi5005-96P151

value: TRIHELIX


description: Library name: AT4G25490_A_lyrata_MN47_DAPi710E07-ORGi5038-96P151


description: Library name: AT2G18550_A_lyrata_MN47_DAPi710E06-ORGi5038-96P151


title: Processed_donor

value: CD8+ T cell


description: Library name: AT5G65310_A_thaliana_Col-0_DAPi710G10-ORGi5005-96P151


description: Library name: AT4G28500_A_lyrata_MN47_DAPi710E05-ORGi5038-96P151


description: Library name: AT5G14960_A_thaliana_Col-0_DAPi710G08-ORGi5005-96P151


description: Library name: XP_013599843.1_A_thaliana_Col-0_DAPi710G08-ORGi5005-96P358


title: NB14 Res2

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60).  GEMM mouse samples were mapped to mm10 and other samples were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (  M22 for GEMM mouse samples; r31, GRCh38.p12 for other samples).
Assembly: GRCh38(hg38) or GRCm38(mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Tumor

growth_protocol: PDX-NB14 tumor were established in CB17 severe combined immunodeficient mice (CB17 scid, Taconic). Transgenic TH-MYCN/ALKF1178L mouse model (GEMM) was provided by Peter Murray and breeded in lab.

extract_protocol:
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: PDX-NB14 mice and MYCN/ALKF1178L mice (GEMM) were treated with vehicle control or indisulam 25 mg/kg according the schedule in the paper. Some tumors from PDX and xenografts developed indisulam resistant. These tumors were isoldated for RNA-seq.

value: Tumor

value: Neuroblastoma

value: indisulam 25mg/kg


description: Library name: AT5G52830_A_thaliana_Col-0_DAPi710G06-ORGi5005-96P151

value: WRKY


description: Library name: AT4G21080_A_thaliana_Col-0_DAPi710G07-ORGi5005-96P151

value: plant


description: Library name: AT1G34670_A_thaliana_Col-0_DAPi710G09-ORGi5005-96P151

value: MYB


description: Library name: Solyc10g018560.2.1_A_thaliana_Col-0_DAPi710G06-ORGi5005-96P358


description: Library name: AT3G12250_A_lyrata_MN47_DAPi710E03-ORGi5038-96P151

value: BZIP


title: NB14 Res1


description: Library name: AL4G46570.t1_A_thaliana_Col-0_DAPi710G05-ORGi5005-96P358

value: SBP


title: NB14 CTRL1

value: Vehicle  treatment


title: NB14 CTRL2


title: wtko_neuts_2

city: Hangzhou

first: Qinyu

last: Luo

state: Zhejiang

address: Yuhangtang road #866

institute: zhejiang university

data_processing:
Low-quality reads were removed using Fastp software (https://github.com/OpenGene/fastp).
HISAT2 (https://ccb.jhu.edu/software/hisat2) was used to map reads to the reference genome of Mus musculus GRCm39.
StringTie (https://ccb.jhu.edu/software/stringtie) was used to estimate the expression levels of all transcripts.
The differentially expressed mRNAs were selected with a fold change > 2 or < 0.5 and with a parametric F test comparing nested linear models (p value < 0.05) by the R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: BALF

extract_protocol:
Total RNA was isolated from BALF neutrophils using TRIzol reagent (Life Technologies, 155896018) following the manufacturer’s protocol.
Libraries for RNA-seq were prepared using the protocol for TruSeq RNA Sample Preparation v.2 (Illumina, RS-122-2001 and RS-122-2002).

value: BALF

value: neutrophils

value: WT

value: E.coli pneumonia model


description: Library name: AT2G42430_A_lyrata_MN47_DAPi710E01-ORGi5038-96P151


description: Library name: Carub.0005s0004.1_A_thaliana_Col-0_DAPi710G01-ORGi5005-96P358


description: Library name: AT1G08320_A_lyrata_MN47_DAPi710D12-ORGi5038-96P151


description: Library name: XP_013591813.1_A_thaliana_Col-0_DAPi710F10-ORGi5005-96P358

value: RWPRK


description: Library name: AT2G26960_A_lyrata_MN47_DAPi710D11-ORGi5038-96P151


description: Library name: AT5G02320_A_thaliana_Col-0_DAPi710G02-ORGi5005-96P151


title: wtko_neuts_1


description: Library name: AT1G28160_A_lyrata_MN47_DAPi710E04-ORGi5038-96P151


description: Library name: AT1G69570_A_thaliana_Col-0_DAPi710F11-ORGi5005-96P151


title: casp1ko_neuts_2


description: Library name: AL5G11070.t1_A_thaliana_Col-0_DAPi710F08-ORGi5005-96P358

value: BBRBPC


description: Library name: AT2G15740_A_thaliana_Col-0_DAPi710F08-ORGi5005-96P151


description: Library name: AT4G01550_A_lyrata_MN47_DAPi710D08-ORGi5038-96P151

value: NAC


title: casp1ko_neuts_1


description: Library name: AT3G10030_A_thaliana_Col-0_DAPi710G03-ORGi5005-96P151

value: TRIHELIX


description: Library name: LOC_Os10g40810.1_A_thaliana_Col-0_DAPi710F06-ORGi5005-96P358


description: Library name: Solyc01g091420.2.1_A_thaliana_Col-0_DAPi710F05-ORGi5005-96P358


description: Library name: LOC_Os08g44050.1_A_thaliana_Col-0_DAPi710F02-ORGi5005-96P358


description: Library name: AT5G22990_A_thaliana_Col-0_DAPi710F02-ORGi5005-96P151


description: Library name: AT3G25990_A_thaliana_Col-0_DAPi710H05-ORGi5005-96P151


description: Library name: AT1G09540_A_thaliana_Col-0_DAPi710F07-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P247

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

organism: Brassica oleracea


description: Library name: AT5G56840_A_lyrata_MN47_DAPi710D01-ORGi5038-96P151

value: MYBRELATED


description: Library name: AL2G34360.t1_A_thaliana_Col-0_DAPi710E10-ORGi5005-96P358


description: Library name: AT5G17300_A_thaliana_Col-0_DAPi710F09-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P247


description: Library name: AT2G33550_A_thaliana_Col-0_DAPi710F01-ORGi5005-96P151


description: Library name: AT1G47655_A_lyrata_MN47_DAPi710D05-ORGi5038-96P151


description: Library name: XP_013620714.1_A_thaliana_Col-0_DAPi710F01-ORGi5005-96P358


description: Library name: AT1G02250_A_lyrata_MN47_DAPi710D09-ORGi5038-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P247


description: Library name: AT1G28470_A_thaliana_Col-0_DAPi710E12-ORGi5005-96P151


description: Library name: AT4G25490_A_thaliana_Col-0_DAPi710E07-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P247


description: Library name: AT2G37590_A_thaliana_Col-0_DAPi710E09-ORGi5005-96P151


description: Library name: AT5G18560_A_lyrata_MN47_DAPi710D07-ORGi5038-96P151


description: Library name: XP_013602065.1_A_thaliana_Col-0_DAPi710E06-ORGi5005-96P358


description: Library name: AT2G18550_A_thaliana_Col-0_DAPi710E06-ORGi5005-96P151

value: HOMEOBOX


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H12-ORGi5021-96P169


description: Library name: AT3G46590_A_lyrata_MN47_DAPi710D06-ORGi5038-96P151


description: Library name: LOC_Os10g07510.1_A_thaliana_Col-0_DAPi710E05-ORGi5005-96P358


description: Library name: AT1G75240_A_lyrata_MN47_DAPi710C12-ORGi5038-96P151

value: ZFHD


description: Library name: AT1G76420_A_lyrata_MN47_DAPi710C10-ORGi5038-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A12-ORGi5021-96P169


description: Library name: AT2G40740_A_lyrata_MN47_DAPi710C11-ORGi5038-96P151

value: WRKY


description: Library name: AT2G01940_A_lyrata_MN47_DAPi710C09-ORGi5038-96P151

value: plant


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709H01-ORGi5021-96P169


description: Library name: AT1G28160_A_thaliana_Col-0_DAPi710E04-ORGi5005-96P151


description: Library name: AT3G12250_A_thaliana_Col-0_DAPi710E03-ORGi5005-96P151


description: Library name: AT4G28500_A_thaliana_Col-0_DAPi710E05-ORGi5005-96P151


description: Library name: AL5G10010.t1_A_thaliana_Col-0_DAPi710E01-ORGi5005-96P358


description: Library name: AT1G08320_A_thaliana_Col-0_DAPi710D12-ORGi5005-96P151


description: Library name: AT2G42430_A_thaliana_Col-0_DAPi710E01-ORGi5005-96P151


description: Library name: AT1G63030_A_lyrata_MN47_DAPi710C07-ORGi5038-96P151


description: Library name: AT3G17730_A_lyrata_MN47_DAPi710C06-ORGi5038-96P151


description: Library name: AT2G26960_A_thaliana_Col-0_DAPi710D11-ORGi5005-96P151

value: MYB


description: Library name: AT5G03150_A_thaliana_Col-0_DAPi710E08-ORGi5005-96P151


description: Library name: Solyc05g009790.1.1_A_thaliana_Col-0_DAPi710D10-ORGi5005-96P358

value: RAV


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H01-ORGi5021-96P166


description: Library name: AT1G02250_A_thaliana_Col-0_DAPi710D09-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A12-ORGi5021-96P166


description: Library name: AT1G77200_A_lyrata_MN47_DAPi710C05-ORGi5038-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711A01-ORGi5021-96P166


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P155


description: Library name: AT5G18560_A_thaliana_Col-0_DAPi710D07-ORGi5005-96P151


description: Library name: AT5G51990_A_lyrata_MN47_DAPi710C04-ORGi5038-96P151


description: Library name: Solyc06g051120.4.1_A_thaliana_Col-0_DAPi710D07-ORGi5005-96P358


description: Library name: AL5G42830.t1_A_thaliana_Col-0_DAPi710D06-ORGi5005-96P358


description: Library name: AT3G46590_A_thaliana_Col-0_DAPi710D06-ORGi5005-96P151


description: Library name: AT3G30210_A_lyrata_MN47_DAPi710C02-ORGi5038-96P151


description: Library name: AT3G10580_A_lyrata_MN47_DAPi710C01-ORGi5038-96P151


description: Library name: Carub.0004s2803.1_A_thaliana_Col-0_DAPi710D05-ORGi5005-96P358


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi711H12-ORGi5021-96P166


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi709A01-ORGi5021-96P169


description: Library name: AT1G47655_A_thaliana_Col-0_DAPi710D05-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P155


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P155


description: Library name: AT5G26170_A_lyrata_MN47_DAPi710B11-ORGi5038-96P151


description: Library name: Solyc02g094290.1.1_A_thaliana_Col-0_DAPi710D04-ORGi5005-96P358

value: TCP


description: Library name: Solyc02g085630.3.1_A_thaliana_Col-0_DAPi710D01-ORGi5005-96P358


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H12-ORGi5021-96P151


description: Library name: AT5G66940_A_lyrata_MN47_DAPi710B10-ORGi5038-96P151


description: Library name: AT1G75240_A_thaliana_Col-0_DAPi710C12-ORGi5005-96P151


description: Library name: AT2G02820_A_lyrata_MN47_DAPi710B09-ORGi5038-96P151


description: Library name: AT5G56840_A_thaliana_Col-0_DAPi710D01-ORGi5005-96P151


description: Library name: XP_013599228.1_A_thaliana_Col-0_DAPi710D02-ORGi5005-96P358


description: Library name: AT4G01550_A_thaliana_Col-0_DAPi710D08-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710A12-ORGi5021-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi710H01-ORGi5021-96P151


description: Library name: AT2G40740_A_thaliana_Col-0_DAPi710C11-ORGi5005-96P151


description: Library name: AT1G63030_A_thaliana_Col-0_DAPi710C07-ORGi5005-96P151


description: Library name: AT1G12630_A_lyrata_MN47_DAPi710B04-ORGi5038-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H01-ORGi5021-96P220


description: Library name: AT3G50410_A_lyrata_MN47_DAPi710B03-ORGi5038-96P151


description: Library name: Solyc05g053240.4.1_A_thaliana_Col-0_DAPi710C06-ORGi5005-96P358

value: SBP


description: Library name: AT1G76420_A_thaliana_Col-0_DAPi710C10-ORGi5005-96P151


description: Library name: AT5G47660_A_lyrata_MN47_DAPi710B06-ORGi5038-96P151


description: Library name: AT2G01940_A_thaliana_Col-0_DAPi710C09-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A01-ORGi5021-96P220


description: Library name: AT1G77200_A_thaliana_Col-0_DAPi710C05-ORGi5005-96P151


description: Library name: LOC_Os01g49830.1_A_thaliana_Col-0_DAPi710C10-ORGi5005-96P358


description: Library name: LOC_Os03g10210.1_A_thaliana_Col-0_DAPi710C01-ORGi5005-96P358


description: Library name: AT3G17730_A_thaliana_Col-0_DAPi710C06-ORGi5005-96P151


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712H12-ORGi5021-96P220


description: Library name: Control_TF_DNA_B_oleracea_TO1000DH3_DAPi712A12-ORGi5021-96P220


description: Library name: AT1G25340_A_lyrata_MN47_DAPi710B01-ORGi5038-96P151


description: Library name: AT2G46270_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P220

value: BZIP


description: Library name: AT5G51990_A_thaliana_Col-0_DAPi710C04-ORGi5005-96P151


description: Library name: AT2G45410_A_lyrata_MN47_DAPi710B02-ORGi5038-96P151


description: Library name: AT5G66940_A_thaliana_Col-0_DAPi710B10-ORGi5005-96P151


description: Library name: LOC_Os01g69980.1_A_thaliana_Col-0_DAPi710C04-ORGi5005-96P358


description: Library name: AT3G30210_A_thaliana_Col-0_DAPi710C02-ORGi5005-96P151


description: Library name: Carub.0001s1299.1_A_thaliana_Col-0_DAPi710B10-ORGi5005-96P358


description: Library name: AT3G10580_A_thaliana_Col-0_DAPi710C01-ORGi5005-96P151


description: Library name: AT5G26170_A_thaliana_Col-0_DAPi710B11-ORGi5005-96P151


description: Library name: AT3G03200_A_lyrata_MN47_DAPi710A10-ORGi5038-96P151


description: Library name: AT1G01250_A_lyrata_MN47_DAPi710B07-ORGi5038-96P151


description: Library name: Carub.0002s1959.1_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P247


description: Library name: AL2G28980.t1_B_oleracea_TO1000DH3_DAPi712H11-ORGi5021-96P247


description: Library name: AT2G47070_B_oleracea_TO1000DH3_DAPi712H10-ORGi5021-96P220


description: Library name: Carub.0006s0445.1_A_thaliana_Col-0_DAPi710B07-ORGi5005-96P358


description: Library name: AT1G01250_A_thaliana_Col-0_DAPi710B07-ORGi5005-96P151


description: Library name: AT2G02820_A_thaliana_Col-0_DAPi710B09-ORGi5005-96P151


description: Library name: AT5G19790_A_lyrata_MN47_DAPi710A07-ORGi5038-96P151


description: Library name: Solyc08g078340.3.1_B_oleracea_TO1000DH3_DAPi712H09-ORGi5021-96P247


description: Library name: AT5G47660_A_thaliana_Col-0_DAPi710B06-ORGi5005-96P151


description: Library name: AL4G44590.t1_A_thaliana_Col-0_DAPi710B05-ORGi5005-96P358


description: Library name: LOC_Os03g61760.1_A_thaliana_Col-0_DAPi710B06-ORGi5005-96P358


description: Library name: AT1G12610_A_lyrata_MN47_DAPi710A11-ORGi5038-96P151


description: Library name: AT1G12630_A_thaliana_Col-0_DAPi710B04-ORGi5005-96P151


description: Library name: AT5G62470_A_lyrata_MN47_DAPi710A08-ORGi5038-96P151


description: Library name: AT2G28810_A_lyrata_MN47_DAPi710A06-ORGi5038-96P151


description: Library name: AT3G50410_A_thaliana_Col-0_DAPi710B03-ORGi5005-96P151


description: Library name: LOC_Os01g17260.2_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P247


description: Library name: Solyc11g022470.2.1_A_thaliana_Col-0_DAPi710B02-ORGi5005-96P358


description: Library name: Carub.0005s0520.1_A_thaliana_Col-0_DAPi710B04-ORGi5005-96P358


description: Library name: AT5G60130_A_lyrata_MN47_DAPi710A04-ORGi5038-96P151


description: Library name: AT5G17300_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P220


description: Library name: AT2G45410_A_thaliana_Col-0_DAPi710B02-ORGi5005-96P151


description: Library name: AT5G62320_A_lyrata_MN47_DAPi710A03-ORGi5038-96P151


description: Library name: AT5G18560_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P220


description: Library name: AT1G25340_A_thaliana_Col-0_DAPi710B01-ORGi5005-96P151


description: Library name: Carub.0003s3279.1_A_thaliana_Col-0_DAPi710B01-ORGi5005-96P358


description: Library name: Solyc03g116010.3.1_A_thaliana_Col-0_DAPi710A11-ORGi5005-96P358


description: Library name: AT3G49530_B_oleracea_TO1000DH3_DAPi712H07-ORGi5021-96P155


description: Library name: XP_013634112.1_B_oleracea_TO1000DH3_DAPi712H08-ORGi5021-96P247


description: Library name: AT1G68320_A_lyrata_MN47_DAPi709H11-ORGi5038-96P169


description: Library name: AL4G45550.t1_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P247


description: Library name: AT3G24050_A_lyrata_MN47_DAPi709H10-ORGi5038-96P169


description: Library name: XP_013637759.1_A_thaliana_Col-0_DAPi710A10-ORGi5005-96P358


description: Library name: AT5G62470_A_thaliana_Col-0_DAPi710A08-ORGi5005-96P151


description: Library name: AT3G03200_A_thaliana_Col-0_DAPi710A10-ORGi5005-96P151


description: Library name: AT3G50410_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P220


description: Library name: AT5G19790_A_thaliana_Col-0_DAPi710A07-ORGi5005-96P151


description: Library name: AT5G11510_B_oleracea_TO1000DH3_DAPi712H06-ORGi5021-96P155


description: Library name: AT1G79180_A_lyrata_MN47_DAPi709H09-ORGi5038-96P169


description: Library name: Carub.0004s2981.1_A_thaliana_Col-0_DAPi710A06-ORGi5005-96P358


description: Library name: AT1G01060_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P220


description: Library name: AT2G28810_A_thaliana_Col-0_DAPi710A06-ORGi5005-96P151


description: Library name: XP_013593496.1_A_thaliana_Col-0_DAPi710A04-ORGi5005-96P358


description: Library name: AT5G08130_A_lyrata_MN47_DAPi709H05-ORGi5038-96P169

value: BHLH


description: Library name: AT5G58850_A_thaliana_Col-0_DAPi710A05-ORGi5005-96P151


description: Library name: AT5G60130_A_thaliana_Col-0_DAPi710A04-ORGi5005-96P151


description: Library name: AT3G60490_A_lyrata_MN47_DAPi710A02-ORGi5038-96P151


description: Library name: AT1G12610_A_thaliana_Col-0_DAPi710A11-ORGi5005-96P151


description: Library name: AT5G61620_B_oleracea_TO1000DH3_DAPi712H05-ORGi5021-96P155


description: Library name: LOC_Os09g12770.1_A_thaliana_Col-0_DAPi710A02-ORGi5005-96P358


description: Library name: Solyc01g102340.3.1_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P247


description: Library name: AT3G60490_A_thaliana_Col-0_DAPi710A02-ORGi5005-96P151


description: Library name: AT5G62320_A_thaliana_Col-0_DAPi710A03-ORGi5005-96P151


description: Library name: AT1G51220_A_lyrata_MN47_DAPi709G12-ORGi5038-96P169


description: Library name: AT3G02940_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P220


description: Library name: AL2G28980.t1_A_thaliana_Col-0_DAPi709H11-ORGi5005-96P354


description: Library name: AT1G71450_A_lyrata_MN47_DAPi709G11-ORGi5038-96P169


description: Library name: AT2G47070_B_oleracea_TO1000DH3_DAPi712H04-ORGi5021-96P155


description: Library name: AT2G46270_A_thaliana_Col-0_DAPi709H11-ORGi5005-96P206


description: Library name: AT1G69180_A_lyrata_MN47_DAPi709G09-ORGi5038-96P169


description: Library name: LOC_Os10g02584.3_A_thaliana_Col-0_DAPi710A09-ORGi5005-96P358


description: Library name: AT2G46270_A_thaliana_Col-0_DAPi709H11-ORGi5005-96P203


description: Library name: AT1G68320_A_thaliana_Col-0_DAPi709H11-ORGi5005-96P169


description: Library name: Carub.0002s1959.1_A_thaliana_Col-0_DAPi709H10-ORGi5005-96P354


description: Library name: AT2G47070_A_thaliana_Col-0_DAPi709H10-ORGi5005-96P206


description: Library name: XP_013629448.1_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P247


description: Library name: AT5G51190_A_lyrata_MN47_DAPi709G07-ORGi5038-96P169


description: Library name: AT5G47230_A_lyrata_MN47_DAPi709G06-ORGi5038-96P169


description: Library name: AT4G36740_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P155


description: Library name: AT1G46768_A_lyrata_MN47_DAPi709H03-ORGi5038-96P169


description: Library name: AT3G24050_A_thaliana_Col-0_DAPi709H10-ORGi5005-96P169


description: Library name: AT2G30250_B_oleracea_TO1000DH3_DAPi712H03-ORGi5021-96P220


description: Library name: Solyc08g078340.3.1_A_thaliana_Col-0_DAPi709H09-ORGi5005-96P354


description: Library name: AT1G34370_A_thaliana_Col-0_DAPi709H09-ORGi5005-96P206


description: Library name: AT1G79180_A_thaliana_Col-0_DAPi709H09-ORGi5005-96P169


description: Library name: AT2G32460_A_lyrata_MN47_DAPi709G05-ORGi5038-96P169


description: Library name: XP_013634112.1_A_thaliana_Col-0_DAPi709H08-ORGi5005-96P354


description: Library name: AT1G50640_A_lyrata_MN47_DAPi709G04-ORGi5038-96P169


description: Library name: AT5G06100_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P155


description: Library name: AT2G22430_B_oleracea_TO1000DH3_DAPi712H02-ORGi5021-96P220


description: Library name: AT5G62020_A_lyrata_MN47_DAPi709G02-ORGi5038-96P169

value: HSF


description: Library name: AT5G17300_A_thaliana_Col-0_DAPi709H08-ORGi5005-96P206


description: Library name: AT5G17300_A_thaliana_Col-0_DAPi709H08-ORGi5005-96P203


description: Library name: LOC_Os01g17260.2_A_thaliana_Col-0_DAPi709H07-ORGi5005-96P354


description: Library name: AT1G29160_A_lyrata_MN47_DAPi709G01-ORGi5038-96P169


description: Library name: XP_013609718.1_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P247


description: Library name: AT5G58850_A_lyrata_MN47_DAPi710A05-ORGi5038-96P151


description: Library name: AT2G47070_A_thaliana_Col-0_DAPi709H10-ORGi5005-96P203


description: Library name: AT5G56110_A_lyrata_MN47_DAPi709F12-ORGi5038-96P169


description: Library name: AT5G18560_A_thaliana_Col-0_DAPi709H07-ORGi5005-96P203


description: Library name: AT5G18560_A_thaliana_Col-0_DAPi709H07-ORGi5005-96P206


description: Library name: AT3G50410_A_thaliana_Col-0_DAPi709H06-ORGi5005-96P206


description: Library name: AL4G45550.t1_A_thaliana_Col-0_DAPi709H06-ORGi5005-96P354


description: Library name: AT1G01060_A_thaliana_Col-0_DAPi709H05-ORGi5005-96P206


description: Library name: AT3G50410_A_thaliana_Col-0_DAPi709H06-ORGi5005-96P203


description: Library name: AT1G01720_A_lyrata_MN47_DAPi709F09-ORGi5038-96P169


description: Library name: AT5G65210_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P155


description: Library name: AT5G64060_A_lyrata_MN47_DAPi709F10-ORGi5038-96P169


description: Library name: AT5G57620_B_oleracea_TO1000DH3_DAPi712G12-ORGi5021-96P155


description: Library name: Solyc03g116890.3.1_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P247


description: Library name: AT5G08130_A_thaliana_Col-0_DAPi709H05-ORGi5005-96P169


description: Library name: AT3G02940_A_thaliana_Col-0_DAPi709H04-ORGi5005-96P206


description: Library name: AT1G49010_A_lyrata_MN47_DAPi709F03-ORGi5038-96P169


description: Library name: XP_013629448.1_A_thaliana_Col-0_DAPi709H03-ORGi5005-96P354


description: Library name: XP_013589913.1_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P247


description: Library name: AT3G02940_A_thaliana_Col-0_DAPi709H04-ORGi5005-96P203


description: Library name: AT5G45300_B_oleracea_TO1000DH3_DAPi712G10-ORGi5021-96P220


description: Library name: AT2G30250_A_thaliana_Col-0_DAPi709H03-ORGi5005-96P206


description: Library name: AT2G30250_A_thaliana_Col-0_DAPi709H03-ORGi5005-96P203


description: Library name: AT3G08500_A_lyrata_MN47_DAPi709F05-ORGi5038-96P169


description: Library name: AT3G01220_A_lyrata_MN47_DAPi709F01-ORGi5038-96P169


description: Library name: LOC_Os10g41200.1_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P247


description: Library name: AT1G46768_A_thaliana_Col-0_DAPi709H03-ORGi5005-96P169


description: Library name: AT1G72740_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P220


description: Library name: AT2G22430_A_thaliana_Col-0_DAPi709H02-ORGi5005-96P206


description: Library name: AT5G09410_B_oleracea_TO1000DH3_DAPi712G11-ORGi5021-96P220

value: CAMTA


description: Library name: AT1G01060_A_thaliana_Col-0_DAPi709H05-ORGi5005-96P203


description: Library name: AT1G19210_A_thaliana_Col-0_DAPi709H02-ORGi5005-96P169


description: Library name: AT2G35530_B_oleracea_TO1000DH3_DAPi712G09-ORGi5021-96P155


description: Library name: AT2G22430_A_thaliana_Col-0_DAPi709H02-ORGi5005-96P203


description: Library name: XP_013609718.1_A_thaliana_Col-0_DAPi709G12-ORGi5005-96P354


description: Library name: AT3G16280_A_lyrata_MN47_DAPi709E11-ORGi5038-96P169


description: Library name: AT4G06746_A_lyrata_MN47_DAPi709E10-ORGi5038-96P169


description: Library name: AL4G38490.t1_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P247


description: Library name: AT1G51220_A_thaliana_Col-0_DAPi709G12-ORGi5005-96P169


description: Library name: AT2G01940_B_oleracea_TO1000DH3_DAPi712G08-ORGi5021-96P220


description: Library name: AT5G09410_A_thaliana_Col-0_DAPi709G11-ORGi5005-96P206


description: Library name: Solyc03g116890.3.1_A_thaliana_Col-0_DAPi709G11-ORGi5005-96P354


description: Library name: AT2G44940_A_lyrata_MN47_DAPi709F02-ORGi5038-96P169


description: Library name: AT5G09410_A_thaliana_Col-0_DAPi709G11-ORGi5005-96P203


description: Library name: Carub.0003s1161.1.p_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P247


description: Library name: AT1G71450_A_thaliana_Col-0_DAPi709G11-ORGi5005-96P169


description: Library name: AT3G57920_A_lyrata_MN47_DAPi709E12-ORGi5038-96P169


description: Library name: AT5G02840_A_lyrata_MN47_DAPi709E07-ORGi5038-96P169


description: Library name: AT5G45300_A_thaliana_Col-0_DAPi709G10-ORGi5005-96P206


description: Library name: AT5G45300_A_thaliana_Col-0_DAPi709G10-ORGi5005-96P203


description: Library name: AT2G20400_A_lyrata_MN47_DAPi709E09-ORGi5038-96P169


description: Library name: AT5G19790_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P220


description: Library name: AT4G23550_A_lyrata_MN47_DAPi709E05-ORGi5038-96P169


description: Library name: AT5G02320_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P220


description: Library name: AT1G72740_A_thaliana_Col-0_DAPi709G09-ORGi5005-96P203


description: Library name: AT4G01280_A_lyrata_MN47_DAPi709E03-ORGi5038-96P169


description: Library name: AL4G38490.t1_A_thaliana_Col-0_DAPi709G08-ORGi5005-96P354


description: Library name: AT2G01940_A_thaliana_Col-0_DAPi709G08-ORGi5005-96P206


description: Library name: AT4G25470_A_lyrata_MN47_DAPi709D11-ORGi5038-96P169


description: Library name: AT1G69180_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P220


description: Library name: AT1G01060_A_lyrata_MN47_DAPi709D10-ORGi5038-96P169


description: Library name: AT1G69180_A_thaliana_Col-0_DAPi709G09-ORGi5005-96P169


description: Library name: XP_013589913.1_A_thaliana_Col-0_DAPi709G10-ORGi5005-96P354


description: Library name: AT5G25810_A_lyrata_MN47_DAPi709E04-ORGi5038-96P169


description: Library name: AT5G19790_A_thaliana_Col-0_DAPi709G07-ORGi5005-96P206


description: Library name: AT5G16820_B_oleracea_TO1000DH3_DAPi712G05-ORGi5021-96P155


description: Library name: Carub.0003s1161.1.p_A_thaliana_Col-0_DAPi709G07-ORGi5005-96P354


description: Library name: AT4G34590_B_oleracea_TO1000DH3_DAPi712G07-ORGi5021-96P155


description: Library name: LOC_Os10g41200.1_A_thaliana_Col-0_DAPi709G09-ORGi5005-96P354


description: Library name: AT5G51190_A_thaliana_Col-0_DAPi709G07-ORGi5005-96P169


description: Library name: AT5G54230_A_lyrata_MN47_DAPi709D07-ORGi5038-96P169


description: Library name: AT5G19790_A_thaliana_Col-0_DAPi709G07-ORGi5005-96P203


description: Library name: AT2G01930_A_lyrata_MN47_DAPi709D06-ORGi5038-96P169


description: Library name: LOC_Os01g18240.1_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P247


description: Library name: AT5G02320_A_thaliana_Col-0_DAPi709G06-ORGi5005-96P206


description: Library name: AT1G46768_B_oleracea_TO1000DH3_DAPi712G04-ORGi5021-96P220


description: Library name: AT5G47230_A_thaliana_Col-0_DAPi709G06-ORGi5005-96P169


description: Library name: AT5G09410_B_oleracea_TO1000DH3_DAPi712G06-ORGi5021-96P155


description: Library name: AT1G72740_A_thaliana_Col-0_DAPi709G09-ORGi5005-96P206


description: Library name: AT5G02320_A_thaliana_Col-0_DAPi709G06-ORGi5005-96P203


description: Library name: AT5G62940_A_lyrata_MN47_DAPi709D05-ORGi5038-96P169


description: Library name: AT1G80840_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P220


description: Library name: AT1G69180_A_thaliana_Col-0_DAPi709G05-ORGi5005-96P206


description: Library name: AT1G69180_A_thaliana_Col-0_DAPi709G05-ORGi5005-96P203


description: Library name: AT4G25480_A_lyrata_MN47_DAPi709D03-ORGi5038-96P169


description: Library name: AT2G01940_A_thaliana_Col-0_DAPi709G08-ORGi5005-96P203


description: Library name: AT1G46768_A_thaliana_Col-0_DAPi709G04-ORGi5005-96P206


description: Library name: AT1G50640_A_thaliana_Col-0_DAPi709G04-ORGi5005-96P169


description: Library name: AT1G46768_A_thaliana_Col-0_DAPi709G04-ORGi5005-96P203


description: Library name: AT3G50060_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P220


description: Library name: AT2G32460_A_thaliana_Col-0_DAPi709G05-ORGi5005-96P169


description: Library name: AL7G19010.t1_A_thaliana_Col-0_DAPi709G03-ORGi5005-96P354


description: Library name: AT2G40260_A_lyrata_MN47_DAPi709C12-ORGi5038-96P169


description: Library name: AT1G36060_A_lyrata_MN47_DAPi709D02-ORGi5038-96P169


description: Library name: AT1G80840_A_thaliana_Col-0_DAPi709G03-ORGi5005-96P206


description: Library name: AT5G10030_A_lyrata_MN47_DAPi709C11-ORGi5038-96P169


description: Library name: AT1G80840_A_thaliana_Col-0_DAPi709G03-ORGi5005-96P203


description: Library name: AT4G01500_B_oleracea_TO1000DH3_DAPi712G02-ORGi5021-96P155


description: Library name: AT1G18330_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P220


description: Library name: Carub.0008s2269.1_A_thaliana_Col-0_DAPi709G02-ORGi5005-96P354

value: ARF


description: Library name: AT3G50060_A_thaliana_Col-0_DAPi709G02-ORGi5005-96P203


description: Library name: AT3G50060_A_thaliana_Col-0_DAPi709G02-ORGi5005-96P206


description: Library name: AT5G62020_A_thaliana_Col-0_DAPi709G02-ORGi5005-96P169


description: Library name: AT1G18330_A_thaliana_Col-0_DAPi709G01-ORGi5005-96P206


description: Library name: AT4G18450_B_oleracea_TO1000DH3_DAPi712G01-ORGi5021-96P155


description: Library name: AT1G13600_B_oleracea_TO1000DH3_DAPi712F12-ORGi5021-96P155


description: Library name: AT1G53230_A_lyrata_MN47_DAPi709C08-ORGi5038-96P169


description: Library name: AT3G11280_A_lyrata_MN47_DAPi709C06-ORGi5038-96P169


description: Library name: AT1G32150_B_oleracea_TO1000DH3_DAPi712G03-ORGi5021-96P155


description: Library name: LOC_Os09g25060.1_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P247


description: Library name: AT1G29160_A_thaliana_Col-0_DAPi709G01-ORGi5005-96P169


description: Library name: AT1G18330_A_thaliana_Col-0_DAPi709G01-ORGi5005-96P203


description: Library name: AL3G51890.t2_A_thaliana_Col-0_DAPi709F12-ORGi5005-96P354


description: Library name: AT3G02940_A_lyrata_MN47_DAPi709C05-ORGi5038-96P169


description: Library name: AT1G76880_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P220


description: Library name: AT5G56110_A_thaliana_Col-0_DAPi709F12-ORGi5005-96P169


description: Library name: AT3G01970_A_lyrata_MN47_DAPi709C04-ORGi5038-96P169


description: Library name: LOC_Os09g25060.1_A_thaliana_Col-0_DAPi709F11-ORGi5005-96P354


description: Library name: AT3G18400_A_lyrata_MN47_DAPi709C10-ORGi5038-96P169


description: Library name: AT1G76880_A_thaliana_Col-0_DAPi709F11-ORGi5005-96P206


description: Library name: AL2G32420.t2_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P247


description: Library name: AL2G32420.t2_A_thaliana_Col-0_DAPi709F10-ORGi5005-96P354


description: Library name: AT4G14770_A_thaliana_Col-0_DAPi709F10-ORGi5005-96P203

value: CPP


description: Library name: AT5G03790_A_lyrata_MN47_DAPi709B12-ORGi5038-96P169


description: Library name: AT3G15170_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P155

value: NAC


description: Library name: Carub.0008s0039.1_A_thaliana_Col-0_DAPi709F09-ORGi5005-96P354


description: Library name: AT5G64060_A_thaliana_Col-0_DAPi709F10-ORGi5005-96P169


description: Library name: AT2G45480_A_thaliana_Col-0_DAPi709F09-ORGi5005-96P206

value: GRF


description: Library name: AT2G45480_A_thaliana_Col-0_DAPi709F09-ORGi5005-96P203


description: Library name: AT2G24430_A_lyrata_MN47_DAPi709B10-ORGi5038-96P169


description: Library name: AT3G52440_A_lyrata_MN47_DAPi709B11-ORGi5038-96P169


description: Library name: AT1G19210_A_lyrata_MN47_DAPi709H02-ORGi5038-96P169


description: Library name: AT1G01720_A_thaliana_Col-0_DAPi709F09-ORGi5005-96P169


description: Library name: AT2G02820_A_thaliana_Col-0_DAPi709F08-ORGi5005-96P203


description: Library name: AT2G02820_A_thaliana_Col-0_DAPi709F08-ORGi5005-96P206


description: Library name: AT1G76880_A_thaliana_Col-0_DAPi709F11-ORGi5005-96P203

value: TRIHELIX


description: Library name: AT2G45480_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P220


description: Library name: AT2G02820_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P220


description: Library name: AT1G22810_A_lyrata_MN47_DAPi709B04-ORGi5038-96P169


description: Library name: AT3G27010_A_lyrata_MN47_DAPi709C02-ORGi5038-96P169


description: Library name: AT4G38000_A_lyrata_MN47_DAPi709B02-ORGi5038-96P169


description: Library name: AT1G03800_A_lyrata_MN47_DAPi709C01-ORGi5038-96P169


description: Library name: XP_013586407.1_A_thaliana_Col-0_DAPi709F07-ORGi5005-96P354


description: Library name: AT5G11260_B_oleracea_TO1000DH3_DAPi712F11-ORGi5021-96P155


description: Library name: AT4G14770_B_oleracea_TO1000DH3_DAPi712F10-ORGi5021-96P220


description: Library name: AT5G52830_A_thaliana_Col-0_DAPi709F07-ORGi5005-96P203


description: Library name: AT5G07680_B_oleracea_TO1000DH3_DAPi712F08-ORGi5021-96P155


description: Library name: AT5G52830_A_thaliana_Col-0_DAPi709F07-ORGi5005-96P206


description: Library name: AT5G65130_A_lyrata_MN47_DAPi709B01-ORGi5038-96P169


description: Library name: Carub.0008s0039.1_B_oleracea_TO1000DH3_DAPi712F09-ORGi5021-96P247

value: MYBRELATED


description: Library name: XP_013586407.1_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P247


description: Library name: AT2G45420_A_thaliana_Col-0_DAPi709F06-ORGi5005-96P206


description: Library name: AT2G01060_A_thaliana_Col-0_DAPi709F05-ORGi5005-96P206


description: Library name: AT5G45580_A_lyrata_MN47_DAPi709A11-ORGi5038-96P169


description: Library name: AT5G52830_B_oleracea_TO1000DH3_DAPi712F07-ORGi5021-96P220


description: Library name: AT2G01060_A_thaliana_Col-0_DAPi709F05-ORGi5005-96P203


description: Library name: AT5G52020_A_lyrata_MN47_DAPi709A10-ORGi5038-96P169


description: Library name: AT3G08500_A_thaliana_Col-0_DAPi709F05-ORGi5005-96P169


description: Library name: AT3G28920_A_lyrata_MN47_DAPi709A08-ORGi5038-96P169

value: ZFHD


description: Library name: AT2G45420_B_oleracea_TO1000DH3_DAPi712F06-ORGi5021-96P220


description: Library name: Solyc08g079120.3.1_A_thaliana_Col-0_DAPi709F03-ORGi5005-96P354


description: Library name: AT4G25480_A_thaliana_Col-0_DAPi709F04-ORGi5005-96P203


description: Library name: AT4G14770_A_thaliana_Col-0_DAPi709F10-ORGi5005-96P206


description: Library name: AT4G25480_B_oleracea_TO1000DH3_DAPi712F04-ORGi5021-96P220


description: Library name: AT2G01060_B_oleracea_TO1000DH3_DAPi712F05-ORGi5021-96P220


description: Library name: Solyc08g079120.3.1_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P247


description: Library name: AT1G49010_A_thaliana_Col-0_DAPi709F03-ORGi5005-96P169


description: Library name: AT1G33240_A_thaliana_Col-0_DAPi709F03-ORGi5005-96P203


description: Library name: AT2G45420_A_thaliana_Col-0_DAPi709F06-ORGi5005-96P203


description: Library name: AT4G31800_A_thaliana_Col-0_DAPi709F02-ORGi5005-96P206

value: WRKY


description: Library name: AT5G07310_A_lyrata_MN47_DAPi709A05-ORGi5038-96P169

value: plant


description: Library name: AT5G52660_A_lyrata_MN47_DAPi709A06-ORGi5038-96P169


description: Library name: AT4G31800_A_thaliana_Col-0_DAPi709F02-ORGi5005-96P203


description: Library name: AT1G33240_B_oleracea_TO1000DH3_DAPi712F03-ORGi5021-96P220


description: Library name: AT2G44940_A_thaliana_Col-0_DAPi709F02-ORGi5005-96P169


description: Library name: Solyc04g078640.3.1_A_thaliana_Col-0_DAPi709F01-ORGi5005-96P354


description: Library name: AT4G31800_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P220


description: Library name: AT5G13910_A_lyrata_MN47_DAPi709A04-ORGi5038-96P169


description: Library name: AT5G47390_A_thaliana_Col-0_DAPi709F01-ORGi5005-96P206


description: Library name: AT3G01220_A_thaliana_Col-0_DAPi709F01-ORGi5005-96P169

value: HOMEOBOX


description: Library name: AT5G47390_A_thaliana_Col-0_DAPi709F01-ORGi5005-96P203


description: Library name: AT5G13790_B_oleracea_TO1000DH3_DAPi712F02-ORGi5021-96P155

value: MADS


description: Library name: AT1G33240_A_thaliana_Col-0_DAPi709F03-ORGi5005-96P206


description: Library name: AT4G25480_A_thaliana_Col-0_DAPi709F04-ORGi5005-96P206


description: Library name: AT3G09600_A_lyrata_MN47_DAPi709A02-ORGi5038-96P169


description: Library name: AT1G28370_A_lyrata_MN47_DAPi709A07-ORGi5038-96P169


description: Library name: Solyc04g078640.3.1_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P247


description: Library name: Solyc05g007180.3.1_A_thaliana_Col-0_DAPi709E12-ORGi5005-96P354


description: Library name: AT1G52880_A_thaliana_Col-0_DAPi709E12-ORGi5005-96P203


description: Library name: AT5G47390_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P220


title: SRSF2_config2

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
Library name: SRSF2_config2
RBR-scan plasmid pool for human SRSF2

library_source: other

data_processing:
Bases were called using Dorado in mode dna_r10.4.1_e8.1_400bps_sup. Reads were subsequently filtered and aligned to the DNA sequence for MS2 coat protein or SRSF2. Mutation frequencies were calculated as the percentage of reads containing the correct mutant codon out of the total reads associated with each barcode. Reads were further categorized as the desired mutation, wild type, or other (i.e., neither mutant nor WT). Mutants linked to barcodes with ≤10 reads or that contained ≥ 50% of reads sourced from WT were excluded from mass spectrometry analysis. In some cases, barcodes associated with mutations outside their expected pool were reassigned to the mutation they were linked to.
Assembly: MS2CP or SRSF2 reference sequence
Supplementary files format and content: Table describes source of reads associated with each peptide barcode (freuqency of WT, expected mutant, other)

molecule: other

organism: Escherichia coli

source_name: NEB 10 beta E coli

extract_protocol:
Plasmids were extracted from an E. coli culture containing an average of 82,500 colony forming units providing a 875x coverage for each individual mutant within a pool of 96 mutants. Plasmid midi preps were prepared using manufacturer’s protocol (Macherey-Nagel). Plasmid quality was confirmed by PCR amplifying the plasmid backbone from the empty vector and the RBR-scan pools. Libraries for nanopore were amplified from the plasmid pool with Q5 Hot Start polymerase using the external primers from OE-PCR. Libraries for nanopore were prepared with the Native Barcoding Kit according to manufacturer’s instructions with minor adjustments (Oxford Nanopore Technologies, SQK-NBD114.24). 200 fmol of PCR product from RBR-scan pools was end-repaired using End Repair Enzyme Mix (Enzymatics, Y9140-LC-L), tailed with deoxyadenine using Klenow (Enzymatics, P7010-HC-L), and ligated to nanopore Native Barcodes. nanopore libraries were pooled, size selected by SPRI (1.0x clean) and ligated to the nanopore sequencing adapter. Residual sequencing adapter was removed by SPRI. DNA was quantified by Qubit fluorimetry (Thermo Fisher) and 10–20 fmol was loaded onto the flow cell (Oxford Nanopore Technologies, FLO-MIN114).
Oxford Nanopore Technologies, SQK-NBD114.24

value: NEB 10 beta E coli


title: SRSF2_config1

description:
Library name: SRSF2_config1
RBR-scan plasmid pool for human SRSF2


description: Library name: AT1G20980_A_thaliana_Col-0_DAPi709E11-ORGi5005-96P203

value: SBP


description: Library name: AT1G20980_A_thaliana_Col-0_DAPi709E11-ORGi5005-96P206


description: Library name: Solyc05g007180.3.1_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P247


description: Library name: AT3G16280_A_thaliana_Col-0_DAPi709E11-ORGi5005-96P169


title: MS2CP_config2

description:
Library name: MS2CP_config2
RBR-scan plasmid pool for MS2 coat protein


description: Library name: Carub.0002s2670.1_A_thaliana_Col-0_DAPi709E11-ORGi5005-96P354


description: Library name: AT4G31060_A_lyrata_MN47_DAPi709A03-ORGi5038-96P169


title: MS2CP_config1

description:
Library name: MS2CP_config1
RBR-scan plasmid pool for MS2 coat protein


description: Library name: AT1G20910_B_oleracea_TO1000DH3_DAPi712F01-ORGi5021-96P155

value: ARID


description: Library name: Solyc10g005080.3.1_A_thaliana_Col-0_DAPi709E10-ORGi5005-96P354


description: Library name: AT1G52880_B_oleracea_TO1000DH3_DAPi712E12-ORGi5021-96P220


description: Library name: AT4G17980_A_thaliana_Col-0_DAPi709E10-ORGi5005-96P203


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712H12-ORGi5037-96P247

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: 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


description: Library name: AT4G06746_A_thaliana_Col-0_DAPi709E10-ORGi5005-96P169


description: Library name: AT4G17980_A_thaliana_Col-0_DAPi709E10-ORGi5005-96P206


description: Library name: Carub.0002s2670.1_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P247


description: Library name: AT3G57920_A_thaliana_Col-0_DAPi709E12-ORGi5005-96P169


description: Library name: AT2G20400_A_thaliana_Col-0_DAPi709E09-ORGi5005-96P169


description: Library name: AT5G14960_A_thaliana_Col-0_DAPi709E08-ORGi5005-96P206


description: Library name: AT1G20980_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P220


description: Library name: XP_013615900.1_A_thaliana_Col-0_DAPi709E09-ORGi5005-96P354


description: Library name: AT5G14960_A_thaliana_Col-0_DAPi709E08-ORGi5005-96P203


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712H01-ORGi5037-96P247


description: Library name: AT4G10350_B_oleracea_TO1000DH3_DAPi712E11-ORGi5021-96P155


description: Library name: AL3G23910.t2_A_thaliana_Col-0_DAPi709E07-ORGi5005-96P354

value: BZIP


description: Library name: AT2G18550_A_thaliana_Col-0_DAPi709E07-ORGi5005-96P206


description: Library name: Solyc10g005080.3.1_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P247


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712A01-ORGi5037-96P247


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi709H12-ORGi5037-96P169


description: Library name: AT2G18550_A_thaliana_Col-0_DAPi709E07-ORGi5005-96P203


description: Library name: AT4G17980_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P220


description: Library name: AT5G56110_A_thaliana_Col-0_DAPi709E06-ORGi5005-96P206

value: MYB


description: Library name: AT5G02840_A_thaliana_Col-0_DAPi709E07-ORGi5005-96P169


description: Library name: AT5G56110_A_thaliana_Col-0_DAPi709E06-ORGi5005-96P203


description: Library name: AT3G60530_A_thaliana_Col-0_DAPi709E05-ORGi5005-96P206


description: Library name: AT5G66300_B_oleracea_TO1000DH3_DAPi712E10-ORGi5021-96P155


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi709A12-ORGi5037-96P169


description: Library name: XP_013615900.1_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P247


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi709H01-ORGi5037-96P169


description: Library name: AT4G23550_A_thaliana_Col-0_DAPi709E05-ORGi5005-96P169


description: Library name: AT5G62020_A_thaliana_Col-0_DAPi709E04-ORGi5005-96P206

value: HSF


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi712A12-ORGi5037-96P247


description: Library name: AT3G15500_B_oleracea_TO1000DH3_DAPi712E09-ORGi5021-96P155


description: Library name: AT5G62020_A_thaliana_Col-0_DAPi709E04-ORGi5005-96P203


description: Library name: AT5G14960_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P220


description: Library name: AT5G25810_A_thaliana_Col-0_DAPi709E04-ORGi5005-96P169


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi709A01-ORGi5037-96P169


description: Library name: AT1G75390_B_oleracea_TO1000DH3_DAPi712E08-ORGi5021-96P155


description: Library name: AT5G64750_A_thaliana_Col-0_DAPi709E03-ORGi5005-96P206


description: Library name: Control_TF_DNA_C_rubella_Monte_Gargano_DAPi711H01-ORGi5037-96P166


description: Library name: LOC_Os02g42970.1_A_thaliana_Col-0_DAPi709E03-ORGi5005-96P354