description: Library name: Solyc02g085630.3.1_O_sativa_Nipponbare_DAPi710D01-ORGi5010-96P358

value: HOMEOBOX


title: MSR-dCas9-Activator MEF, timecourse, post-induction 12h, rep2

status: Public on Jun 05 2025

type: SRA

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Library name: vpr_12_2
Illumina HiSeq 3000

library_source: transcriptomic

data_processing:
Unprocessed reads were first quality and adapter trimmed using cutadapt55 version 1.8.1 using a quality threshold of 20. Reads were then aligned to the GRCm38 genome from Ensembl using STAR56 version 2.5.2b, with settings as recommended by TEtranscripts57. Both repeats and genes were then quantified using TEtranscripts version 2.0.3
Assembly: mm10
Supplementary files format and content: countData.tsv

molecule: total RNA

organism: Mus musculus

source_name: mouse embryonic fibroblast

growth_protocol: Cells were maintained in high glucose DMEM containing 10% tet-free FBS, 2 mM L-glutamine, 0.1 mM b-mercaptoethanol, 1x non-essential amino acids, 1 mM sodium pyruvate, and 400 mg/ml hygromycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRI Reagent and ethanol precipitated. 10 ug of total RNA was further processed to remove the remaining DNA with TURBO DNase and column purified prior to library construction.
Total RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020598) following manufacturer's protocol.

treatment_protocol: MSR-dCas9-Activator MEF cells were treated with 10 ng/ml doxycycline for 6 hrs, MSR-dCas9-Repressor MEF cells were treated with 100 ng/ml doxycycline for 24 hrs, and MSR-dCas9-Control MEF cells were treated with 10 ng/ml doxycycline for 24 hrs.

tag: cell type

value: mouse embryonic fibroblast

tag: genotype

value: inducible expression of MSR-dCas9-Activator

tag: treatment

value: post-induction, fresh media, 12 hr


title: p26688_28474/131

city: Zurich

first: Christelle

last: Le Foll

address: Winterthurerstrasse 260

department: Vetsuisse faculty

country: Switzerland

institute: Univeristy Of Zurich

description: Library name: Brain_region_131

data_processing:
Trimming performed with fastp v0.20
Transcript abundance estimation performed with kallisto v0.46.1
Assembly: GRCm39
Supplementary files format and content: tab-delimited transcript abundances

source_name: Brain tissue

extract_protocol:
mRNA was extracted from the brain punches with the reliaprep promega tissue kit (Z6212)
The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20.

tag: tissue

value: Brain tissue

value: ARC

value: sCT 150 nmol/kg


title: MSR-dCas9-Activator MEF, timecourse, post-induction 12h, rep3

description:
Library name: vpr_12_3
Illumina HiSeq 3000


city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

country: USA

institute: DOE Joint Genome Institute

description: Library name: LOC_Os01g49830.1_O_sativa_Nipponbare_DAPi710C10-ORGi5010-96P358

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: Oryza sativa Nipponbare: MSU via Phytozome v7.0
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: Oryza sativa

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.

value: plant

value: Nipponbare

tag: tf id

tag: tf family

value: RAV

tag: multidap sample_id

tag: 96 well_plate_id

tag: tf source_species


description: Library name: LOC_Os01g69980.1_O_sativa_Nipponbare_DAPi710C04-ORGi5010-96P358

value: TCP


title: MSR-dCas9-Activator MEF, timecourse, post-induction 12h, rep1

description:
Library name: vpr_12_1
Illumina HiSeq 3000


description: Library name: LOC_Os03g10210.1_O_sativa_Nipponbare_DAPi710C01-ORGi5010-96P358


description: Library name: AL5G42830.t1_O_sativa_Nipponbare_DAPi710D06-ORGi5010-96P358


description: Library name: Carub.0001s1299.1_O_sativa_Nipponbare_DAPi710B10-ORGi5010-96P358


title: MSR-dCas9-Activator MEF, timecourse, post-induction 6h, rep3

description:
Library name: vpr_6_3
Illumina HiSeq 3000

value: post-induction, fresh media, 6 hr


title: MSR-dCas9-Activator MEF, timecourse, post-induction 6h, rep2

description:
Library name: vpr_6_2
Illumina HiSeq 3000


title: p26688_28474/129

description: Library name: Brain_region_129

value: AM833 0.3 nmol/kg


description: Library name: LOC_Os03g61760.1_O_sativa_Nipponbare_DAPi710B06-ORGi5010-96P358

value: SBP


description: Library name: Carub.0006s0445.1_O_sativa_Nipponbare_DAPi710B07-ORGi5010-96P358

value: TRIHELIX


description: Library name: Carub.0005s0520.1_O_sativa_Nipponbare_DAPi710B04-ORGi5010-96P358


description: Library name: AL4G44590.t1_O_sativa_Nipponbare_DAPi710B05-ORGi5010-96P358


description: Library name: Solyc11g022470.2.1_O_sativa_Nipponbare_DAPi710B02-ORGi5010-96P358


description: Library name: Carub.0003s3279.1_O_sativa_Nipponbare_DAPi710B01-ORGi5010-96P358


title: MSR-dCas9-Activator MEF, timecourse, post-induction 3h, rep3

description:
Library name: vpr_3_3
Illumina HiSeq 3000

value: post-induction, fresh media, 3 hr


title: p26688_28474/127

description: Library name: Brain_region_127


description: Library name: Solyc05g053240.4.1_O_sativa_Nipponbare_DAPi710C06-ORGi5010-96P358


description: Library name: XP_013637759.1_O_sativa_Nipponbare_DAPi710A10-ORGi5010-96P358


title: p26688_28474/124

description: Library name: Brain_region_124


title: p26688_28474/13

description: Library name: Brain_region_13

value: AP


title: p26688_28474/126

description: Library name: Brain_region_126


description: Library name: LOC_Os10g02584.3_O_sativa_Nipponbare_DAPi710A09-ORGi5010-96P358

value: BBRBPC


description: Library name: Carub.0004s2981.1_O_sativa_Nipponbare_DAPi710A06-ORGi5010-96P358


title: p26688_28474/122

description: Library name: Brain_region_122

value: Vehicle


description: Library name: XP_013593496.1_O_sativa_Nipponbare_DAPi710A04-ORGi5010-96P358


title: MSR-dCas9-Activator MEF, timecourse, post-induction 3h, rep1

description:
Library name: vpr_3_1
Illumina HiSeq 3000

value: mouse embryonic fibroblast

value: inducible expression of MSR-dCas9-Activator


description: Library name: LOC_Os09g12770.1_O_sativa_Nipponbare_DAPi710A02-ORGi5010-96P358


title: MSR-dCas9-Activator MEF, timecourse, induced, rep3

description:
Library name: vpr_0_3
Illumina HiSeq 3000

value: 10 ng/ml doxycycline, 6 hr


title: MSR-dCas9-Activator MEF, timecourse, post-induction 6h, rep1

description:
Library name: vpr_6_1
Illumina HiSeq 3000


description: Library name: Carub.0002s1959.1_O_sativa_Nipponbare_DAPi709H10-ORGi5010-96P354

value: MYBRELATED


title: MSR-dCas9-Activator MEF, timecourse, induced, rep2

description:
Library name: vpr_0_2
Illumina HiSeq 3000


description: Library name: AL2G28980.t1_O_sativa_Nipponbare_DAPi709H11-ORGi5010-96P354

value: HOMEOBOX


description: Library name: Solyc08g078340.3.1_O_sativa_Nipponbare_DAPi709H09-ORGi5010-96P354

value: plant


title: p26688_28474/121

description: Library name: Brain_region_121

value: Brain tissue

value: ARC


description: Library name: XP_013634112.1_O_sativa_Nipponbare_DAPi709H08-ORGi5010-96P354

value: Nipponbare

value: BZIP


title: p26688_28474/128

description: Library name: Brain_region_128

value: AM833 0.3 nmol/kg


description: Library name: Solyc03g116010.3.1_O_sativa_Nipponbare_DAPi710A11-ORGi5010-96P358

value: RWPRK


title: MSR-dCas9-Activator MEF, timecourse, induced, rep1

description:
Library name: vpr_0_1
Illumina HiSeq 3000


title: MSR-dCas9-Activator MEF, timecourse, post-induction 3h, rep2

description:
Library name: vpr_3_2
Illumina HiSeq 3000


title: p26688_28474/119

description: Library name: Brain_region_119


description: Library name: LOC_Os01g17260.2_O_sativa_Nipponbare_DAPi709H07-ORGi5010-96P354


description: Library name: AL4G45550.t1_O_sativa_Nipponbare_DAPi709H06-ORGi5010-96P354


description: Library name: XP_013609718.1_O_sativa_Nipponbare_DAPi709G12-ORGi5010-96P354


title: p26688_28474/116

description: Library name: Brain_region_116


title: MSR-dCas9-Activator MEF, timecourse, uninduced, rep2

description:
Library name: vpr_-24_2
Illumina HiSeq 3000

value: untreated


title: p26688_28474/115

description: Library name: Brain_region_115

value: sCT 150 nmol/kg


title: MSR-dCas9-Activator MEF, timecourse, uninduced, rep1

description:
Library name: vpr_-24_1
Illumina HiSeq 3000


description: Library name: XP_013589913.1_O_sativa_Nipponbare_DAPi709G10-ORGi5010-96P354


description: Library name: LOC_Os10g41200.1_O_sativa_Nipponbare_DAPi709G09-ORGi5010-96P354


title: p26688_28474/114

description: Library name: Brain_region_114


description: Library name: AL4G38490.t1_O_sativa_Nipponbare_DAPi709G08-ORGi5010-96P354


description: Library name: AL7G19010.t1_O_sativa_Nipponbare_DAPi709G03-ORGi5010-96P354

value: MYB


title: p26688_28474/113

description: Library name: Brain_region_113


description: Library name: Carub.0003s1161.1.p_O_sativa_Nipponbare_DAPi709G07-ORGi5010-96P354


title: p26688_28474/118

description: Library name: Brain_region_118


description: Library name: LOC_Os09g25060.1_O_sativa_Nipponbare_DAPi709F11-ORGi5010-96P354

value: WRKY


description: Library name: AL3G51890.t2_O_sativa_Nipponbare_DAPi709F12-ORGi5010-96P354


title: MSR-dCas9-Control MEF, timecourse, post-induction 24h, rep2

description:
Library name: dcas9_24_2
Illumina HiSeq 3000

value: inducible expression of MSR-dCas9-Control

value: post-induction, fresh media, 24 hr


description: Library name: XP_013629448.1_O_sativa_Nipponbare_DAPi709H03-ORGi5010-96P354


description: Library name: Carub.0008s0039.1_O_sativa_Nipponbare_DAPi709F09-ORGi5010-96P354


description: Library name: Carub.0008s2269.1_O_sativa_Nipponbare_DAPi709G02-ORGi5010-96P354

value: ARF


title: MSR-dCas9-Activator MEF, timecourse, uninduced, rep3

description:
Library name: vpr_-24_3
Illumina HiSeq 3000

value: mouse embryonic fibroblast

value: inducible expression of MSR-dCas9-Activator


description: Library name: AL2G32420.t2_O_sativa_Nipponbare_DAPi709F10-ORGi5010-96P354

value: MYBRELATED


title: MSR-dCas9-Control MEF, timecourse, post-induction 12h, rep3

description:
Library name: dcas9_12_3
Illumina HiSeq 3000

value: post-induction, fresh media, 12 hr


title: MSR-dCas9-Control MEF, timecourse, post-induction 24h, rep1

description:
Library name: dcas9_24_1
Illumina HiSeq 3000


description: Library name: XP_013586407.1_O_sativa_Nipponbare_DAPi709F07-ORGi5010-96P354

value: plant


title: p26688_28474/111

description: Library name: Brain_region_111

value: Brain tissue

value: ARC


title: MSR-dCas9-Control MEF, timecourse, post-induction 12h, rep2

description:
Library name: dcas9_12_2
Illumina HiSeq 3000


title: p26688_28474/110

description: Library name: Brain_region_110


description: Library name: Solyc08g079120.3.1_O_sativa_Nipponbare_DAPi709F03-ORGi5010-96P354

value: Nipponbare

value: NAC


description: Library name: Solyc03g116890.3.1_O_sativa_Nipponbare_DAPi709G11-ORGi5010-96P354


title: MSR-dCas9-Control MEF, timecourse, post-induction 24h, rep3

description:
Library name: dcas9_24_3
Illumina HiSeq 3000


title: p26688_28474/112

description: Library name: Brain_region_112


description: Library name: Solyc05g007180.3.1_O_sativa_Nipponbare_DAPi709E12-ORGi5010-96P354

value: HOMEOBOX


title: p26688_28474/11

description: Library name: Brain_region_11

value: AP

value: AM833 0.3 nmol/kg


description: Library name: Carub.0002s2670.1_O_sativa_Nipponbare_DAPi709E11-ORGi5010-96P354


description: Library name: Solyc04g078640.3.1_O_sativa_Nipponbare_DAPi709F01-ORGi5010-96P354


title: MSR-dCas9-Control MEF, timecourse, post-induction 12h, rep1

description:
Library name: dcas9_12_1
Illumina HiSeq 3000


title: MSR-dCas9-Control MEF, timecourse, post-induction 6h, rep3

description:
Library name: dcas9_6_3
Illumina HiSeq 3000

value: post-induction, fresh media, 6 hr


description: Library name: XP_013615900.1_O_sativa_Nipponbare_DAPi709E09-ORGi5010-96P354


title: p26688_28474/108

description: Library name: Brain_region_108

value: sCT 150 nmol/kg


title: MSR-dCas9-Control MEF, timecourse, post-induction 6h, rep2

description:
Library name: dcas9_6_2
Illumina HiSeq 3000

value: inducible expression of MSR-dCas9-Control


description: Library name: AL3G23910.t2_O_sativa_Nipponbare_DAPi709E07-ORGi5010-96P354

value: BZIP


title: MSR-dCas9-Control MEF, timecourse, post-induction 3h, rep3

description:
Library name: dcas9_3_3
Illumina HiSeq 3000

value: post-induction, fresh media, 3 hr


title: p26688_28474/106

description: Library name: Brain_region_106


description: Library name: AL8G38770.t1_O_sativa_Nipponbare_DAPi709E02-ORGi5010-96P354

value: ARF


title: p26688_28474/105

description: Library name: Brain_region_105


title: MSR-dCas9-Control MEF, timecourse, post-induction 3h, rep2

description:
Library name: dcas9_3_2
Illumina HiSeq 3000

value: mouse embryonic fibroblast


description: Library name: LOC_Os08g06110.3_O_sativa_Nipponbare_DAPi709D10-ORGi5010-96P354

value: MYBRELATED


title: MSR-dCas9-Control MEF, timecourse, post-induction 3h, rep1

description:
Library name: dcas9_3_1
Illumina HiSeq 3000


title: p26688_28474/104

description: Library name: Brain_region_104


description: Library name: Carub.0008s0285.1_O_sativa_Nipponbare_DAPi709D08-ORGi5010-96P354


description: Library name: Solyc01g095460.3.1_O_sativa_Nipponbare_DAPi709D07-ORGi5010-96P354


description: Library name: AL8G10650.t1_O_sativa_Nipponbare_DAPi709D09-ORGi5010-96P354


title: p26688_28474/102

description: Library name: Brain_region_102


title: MSR-dCas9-Control MEF, timecourse, induced, rep3

description:
Library name: dcas9_0_3
Illumina HiSeq 3000

value: 10 ng/ml doxycycline, 24 hr


title: p26688_28474/103

description: Library name: Brain_region_103


description: Library name: Solyc10g005080.3.1_O_sativa_Nipponbare_DAPi709E10-ORGi5010-96P354

value: plant


title: p26688_28474/107

description: Library name: Brain_region_107

value: Brain tissue


title: MSR-dCas9-Control MEF, timecourse, post-induction 6h, rep1

description:
Library name: dcas9_6_1
Illumina HiSeq 3000


description: Library name: LOC_Os10g26500.1_O_sativa_Nipponbare_DAPi709D12-ORGi5010-96P354


description: Library name: LOC_Os02g42970.1_O_sativa_Nipponbare_DAPi709E03-ORGi5010-96P354


title: MSR-dCas9-Control MEF, timecourse, induced, rep1

description:
Library name: dcas9_0_1
Illumina HiSeq 3000


description: Library name: Carub.0002s1646.1_O_sativa_Nipponbare_DAPi709C12-ORGi5010-96P354


description: Library name: LOC_Os06g07030.1_O_sativa_Nipponbare_DAPi709E01-ORGi5010-96P354


description: Library name: LOC_Os02g33430.1_O_sativa_Nipponbare_DAPi709D05-ORGi5010-96P354


title: p26688_28474/101

description: Library name: Brain_region_101

value: ARC


description: Library name: Carub.0001s0116.1_O_sativa_Nipponbare_DAPi709C10-ORGi5010-96P354

value: Nipponbare


title: MSR-dCas9-Control MEF, timecourse, induced, rep2

description:
Library name: dcas9_0_2
Illumina HiSeq 3000


description: Library name: Carub.0001s3581.1.p_O_sativa_Nipponbare_DAPi709D01-ORGi5010-96P354


description: Library name: AL2G40550.t1_O_sativa_Nipponbare_DAPi709C11-ORGi5010-96P354

value: WRKY


title: p26688_28474/10

description: Library name: Brain_region_10


description: Library name: LOC_Os01g46970.1_O_sativa_Nipponbare_DAPi709C07-ORGi5010-96P354


title: p26688_28474/100

description: Library name: Brain_region_100


title: MSR-dCas9-Control MEF, timecourse, uninduced, rep3

description:
Library name: dcas9_-24_3
Illumina HiSeq 3000

value: untreated


description: Library name: XP_013602769.1_O_sativa_Nipponbare_DAPi709C03-ORGi5010-96P354

value: NAC


description: Library name: Solyc07g040920.2.1_O_sativa_Nipponbare_DAPi709B11-ORGi5010-96P354


description: Library name: XP_013613838.1_O_sativa_Nipponbare_DAPi709C08-ORGi5010-96P354


title: MSR-dCas9-Control MEF, timecourse, uninduced, rep2

description:
Library name: dcas9_-24_2
Illumina HiSeq 3000


title: brassica-mix,root,rep5

description: Library name: NXHYU

library_source: transcriptomic single cell

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

molecule: polyA RNA

organism:
Arabidopsis thaliana
Brassica oleracea
Arabidopsis lyrata
Capsella rubella

source_name: seedling root

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

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

value: seedling root

tag: tissue condition

value: frozen

tag: platform

value: 10X Chromium

tag: number of_multiplexed_species


description: Library name: Carub.0001s1194.1_O_sativa_Nipponbare_DAPi709D03-ORGi5010-96P354


title: GEMM_Ctr2_MultiOME GEX

city: Memphis

first: Xiang

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Computational Biology

institute: St.Jude Children's Research Hospital

description:
Library name: GEMM_Ctr2_GEX
GEMM_Ctr2_MultiOME GEX

data_processing:
Cellranger ARC
Assembly: mm10-2020-A
Supplementary files format and content: Fastq files

source_name: Tumor

extract_protocol: 10X Genomics- ScMultiOME ATAC + Gene expression

value: Tumor


description: Library name: Solyc08g068320.3.1_O_sativa_Nipponbare_DAPi709C04-ORGi5010-96P354

value: MYB


description: Library name: LOC_Os03g21800.1_O_sativa_Nipponbare_DAPi709B09-ORGi5010-96P354

value: BZIP


title: GEMM_Ctr1_MultiOME GEX

description:
Library name: GEMM_Ctr1_GEX
GEMM_Ctr1_MultiOME GEX


title: brassica-mix,fresh-root,rep2

description: Library name: NXHYP

value: fresh


title: GEMM_Ctr2_MultiOME ATAC

description:
Library name: GEMM_Ctr2_ATAC
GEMM_Ctr2_MultiOME ATAC


description: Library name: AL1G53260.t1_O_sativa_Nipponbare_DAPi709B01-ORGi5010-96P354


title: MSR-dCas9-Control MEF, timecourse, uninduced, rep1

description:
Library name: dcas9_-24_1
Illumina HiSeq 3000

value: mouse embryonic fibroblast

value: inducible expression of MSR-dCas9-Control


title: p26688_28474/1

description: Library name: Brain_region_1

value: AP

value: Vehicle


description: Library name: XP_013587350.1_O_sativa_Nipponbare_DAPi709B10-ORGi5010-96P354

value: plant

value: MYBRELATED


title: GEMM_Inte1_MultiOME ATAC

description:
Library name: GEMM_Inte1_ATAC
GEMM_Inte1_MultiOME ATAC


title: brassica-mix,fresh-root,rep1

description: Library name: NXHYO


description: Library name: Carub.0004s2291.1_O_sativa_Nipponbare_DAPi709A09-ORGi5010-96P354

value: Nipponbare


title: brassica-mix,root,rep3

description: Library name: NUUHN


title: GEMM_Inte1_MultiOME GEX

description:
Library name: GEMM_Inte1_GEX
GEMM_Inte1_MultiOME GEX


description: Library name: AL8G13510.t2_O_sativa_Nipponbare_DAPi709B08-ORGi5010-96P354


title: brassica-mix,root,rep4

description: Library name: NXHYS


description: Library name: Carub.0007s0775.1_O_sativa_Nipponbare_DAPi709A04-ORGi5010-96P354


description: Library name: Carub.0004s2898.1.p_O_sativa_Nipponbare_DAPi709B07-ORGi5010-96P354


description: Library name: AL1G23550.t1_O_sativa_Nipponbare_DAPi709B03-ORGi5010-96P354


description: Library name: AL1G11460.t1_O_sativa_Nipponbare_DAPi709A10-ORGi5010-96P354


title: brassica-mix,shoot,rep1

description: Library name: NUUHG

source_name: seedling shoot

value: seedling shoot


title: E14.5GFP&RFP_K5

city: Boston

first: Andrew

middle: Bruce

last: Lassar

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Raw reads were examined for quality issues using FastQC
STAR as used to align reads to the genome and create BAM files to check for evenness of coverage, rRNA content, genomic context of alignments
Abundance estimates were  generated by quasialignment using Salmon and counts per gene estimated using tximport
DESeq2 was used to generate normalized count and identify significantly DE genes
Assembly: mm10
Supplementary files format and content: Comma separated file with normalized counts for each sample

source_name: Knee

extract_protocol:
RNA from FAC-sorted cells (~250K to ~500K cells per sample) was purified using the Qiagen RNeasy Plus Micro Kit. RNA quality and quantity were assessed on an Agilent Tape Station.
RNA-Seq libraries were created using the Nextera XT DNA Library Preparation kit (Illumina).

value: Knee

value: GFP&RFP

tag: isolation date

tag: litter


description: Library name: Solyc11g064950.3.1_O_sativa_Nipponbare_DAPi709A08-ORGi5010-96P354


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712A12-ORGi5012-96P247

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: Solanum tuberosum DM1-3-516-R44: MSU via Phytozome v6.1
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: Solanum tuberosum


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712H01-ORGi5012-96P247


title: GEMM_Ctr1_MultiOME ATAC

description:
Library name: GEMM_Ctr1_ATAC
GEMM_Ctr1_MultiOME ATAC


title: brassica-mix,shoot,rep2

description: Library name: NUUHH


description: Library name: XP_013631386.1_O_sativa_Nipponbare_DAPi709A07-ORGi5010-96P354


title: E14.5GFP_K5

value: GFP


title: E14.5RFP_K5

value: RFP


description: Library name: LOC_Os01g51154.1_O_sativa_Nipponbare_DAPi709A11-ORGi5010-96P354


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712H12-ORGi5012-96P247


title: brassica-mix,root,rep2

description: Library name: NUUHC

value: seedling root

value: frozen

value: 10X Chromium


title: E14.5GFP&RFP_K2


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712A01-ORGi5012-96P247


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712H12-ORGi5012-96P220


title: brassica-mix,root,rep1

description: Library name: NUUHB


description: Library name: AT2G46270_S_tuberosum_DM_1-3-516-R44_DAPi712H11-ORGi5012-96P220

value: BZIP


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712H01-ORGi5012-96P220


title: E14.5RFP_K2


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712H12-ORGi5038-96P247

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: 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


title: E14.5RFP_K1


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712A12-ORGi5038-96P247


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712A01-ORGi5038-96P247


description: Library name: AT5G18560_S_tuberosum_DM_1-3-516-R44_DAPi712H07-ORGi5012-96P220


description: Library name: LOC_Os01g17260.2_S_tuberosum_DM_1-3-516-R44_DAPi712H07-ORGi5012-96P247


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi709H12-ORGi5038-96P169


title: Sbicolor,leaf,rep1

description: Library name: OUGHZ

organism: Sorghum bicolor

source_name: leaf

value: leaf

value: BD Rhapsody


description: Library name: AL4G45550.t1_S_tuberosum_DM_1-3-516-R44_DAPi712H06-ORGi5012-96P247


title: E14.5GFP_K2


description: Library name: Carub.0002s1959.1_S_tuberosum_DM_1-3-516-R44_DAPi712H10-ORGi5012-96P247


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi709H01-ORGi5038-96P169


description: Library name: AT1G01060_S_tuberosum_DM_1-3-516-R44_DAPi712H05-ORGi5012-96P220


description: Library name: Solyc01g102340.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712H04-ORGi5012-96P247

value: MYB


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712H01-ORGi5038-96P247


description: Library name: AT3G02940_S_tuberosum_DM_1-3-516-R44_DAPi712H04-ORGi5012-96P220


description: Library name: Solyc08g078340.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712H09-ORGi5012-96P247


title: E14_5_Prx1Cre_iCreb55

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Raw reads were examined for quality issues using FastQC
STAR as used to align reads to the genome and create BAM files to check for evenness of coverage, rRNA content, genomic context of alignments
Abundance estimates were  generated by quasialignment using Salmon and counts per gene estimated using tximport
DESeq2 was used to generate normalized count and identify significantly DE genes
Assembly: mm10 + bovine Creb5 (custom genome)
Supplementary files format and content: Comma separated file with normalized counts for each sample

tag: dev stage

tag: batch


description: Library name: AL2G28980.t1_S_tuberosum_DM_1-3-516-R44_DAPi712H11-ORGi5012-96P247

value: HOMEOBOX


description: Library name: XP_013629448.1_S_tuberosum_DM_1-3-516-R44_DAPi712H03-ORGi5012-96P247


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi709A01-ORGi5038-96P169


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712A01-ORGi5012-96P220


title: E14.5GFP&RFP_K1


title: E14_5_Prx1Cre_iTdtomato5b

source_name: Tdtomato

value: Tdtomato


description: Library name: AT5G17300_S_tuberosum_DM_1-3-516-R44_DAPi712H08-ORGi5012-96P220

value: plant


description: Library name: XP_013634112.1_S_tuberosum_DM_1-3-516-R44_DAPi712H08-ORGi5012-96P247


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi711H12-ORGi5038-96P166


description: Library name: Solyc03g116890.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712G11-ORGi5012-96P247

value: WRKY


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi711H01-ORGi5038-96P166


title: E14.5GFP_K1


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi711A12-ORGi5038-96P166


description: Library name: AT3G50410_S_tuberosum_DM_1-3-516-R44_DAPi712H06-ORGi5012-96P220


title: E14_5_Prx1Cre_iCreb56


title: E14_5_Prx1Cre_iCreb53c


description: Library name: AT1G72740_S_tuberosum_DM_1-3-516-R44_DAPi712G09-ORGi5012-96P220

value: MYBRELATED


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi711A01-ORGi5038-96P166


title: E14_5_Prx1Cre_iTdtomato3c


description: Library name: AT2G47070_S_tuberosum_DM_1-3-516-R44_DAPi712H10-ORGi5012-96P220

value: SBP


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712H12-ORGi5038-96P155


title: E14_5_Prx1Cre_iCreb53b


title: E14_5_Prx1Cre_iTdtomato6d


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi709A12-ORGi5038-96P169


description: Library name: Carub.0003s1161.1.p_S_tuberosum_DM_1-3-516-R44_DAPi712G07-ORGi5012-96P247


title: p26688_28474/109

description: Library name: Brain_region_109

value: Brain tissue

value: ARC

value: sCT 150 nmol/kg


title: E14_5_Prx1Cre_iCreb54a


description: Library name: XP_013609718.1_S_tuberosum_DM_1-3-516-R44_DAPi712G12-ORGi5012-96P247


description: Library name: AT2G22430_S_tuberosum_DM_1-3-516-R44_DAPi712H02-ORGi5012-96P220


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712A12-ORGi5038-96P155


description: Library name: AT5G09410_S_tuberosum_DM_1-3-516-R44_DAPi712G11-ORGi5012-96P220

value: CAMTA


title: E14_5_Prx1Cre_iTdtomato3b


title: E14_5_Prx1Cre__iCreb53a


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712A01-ORGi5038-96P155


description: Library name: AT5G02320_S_tuberosum_DM_1-3-516-R44_DAPi712G06-ORGi5012-96P220


title: E14_5_Prx1Cre_iTdtomato4a


description: Library name: AT5G45300_S_tuberosum_DM_1-3-516-R44_DAPi712G10-ORGi5012-96P220


description: Library name: XP_013589913.1_S_tuberosum_DM_1-3-516-R44_DAPi712G10-ORGi5012-96P247


description: Library name: AT1G46768_S_tuberosum_DM_1-3-516-R44_DAPi712G04-ORGi5012-96P220


title: E14_5_Prx1Cre_iTdtomato3a


description: Library name: LOC_Os10g41200.1_S_tuberosum_DM_1-3-516-R44_DAPi712G09-ORGi5012-96P247


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi710H01-ORGi5038-96P151


description: Library name: XP_013587997.1_O_sativa_Nipponbare_DAPi709D11-ORGi5010-96P354

value: Nipponbare


description: Library name: AT2G30250_S_tuberosum_DM_1-3-516-R44_DAPi712H03-ORGi5012-96P220


description: Library name: AT3G50060_S_tuberosum_DM_1-3-516-R44_DAPi712G02-ORGi5012-96P220


description: Library name: AT2G01940_S_tuberosum_DM_1-3-516-R44_DAPi712G08-ORGi5012-96P220


description: Library name: AT1G69180_S_tuberosum_DM_1-3-516-R44_DAPi712G05-ORGi5012-96P220


description: Library name: AT5G19790_S_tuberosum_DM_1-3-516-R44_DAPi712G07-ORGi5012-96P220


description: Library name: AL4G38490.t1_S_tuberosum_DM_1-3-516-R44_DAPi712G08-ORGi5012-96P247


title: HoxA11GFP_Creb5RFP_F6_HA_6

data_processing:
All samples were processed using an ATAC-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Raw reads were examined for quality issues using FastQC and reads were filtered and trimmed with Atropos
Bowtie2 was used to map reads to the genome
Mapped reads were filtered to retain properly paired reads with high mapping quality (MAPQ score >10, non-duplicates, qualified reads) using Sambamba
Macs2 was used to call peaks on unique reads
Assembly: mm10
Supplementary files format and content: narrowPeak files (BED format)
Library strategy: Cut&Run

extract_protocol:
Cut&Run-Seq (Cleavage Under Targets and Release Using Nuclease) was performed using a CUTANA™ ChIC/CUT&RUN Kit (Epicypher, Cat#: 14-1048) according to the manufacturer’s protocol
The sequencing libraries were prepared using a NEBNext® UltraTM II DNA Library Prep Kit (New England Biolabs, Cat#: E7645L). PCR products in the libraries that were bigger than 350 bp and smaller than 150 bp were removed by two rounds of selection using AMPure beads (Beckman Coulter

tag: chip antibody

value: HA

tag: dataset


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi710A12-ORGi5038-96P151

tag: genotype


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712H12-ORGi5038-96P220


title: HoxA11GFP_Creb5RFP_F6_IgG_6

value: IgG


description: Library name: Carub.0008s0039.1_S_tuberosum_DM_1-3-516-R44_DAPi712F09-ORGi5012-96P247


description: Library name: LOC_Os01g18240.1_S_tuberosum_DM_1-3-516-R44_DAPi712G04-ORGi5012-96P247


description: Library name: AT1G80840_S_tuberosum_DM_1-3-516-R44_DAPi712G03-ORGi5012-96P220


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712A12-ORGi5038-96P220


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712H01-ORGi5038-96P220


description: Library name: AL2G32420.t2_S_tuberosum_DM_1-3-516-R44_DAPi712F10-ORGi5012-96P247


title: HoxA11GFP_Creb5RFP_H5_Creb5_5


description: Library name: AT1G76880_S_tuberosum_DM_1-3-516-R44_DAPi712F11-ORGi5012-96P220

value: TRIHELIX


title: HoxA11GFP_Creb5RFP_F6_Creb5_6


description: Library name: AT2G45480_S_tuberosum_DM_1-3-516-R44_DAPi712F09-ORGi5012-96P220

value: GRF


description: Library name: XP_013586407.1_S_tuberosum_DM_1-3-516-R44_DAPi712F07-ORGi5012-96P247

value: BZIP


title: HoxA11GFP_Creb5RFP_H3_Creb5_3


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi712A01-ORGi5038-96P220


description: Library name: LOC_Os09g25060.1_S_tuberosum_DM_1-3-516-R44_DAPi712F11-ORGi5012-96P247


description: Library name: AT2G02820_S_tuberosum_DM_1-3-516-R44_DAPi712F08-ORGi5012-96P220

value: MYB


description: Library name: AT4G25480_S_tuberosum_DM_1-3-516-R44_DAPi712F04-ORGi5012-96P220


description: Library name: AT2G45420_S_tuberosum_DM_1-3-516-R44_DAPi712F06-ORGi5012-96P220


title: Knee_Creb5RFP_Creb5_2


title: Knee_Sox9GFP_Creb5RFP_Creb5_2


description: Library name: AT5G52830_S_tuberosum_DM_1-3-516-R44_DAPi712F07-ORGi5012-96P220


description: Library name: AL2G28980.t1_A_lyrata_MN47_DAPi712H11-ORGi5038-96P247

value: HOMEOBOX


description: Library name: AT2G46270_A_lyrata_MN47_DAPi712H11-ORGi5038-96P220


description: Library name: Solyc08g079120.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712F03-ORGi5012-96P247

value: NAC


description: Library name: AT4G14770_S_tuberosum_DM_1-3-516-R44_DAPi712F10-ORGi5012-96P220

value: plant

value: CPP


description: Library name: AT1G33240_S_tuberosum_DM_1-3-516-R44_DAPi712F03-ORGi5012-96P220


description: Library name: Carub.0002s1959.1_A_lyrata_MN47_DAPi712H10-ORGi5038-96P247

value: MYBRELATED


title: Knee_Creb5RFP_Creb5_1


title: Knee_Sox9GFP_Creb5RFP_Creb5_1


description: Library name: AT2G47070_A_lyrata_MN47_DAPi712H10-ORGi5038-96P220

value: SBP


description: Library name: Solyc04g078640.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712F01-ORGi5012-96P247


description: Library name: AT4G31800_S_tuberosum_DM_1-3-516-R44_DAPi712F02-ORGi5012-96P220

value: WRKY


title: E14.5RFP_K2

data_processing:
All samples were processed using an ATAC-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Raw reads were examined for quality issues using FastQC and reads were filtered and trimmed with Atropos
Bowtie2 was used to map reads to the genome
Mapped reads were filtered to retain properly paired reads with high mapping quality (MAPQ score >10, non-duplicates, qualified reads) and remove remove mitochondrial DNA using Sambamba
Macs2 was used to call peaks on unique reads
Assembly: mm10
Supplementary files format and content: narrowPeak files (BED format)

extract_protocol:
After FACS, cells were washed twice in ice-cold PBS, and 50,000 cells (per sample) were used to perform ATAC-Seq. Cells were resuspended in 50 μl ice-cold ATAC Lysis Buffer , and centrifuged at 500 g at 4 °C to isolate nuclear pellets
Nuclear pellets were treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) in a 50 μl reaction for 30 min at 37 °C.  Transposed DNA was immediately isolated using a Qiagen MinElute PCR Purification Kit, and then PCR amplified in a 50 μl reaction using a common forward primer and different reverse primers with unique barcodes for each sample

value: Knee

tag: cell type

value: RFP


description: Library name: Solyc05g007180.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712E12-ORGi5012-96P247

tag: tissue


description: Library name: AT1G52880_S_tuberosum_DM_1-3-516-R44_DAPi712E12-ORGi5012-96P220

tag: tf id


description: Library name: AT5G47390_S_tuberosum_DM_1-3-516-R44_DAPi712F01-ORGi5012-96P220

tag: tf family


description: Library name: AT2G01060_S_tuberosum_DM_1-3-516-R44_DAPi712F05-ORGi5012-96P220

tag: multidap sample_id


title: E14.5GFP&RFP_K2

value: GFP&RFP


description: Library name: Solyc08g078340.3.1_A_lyrata_MN47_DAPi712H09-ORGi5038-96P247

tag: 96 well_plate_id


description: Library name: Carub.0002s2670.1_S_tuberosum_DM_1-3-516-R44_DAPi712E11-ORGi5012-96P247

tag: tf source_species


description: Library name: AT1G20980_S_tuberosum_DM_1-3-516-R44_DAPi712E11-ORGi5012-96P220


description: Library name: Solyc10g005080.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712E10-ORGi5012-96P247


title: E14.5GFP_K2

value: GFP


description: Library name: AT5G17300_A_lyrata_MN47_DAPi712H08-ORGi5038-96P220


description: Library name: XP_013615900.1_S_tuberosum_DM_1-3-516-R44_DAPi712E09-ORGi5012-96P247


description: Library name: AT1G18330_S_tuberosum_DM_1-3-516-R44_DAPi712G01-ORGi5012-96P220


title: E14.5RFP_K1


description: Library name: LOC_Os01g17260.2_A_lyrata_MN47_DAPi712H07-ORGi5038-96P247


description: Library name: AT4G17980_S_tuberosum_DM_1-3-516-R44_DAPi712E10-ORGi5012-96P220


title: E14.5GFP&RFP_K1


description: Library name: AT2G18550_S_tuberosum_DM_1-3-516-R44_DAPi712E07-ORGi5012-96P220


description: Library name: AT5G56110_S_tuberosum_DM_1-3-516-R44_DAPi712E06-ORGi5012-96P220


title: E14_5_Prx1Cre_iCreb53c

tag: prep date


title: E14.5GFP_K1


description: Library name: AT5G62020_S_tuberosum_DM_1-3-516-R44_DAPi712E04-ORGi5012-96P220

value: HSF


description: Library name: AL3G23910.t2_S_tuberosum_DM_1-3-516-R44_DAPi712E07-ORGi5012-96P247


description: Library name: AT5G18560_A_lyrata_MN47_DAPi712H07-ORGi5038-96P220


title: E14_5_Prx1Cre_iTdtomato3c

source_name: iTdtomato

value: iTdtomato


description: Library name: XP_013634112.1_A_lyrata_MN47_DAPi712H08-ORGi5038-96P247


description: Library name: AT3G49530_A_lyrata_MN47_DAPi712H07-ORGi5038-96P155


description: Library name: AL4G45550.t1_A_lyrata_MN47_DAPi712H06-ORGi5038-96P247


description: Library name: AT5G64750_S_tuberosum_DM_1-3-516-R44_DAPi712E03-ORGi5012-96P220


description: Library name: AT3G50410_A_lyrata_MN47_DAPi712H06-ORGi5038-96P220


description: Library name: LOC_Os02g42970.1_S_tuberosum_DM_1-3-516-R44_DAPi712E03-ORGi5012-96P247


description: Library name: Control_TF_DNA_S_tuberosum_DM_1-3-516-R44_DAPi712A12-ORGi5012-96P220


title: E14_5_Prx1Cre_iCreb53b


description: Library name: LOC_Os10g26500.1_S_tuberosum_DM_1-3-516-R44_DAPi712D12-ORGi5012-96P247


description: Library name: AT5G11510_A_lyrata_MN47_DAPi712H06-ORGi5038-96P155


description: Library name: AT5G14960_S_tuberosum_DM_1-3-516-R44_DAPi712E08-ORGi5012-96P220


description: Library name: LOC_Os06g07030.1_S_tuberosum_DM_1-3-516-R44_DAPi712E01-ORGi5012-96P247


description: Library name: AT1G01060_A_lyrata_MN47_DAPi712H05-ORGi5038-96P220


description: Library name: AT5G11260_S_tuberosum_DM_1-3-516-R44_DAPi712D12-ORGi5012-96P220


description: Library name: AT1G13260_S_tuberosum_DM_1-3-516-R44_DAPi712E01-ORGi5012-96P220

value: RAV


title: E14_5_Prx1Cre_iCreb53a


description: Library name: AT3G18990_S_tuberosum_DM_1-3-516-R44_DAPi712D11-ORGi5012-96P220


description: Library name: XP_013587997.1_S_tuberosum_DM_1-3-516-R44_DAPi712D11-ORGi5012-96P247


description: Library name: AT3G60530_S_tuberosum_DM_1-3-516-R44_DAPi712E05-ORGi5012-96P220


description: Library name: AT5G61620_A_lyrata_MN47_DAPi712H05-ORGi5038-96P155


title: E14_5_Prx1Cre_iTdtomato3a


description: Library name: LOC_Os08g06110.3_S_tuberosum_DM_1-3-516-R44_DAPi712D10-ORGi5012-96P247


description: Library name: AL8G10650.t1_S_tuberosum_DM_1-3-516-R44_DAPi712D09-ORGi5012-96P247


description: Library name: Solyc01g102340.3.1_A_lyrata_MN47_DAPi712H04-ORGi5038-96P247


description: Library name: Carub.0008s0285.1_S_tuberosum_DM_1-3-516-R44_DAPi712D08-ORGi5012-96P247


title: Single cell BH9 from colon

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

source_name: colon

extract_protocol:
Lysis in sodium bisulfite
sc-DEEP-mC

value: colon


description: Library name: AT3G02940_A_lyrata_MN47_DAPi712H04-ORGi5038-96P220


description: Library name: AT5G03150_S_tuberosum_DM_1-3-516-R44_DAPi712D08-ORGi5012-96P220


title: E14_5_Prx1Cre_iTdtomato3b


description: Library name: Solyc01g095460.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712D07-ORGi5012-96P247

value: BZIP


description: Library name: XP_013629448.1_A_lyrata_MN47_DAPi712H03-ORGi5038-96P247

value: MYB


description: Library name: AT2G47070_A_lyrata_MN47_DAPi712H04-ORGi5038-96P155


description: Library name: Control_TF_DNA_A_lyrata_MN47_DAPi710H12-ORGi5038-96P151


description: Library name: AT2G01930_S_tuberosum_DM_1-3-516-R44_DAPi712D05-ORGi5012-96P220

value: BBRBPC


description: Library name: AT1G74480_S_tuberosum_DM_1-3-516-R44_DAPi712D07-ORGi5012-96P220

value: RWPRK


description: Library name: Carub.0001s1194.1_S_tuberosum_DM_1-3-516-R44_DAPi712D03-ORGi5012-96P247

value: plant

value: NAC


description: Library name: LOC_Os02g33430.1_S_tuberosum_DM_1-3-516-R44_DAPi712D05-ORGi5012-96P247


title: Single cell BH7 from colon


description: Library name: AT3G50260_S_tuberosum_DM_1-3-516-R44_DAPi712D02-ORGi5012-96P220


description: Library name: AT3G57920_S_tuberosum_DM_1-3-516-R44_DAPi712D06-ORGi5012-96P220


description: Library name: Carub.0001s3581.1.p_S_tuberosum_DM_1-3-516-R44_DAPi712D01-ORGi5012-96P247


title: Single cell BH6 from colon


title: Single cell BH8 from colon


title: Single cell BH4 from colon


description: Library name: Carub.0001s0116.1_S_tuberosum_DM_1-3-516-R44_DAPi712C10-ORGi5012-96P247

value: MYBRELATED


description: Library name: AT5G65410_S_tuberosum_DM_1-3-516-R44_DAPi712D03-ORGi5012-96P220

value: ZFHD


title: Single cell BH5 from colon


description: Library name: AT1G76420_S_tuberosum_DM_1-3-516-R44_DAPi712C09-ORGi5012-96P220


title: Single cell BH12 from colon


description: Library name: AT5G62470_S_tuberosum_DM_1-3-516-R44_DAPi712C08-ORGi5012-96P220


title: Single cell BH2 from colon


description: Library name: AT5G60130_S_tuberosum_DM_1-3-516-R44_DAPi712C07-ORGi5012-96P220


description: Library name: Carub.0002s1646.1_S_tuberosum_DM_1-3-516-R44_DAPi712C12-ORGi5012-96P247

value: HOMEOBOX


description: Library name: AT1G12260_S_tuberosum_DM_1-3-516-R44_DAPi712C12-ORGi5012-96P220


description: Library name: AL2G40550.t1_S_tuberosum_DM_1-3-516-R44_DAPi712C11-ORGi5012-96P247

value: WRKY


title: Single cell BH3 from colon


description: Library name: AT4G00730_S_tuberosum_DM_1-3-516-R44_DAPi712C11-ORGi5012-96P220


description: Library name: AT5G03790_S_tuberosum_DM_1-3-516-R44_DAPi712C06-ORGi5012-96P220


description: Library name: Solyc06g048630.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712C09-ORGi5012-96P247


description: Library name: AT1G27730_S_tuberosum_DM_1-3-516-R44_DAPi712C01-ORGi5012-96P220


description: Library name: LOC_Os01g46970.1_S_tuberosum_DM_1-3-516-R44_DAPi712C07-ORGi5012-96P247


title: Single cell BH1 from colon


title: Single cell BG9 from colon


description: Library name: XP_013602769.1_S_tuberosum_DM_1-3-516-R44_DAPi712C03-ORGi5012-96P247


title: Single cell BH11 from colon


description: Library name: AT2G40620_S_tuberosum_DM_1-3-516-R44_DAPi712B12-ORGi5012-96P220


description: Library name: XP_013613838.1_S_tuberosum_DM_1-3-516-R44_DAPi712C08-ORGi5012-96P247


title: Single cell BG5 from colon


title: Single cell BG8 from colon


description: Library name: AT1G69690_S_tuberosum_DM_1-3-516-R44_DAPi712C02-ORGi5012-96P220

value: TCP


description: Library name: Solyc08g068320.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712C04-ORGi5012-96P247


title: Single cell BG7 from colon


description: Library name: XP_013589953.1_S_tuberosum_DM_1-3-516-R44_DAPi712B12-ORGi5012-96P247


title: Single cell BG6 from colon


description: Library name: AT3G27010_S_tuberosum_DM_1-3-516-R44_DAPi712C04-ORGi5012-96P220


description: Library name: XP_013587350.1_S_tuberosum_DM_1-3-516-R44_DAPi712B10-ORGi5012-96P247


description: Library name: AT1G20910_S_tuberosum_DM_1-3-516-R44_DAPi712B10-ORGi5012-96P220

value: ARID


description: Library name: LOC_Os03g21800.1_S_tuberosum_DM_1-3-516-R44_DAPi712B09-ORGi5012-96P247


description: Library name: Carub.0004s2898.1.p_S_tuberosum_DM_1-3-516-R44_DAPi712B07-ORGi5012-96P247


description: Library name: Solyc07g040920.2.1_S_tuberosum_DM_1-3-516-R44_DAPi712B11-ORGi5012-96P247


description: Library name: AT1G79580_S_tuberosum_DM_1-3-516-R44_DAPi712B09-ORGi5012-96P220


title: Single cell BG4 from colon


description: Library name: AT3G08500_S_tuberosum_DM_1-3-516-R44_DAPi712B05-ORGi5012-96P220


title: Single cell BG3 from colon


title: Single cell BG2 from colon


description: Library name: AL8G13510.t2_S_tuberosum_DM_1-3-516-R44_DAPi712B08-ORGi5012-96P247


description: Library name: AT4G25470_S_tuberosum_DM_1-3-516-R44_DAPi712B06-ORGi5012-96P220


title: Single cell BG10 from colon


description: Library name: Solyc03g116890.3.1_A_lyrata_MN47_DAPi712G11-ORGi5038-96P247


description: Library name: XP_013589913.1_A_lyrata_MN47_DAPi712G10-ORGi5038-96P247


description: Library name: AT4G36740_A_lyrata_MN47_DAPi712H03-ORGi5038-96P155


description: Library name: XP_013631649.1_S_tuberosum_DM_1-3-516-R44_DAPi712B05-ORGi5012-96P247


description: Library name: AT2G01940_A_lyrata_MN47_DAPi712G08-ORGi5038-96P220


description: Library name: AT2G22430_A_lyrata_MN47_DAPi712H02-ORGi5038-96P220


description: Library name: AT5G65210_A_lyrata_MN47_DAPi712G11-ORGi5038-96P155


description: Library name: AT5G57620_A_lyrata_MN47_DAPi712G12-ORGi5038-96P155


description: Library name: AT1G72740_A_lyrata_MN47_DAPi712G09-ORGi5038-96P220


description: Library name: AT2G35530_A_lyrata_MN47_DAPi712G09-ORGi5038-96P155


description: Library name: AT5G45300_A_lyrata_MN47_DAPi712G10-ORGi5038-96P220


description: Library name: AT5G06100_A_lyrata_MN47_DAPi712H02-ORGi5038-96P155


description: Library name: LOC_Os10g41200.1_A_lyrata_MN47_DAPi712G09-ORGi5038-96P247


description: Library name: XP_013609718.1_A_lyrata_MN47_DAPi712G12-ORGi5038-96P247


description: Library name: AL4G38490.t1_A_lyrata_MN47_DAPi712G08-ORGi5038-96P247


description: Library name: AT2G30250_A_lyrata_MN47_DAPi712H03-ORGi5038-96P220


description: Library name: AT5G09410_A_lyrata_MN47_DAPi712G11-ORGi5038-96P220

value: CAMTA


title: Single cell BG11 from colon


description: Library name: AT5G19790_A_lyrata_MN47_DAPi712G07-ORGi5038-96P220


description: Library name: Carub.0003s1161.1.p_A_lyrata_MN47_DAPi712G07-ORGi5038-96P247


description: Library name: AL1G53260.t1_S_tuberosum_DM_1-3-516-R44_DAPi712B01-ORGi5012-96P247


description: Library name: AL1G23550.t1_S_tuberosum_DM_1-3-516-R44_DAPi712B03-ORGi5012-96P247


description: Library name: AT4G34590_A_lyrata_MN47_DAPi712G07-ORGi5038-96P155


title: Single cell BF9 from cecum

source_name: cecum

value: cecum


description: Library name: AT3G56400_S_tuberosum_DM_1-3-516-R44_DAPi712B02-ORGi5012-96P220


description: Library name: LOC_Os01g51154.1_S_tuberosum_DM_1-3-516-R44_DAPi712A11-ORGi5012-96P247


description: Library name: AT1G29160_S_tuberosum_DM_1-3-516-R44_DAPi712B04-ORGi5012-96P220


description: Library name: AT5G67300_S_tuberosum_DM_1-3-516-R44_DAPi712B01-ORGi5012-96P220


description: Library name: AT5G02320_A_lyrata_MN47_DAPi712G06-ORGi5038-96P220


title: Single cell BG1 from colon


title: Single cell BF8 from cecum


description: Library name: AL1G11460.t1_S_tuberosum_DM_1-3-516-R44_DAPi712A10-ORGi5012-96P247


description: Library name: AT5G09410_A_lyrata_MN47_DAPi712G06-ORGi5038-96P155


description: Library name: AT5G05550_S_tuberosum_DM_1-3-516-R44_DAPi712A10-ORGi5012-96P220

value: TRIHELIX


description: Library name: Solyc11g064950.3.1_S_tuberosum_DM_1-3-516-R44_DAPi712A08-ORGi5012-96P247


title: Single cell BF7 from cecum


description: Library name: AT4G25490_S_tuberosum_DM_1-3-516-R44_DAPi712A08-ORGi5012-96P220


description: Library name: AT5G62940_S_tuberosum_DM_1-3-516-R44_DAPi712A05-ORGi5012-96P220


description: Library name: AT3G12250_S_tuberosum_DM_1-3-516-R44_DAPi712A07-ORGi5012-96P220


title: Single cell BF2 from cecum


description: Library name: AT5G16820_A_lyrata_MN47_DAPi712G05-ORGi5038-96P155

value: HSF


title: Single cell BF12 from cecum


description: Library name: XP_013631386.1_S_tuberosum_DM_1-3-516-R44_DAPi712A07-ORGi5012-96P247


description: Library name: AT1G69180_A_lyrata_MN47_DAPi712G05-ORGi5038-96P220


description: Library name: LOC_Os08g37970.1_S_tuberosum_DM_1-3-516-R44_DAPi712A06-ORGi5012-96P247


description: Library name: LOC_Os01g18240.1_A_lyrata_MN47_DAPi712G04-ORGi5038-96P247


title: Single cell BF3 from cecum


description: Library name: AT1G49480_S_tuberosum_DM_1-3-516-R44_DAPi712A04-ORGi5012-96P220

value: REM


description: Library name: AT1G46768_A_lyrata_MN47_DAPi712G04-ORGi5038-96P220


description: Library name: AT5G39760_S_tuberosum_DM_1-3-516-R44_DAPi712A02-ORGi5012-96P220


title: Single cell BF10 from cecum


description: Library name: AT1G69780_S_tuberosum_DM_1-3-516-R44_DAPi712A03-ORGi5012-96P220


title: Single cell BF11 from cecum


title: compound 8 and oxacillin cotreated biol rep_C

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

department: Chemistry

institute: High Point University

description:
Library name: Sample 18
Cmpd8_Ox_C

data_processing:
Quality control of resulting reads included removing adapter-containing reads, removing reads where “N” was > 10%, and removing low-quality reads where the quality value of over 50% of the bases was ≤ 5.
The remaining reads were mapped to the reference genome (USA300_FPR3757) using Bowtie2.
Gene expression levels were quantified as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and averaged among biological triplicate samples.
Assembly: USA300_FPR3757 https://www.ncbi.nlm.nih.gov/nuccore/87159884
Supplementary files format and content: An Excel spreadsheet for all treatment comparison groups that contain all analyzed replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: S. aureus BAA-1556 was purchased from the American Type Culture Collection. Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 105 CFU mL–1 in CAMHB.

extract_protocol:
Total RNA was purified from 3mL of culture using a Qiagen RNeasy kit and Thermo's Turbo DNase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cell suspension (3 mL) was aliquoted into sterile culture tubes, and loratadine was added to the appropriate concentration (≤25% of the compound MIC = 50 uM). Compound 8 was added to the appropriate concentration (≤25% of the compound MIC = 20 uM) Oxacillin was added to a separate culture tube at 4 ug/mL. Cotreatment consisted of both oxacillin (4 ug/mL) and loratadine (50uM) or compound 8 (25uM). Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.

value: bacterial cells

tag: cell line

value: bacterial

tag: treatment

value: cotreated w/oxacillin and compound 8


title: loratadine and oxacillin cotreated biol rep_C

description:
Library name: Sample 17
Lor_Ox_C

value: cotreated w/oxacillin and loratadine


description: Library name: AT5G10030_S_tuberosum_DM_1-3-516-R44_DAPi712A06-ORGi5012-96P220

value: plant

value: BZIP


title: Single cell BE9 from cecum


description: Library name: AT1G32150_A_lyrata_MN47_DAPi712G03-ORGi5038-96P155


description: Library name: Carub.0004s2291.1_S_tuberosum_DM_1-3-516-R44_DAPi712A09-ORGi5012-96P247


title: loratadine treated biol rep_C

description:
Library name: Sample 15
Lor_C

value: loratadine treated, 50 uM


title: compound 8 treated biol rep_C

description:
Library name: Sample 16
Cmpd8_C

value: compound 8 treated, 25uM


title: untreated biol rep_C

description:
Library name: Sample 13
Un_C

value: untreated, DMSO only


title: compound 8 and oxacillin cotreated biol rep_B

description:
Library name: Sample 12
USA3008oxB


description: Library name: AT3G50060_A_lyrata_MN47_DAPi712G02-ORGi5038-96P220

value: MYB


title: oxacillin treated biol rep_C

description:
Library name: Sample 14
Ox_C

value: oxacillin treated, 4 ug/mL


title: Single cell BE7 from cecum


title: Single cell BE8 from cecum


title: Single cell BE5 from cecum


title: compound 8 treated biol rep_B

description:
Library name: Sample 10
USA3008B


description: Library name: AT4G18450_A_lyrata_MN47_DAPi712G01-ORGi5038-96P155


title: loratadine and oxacillin cotreated biol rep_B

description:
Library name: Sample 11
USA300loroxB


description: Library name: AT4G01500_A_lyrata_MN47_DAPi712G02-ORGi5038-96P155


description: Library name: AT1G13600_A_lyrata_MN47_DAPi712F12-ORGi5038-96P155


title: loratadine treated biol rep_B

description:
Library name: Sample 9
USA300lorB


title: Single cell BE6 from cecum


title: Single cell BE4 from cecum


description: Library name: LOC_Os09g25060.1_A_lyrata_MN47_DAPi712F11-ORGi5038-96P247

value: WRKY


title: compound 8 and oxacillin cotreated biol rep_A

description:
Library name: Sample 6
Cmpd8_Ox_A


title: loratadine and oxacillin cotreated biol rep_A

description:
Library name: Sample 5
Lor_Ox_A


title: untreated biol rep_B

description:
Library name: Sample 7
USA300unB


title: Single cell BE3 from cecum


title: compound 8 treated biol rep_A

description:
Library name: Sample 4
Cmpd8_A


title: loratadine treated biol rep_A

description:
Library name: Sample 3
Lor_A


title: oxacillin treated biol rep_A

description:
Library name: Sample 2
Ox_A


description: Library name: AT1G76880_A_lyrata_MN47_DAPi712F11-ORGi5038-96P220


title: Single cell BE2 from cecum


title: oxacillin treated biol rep_B

description:
Library name: Sample 8
USA300oxB


description: Library name: AT1G18330_A_lyrata_MN47_DAPi712G01-ORGi5038-96P220

value: MYBRELATED


description: Library name: AT5G11260_A_lyrata_MN47_DAPi712F11-ORGi5038-96P155


title: untreated biol rep_A

description:
Library name: Sample 1
Un_A


description: Library name: AL2G32420.t2_A_lyrata_MN47_DAPi712F10-ORGi5038-96P247


description: Library name: AT1G80840_A_lyrata_MN47_DAPi712G03-ORGi5038-96P220


title: Single cell BE12 from cecum

value: cecum


title: KO_84_T12 (biol rep 1)

city: London

first: Richard

last: Treisman

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: Sample 22

data_processing:
Nextflow version 21.10.3 - nf-core/rna-seq v3.5
Assembly: GRCm38
Supplementary files format and content: salmon quant.sf files: transcript name, length, effective length, TPM and NumReads

source_name: MEF 84

growth_protocol: All MEFs were maintained in DMEM with 10% fetal bovine serum and 1% PenStrep in a humidified incubator with 10% CO2 at 37C.

extract_protocol:
RNA was extracted using GenElute mammalian RNA miniprep kit (RTN350 , Sigma)
polyA_KAPA_mRNA_Hyper_Prep (Roche) according to manufacturer's protocol.

treatment_protocol: Cells were collected on day 0, 2, 4 or 12 after 1µM 4-OHT treatment to inactivate MRTFs. 4-OHT was left on for 48 hours before returning cells to regular growth medium.

value: MEF 84

value: Mouse embryonic fibroblasts

value: MRTF-floxed

tag: time point

value: 12 days


title: KO_89_T12 (biol rep 3)

description: Library name: Sample 24

source_name: MEF 89

value: MEF 89


title: WT_80_T12 (biol rep 2)

description: Library name: Sample 20

source_name: MEF 80

value: MEF 80

value: WT


description: Library name: AT4G14770_A_lyrata_MN47_DAPi712F10-ORGi5038-96P220

value: plant

value: CPP


title: Single cell BE11 from cecum


title: KO_86_T12 (biol rep 2)

description: Library name: Sample 23

source_name: MEF 86

value: MEF 86


title: WT_82_T12 (biol rep 3)

description: Library name: Sample 21

source_name: MEF 82

value: MEF 82


description: Library name: AT3G15170_A_lyrata_MN47_DAPi712F10-ORGi5038-96P155

value: NAC


title: WT_79_T12 (biol rep 1)

description: Library name: Sample 19

source_name: MEF 79

value: MEF 79


title: KO_89_T4 (biol rep 3)

description: Library name: Sample 18

value: 4 days


title: Single cell BE10 from cecum


title: Single cell BD9 from distal small intestine

source_name: distal small intestine

value: distal small intestine


description: Library name: AT2G45480_A_lyrata_MN47_DAPi712F09-ORGi5038-96P220

source_name: plant

value: GRF


title: KO_86_T4 (biol rep 2)

description: Library name: Sample 17


title: KO_84_T4 (biol rep 1)

description: Library name: Sample 16


title: Single cell BE1 from cecum

value: cecum


title: WT_80_T4 (biol rep 2)

description: Library name: Sample 14


description: Library name: Carub.0008s0039.1_A_lyrata_MN47_DAPi712F09-ORGi5038-96P247

value: MYBRELATED


description: Library name: AT2G02820_A_lyrata_MN47_DAPi712F08-ORGi5038-96P220

value: MYB


title: WT_82_T4 (biol rep 3)

description: Library name: Sample 15

value: Mouse embryonic fibroblasts


title: Single cell BD7 from distal small intestine


title: WT_79_T4 (biol rep 1)

description: Library name: Sample 13


title: KO_89_T2 (biol rep 3)

description: Library name: Sample 12

value: MRTF-floxed

value: 2 days


title: KO_86_T2 (biol rep 2)

description: Library name: Sample 11


description: Library name: AT5G07680_A_lyrata_MN47_DAPi712F08-ORGi5038-96P155


title: WT_80_T2 (biol rep 2)

description: Library name: Sample 8

value: MEF 80


title: Single cell BD4 from distal small intestine


title: WT_79_T2 (biol rep 1)

description: Library name: Sample 7

value: WT


title: KO_84_T2 (biol rep 1)

description: Library name: Sample 10

value: MEF 84


title: Single cell BD5 from distal small intestine


description: Library name: AT5G52830_A_lyrata_MN47_DAPi712F07-ORGi5038-96P220

value: plant

value: WRKY


description: Library name: XP_013586407.1_A_lyrata_MN47_DAPi712F07-ORGi5038-96P247

value: BZIP


title: Single cell BD8 from distal small intestine


description: Library name: AT2G45420_A_lyrata_MN47_DAPi712F06-ORGi5038-96P220


title: KO_86_T0 (biol rep 2)

description: Library name: Sample 5

value: MEF 86

value: 0 days


title: WT_82_T2 (biol rep 3)

description: Library name: Sample 9

value: MEF 82


title: KO_89_T0 (biol rep 3)

description: Library name: Sample 6

value: MEF 89


title: Single cell BD2 from distal small intestine

value: distal small intestine


title: Single cell BD3 from distal small intestine


title: KO_84_T0 (biol rep 1)

description: Library name: Sample 4


description: Library name: AT4G25480_A_lyrata_MN47_DAPi712F04-ORGi5038-96P220


title: Single cell BD11 from distal small intestine


description: Library name: AT2G01060_A_lyrata_MN47_DAPi712F05-ORGi5038-96P220


title: WT_82_T0 (biol rep 3)

description: Library name: Sample 3


title: E13.5_Molar, Smad4_ChIP

city: New Orleans

first: Qinghuang

last: Tang

state: LA

address: 2000 Percival Stern Hall

department: Cell and Molecular Biology

institute: Tulane University

description:
Library name: E13.5_Molar_Smad4
Peaks identified by BCP_TF are represented in a 7-column BED format that includes: chromosome name, start position, end position, peak length, enrichment score, p-value, and summit location.

data_processing:
After generating raw data from the Illumina HiSeq 4000 platform using bcl2fastq conversion, BGI program SOAPnuke was applied to remove adapter sequences, contaminants, and low-quality reads. The resulting clean reads were stored in FASTQ format.
The clean 50-bp single-end reads were aligned to the mouse reference genome (mm10) using Bowtie2. The resulting SAM files were converted to BAM format using SAMtools. These BAM files were then filtered and converted to BED format using BEDtools prior to peak calling with BCP.
Heatmaps of ChIP-seq signals centered on transcription start sites (TSSs) were generated using the plotHeatmap function of deepTools.
Assembly: mm10
Supplementary files format and content: BED, peaks that identified by BCP_TF through comparison of ChIP and Input BED files.

source_name: E13.5 Molar

extract_protocol:
E13.5 limb or molar tissues were fixed with 1% formaldehyde at room temperature for 15 minutes. After stopping fixation and cell lysis, chromatin was sonicated using a Diagenode Bioruptor Sonicator. ChIP was performed following the manufacturer's protocol provided by Active Motif ChIP-IT High Sensitivity Kit.
Illuminina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of DNA-end repair, 3'-dA overhang, and adaptor ligation. After PCR amplification and size selection, the resulting DNA libraries were quantified and sequenced with an Illumina HiSeq 4000 instrument.

value: E13.5 Molar

value: Smad4 (Abcam, #ab3219)

value: wildtype


title: E13.5_Molar, pSmad15_ChIP

description:
Library name: E13.5_Molar_pSmad15
Peaks identified by BCP_TF are represented in a 7-column BED format that includes: chromosome name, start position, end position, peak length, enrichment score, p-value, and summit location.

value: pSmad1/5 (Cell signaling technology, #11971)


title: Single cell BD6 from distal small intestine


title: Single cell BD10 from distal small intestine


description: Library name: Solyc08g079120.3.1_A_lyrata_MN47_DAPi712F03-ORGi5038-96P247

value: NAC


description: Library name: AT1G33240_A_lyrata_MN47_DAPi712F03-ORGi5038-96P220

value: TRIHELIX


title: E13.5_Molar, Input

description: Library name: E13.5_Molar_Input


title: Single cell BD1 from distal small intestine


title: E13.5_Limb, Smad4_ChIP

description:
Library name: E13.5_Limb_Smad4
Peaks identified by BCP_TF are represented in a 7-column BED format that includes: chromosome name, start position, end position, peak length, enrichment score, p-value, and summit location.

source_name: E13.5 Limb

value: E13.5 Limb


title: E13.5_Limb, pSmad15_ChIP

description:
Library name: E13.5_Limb_pSmad15
Peaks identified by BCP_TF are represented in a 7-column BED format that includes: chromosome name, start position, end position, peak length, enrichment score, p-value, and summit location.


title: WT_80_T0 (biol rep 2)

description: Library name: Sample 2

value: MEF 80

value: Mouse embryonic fibroblasts

value: WT


title: E13.5_Limb, Input

description: Library name: E13.5_Limb_Input


title: WT_79_T0 (biol rep 1)

description: Library name: Sample 1

value: MEF 79


title: b1

city: Zhan Jiang

first: Guozhu

last: Ning

state: Guangdong

address: Nr. 57 Renmin Dadao Nan, Xiashan  Zhanjiang, P. R. China

country: China

institute: Affiliated Hospital of Guangdong Medical University

description:
Library name: sample1
M

data_processing:
The difference in the number of alternative splicing events between groups was analyzed using rMATS (version 4.1.0)
Assembly: GRCz11
Supplementary files format and content: Gene expression matrix

organism: Danio rerio

source_name: embryo

extract_protocol:
Embryos were collected at the 10-somite stage and gently transferred into lysis buffer. Reverse transcription was performed using a SMARTer Ultra Low RNA Kit (Clontech, 634437) directly from the cell lysates.
The cDNA library was prepared using an Advantage 2 PCR Kit (Clontech，639206) and then sequenced via the Illumina sequencing platform (NovaSeq 6000).

value: embryo


description: Library name: AT5G13790_A_lyrata_MN47_DAPi712F02-ORGi5038-96P155

value: plant

value: MADS


title: Single cell BC9 from distal small intestine


title: b14

description:
Library name: sample2
MG

value: Heterozygote


description: Library name: AT4G31800_A_lyrata_MN47_DAPi712F02-ORGi5038-96P220

value: WRKY


title: Single cell BC8 from distal small intestine

value: distal small intestine


description: Library name: Solyc04g078640.3.1_A_lyrata_MN47_DAPi712F01-ORGi5038-96P247


title: Single cell BC7 from distal small intestine


description: Library name: AT1G20910_A_lyrata_MN47_DAPi712F01-ORGi5038-96P155

value: ARID


description: Library name: AT5G47390_A_lyrata_MN47_DAPi712F01-ORGi5038-96P220

value: MYBRELATED


title: Single cell BC4 from distal small intestine


description: Library name: Solyc05g007180.3.1_A_lyrata_MN47_DAPi712E12-ORGi5038-96P247

value: HOMEOBOX


title: Single cell BC3 from distal small intestine


description: Library name: AT1G52880_A_lyrata_MN47_DAPi712E12-ORGi5038-96P220


title: Single cell BC6 from distal small intestine


title: Single cell BC2 from distal small intestine


description: Library name: Carub.0002s2670.1_A_lyrata_MN47_DAPi712E11-ORGi5038-96P247


title: Single cell BC12 from distal small intestine


description: Library name: AT1G20980_A_lyrata_MN47_DAPi712E11-ORGi5038-96P220

value: SBP


title: Single cell BC11 from distal small intestine


description: Library name: AT4G10350_A_lyrata_MN47_DAPi712E11-ORGi5038-96P155

value: NAC


title: Single cell BC10 from distal small intestine


description: Library name: Solyc10g005080.3.1_A_lyrata_MN47_DAPi712E10-ORGi5038-96P247


title: Single cell BC1 from distal small intestine


title: Single cell BB9 from proximal small intestine

source_name: proximal small intestine

value: proximal small intestine


description: Library name: AT4G17980_A_lyrata_MN47_DAPi712E10-ORGi5038-96P220


description: Library name: AT5G66300_A_lyrata_MN47_DAPi712E10-ORGi5038-96P155


title: Single cell BB8 from proximal small intestine


description: Library name: AT3G15500_A_lyrata_MN47_DAPi712E09-ORGi5038-96P155


description: Library name: XP_013615900.1_A_lyrata_MN47_DAPi712E09-ORGi5038-96P247


title: Single cell BB6 from proximal small intestine


title: Single cell BB7 from proximal small intestine


title: Single cell BB5 from proximal small intestine


description: Library name: AT5G14960_A_lyrata_MN47_DAPi712E08-ORGi5038-96P220


description: Library name: AT1G75390_A_lyrata_MN47_DAPi712E08-ORGi5038-96P155

value: BZIP


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710G12-ORGi5005-96P358

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

organism: Arabidopsis thaliana


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H12-ORGi5005-96P354


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710A12-ORGi5005-96P358


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H12-ORGi5005-96P155


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A01-ORGi5005-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H01-ORGi5005-96P354


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A01-ORGi5005-96P364


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A12-ORGi5005-96P364


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H12-ORGi5005-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712G12-ORGi5005-96P364


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710H01-ORGi5005-96P358


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711A12-ORGi5005-96P166


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711H12-ORGi5005-96P166


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H12-ORGi5005-96P169


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711H01-ORGi5005-96P166


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711A01-ORGi5005-96P166


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H01-ORGi5005-96P169


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A01-ORGi5005-96P354


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A12-ORGi5005-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711H01-ORGi5005-96P361


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H12-ORGi5005-96P364


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H01-ORGi5005-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710H12-ORGi5005-96P358


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711A01-ORGi5005-96P361


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi711H12-ORGi5005-96P361


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A01-ORGi5005-96P169


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A12-ORGi5005-96P169


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710A01-ORGi5005-96P358


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H01-ORGi5005-96P364


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A12-ORGi5005-96P155


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710H12-ORGi5005-96P151


title: Single cell BB4 from proximal small intestine


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H12-ORGi5005-96P220


title: Single cell BB10 from proximal small intestine


description: Library name: AT5G62020_A_lyrata_MN47_DAPi712E04-ORGi5038-96P220

value: HSF


title: Single cell BA9 from proximal small intestine


description: Library name: AT1G76880_A_lyrata_MN47_DAPi712E06-ORGi5038-96P155

value: TRIHELIX


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712H01-ORGi5005-96P220


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H12-ORGi5005-96P206


description: Library name: AL3G23910.t2_A_lyrata_MN47_DAPi712E07-ORGi5038-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710H01-ORGi5005-96P151


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A01-ORGi5005-96P220


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A01-ORGi5005-96P155


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H01-ORGi5005-96P206


title: Single cell BB11 from proximal small intestine


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi712A12-ORGi5005-96P220


description: Library name: AT2G18550_A_lyrata_MN47_DAPi712E07-ORGi5038-96P220


description: Library name: AT5G56110_A_lyrata_MN47_DAPi712E06-ORGi5038-96P220

value: MYB


title: Single cell BB1 from proximal small intestine


description: Library name: AT4G00730_A_lyrata_MN47_DAPi712E05-ORGi5038-96P155


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H12-ORGi5005-96P203


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A01-ORGi5005-96P206


title: Single cell BB2 from proximal small intestine


description: Library name: AT3G60530_A_lyrata_MN47_DAPi712E05-ORGi5038-96P220


title: Single cell BA8 from proximal small intestine


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709H01-ORGi5005-96P203


description: Library name: AT5G64750_A_lyrata_MN47_DAPi712E03-ORGi5038-96P220


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi710A12-ORGi5005-96P151


description: Library name: LOC_Os06g07030.1_A_lyrata_MN47_DAPi712E01-ORGi5038-96P247


title: Single cell BB12 from proximal small intestine


description: Library name: Carub.0002s1959.1_A_thaliana_Col-0_DAPi712H10-ORGi5005-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A12-ORGi5005-96P206


title: Single cell BA5 from proximal small intestine


title: Single cell BA7 from proximal small intestine


description: Library name: LOC_Os02g42970.1_A_lyrata_MN47_DAPi712E03-ORGi5038-96P247


description: Library name: AT2G46270_A_thaliana_Col-0_DAPi712H11-ORGi5005-96P220


title: Single cell BA6 from proximal small intestine


description: Library name: AT1G13260_A_lyrata_MN47_DAPi712E01-ORGi5038-96P220

value: RAV


description: Library name: AT4G21030_A_lyrata_MN47_DAPi712E02-ORGi5038-96P155


description: Library name: AL2G28980.t1_A_thaliana_Col-0_DAPi712H11-ORGi5005-96P247


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A01-ORGi5005-96P203


title: Single cell BA2 from proximal small intestine


title: Single cell BA3 from proximal small intestine


title: Single cell BA4 from proximal small intestine


description: Library name: Control_TF_DNA_A_thaliana_Col-0_DAPi709A12-ORGi5005-96P203


description: Library name: XP_013634112.1_A_thaliana_Col-0_DAPi712H08-ORGi5005-96P247


description: Library name: AT5G18560_A_thaliana_Col-0_DAPi712H07-ORGi5005-96P220


description: Library name: AT5G17300_A_thaliana_Col-0_DAPi712H08-ORGi5005-96P220


description: Library name: Carub.0005s0095.1_A_thaliana_Col-0_DAPi712H08-ORGi5005-96P364

value: BBRBPC


description: Library name: AL1G24970.t1_A_thaliana_Col-0_DAPi712H09-ORGi5005-96P364

value: plant


description: Library name: AT2G47070_A_thaliana_Col-0_DAPi712H10-ORGi5005-96P220


title: Single cell BA12 from proximal small intestine


description: Library name: LOC_Os01g17260.2_A_thaliana_Col-0_DAPi712H07-ORGi5005-96P247


description: Library name: LOC_Os10g26500.1_A_lyrata_MN47_DAPi712D12-ORGi5038-96P247


description: Library name: XP_013587997.1_A_lyrata_MN47_DAPi712D11-ORGi5038-96P247


description: Library name: AT5G11260_A_lyrata_MN47_DAPi712D12-ORGi5038-96P220


title: Single cell BA11 from proximal small intestine


description: Library name: XP_013635977.1_A_thaliana_Col-0_DAPi712H05-ORGi5005-96P364


description: Library name: AT3G18990_A_lyrata_MN47_DAPi712D11-ORGi5038-96P220


description: Library name: Solyc08g078340.3.1_A_thaliana_Col-0_DAPi712H09-ORGi5005-96P247


description: Library name: AL4G45550.t1_A_thaliana_Col-0_DAPi712H06-ORGi5005-96P247


description: Library name: AT5G11510_A_thaliana_Col-0_DAPi712H06-ORGi5005-96P155


title: Single cell BA10 from proximal small intestine


description: Library name: AT5G61620_A_thaliana_Col-0_DAPi712H05-ORGi5005-96P155


description: Library name: LOC_Os10g28340.1_A_thaliana_Col-0_DAPi712H04-ORGi5005-96P364


description: Library name: AT3G49530_A_thaliana_Col-0_DAPi712H07-ORGi5005-96P155


description: Library name: AT1G01060_A_thaliana_Col-0_DAPi712H05-ORGi5005-96P220


title: Single cell AH8 from colon

value: colon


description: Library name: LOC_Os08g06110.3_A_lyrata_MN47_DAPi712D10-ORGi5038-96P247


description: Library name: Solyc01g102340.3.1_A_thaliana_Col-0_DAPi712H04-ORGi5005-96P247


description: Library name: AT2G46770_A_lyrata_MN47_DAPi712D10-ORGi5038-96P155


description: Library name: AT3G56850_A_lyrata_MN47_DAPi712D12-ORGi5038-96P155


description: Library name: AL8G10650.t1_A_lyrata_MN47_DAPi712D09-ORGi5038-96P247


title: Single cell AH6 from colon


description: Library name: XP_013629448.1_A_thaliana_Col-0_DAPi712H03-ORGi5005-96P247


description: Library name: AT4G36740_A_thaliana_Col-0_DAPi712H03-ORGi5005-96P155


title: Single cell AH9 from colon


description: Library name: Carub.0008s0285.1_A_lyrata_MN47_DAPi712D08-ORGi5038-96P247


description: Library name: AT2G22430_A_thaliana_Col-0_DAPi712H02-ORGi5005-96P220


title: Single cell AH5 from colon


title: Single cell AH3 from colon


description: Library name: AT5G57620_A_thaliana_Col-0_DAPi712G12-ORGi5005-96P155


description: Library name: AT3G02940_A_thaliana_Col-0_DAPi712H04-ORGi5005-96P220


description: Library name: Solyc03g116890.3.1_A_thaliana_Col-0_DAPi712G11-ORGi5005-96P247


description: Library name: XP_013609718.1_A_thaliana_Col-0_DAPi712G12-ORGi5005-96P247


description: Library name: AT5G65210_A_thaliana_Col-0_DAPi712G11-ORGi5005-96P155


description: Library name: Solyc01g095460.3.1_A_lyrata_MN47_DAPi712D07-ORGi5038-96P247


title: Single cell AH2 from colon


description: Library name: AT5G09410_A_thaliana_Col-0_DAPi712G11-ORGi5005-96P220

value: CAMTA


description: Library name: AT1G74480_A_lyrata_MN47_DAPi712D07-ORGi5038-96P220

value: RWPRK


description: Library name: AT2G30250_A_thaliana_Col-0_DAPi712H03-ORGi5005-96P220

value: WRKY


description: Library name: Carub.0002s2128.1_A_thaliana_Col-0_DAPi712G10-ORGi5005-96P364


title: Single cell AH12 from colon


description: Library name: AT2G47070_A_thaliana_Col-0_DAPi712H04-ORGi5005-96P155


description: Library name: XP_013589913.1_A_thaliana_Col-0_DAPi712G10-ORGi5005-96P247


description: Library name: LOC_Os10g41200.1_A_thaliana_Col-0_DAPi712G09-ORGi5005-96P247


title: Single cell AH7 from colon


title: Single cell AH11 from colon


description: Library name: AT3G57920_A_lyrata_MN47_DAPi712D06-ORGi5038-96P220


description: Library name: AT5G06100_A_thaliana_Col-0_DAPi712H02-ORGi5005-96P155


title: Single cell AH10 from colon


description: Library name: AT1G72740_A_thaliana_Col-0_DAPi712G09-ORGi5005-96P220


description: Library name: AT1G20980_A_lyrata_MN47_DAPi712D06-ORGi5038-96P155


description: Library name: AT5G03150_A_lyrata_MN47_DAPi712D08-ORGi5038-96P220


description: Library name: AT2G35530_A_thaliana_Col-0_DAPi712G09-ORGi5005-96P155


title: Single cell AH1 from colon


description: Library name: AT5G39610_A_lyrata_MN47_DAPi712D07-ORGi5038-96P155


description: Library name: XP_013599843.1_A_thaliana_Col-0_DAPi712G08-ORGi5005-96P364


description: Library name: AT3G50410_A_thaliana_Col-0_DAPi712H06-ORGi5005-96P220


description: Library name: LOC_Os02g33430.1_A_lyrata_MN47_DAPi712D05-ORGi5038-96P247


description: Library name: AT5G45300_A_thaliana_Col-0_DAPi712G10-ORGi5005-96P220


description: Library name: AT2G01940_A_thaliana_Col-0_DAPi712G08-ORGi5005-96P220


description: Library name: AL4G38490.t1_A_thaliana_Col-0_DAPi712G08-ORGi5005-96P247


description: Library name: AT2G01930_A_lyrata_MN47_DAPi712D05-ORGi5038-96P220


description: Library name: AT5G19790_A_thaliana_Col-0_DAPi712G07-ORGi5005-96P220


description: Library name: Carub.0003s1161.1.p_A_thaliana_Col-0_DAPi712G07-ORGi5005-96P247


title: Single cell AG9 from colon


title: Single cell AG8 from colon


description: Library name: AT4G34590_A_thaliana_Col-0_DAPi712G07-ORGi5005-96P155


description: Library name: AT5G02320_A_thaliana_Col-0_DAPi712G06-ORGi5005-96P220


description: Library name: AT5G45300_A_lyrata_MN47_DAPi712D04-ORGi5038-96P155


description: Library name: AT3G20770_A_lyrata_MN47_DAPi712D05-ORGi5038-96P155

value: EIL


title: Single cell AG3 from colon


description: Library name: Carub.0001s1194.1_A_lyrata_MN47_DAPi712D03-ORGi5038-96P247


description: Library name: AT1G69180_A_thaliana_Col-0_DAPi712G05-ORGi5005-96P220


description: Library name: AT5G09410_A_thaliana_Col-0_DAPi712G06-ORGi5005-96P155


title: Single cell AG5 from colon


description: Library name: AT4G17980_A_lyrata_MN47_DAPi712D03-ORGi5038-96P155


description: Library name: AT5G65410_A_lyrata_MN47_DAPi712D03-ORGi5038-96P220

value: ZFHD


title: Single cell AG4 from colon


title: Single cell AG11 from colon


description: Library name: AT5G16820_A_thaliana_Col-0_DAPi712G05-ORGi5005-96P155


description: Library name: AT1G46768_A_thaliana_Col-0_DAPi712G04-ORGi5005-96P220


description: Library name: AL4G46570.t1_A_thaliana_Col-0_DAPi712G05-ORGi5005-96P364


title: Single cell AG10 from colon


description: Library name: Solyc10g018560.2.1_A_thaliana_Col-0_DAPi712G06-ORGi5005-96P364


description: Library name: AT3G50060_A_thaliana_Col-0_DAPi712G02-ORGi5005-96P220


title: Single cell AG12 from colon


description: Library name: AT1G32150_A_thaliana_Col-0_DAPi712G03-ORGi5005-96P155


description: Library name: LOC_Os01g18240.1_A_thaliana_Col-0_DAPi712G04-ORGi5005-96P247


description: Library name: Carub.0005s0004.1_A_thaliana_Col-0_DAPi712G01-ORGi5005-96P364


description: Library name: Carub.0001s3581.1.p_A_lyrata_MN47_DAPi712D01-ORGi5038-96P247


title: Single cell AF9 from cecum

value: cecum


description: Library name: AT1G18330_A_thaliana_Col-0_DAPi712G01-ORGi5005-96P220

value: MYBRELATED


description: Library name: AT4G18450_A_thaliana_Col-0_DAPi712G01-ORGi5005-96P155


description: Library name: AT1G13600_A_thaliana_Col-0_DAPi712F12-ORGi5005-96P155


title: Single cell AF5 from cecum


description: Library name: AT1G76880_A_thaliana_Col-0_DAPi712F11-ORGi5005-96P220


title: Single cell AF6 from cecum


description: Library name: AT4G14770_A_thaliana_Col-0_DAPi712F10-ORGi5005-96P220

value: CPP


title: Single cell AF7 from cecum


description: Library name: AT3G15170_A_thaliana_Col-0_DAPi712F10-ORGi5005-96P155

value: NAC


description: Library name: LOC_Os09g25060.1_A_thaliana_Col-0_DAPi712F11-ORGi5005-96P247


description: Library name: AT1G12260_A_lyrata_MN47_DAPi712C12-ORGi5038-96P220


description: Library name: AT1G80840_A_thaliana_Col-0_DAPi712G03-ORGi5005-96P220


description: Library name: AL2G32420.t2_A_thaliana_Col-0_DAPi712F10-ORGi5005-96P247


description: Library name: AT5G11260_A_thaliana_Col-0_DAPi712F11-ORGi5005-96P155

value: BZIP


description: Library name: Carub.0002s1646.1_A_lyrata_MN47_DAPi712C12-ORGi5038-96P247

value: HOMEOBOX


description: Library name: AL2G40550.t1_A_lyrata_MN47_DAPi712C11-ORGi5038-96P247


title: Single cell AF8 from cecum


description: Library name: AT2G45480_A_thaliana_Col-0_DAPi712F09-ORGi5005-96P220

value: GRF


description: Library name: AT4G00730_A_lyrata_MN47_DAPi712C11-ORGi5038-96P220


description: Library name: AL5G11070.t1_A_thaliana_Col-0_DAPi712F08-ORGi5005-96P364


title: Single cell AF3 from cecum


title: Single cell AF4 from cecum


description: Library name: AT4G36620_A_lyrata_MN47_DAPi712D02-ORGi5038-96P155


description: Library name: AT2G02820_A_thaliana_Col-0_DAPi712F08-ORGi5005-96P220

value: MYB


description: Library name: AT1G43700_A_lyrata_MN47_DAPi712C11-ORGi5038-96P155


description: Library name: Carub.0008s0039.1_A_thaliana_Col-0_DAPi712F09-ORGi5005-96P247


description: Library name: Carub.0001s0116.1_A_lyrata_MN47_DAPi712C10-ORGi5038-96P247


description: Library name: AT4G01500_A_thaliana_Col-0_DAPi712G02-ORGi5005-96P155


title: Single cell AG1 from colon


description: Library name: AT3G50260_A_lyrata_MN47_DAPi712D02-ORGi5038-96P220


description: Library name: XP_013591813.1_A_thaliana_Col-0_DAPi712F10-ORGi5005-96P364


description: Library name: AT1G06850_A_lyrata_MN47_DAPi712C12-ORGi5038-96P155


description: Library name: AT5G18270_A_lyrata_MN47_DAPi712C10-ORGi5038-96P155


title: Single cell AF12 from cecum


description: Library name: LOC_Os10g40810.1_A_thaliana_Col-0_DAPi712F06-ORGi5005-96P364


description: Library name: AT2G45420_A_thaliana_Col-0_DAPi712F06-ORGi5005-96P220


description: Library name: Solyc06g048630.3.1_A_lyrata_MN47_DAPi712C09-ORGi5038-96P247


description: Library name: AT5G07680_A_thaliana_Col-0_DAPi712F08-ORGi5005-96P155


description: Library name: XP_013586407.1_A_thaliana_Col-0_DAPi712F07-ORGi5005-96P247


description: Library name: AT5G52830_A_thaliana_Col-0_DAPi712F07-ORGi5005-96P220


title: Single cell AF2 from cecum


title: Single cell AF10 from cecum


description: Library name: AT1G76420_A_lyrata_MN47_DAPi712C09-ORGi5038-96P220


title: Single cell AF1 from cecum


description: Library name: AT2G01060_A_thaliana_Col-0_DAPi712F05-ORGi5005-96P220


description: Library name: AT1G33240_A_thaliana_Col-0_DAPi712F03-ORGi5005-96P220

value: TRIHELIX


description: Library name: AT4G25480_A_thaliana_Col-0_DAPi712F04-ORGi5005-96P220


description: Library name: LOC_Os08g44050.1_A_thaliana_Col-0_DAPi712F02-ORGi5005-96P364


description: Library name: LOC_Os01g46970.1_A_lyrata_MN47_DAPi712C07-ORGi5038-96P247


description: Library name: XP_013613838.1_A_lyrata_MN47_DAPi712C08-ORGi5038-96P247


title: Single cell AE9 from cecum


description: Library name: AT5G13790_A_thaliana_Col-0_DAPi712F02-ORGi5005-96P155

value: MADS


description: Library name: XP_013620714.1_A_thaliana_Col-0_DAPi712F01-ORGi5005-96P364

value: plant


title: Single cell AE8 from cecum


description: Library name: Solyc08g079120.3.1_A_thaliana_Col-0_DAPi712F03-ORGi5005-96P247


description: Library name: AT4G31800_A_thaliana_Col-0_DAPi712F02-ORGi5005-96P220


description: Library name: Solyc04g078640.3.1_A_thaliana_Col-0_DAPi712F01-ORGi5005-96P247


title: Single cell AE7 from cecum


description: Library name: Solyc01g091420.2.1_A_thaliana_Col-0_DAPi712F05-ORGi5005-96P364


description: Library name: AT5G60130_A_lyrata_MN47_DAPi712C07-ORGi5038-96P220


description: Library name: AT5G47390_A_thaliana_Col-0_DAPi712F01-ORGi5005-96P220


description: Library name: AT5G62470_A_lyrata_MN47_DAPi712C08-ORGi5038-96P220


description: Library name: AT1G20910_A_thaliana_Col-0_DAPi712F01-ORGi5005-96P155

value: ARID


description: Library name: AT3G62420_A_lyrata_MN47_DAPi712C07-ORGi5038-96P155


description: Library name: AT1G52880_A_thaliana_Col-0_DAPi712E12-ORGi5005-96P220


description: Library name: Solyc05g007180.3.1_A_thaliana_Col-0_DAPi712E12-ORGi5005-96P247


title: Single cell AE5 from cecum


description: Library name: Carub.0002s2670.1_A_thaliana_Col-0_DAPi712E11-ORGi5005-96P247


title: Single cell AE6 from cecum


title: Single cell AE4 from cecum


description: Library name: AT1G20980_A_thaliana_Col-0_DAPi712E11-ORGi5005-96P220

value: SBP


description: Library name: Solyc10g005080.3.1_A_thaliana_Col-0_DAPi712E10-ORGi5005-96P247


description: Library name: AT4G17980_A_thaliana_Col-0_DAPi712E10-ORGi5005-96P220


description: Library name: Solyc08g068320.3.1_A_lyrata_MN47_DAPi712C04-ORGi5038-96P247


title: Single cell AE3 from cecum


description: Library name: AT5G66300_A_thaliana_Col-0_DAPi712E10-ORGi5005-96P155


description: Library name: AT4G32730_A_lyrata_MN47_DAPi712C05-ORGi5038-96P155


description: Library name: AL2G34360.t1_A_thaliana_Col-0_DAPi712E10-ORGi5005-96P364

value: RWPRK


description: Library name: AT3G27010_A_lyrata_MN47_DAPi712C04-ORGi5038-96P220

value: TCP


title: Single cell AE12 from cecum


description: Library name: XP_013615900.1_A_thaliana_Col-0_DAPi712E09-ORGi5005-96P247


description: Library name: AT4G14770_A_lyrata_MN47_DAPi712C04-ORGi5038-96P155


description: Library name: AT3G15500_A_thaliana_Col-0_DAPi712E09-ORGi5005-96P155


title: Single cell AF11 from cecum


title: Single cell AE2 from cecum


description: Library name: AT5G03790_A_lyrata_MN47_DAPi712C06-ORGi5038-96P220


description: Library name: XP_013602769.1_A_lyrata_MN47_DAPi712C03-ORGi5038-96P247


description: Library name: AT5G14960_A_thaliana_Col-0_DAPi712E08-ORGi5005-96P220


title: Single cell AE11 from cecum


description: Library name: AT1G75390_A_thaliana_Col-0_DAPi712E08-ORGi5005-96P155


description: Library name: AT1G69690_A_lyrata_MN47_DAPi712C02-ORGi5038-96P220


description: Library name: AT4G10350_A_thaliana_Col-0_DAPi712E11-ORGi5005-96P155


title: Single cell AE10 from cecum


description: Library name: AT2G18550_A_thaliana_Col-0_DAPi712E07-ORGi5005-96P220


description: Library name: AL3G23910.t2_A_thaliana_Col-0_DAPi712E07-ORGi5005-96P247


title: Single cell AE1 from cecum


description: Library name: AT5G56110_A_thaliana_Col-0_DAPi712E06-ORGi5005-96P220


description: Library name: AT1G27730_A_lyrata_MN47_DAPi712C01-ORGi5038-96P220


description: Library name: AT5G17800_A_lyrata_MN47_DAPi712C02-ORGi5038-96P155


title: Single cell AD9 from distal small intestine

value: distal small intestine


description: Library name: XP_013602065.1_A_thaliana_Col-0_DAPi712E06-ORGi5005-96P364


description: Library name: AT1G76880_A_thaliana_Col-0_DAPi712E06-ORGi5005-96P155


description: Library name: AT3G60530_A_thaliana_Col-0_DAPi712E05-ORGi5005-96P220


description: Library name: XP_013589953.1_A_lyrata_MN47_DAPi712B12-ORGi5038-96P247


title: Single cell AD8 from distal small intestine


description: Library name: LOC_Os10g07510.1_A_thaliana_Col-0_DAPi712E05-ORGi5005-96P364


description: Library name: AT4G00730_A_thaliana_Col-0_DAPi712E05-ORGi5005-96P155


description: Library name: AT5G62020_A_thaliana_Col-0_DAPi712E04-ORGi5005-96P220

value: HSF


title: Single cell AD7 from distal small intestine


description: Library name: LOC_Os02g42970.1_A_thaliana_Col-0_DAPi712E03-ORGi5005-96P247


description: Library name: AT4G21030_A_thaliana_Col-0_DAPi712E02-ORGi5005-96P155


description: Library name: Solyc07g040920.2.1_A_lyrata_MN47_DAPi712B11-ORGi5038-96P247


description: Library name: AT1G52880_A_lyrata_MN47_DAPi712B12-ORGi5038-96P155