title: Mulitome, WT, E14.5, GEX

first: Shanshan

last: Yi

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: College of Life Science and Technology

institute: Tongji University

description:
Library name: WT145_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
WT145_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz

data_processing:
The 10X Genomics CellRanger-ARC (v2.0.2) pipeline were used to process multiome data. The raw fastq files of RNA-seq and ATAC-seq libraries from the sample were aligned to UCSC mouse genome (mm10) and quantified using 'cellranger-arc count'.
Assembly: mm10
Supplementary files format and content: h5 file: contains both RNA-seq counts and ATAC-seq counts; tsv.gz: fragments file for ATAC-seq; tsv.gz.tbi: fragment file index for ATAC-seq

molecule: nuclear RNA

source_name: placenta

growth_protocol: For natural fertilization, female C57BL/6n mice were mated with male PWK/PhJ mice, followed by placental tissue collection at specified developmental stages. For nuclear transfer, cumulus cells from BPF1 (female C57BL/6n×male PWK/PhJ) female mice were injected into enucleated oocytes. The reconstructed oocytes were then incubated in CZB medium for 1 h before activation. Activation was performed by incubation in Ca2+-free CZB medium containing 1 mM SrCl2 and 5 mg/mL CB for 6 h, and then the oocytes were thoroughly washed and cultured in G-1 PLUS medium (Vitrolife) at 37℃ under 5% CO2. The SCNT embryos were transplanted into the uterus of pseudopregnant recipients at the stage of 2-cell development, and the samples were collected at the appropriate day.

extract_protocol:
Placental samples were collected from SCNT and naturally fertilized pregnant mice. Pregnant ICR mice at E12.5, E14.5 and E18.5 were humanely sacrificed and their placenta were dissected. Placentas were washed with PBS to remove blood and blotted dry with absorbent paper. The treated placentas were snap-frozen in liquid nitrogen and stored to a liquid nitrogen tank. Placental tissue was thoroughly washed in ice-cold PBS to eliminate blood contaminants and precisely weighed (2-3 g). The tissue was then carefully minced into ~1 mm³ fragments using sterile scissors before enzymatic digestion in pre-warmed DMEM/F12 medium (Gibco) containing 0.5 mg/mL collagenase IV (Thermo Fisher Scientific, 17104019) and 0.2 mg/mL DNase I (Roche 10104159001). The digestion was performed at 37°C for 20 minutes in a shaking water bath with gentle manual inversion every 10 minutes.
Libraries were constructed by following the 10X Genomics Chromiun Next GEM Sing Cell Multiome ATAC + Gene Expression protocol (CG000338).

treatment_protocol: Small molecule treatments were performed with 50nM Farrerol for 16h starting after activation.

value: placenta

tag: developmental stage

value: embryonic day (E) 14.5

tag: origin

value: Naturally fertilized

value: C57BL/6n x PWK/PhJ

tag: library type

value: mRNA


title: WT_rep3

status: Public on Jun 18 2026

type: SRA

city: New York

first: David

middle: W. J.

last: McQuarrie

state: NY

address: 1300 York Avenue

department: Pharmacology

country: USA

institute: Weill Cornell Medicine, Cornell University

description: Library name: Sample3

library_source: transcriptomic

data_processing:
Sequencing quality was assessed using a standard quality-control pipeline. Adapter sequences were removed with Trim Galore (v0.6.7), and reads were aligned to the D. melanogaster dm6 reference genome using STAR (v2.7.11a). Gene-level counts were generated with FeatureCounts (v2.0.8) and used for differential gene expression analysis with DESeq2 (v1.40.2) under default parameters.
Assembly: dm6
Supplementary files format and content: tab-delimited text file with counts for each sample replicate

molecule: total RNA

organism: Drosophila melanogaster

source_name: Embryo

extract_protocol:
RNA was extracted with Trizol followed by phenol chloroform extraction.
mRNA was enriched from total RNA by poly(A) selection. Sequencing libraries were constructed by Novogene (UK) Company Limited using their standard Illumina-compatible mRNA library preparation protocol (Plant and Animal Eukaryotic mRNA, WOBI) and sequenced on an Illumina NovaSeq X Plus system.

tag: tissue

value: Embryo

tag: genotype

value: Wild type control (elav[e5]/FM7) rep3


title: E15 n1 Xenium

type: RNA

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

hyb_protocol: Samples were incubated in a probe solution for 16-24 hours at 50°C. For all datasets, the solution contained the same set of 347-gene targeting probes: 247 from the 10x Genomics predesigned mouse brain panel, and 100 from a custom add-on that allowed better resolution of key cell types within the ventricular-subventricular zone. Nonspecific probe binding was next washed off via PBS-T, a 30-minute incubation in post-hybridization buffer at 37°C, and additional PBS-T washes. Ligation of the hybridized probes was performed by incubating the samples in ligation enzymes for 2 hours at 37°C. After a series of PBS-T washes, the ligated probes were amplified via rolling circle amplification; to achieve this, samples were incubated with amplification enzyme for 2 hours at 30°C. These steps were next followed by autoflorescence quenching and nuclear staining.

scan_protocol: Image processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system. Data was acquired on instrument software versions 2.0.1.0 to 3.1.0.0, and onboard analysis versions 2.0.0.10 to 3.1.0.4.

data_processing: Following on-instrument analysis, all datasets were run through 10x Genomics Xenium Ranger v3 software (xeniumranger resegment function) with settings as recommended by the manufacturer to assign transcripts to the closest nucleus within a maximum distance of 2 µm.

label: Xenium probe set

organism: Mus musculus

source_name: Brain (embryonic coronal brain sections containing the lateral ventricles)

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Brain tissue was collected from mice at E15, E18, and P2. Samples were fixed in 4% paraformaldehyde (Electron Microscopy Sciences) for 24 hours at 4°C and subsequently cryopreserved in 30% sucrose for 48 hours. Samples were embedded in O.C.T. (Tissue-Tek) and cryosectioned coronally onto Xenium slides (chemistry v1) at a thickness of 10 μm. Afterwards, all samples were processed as per the Xenium worflow for fixed frozen tissue, which involved washes in PBS, water, 100% ethanol, and 70% ethanol, followed by decrosslinking.

treatment_protocol: E15 samples were collected from pregnant mice that were intraperitoneally administered 200 µL of 0.1% BSA in PBS 48 hours prior to collection.

tag: tissue preservation method

value: Other

tag: preservation method

value: Fixed frozen

tag: treatment

value: Pregnant mice were intraperitoneally administered 200 µL of 0.1% BSA in PBS 48 hours prior to collection.


title: KO_MHCneg_rep4

status: Public on Jun 17 2026

city: Glasgow

first: Heather

last: Mathie

state: --None--

address: Sir Graeme Davies Building, 126 University Place

country: United Kingdom

institute: University of Glasgow

description:
Library name: Sample25
Sorted MHCII-ve Lung macrophages
ES_CC.csv
KO_MHCN4_EKRN240061774-1A_22JKL2LT4

data_processing:
Raw reads of fastq format were processed through in-house scripts, removing adapter, poly-N and low-quality reads from raw data. Index of the reference genome was built and paired-end clean 1 reads were aligned using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads for each gene. Differential expression analysis of two conditions/groups was performed using the DESeq2Rpackage (1.20.0). The resulting p-values were adjusted suing the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed
Assembly: mm10
Supplementary files format and content: csv file containing the read counts from this experiment

source_name: Lung

extract_protocol:
Peritoneal lavage cells were isolated by injecting 10 ml PBS containing EDTA into the peritoneal cavity of euthanized mice and collecting the fluid with a syringe. Bone marrow cells were obtained by dissecting the hind limbs, removing the muscle, cutting the femur and tibia bones and flushing with 1 ml PBS containing EDTA. Lungs were removed and chopped finely, before digestion with 0.8 mg/mL Dispase II, 0.2 mg/mL Collagenase P, and 0.1 mg/mL DNase I (Roche) in HBSS shaken at 800 rpm, at 37°C for 45 min. Lungs were filtered through a 40 µm EASYstrainer mesh (Greiner Bio-One), and RBC were lysed. FACS sorted monocytes from the bone marrow, MHCII negative macrophages from the lungs, and SPMs from the peritoneal cavity of WT and ACKR2-/- mice were isolated. RNA extraction was performed on sorted samples for RNA sequencing. RNA was extracted using the RNeasy Microkit with on-column DNAse I digestion (Qiagen), following manufacturer’s instructions. RNA samples were then sent to a commercial sequencing provider (Novogene), for RNA QC, mRNA library preparation (poly-A enrichment) and Illumina Sequencing.
Total RNA was amplified using  SMARTer Ultra Low Input RNA Kit for Sequencing and reverse transcribed into the first-strand cDNA. The double-strand cDNA was synthesized by LD-PCR amplification, followed by the purification with AMPure XP beads and quantification with Qubit. The cDNA samples were then fragmented, end-repaired, A-tailed, and ligated with adaptors. After size selection and PCR enrichment, the RNA library was ready for sequencing.

treatment_protocol: Naïve WT and ACKR2-/- female mice.

value: Lung

tag: cell type

value: MHCII negative macrphage

value: Naïve


title: KO_MHCneg_rep3

description:
Library name: Sample24
Sorted MHCII-ve Lung macrophages
ES_CC.csv
KO_MHCN3_EKRN240061773-1A_22JKL2LT4


title: KO_MHCneg_rep5

description:
Library name: Sample26
Sorted MHCII-ve Lung macrophages
ES_CC.csv
KO_MHCN5_EKRN240061775-1A_22JKL2LT4


title: KO_MHCneg_rep2

description:
Library name: Sample23
Sorted MHCII-ve Lung macrophages
ES_CC.csv
KO_MHCN2_EKRN240061772-1A_22JKL2LT4


title: KO_MHCneg_rep1

description:
Library name: Sample22
Sorted MHCII-ve Lung macrophages
ES_CC.csv
KO_MHCN1_EKRN240061771-1A_22JKL2LT4


title: WT_MHCneg_rep4

description:
Library name: Sample20
Sorted MHCII-ve Lung macrophages
ES_CC.csv
WT_MHCN4_EKRN240061764-1A_22JKL2LT4

value: WT


title: WT_MHCneg_rep5

description:
Library name: Sample21
Sorted MHCII-ve Lung macrophages
ES_CC.csv
WT_MHCN5_EKRN240061765-1A_22JKL2LT4


title: WT_MHCneg_rep2

description:
Library name: Sample18
Sorted MHCII-ve Lung macrophages
ES_CC.csv
WT_MHCN2_EKRN240061762-1A_22JKL2LT4


title: WT_MHCneg_rep1

description:
Library name: Sample17
Sorted MHCII-ve Lung macrophages
ES_CC.csv
WT_MHCN1_EKRN240061761-1A_22JKL2LT4


title: WT_MHCneg_rep3

description:
Library name: Sample19
Sorted MHCII-ve Lung macrophages
ES_CC.csv
WT_MHCN3_EKRN240061763-1A_22JKL2LT4


title: KO_SPM_4

description:
Library name: Sample16
Sorted small perioneal macrophages
gene_countA.csv
KO4

source_name: Peritoneal Lavage

value: Peritoneal Lavage

value: Small peritoneal macrophage


title: KO_SPM_3

description:
Library name: Sample15
Sorted small perioneal macrophages
gene_countA.csv
KO3


title: KO_SPM_2

description:
Library name: Sample14
Sorted small perioneal macrophages
gene_countA.csv
KO2


title: KO_SPM_1

description:
Library name: Sample13
Sorted small perioneal macrophages
gene_countA.csv
KO1


title: WT_SPM_rep3

description:
Library name: Sample11
Sorted small perioneal macrophages
gene_countA.csv
WT3


title: WT_SPM_rep4

description:
Library name: Sample12
Sorted small perioneal macrophages
gene_countA.csv
WT4


title: KO_mono_rep4

description:
Library name: Sample8
Sorted bone marrow monocytes
gene_countBB.csv
KOH4

source_name: Bone marrow

value: Bone marrow

value: Monocyte


title: WT_SPM_rep1

description:
Library name: Sample9
Sorted small perioneal macrophages
gene_countA.csv
WT1


title: KO_mono_rep2

description:
Library name: Sample6
Sorted bone marrow monocytes
gene_countBB.csv
KOH2


title: KO_mono_rep3

description:
Library name: Sample7
Sorted bone marrow monocytes
gene_countBB.csv
KOH3


title: WT_mono_rep4

description:
Library name: Sample4
Sorted bone marrow monocytes
gene_countBB.csv
WTH4


title: KO_mono_rep1

description:
Library name: Sample5
Sorted bone marrow monocytes
gene_countBB.csv
KOH1


title: WT_mono_rep3

description:
Library name: Sample3
Sorted bone marrow monocytes
gene_countBB.csv
WTH3


title: WT_mono_rep1

description:
Library name: Sample1
Sorted bone marrow monocytes
gene_countBB.csv
WTH1


title: WT_mono_rep2

description:
Library name: Sample2
Sorted bone marrow monocytes
gene_countBB.csv
WTH2


title: PNA_4_RNA

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description: Library name: 13513-LB-9-RNA

library_source: transcriptomic single cell

data_processing:
Mulitiome files were demultiplexed with CellRanger mkfastq
Demultiplexed data were processed with CellRanger count pipeline
Assembly: mm10
Supplementary files format and content: CellRanger output files: raw feature barcode h5

source_name: Preoptic area

extract_protocol:
Nuclear isolation: Tissue was homogenized in ice-cold buffer (250mM sucrose, 20mM Tricine-KOH pH 7.5, 5mM MgCl2, 25mM KCl, spermine, spermidine, DTT, protease and RNase inhibitors) using sequential Dounce pestle strokes with 0.30% NP-40, then filtered (40µM) and centrifuged (500 x g, 10 min, 4°C). Nuclei were enriched using anti-nuclei MicroBeads (Miltenyi Biotec) and magnetic column separation, pelleted (1000 x g, 10 min, 4°C), and resuspended in 1X nuclei buffer. Samples were submitted to the University of Michigan Advanced Genomics Core for library preparation and sequencing.
Nuclei were counted (LunaFx7 with AO/PI staining), diluted to 1200-5000 nuclei/μl, bulk transposed to fragment accessible chromatin and add adapters, then encapsulated in barcoded GEMs using the Chromium Controller for reverse transcription following 10X Genomics Multiome ATAC + Gene Expression protocols. Barcoded cDNA and tagmented DNA were PCR amplified, the ATAC library was generated via indexing PCR, the GEX library was created by enzymatic fragmentation with size optimization and adapter ligation followed by indexing PCR, and libraries were quality-checked (LabChip GX Touch HT), quantified (Qubit, TapeStation 4200), pooled, and sequenced on the Illumina NovaSeqx Plus with 50,000 reads/cell paired-end sequencing.

value: Preoptic area

value: PNA


title: PNA_3_RNA

description: Library name: 13513-LB-8-RNA


title: PNA_2_RNA

description: Library name: 13513-LB-7-RNA


title: PNA_1_RNA

description: Library name: 13513-LB-6-RNA


title: WT_SPM_rep2

description:
Library name: Sample10
Sorted small perioneal macrophages
gene_countA.csv
WT2


title: VEH_3_RNA

description: Library name: 13513-LB-3-RNA

value: VEH


title: VEH_4_RNA

description: Library name: 13513-LB-4-RNA


title: VEH_1_RNA

description: Library name: 13513-LB-1-RNA


title: VEH_2_RNA

description: Library name: 13513-LB-2-RNA


title: PNA_3_ATAC

description: Library name: 13513-LB-8-ATAC

library_source: genomic single cell

molecule: genomic DNA


title: PNA_2_ATAC

description: Library name: 13513-LB-7-ATAC


title: PNA_4_ATAC

description: Library name: 13513-LB-9-ATAC


title: VEH_4_ATAC

description: Library name: 13513-LB-4-ATAC


title: VEH_3_ATAC

description: Library name: 13513-LB-3-ATAC


title: PNA_1_ATAC

description: Library name: 13513-LB-6-ATAC


title: VEH_2_ATAC

description: Library name: 13513-LB-2-ATAC


title: VEH_1_ATAC

description: Library name: 13513-LB-1-ATAC


title: SKG-RA mouse BMDC, Poly(I:C) stimulated, Mouse 48, biol rep5

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

description: Library name: SKG_RA_PolyIC_48

data_processing:
Low-quality bases (Phred < 33) and adaptor sequences were removed with the Trimmomatic v.0.36 tool using the following arguments: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:TRUE HEADCROP:4 LEADING:5 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Trimmed reads were aligned to the mouse GRCm38 (mm10) reference genome using HISAT2 v2.2.1.
Raw counts were quantified by counting the number of strand-specific reads aligning to gene exon features using featureCounts (Subread package v1.5.2).
Raw read count libraries were filtered to remove residual rRNA reads and to retain genes expressed above 5 counts per million reads (CPM) in at least 2 samples, for a total of 11,307 expressed genes.
Assembly: mm10
Supplementary files format and content: For all samples, a matrix with raw counts for all genes (.txt format)
Supplementary files format and content: For all samples, a matrix with CPM values for all genes expressed at or greater than 5 CPM in at least 2 samples (.txt format)

source_name: Mouse Primary Cells

extract_protocol:
BMDCs stimulated in culture for 12 hours were harvested and stained with fluorophore-conjugated antibodies anti-CD11c APC (Biolegend, N418, #117310) and anti-CD11b PerCP-Cy5.5 (Thermo Fisher, M1/70, #45-0112-82), and with the viability dye DAPI (BioLegend) for dead cell exclusion. BMDCs were sorted on the FACSAria Fusion (BD Biosciences) into the Mag-MAX Lysis Buffer (Ambion, AM1830). RNA was isolated using the Mag-MAX total RNA kit (Ambion, AM1830) according to the manufacturer’s protocol, and RNA yields and quality were assessed on Bioanalyzer (Agilent).
rRNA depletion and library preparation were performed using the KAPA RNA HyperPrep Kit with RiboErase (Roche).

treatment_protocol:
SKG mouse line carries a homozygous G-to-T substitution at nucleotide 489 in the Zap70 gene on the BALB/c genetic background. Rheumatoid arthritis disease was induced in the mice with an intraperitoneal injection of zymosan (Millipore-Sigma, 58856-83-2) at 5 mg per mouse at the age of 8-10 weeks. Control mice received an equal volume of PBS as the vehicle control. The mice were analyzed at ≥5 weeks after the zymosan treatment when the animals had a clinical score of 8-16, indicating medium to severe arthritis disease.
Primary cell culture protocol: Bone marrow cells collected from SKG-PBS or SKG-RA mice and were resuspended at 10E7 per mL and seeded dropwise at 75 μL per well into 6-well non-tissue culture treated plates (Fisher Scientific) containing 3 mL/well of RPMI-1640 media, with 10% FCS (both from ThermoFisher Scientific), 2 mM L-glutamine (Wisent), 100 U/mL penicillin/streptomycin (Wisent), 50 μM β-mercaptoethanol (Millipore-Sigma), and 20 ng/mL granulocyte-macrophage colony-stimulating factor (GM-CSF, #315-03, PeproTech, ThermoFisher Scientific). Magnetic depletion of mature immune cells from the bone marrow samples was performed using the EasySep Streptavidin RapidSpheres Isolation Kit (#19860, Stem Cell Technologies) and biotin-conjugated antibodies against the major blood and immune lineage markers: CD3 (BioLegend #100244, 17A2), CD19 (BioLegend #115504, 6D5), NK1.1 (BioLegend #108704, PK-136), TER119 (BioLegend #116204), Ly6G (BioLegend #127604, 1A8), and F4/80 (BioLegend #123106). The resulting lineage depleted murine bone marrow cells were resuspended at 10E7 per mL and seeded dropwise at 70 μL per well into the same plates and media as described above. All BMDC cultures were fed with fresh media at days 3 and 6.
Primary cell stimulation protocol: BMDCs were harvested at days 8-9, counted, and seeded at 10E6 cells/mL for stimulation with polyinosinic–polycytidylic acid (poly(I:C), Millipore-Sigma, 20 μg/mL), (1→3)-β-D-glucan from Alcaligenes faecalis (Millipore-Sigma, 5 μg/mL), or PBS for 16 hours.

value: Bone Marrow-Derived Dendritic Cells (BMDC)

tag: mouse genotype

value: SKG (Zap70 G489T)

tag: mouse strain

value: BALB/c

tag: mouse treatment

value: Intraperitoneal Zymosan (5 mg per mouse)

tag: bmdc stimulation

value: Poly(I:C) [20 ug/mL] for 16 h

tag: group id


title: SKG-RA mouse BMDC, Poly(I:C) stimulated, Mouse 45, biol rep4

description: Library name: SKG_RA_PolyIC_45


title: SKG-RA mouse BMDC, Poly(I:C) stimulated, Mouse 39, biol rep2

description: Library name: SKG_RA_PolyIC_39


title: SKG-RA mouse BMDC, Poly(I:C) stimulated, Mouse 42, biol rep3

description: Library name: SKG_RA_PolyIC_42


title: SKG-RA mouse BMDC, Poly(I:C) stimulated, Mouse 36, biol rep1

description: Library name: SKG_RA_PolyIC_36


title: SKG-RA mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 47, biol rep5

description: Library name: SKG_RA_betaGlu_47

value: (1>3)-beta-D-glucan from Alcaligenes faecalis [5 ug/mL] for 16 h


title: SKG-RA mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 44, biol rep4

description: Library name: SKG_RA_betaGlu_44


title: SKG-RA mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 38, biol rep2

description: Library name: SKG_RA_betaGlu_38


title: SKG-RA mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 41, biol rep3

description: Library name: SKG_RA_betaGlu_41


title: SKG-RA mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 35, biol rep1

description: Library name: SKG_RA_betaGlu_35


title: SKG-RA mouse BMDC, Unstimulated, Mouse 46, biol rep4

description: Library name: SKG_RA_Unstim_46

value: PBS [unstimulated] for 16 h


title: SKG-RA mouse BMDC, Unstimulated, Mouse 40, biol rep2

description: Library name: SKG_RA_Unstim_40


title: SKG-RA mouse BMDC, Unstimulated, Mouse 43, biol rep3

description: Library name: SKG_RA_Unstim_43


title: SKG-RA mouse BMDC, Unstimulated, Mouse 34, biol rep1

description: Library name: SKG_RA_Unstim_34


title: SKG-PBS mouse BMDC, Poly(I:C) stimulated, Mouse 33, biol rep4

description: Library name: SKG_PBS_PolyIC_33

value: Intraperitoneal PBS (Control)


title: SKG-PBS mouse BMDC, Poly(I:C) stimulated, Mouse 27, biol rep3

description: Library name: SKG_PBS_PolyIC_27


title: SKG-PBS mouse BMDC, Poly(I:C) stimulated, Mouse 21, biol rep1

description: Library name: SKG_PBS_PolyIC_21


title: SKG-PBS mouse BMDC, Poly(I:C) stimulated, Mouse 24, biol rep2

description: Library name: SKG_PBS_PolyIC_24


title: SKG-PBS mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 26, biol rep3

description: Library name: SKG_PBS_betaGlu_26


title: SKG-PBS mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 32, biol rep4

description: Library name: SKG_PBS_betaGlu_32


title: SKG-PBS mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 23, biol rep2

description: Library name: SKG_PBS_betaGlu_23


title: SKG-PBS mouse BMDC, (1>3)-beta-D-glucan stimulated, Mouse 20, biol rep1

description: Library name: SKG_PBS_betaGlu_20


title: SKG-PBS mouse BMDC, Unstimulated, Mouse 31, biol rep4

description: Library name: SKG_PBS_Unstim_31


title: SKG-PBS mouse BMDC, Unstimulated, Mouse 25, biol rep3

description: Library name: SKG_PBS_Unstim_25


title: SKG-PBS mouse BMDC, Unstimulated, Mouse 22, biol rep2

description: Library name: SKG_PBS_Unstim_22


title: SKG-PBS mouse BMDC, Unstimulated, Mouse 19, biol rep1

description: Library name: SKG_PBS_Unstim_19


title: Vehicle, 3, KU034, scRNASeq

first: Lorenzo

last: Tomassoni

address: 1130 St Nicholas Avenue

institute: Columbia University

description: 10x Genomics

data_processing:
Raw data was aligned using CellRanger (v. 5.0.1)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic Tumor Tissue

growth_protocol: All animal research experiments were approved by the Columbia University Irving Medical Center (CUIMC) Institutional Animal Care and Use Committee (IACUC). Mouse colonies were bred and maintained with standard mouse chow and water, ad libitum, under a standard 12hr light/12 hr dark cycle. KPC (KrasLSL.G12D/+; p53LSL.R172H/+; Pdx1-Cretg/+) mice were generated in the Olive Laboratory at Columbia University.

extract_protocol:
24 h after treatment, mice were sacrificed and tumors were collected for single cell RNA-Seq analysis. Single cell suspension was prepared using Miltenyi Tumor Dissociation Kit.
Libraries were generated at the Sulzberg Genome Center at Columbia University

treatment_protocol: Tumor formation in KPC mice was monitored by bi-weekly palpation. Upon detection of a 4–7 mm diameter tumor by ultrasound, KPC mice were randomized and treated with Vehicle (n=3) or TRAM/HCQ (1 mg/kg, po; 40 mg/kg, po; n=3).

value: Pancreatic Tumor Tissue

value: Vehicle - corn oil, water


title: Treated, 3, KU031, scRNASeq

description: 10x Genomics

value: Trametinib (1mg/kg)/Hydroxychloroquine (40 mg/kg)


title: Vehicle, 2, KU030, scRNASeq

description: 10x Genomics


title: Treated, 2, KU021, scRNASeq

description: 10x Genomics


title: Vehicle, 1, KA001, scRNASeq

description: 10x Genomics


title: Treated, 1, KU020, scRNASeq

description: 10x Genomics


title: VPR-D4_rep2

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Read pairs were processed to remove sequencing adapters using trim_galore (version 0.6.3).
To remove rRNA contamination, reads were mapped to a reference of rDNA annotations using STAR (version 2.7.2b) with the following parameters: --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd --winAnchorMultimapNmax 2000 --outFilterMultimapNmax 10000 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.2 --seedMultimapNmax 20000 --outSAMtype None --outReadsUnmapped Fastx.
To map libraries, an N-masked mm10 genome was generated based on SNP annotations of the PGK12.1 cell line using bedtools maskfasta (version 2.29.2).
To quantify gene and single repeat element expression, read pairs were mapped to the N-masked genome using STAR (version 2.7.2b) to report uniquely mapped reads: --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03 --outSAMattributes NH HI NM MD --outSAMmultNmax 1 --outSAMtype BAM Unsorted. On the other hand, to quantify repeat expression by subfamily, multi-mapping read pairs were saved by randomly asigning them to one of the possible hits using the following parameters: --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd --winAnchorMultimapNmax 2000 --outFilterMultimapNmax 10000 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03 --seedMultimapNmax 20000 --outSAMattributes NH HI NM MD --outSAMmultNmax 1 --outSAMtype BAM Unsorted.
BAM files were filtered to remove singletons with samtools view (version 1.9) and the following options: -b -f 0x2. In addition, mitochondrial reads were filtered out using samtools view and the grep command (grep -v chrM).
To assign read pairs to specific alleles, filtered BAM files and PGK12.1 SNP annotations were used as input of SNPsplit (version 0.3.4) with the following options: --paired --no_sort. SNPsplit generated one BAM file for each allele (129 and PGK) and one for unassigned reads. These 3 BAM files were merged using samtools merge to generate a BAM file with total signal.
BAM files were sorted by coordinate using picard SortSam (version 2.20.8).
Total and allele-specific quantification of gene and repeat expression was performed using featureCounts (version 2.0.1) with ENSEMBL gene annotations (v98) and RepeatMasker annotations (discarding simple, low complexity and exonic repeats), respectively, and with the following parameters: a) for genes, -C -p -s 2 -t exon -g gene_id; b) for single repeats, -C -p -s 2; c) for repeat subfamilies, -C -p -s 2 -M. Repeat coordinates were specified as repeat ids in the SAF file used by featureCounts.
Single repeat elements with less than 10 reads across libraries were filtered out from the results obtained by considering uniquely mapped read pairs.
The final subfamily quantification was obtained by summing counts of all repeats according to their classification.
Assembly: mm10
Supplementary files format and content: Tab-separated counts of uniquely mapped read pairs for genes and repeats
Supplementary files format and content: Tab-separated counts of randomly assigned read pairs for repeat subfamilies

growth_protocol: Cell lines derived from PGK12.1 mouse embryonic stem cells were maintained on gelatin-coated flasks in serum-containing ES cell medium (DMEM) supplemented with 15% ESC-grade foetal bovine serum (FBS), 1000U/ml leukemia inhibitory factor (LIF, Millipore) and 0.1mM B-mercaptoethanol in humidified atmosphere at 37°C with 8% CO2.

extract_protocol:
Cells were briefly washed in 1XPBS and harvested directly in Trizol (Invitrogen). Total RNAs were extracted from Trizol with choloroform by phase separation. The aqueous phase was then mixed with an equal volume of 70% ethanol and transferred to a silica column from the RNeasy Mini kit (Qiagen). Total RNA was purified according to the instructions of the manufacturer, including on-column DNAseI digestion. 800ng of DNAse-treated total RNAs were used for library preparation.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq stranded total RNA Library Prep kit following the manufacturer's protocols. Sequencing was performed in 100pb paired-end reads using a NovaSeq 6000 instrument, with 90-100 millions paired reads per sample on average.

treatment_protocol: For induction of the engineered effectors and for each cell line, cells were plated on gelatin-coated wells from a 6-well plate and treated without or with 1µg/ml doxycycline (Sigma) for 48h.

tag: cell line

value: embryonic stem cells

value: dCas9-VPR effector with sgRNA-encoding transgene

value: mock

tag: time


title: VPR-D4_DOX_rep2

value: doxycycline


title: VPR-B4_DOX_rep2


title: VPR-B4_rep2


title: VPR-D4_rep1


title: VPR-D4_DOX_rep1


title: VPR-B4_rep1


title: VPR-B4_DOX_rep1


title: VPR-B7_DOX_rep2

value: dCas9-VPR effector


title: VPR-B7_rep2


title: VPR-B7_DOX_rep1


title: VPR-B7_rep1


title: LKF-A6_rep2

value: LKFeffector


title: LKF-A6_DOX_rep2


title: AKF-B5_rep2

value: AKF effector


title: AKF-B5_DOX_rep2


title: AKF-B5_DOX_rep1


title: LKF-A6_DOX_rep1


title: AKF-B5_rep1


title: LKF-A6_rep1


title: F4

city: Henan

first: xiaolong

last: Dai

address: kai feng

country: China

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Assembly: TBX20
Supplementary files format and content: core_table_gene

source_name: skin

extract_protocol:
RNA was harvested using Trizol reagent. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1).  The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C.  After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C.  After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet.  Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA.  Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA.  Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature.  Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis.  afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair.  The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution.  The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control.  The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library.  The single strand circle DNA (ssCir DNA) was formatted as the final library.  The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

value: skin

value: tbx20 flox/flox


title: F3


title: F2


title: F1


title: C4

value: tbx20 k14 conditional knockout


title: C1


title: C2


title: C3


title: Biq,60DAA,bio rep 3

city: Viçosa

first: Wesley Elias

middle: Bhering

last: Barrios

email: wesley.barrios@ufv.br, wesb18@gmail.com

state: Minas Gerais

address: Ph. Rolfs, Av., UFV campus, Unidade de Crescimento de Plantas

department: Plant Biology

country: Brazil

institute: Universidade Federal de Viçosa

description:
Library name: sample_24
Pericarp of C. chinense cv. Biquinho at 60 DAA, biological replicate 1

data_processing:
Step 1 - Quality trimming: Raw reads were trimmed using fastp v0.23.1 to remove adapter sequences and low-quality bases. Reads with mean Phred quality score below 20 were filtered using a sliding window of size 3.
Step 2 - Quantification: Trimmed reads were quasi-mapped using Salmon v1.6.0 against a Capsicum annuum Zunla-1 reference transcriptome index in paired-end mode with automatic library type detection (-l A), sequence-specific bias correction (--seqBias), GC-content bias correction (--gcBias), and selective alignment (--validateMappings).
Step 3 - Import and summarization: Salmon output files were imported into R v4.2.0 using the tximport package. Raw read counts were summarized at the gene level and filtered to remove genes with zero expression across all samples.
Step 4 - Differential expression: Differentially expressed genes (DEGs) were identified using DESeq2 v1.36.0. Genes were considered differentially expressed when adjusted p-value (Benjamini-Hochberg FDR) < 0.05 and |log2 fold change| ≥ 1.
Step 5 - Orthology validation: Cross-mapping bias was assessed by identifying 1:1 orthologs among C. chinense (PI159236) and C. annum (Zunla-1 and UCD-10X-F1) mappings using OrthoFinder v2.5.4. Mean TPM values per orthogroup were calculated per tissue-stage combination and pairwise Spearman correlations were computed on log10(TPM+1)-transformed values betwen
Assembly: Capsicum annuum Zunla-1 reference genome and transcriptome (Qin et al., 2014)
Supplementary files format and content: Gene-level vst normalized count matrix (vst_normalized_data.txt): rows = genes, columns = samples, values = VST normalized read counts estimated by Salmon/tximport and normalized by R v.4.2.0

organism: Capsicum chinense

source_name: fruit pericarp

growth_protocol: Seeds were germinated on commercial substrate (Tropstrato HT hortaliças, Vida Verde) and transplanted 25 days after sowing into 5 dm3 pots with soil:substrate (1:1 w/w), fertilized with 5.62 g of 20-5-20 (N-P2O5-K2O). Plants were grown in a greenhouse in Viçosa, MG, Brazil (20°45'S; 42°51'W; 642 m a.s.l.) with regular irrigation and weekly fertilization using 40 mL per pot of a solution containing 5 g L-1 (NH4)2SO4 and 2.5 g L-1 KCl.

extract_protocol:
Total RNA was extracted from pericarp tissues using TRIzol reagent (Invitrogen, Cat. No. 15596018) following manufacturer's instructions. Residual genomic DNA was removed with RQ1 RNase-Free DNase I (Promega, Cat. No. M6101). RNA quality was assessed by agarose gel electrophoresis, NanoDrop spectrophotometry (OD260/280: 1.8–2.2; OD260/230 ≥ 1.8), and Agilent 2100 Bioanalyzer with RNA 6000 Nano Kit. Only samples with RIN > 8.0 were used.
cDNA libraries were prepared using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, Cat. No. PE-401-3001) following manufacturer's instructions. Sequencing was performed on an Illumina HiSeq 2500 with a 12-hour high-output (HO) run to generate paired-end 100 bp reads.

treatment_protocol: No treatment applied. Flowers were tagged at anthesis to track fruit age. Pericarp samples were collected at 20 and 60 days after anthesis (DAA), snap-frozen in liquid nitrogen, and stored at -80°C until processing.

value: fruit pericarp

value: Biquinho

value: 60 Days After Anthesis


title: Biq,60DAA,bio rep 1

description:
Library name: sample_22
Pericarp of C. chinense cv. Biquinho at 60 DAA, biological replicate 1


title: Hab,60DAA,bio rep 2

description:
Library name: sample_20
Pericarp of C. chinense cv. Habanero at 60 DAA, biological replicate 2

value: Habanero


title: Biq,60DAA,bio rep 2

description:
Library name: sample_23
Pericarp of C. chinense cv. Biquinho at 60 DAA, biological replicate 1


title: Hab,60DAA,bio rep 1

description:
Library name: sample_19
Pericarp of C. chinense cv. Habanero at 60 DAA, biological replicate 1


title: A101,60DAA,bio rep 3

description:
Library name: sample_18
Pericarp of C. chinense accession A101 at 60 DAA, biological replicate 3


title: A101,60DAA,bio rep 2

description:
Library name: sample_17
Pericarp of C. chinense accession A101 at 60 DAA, biological replicate 2


title: A18,60DAA,bio rep 3

description:
Library name: sample_15
Pericarp of C. chinense accession A18 at 60 DAA, biological replicate 3


title: A101,60DAA,bio rep 1

description:
Library name: sample_16
Pericarp of C. chinense accession A101 at 60 DAA, biological replicate 1


title: A18,60DAA,bio rep 2

description:
Library name: sample_14
Pericarp of C. chinense accession A18 at 60 DAA, biological replicate 2


title: A18,60DAA,bio rep 1

description:
Library name: sample_13
Pericarp of C. chinense accession A18 at 60 DAA, biological replicate 1


title: Biq,20DAA,bio rep 1

description:
Library name: sample_10
Pericarp of C. chinense cv. Biquinho at 20 DAA, biological replicate 1

value: 20 Days After Anthesis


title: Biq,20DAA,bio rep 2

description:
Library name: sample_11
Pericarp of C. chinense cv. Biquinho at 20 DAA, biological replicate 2


title: Biq,20DAA,bio rep 3

description:
Library name: sample_12
Pericarp of C. chinense cv. Biquinho at 20 DAA, biological replicate 3


title: Hab,20DAA,bio rep 3

description:
Library name: sample_09
Pericarp of C. chinense cv. Habanero at 20 DAA, biological replicate 3


title: Hab,20DAA,bio rep 2

description:
Library name: sample_08
Pericarp of C. chinense cv. Habanero at 20 DAA, biological replicate 2


title: Hab,20DAA,bio rep 1

description:
Library name: sample_07
Pericarp of C. chinense cv. Habanero at 20 DAA, biological replicate 1


title: A101,20DAA,bio rep 3

description:
Library name: sample_06
Pericarp of C. chinense accession A101 at 20 DAA, biological replicate 3


title: A101,20DAA,bio rep 2

description:
Library name: sample_05
Pericarp of C. chinense accession A101 at 20 DAA, biological replicate 2


title: A101,20DAA,bio rep 1

description:
Library name: sample_04
Pericarp of C. chinense accession A101 at 20 DAA, biological replicate 1


title: A18,20DAA,bio rep 2

description:
Library name: sample_03
Pericarp of C. chinense accession A18 at 20 DAA, biological replicate 2


title: A18,20DAA,bio rep 1

description:
Library name: sample_02
Pericarp of C. chinense accession A18 at 20 DAA, biological replicate 1


title: RYs15_BCR

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description:
Library name: s008_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.

data_processing:
Cellranger v6.1.2 multi was used to obtain antigen barcode counts using the antigen barcode library and VDJ library. The VDJ reference that was used with multi was created using the fetch-imgt utility of cell ranger 6.0.2 for Macaca mulatta on 17th March 2023. The constant region sequences from Ramesh et al. were added to the IMGT sequences. Since the multi option is only available with newer versions of cellranger which have specific requirements for VDJ reference, we used another VDJ reference comprised of heavy chain V gene sequences from Cirelli et al., KimDB v1.1, and IMPre in addition to IMGT sequences to start with a comprehensive database for assembly with cellranger v3.1.0. The assembled sequences were once again annotated with the Cirelli et al. database using IgBLAST v1.21.0. The sequences were filtered to keep only those that were productive and with a predicted CDR3 region. After filtering Ig sequences, cells with only a single heavy and a single light chain were used downstream.
Assembly: mmul10
Supplementary files format and content: Processed data files include per-sample outputs from Cell Ranger v6.1.2 multi. Count matrices are provided in Market Exchange Format (MEX): barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene and antigen barcode features), and matrix.mtx.gz (sparse UMI count matrix). V(D)J outputs are provided as: airr_rearrangement.tsv (BCR rearrangements in AIRR Community standard format), filtered_contig_annotations.csv (per-contig V(D)J gene annotations), filtered_contig.fasta (filtered contig sequences), and clonotypes.csv (clonotype assignments). All files are prefixed with a sample identifier (s001–s008) corresponding to the sample listed in each GEO record.
Library strategy: BCR-Seq

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMCs

extract_protocol:
PBMCs were isolated from WB post BG505 vaccination.
Single cell suspensions of FACS enriched memory B cells were prepared and loaded onto the 10X Genomics Chromium Controller using the Chromium NextGEM Single Cell 5’ Library & Gel Bead kit to capture individual cells and barcoded gel beads within droplets. For RM experiments, counting steps were skipped due to low number of antigen specific B cells isolated via FACS. VDJ and feature barcode libraries were prepared according to manufacturer instructions. They were then sequenced on an Illumina NovaSeq 6000 with a paired-end 26x91 configuration targeting a depth of 5,000 reads for both surface barcode libraries and VDJ libraires. Cell Ranger software was used to perform demultiplexing of cellular transcript data, as well as mapping and annotation of UMIs and transcripts for downstream data analysis.

tag: animal id

value: PBMCs

value: Memory B Cells


title: RYs15_ADT

description:
Library name: s008_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.

library_source: other

data_processing:
Cellranger v6.1.2 multi was used to obtain antigen barcode counts using the antigen barcode library and VDJ library. The VDJ reference that was used with multi was created using the fetch-imgt utility of cell ranger 6.0.2 for Macaca mulatta on 17th March 2023. The constant region sequences from Ramesh et al. were added to the IMGT sequences. Since the multi option is only available with newer versions of cellranger which have specific requirements for VDJ reference, we used another VDJ reference comprised of heavy chain V gene sequences from Cirelli et al., KimDB v1.1, and IMPre in addition to IMGT sequences to start with a comprehensive database for assembly with cellranger v3.1.0. The assembled sequences were once again annotated with the Cirelli et al. database using IgBLAST v1.21.0. The sequences were filtered to keep only those that were productive and with a predicted CDR3 region. After filtering Ig sequences, cells with only a single heavy and a single light chain were used downstream.
Assembly: mmul10
Supplementary files format and content: Processed data files include per-sample outputs from Cell Ranger v6.1.2 multi. Count matrices are provided in Market Exchange Format (MEX): barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene and antigen barcode features), and matrix.mtx.gz (sparse UMI count matrix). V(D)J outputs are provided as: airr_rearrangement.tsv (BCR rearrangements in AIRR Community standard format), filtered_contig_annotations.csv (per-contig V(D)J gene annotations), filtered_contig.fasta (filtered contig sequences), and clonotypes.csv (clonotype assignments). All files are prefixed with a sample identifier (s001–s008) corresponding to the sample listed in each GEO record.
Library strategy: CITE-seq

molecule: other


title: RLk15_ADT

description:
Library name: s007_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RIr15_BCR

description:
Library name: s006_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RIr15_ADT

description:
Library name: s006_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RLk15_BCR

description:
Library name: s007_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RHe16_ADT

description:
Library name: s005_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RHe16_BCR

description:
Library name: s005-BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: 275_12_ADT

description:
Library name: s004_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: 275_12_BCR

description:
Library name: s004_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RUp16_BCR

description:
Library name: s003_BCR
10x Genomics 5' V(D)J B cell receptor library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: RUp16_ADT

description:
Library name: s003_ADT
10x Genomics 5' antigen barcode (LIBRA-seq) library; 26x91 configuration targeting a depth of 5,000 reads per cell.


title: TGIF2 (fused to YFP, MNase, NLS), rep 2

city: Rehovot

first: Naama

last: Barkai

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Library name: TGIF2_2
Human TF ChEC-seq profile in budding yeast

library_source: genomic

data_processing:
After demultiplexing using bcl2fastq (Illumina), reads were filtered using cutadapt with the following parameters: ‘--pair-filter=any -m 15 --action=trim’.
Alignment to the S. cerevisiae genome R64-1-1 was done using Bowtie2 (‘--very-sensitive --trim-to 30 --dovetail’).
genomeCoverageBed (‘-5 -fs 1 -d’) was used to achieve single bp resolution of MNase cut sites.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content:
*.out file contains genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
*.bam.bw file contains normalized genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria). Normalization: ribosomal locus (chr12: 450,000-490,001), CUP1 and CUP2 sites (chr8: 212,408-215,118), and partial GAL11 promoter (chr15: 234,421 - 234,548) were filtered out contains genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Library strategy: ChEC-seq

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Stationary phase cultures from freshly picked colonies were diluted into 5 mL fresh SD media and grown overnight to OD600 = 4.

extract_protocol:
Samples were treated with Proteinase K (0.5 mg/mL, 55°C, 30 min), extracted with equal volume phenol-chloroform pH 8 (Sigma-Aldrich), vortexed, and centrifuged (17,000g, 15 min). DNA was precipitated with 3 volumes cold 96% EtOH, 45 mg Glycoblue, and 20 mM sodium acetate (–80°C, >1 hr), pelleted (17,000g, 4°C, 10 min), washed with 70% EtOH, dried, and resuspended in 30 µL RNase A solution (0.33 mg/mL in TE: 10 mM Tris, 1 mM EDTA) for 20 min at 37°C. Small fragments were enriched by SPRI cleanup (Ampure XP): 0.8× (24 µL) beads for reverse cleanup (5 min, RT), supernatant retained; then 1× (30 µL) beads plus 5.4× (162 µL) isopropanol (5 min, RT). Beads were washed twice with 85% EtOH and DNA eluted in 30 µL 0.1× TE.
Following RNase treatment and reverse SPRI cleanup, DNA fragments were used for end-repair and A-tailing (ERA). A 5.4 µL ERA mix (1× T4 DNA ligase buffer [NEB], 0.5 mM dNTPs, 0.25 mM ATP, 2.75% PEG 4000, 6 U T4 PNK [NEB], 0.5 U T4 DNA Polymerase [Thermo Scientific], 0.5 U Taq DNA polymerase [Bioline]) was added to 14.6 µL sample and incubated at 12°C for 20 min, 37°C for 15 min, and 58°C for 45 min. ERA products were subjected to reverse SPRI cleanup with 0.5× (10 µL) SPRI beads (Ampure XP, Beckman Coulter); supernatant was retained, and small fragments were purified with 1.3× (26 µL) SPRI beads plus 5.4× (108 µL) isopropanol. After two 85% EtOH washes, DNA was eluted in 17 µL 0.1× TE. For ligation, 16.4 µL eluate was added to a 40 µL reaction (1× Quick ligase buffer [NEB], 4000 U Quick ligase [NEB], 6.4 nM Y-shaped barcode adaptors with T-overhang) and incubated 15 min at 20°C. Ligation products were cleaned by double SPRI: first 1.2× (48 µL) SPRI, eluted in 30 µL 0.1× TE; then without bead separation, 1.3× (39 µL) HXN buffer (2.5 M NaCl, 20% PEG 8000) was added and DNA eluted in 24 µL 0.1× TE. Next, 23 µL eluate was amplified in a 50 µL PCR (1× Kappa HIFI [Roche], 0.32 µM barcoded forward and reverse primers) with 45 s at 98°C; 16 cycles of 15 s at 98°C and 15 s at 60°C; and 1 min at 72°C. Final libraries were cleaned with 1.1× (55 µL) SPRI and eluted in 15 µL 0.1× TE. Concentration and size distribution were assessed by Qbit (Thermo Scientific) and TapeStation (Agilent). Libraries were pooled equimolarly, diluted to 2 nM, and sequenced on NovaSeq 6000/NovaSeq X (Illumina) with the following parameters: Read1, 61 nt; Index1, 8 nt; Index2, 8 nt; Read2, 61 nt.

treatment_protocol: Cells were pelleted (1,500g, 2 min), resuspended in 0.5 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1× cOmplete EDTA-free protease inhibitors [Roche; one tablet per 50 mL], 1 mM PMSF), transferred to 2 mL 96-well plates (Thermo Scientific), and washed twice with 1 mL Buffer A. Cells were resuspended in 150 µL Buffer A + 0.1% digitonin, transferred to an Eppendorf 96-well plate, and permeabilized at 30°C for 5 min. CaCl₂ was added to 2 mM and incubated for 30 s to activate MNase, then stopped with an equal volume of stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA, 1% SDS).

tag: strain genotype

value: Saccharomyces cerevisiae cells

tag: human tf

tag: locus

value: HO

tag: promoter


title: TGIF2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: TGIF2_1
Human TF ChEC-seq profile in budding yeast


title: TGIF2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: TGIF2_3
Human TF ChEC-seq profile in budding yeast


title: TGIF2LY (fused to YFP, MNase, NLS), rep 4

description:
Library name: TGIF2LY_4
Human TF ChEC-seq profile in budding yeast


title: TGIF2LY (fused to YFP, MNase, NLS), rep 2

description:
Library name: TGIF2LY_2
Human TF ChEC-seq profile in budding yeast


title: TGIF2LY (fused to YFP, MNase, NLS), rep 3

description:
Library name: TGIF2LY_3
Human TF ChEC-seq profile in budding yeast


title: TGIF2LY (fused to YFP, MNase, NLS), rep 1

description:
Library name: TGIF2LY_1
Human TF ChEC-seq profile in budding yeast


title: TGIF2LY (fused to YFP, MNase, NLS), rep 5

description:
Library name: TGIF2LY_5
Human TF ChEC-seq profile in budding yeast


title: TGIF2LX (fused to YFP, MNase, NLS), rep 2

description:
Library name: TGIF2LX_2
Human TF ChEC-seq profile in budding yeast


title: TGIF1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: TGIF1_3
Human TF ChEC-seq profile in budding yeast


title: TGIF2LX (fused to YFP, MNase, NLS), rep 1

description:
Library name: TGIF2LX_1
Human TF ChEC-seq profile in budding yeast


title: TGIF1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: TGIF1_1
Human TF ChEC-seq profile in budding yeast


title: SOX9-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX9_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX9-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX9_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX9-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX9_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX9-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX9_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX9-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX9_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX9 (fused to YFP, MNase, NLS), rep 5

description:
Library name: SOX9_5
Human TF ChEC-seq profile in budding yeast


title: RS2Z36-1 mutant, Replicate 2

city: Frankfurt am Main

first: Remus

middle: Richard Elrik

last: Rosenkranz

address: Max-von-Laue-Str. 9

country: Germany

institute: Goethe University Frankfurt

description: Library name: 20103R-01-05

data_processing:
Raw reads were mapped against the tomato reference genome (S. lycopersicum cv. Heinz 1706, genome build 4.0; ITAG 4.0) in a splice-aware manner using Star (Galaxy version 2.7.8a) with default settings, except for the following changes: --genomeSAindexNbases 14, --sjdbGTFfile ITAG4.0_gene_models.gff, -- sjdbOverhang 149, --chimOutType don’t report, --outFilterType yes, --outFilterMultimapNmax 1, -- outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.05.
Reads per gene were counted using htseq-count (Galaxy version 0.9.1) with the following settings: --mode union. –stranded no, --minaqual 10, --type gene, --idattr ID
Read counts per gene (ITAG 4.0 annotation) are deposited as processed data.
Assembly: Tomato Genome version SL4.0
Supplementary files format and content: tab-delimited text files contain read counts for each sample

organism: Solanum lycopersicum

source_name: Ovary

extract_protocol:
Total RNA was isolated using TriZol (Invitrogen) followed by DirectZol (Zymo Research)
RNA libraries for RNA-seq were prepared using the NEBNext Ultra II non-directional RNA Library Kit with polyA selection

tag: tissue

value: Ovary

tag: genotype

value: RS2Z36 KO

value: control


title: T_10

city: Pamplona

first: Josune

last: Orbe

address: Avenida Pio XII 55

country: Spain

institute: CIMA

description: Library name: 8_S8

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR 2.7.9a with default parameters.
UMI deduplication was performed using UMI-tools v1.0.0
featureCounts v1.6.0 software and Gencode v47 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

organism: Homo sapiens

source_name: Plasma EVs

extract_protocol:
EVs were isolated by centrifugation at 20.000 xg during 70 min from frozen  citrate  plasma samples at -80°C after double centrifugation (10 min 2000 xg and 15 min 2500 xg)
Plasma EVs were resuspended in 100 μL of lysis/binding Buffer (Invitrogen). RNA transcripts were captured with dynabeads oligo (dT) (Invitrogen) and reverse transcribed. RNA samples underwent a linear amplification by in vitro transcription followed by a fragmentation into 250–350 bp. Partial Illumina adaptor sequences were used, and a second reverse transcription reaction was performed. Full Illumina adaptor sequences were successfully added and the libraries sequenced (NextSeq 2000, Illumina)

value: Plasma EVs

tag: batch


title: SOX9 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX9_3
Human TF ChEC-seq profile in budding yeast


title: SOX9 (fused to YFP, MNase, NLS), rep 4

description:
Library name: SOX9_4
Human TF ChEC-seq profile in budding yeast


title: SOX9 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX9_2
Human TF ChEC-seq profile in budding yeast


title: SOX7-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX7_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX9 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX9_1
Human TF ChEC-seq profile in budding yeast


title: SOX7-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX7_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX7-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX7_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX9-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX9_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX7-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX7_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX7 (fused to YFP, MNase, NLS), rep 5

description:
Library name: SOX7_5
Human TF ChEC-seq profile in budding yeast


title: SOX7-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX7_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX7 (fused to YFP, MNase, NLS), rep 4

description:
Library name: SOX7_4
Human TF ChEC-seq profile in budding yeast


title: SOX7 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX7_3
Human TF ChEC-seq profile in budding yeast


title: SOX7 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX7_2
Human TF ChEC-seq profile in budding yeast


title: SOX6-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX6_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX6-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX6_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX6-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX6_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX6-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX6_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX6-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX6_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX6 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX6_3
Human TF ChEC-seq profile in budding yeast


title: SOX6 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX6_2
Human TF ChEC-seq profile in budding yeast


title: SOX6 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX6_1
Human TF ChEC-seq profile in budding yeast


title: SOX5-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX5_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX5-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX5_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX5-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX5_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX5-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX5_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX5 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX5_2
Human TF ChEC-seq profile in budding yeast


title: SOX4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX4_3
Human TF ChEC-seq profile in budding yeast


title: SOX4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX4_2
Human TF ChEC-seq profile in budding yeast


title: SOX4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX4_1
Human TF ChEC-seq profile in budding yeast


title: SOX30-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX30_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX30-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX30_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX30-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX30_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX30-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX30_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX30-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX30_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX30-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX30_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX30 (fused to YFP, MNase, NLS), rep 4

description:
Library name: SOX30_4
Human TF ChEC-seq profile in budding yeast


title: SOX30 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX30_2
Human TF ChEC-seq profile in budding yeast


title: SOX30 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX30_3
Human TF ChEC-seq profile in budding yeast


title: SOX30 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX30_1
Human TF ChEC-seq profile in budding yeast


title: SOX17-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX17_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX17-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX17_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX17-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX17_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX17-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX17_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX17-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX17_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX17-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX17_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX17 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX17_2
Human TF ChEC-seq profile in budding yeast


title: SOX17 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX17_3
Human TF ChEC-seq profile in budding yeast


title: SOX17 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX17_1
Human TF ChEC-seq profile in budding yeast


title: SOX15 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX15_2
Human TF ChEC-seq profile in budding yeast


title: SOX15 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX15_1
Human TF ChEC-seq profile in budding yeast


title: SOX13-nonDBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX13_nonDBD_only_3
Human TF ChEC-seq profile in budding yeast


title: SOX13-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX13_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX13-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX13_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX13-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX13_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: SOX13 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX13_2
Human TF ChEC-seq profile in budding yeast


title: SOX11 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX11_3
Human TF ChEC-seq profile in budding yeast


title: SOX11 (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX11_2
Human TF ChEC-seq profile in budding yeast


title: SOX11 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX11_1
Human TF ChEC-seq profile in budding yeast


title: POU3F4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: POU3F4_3
Human TF ChEC-seq profile in budding yeast


title: SOX13-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX13_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: SOX13 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX13_3
Human TF ChEC-seq profile in budding yeast


title: POU3F4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: POU3F4_2
Human TF ChEC-seq profile in budding yeast


title: TGIF2LX (fused to YFP, MNase, NLS), rep 3

description:
Library name: TGIF2LX_3
Human TF ChEC-seq profile in budding yeast


title: TGIF1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: TGIF1_2
Human TF ChEC-seq profile in budding yeast


title: POU3F4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: POU3F4_1
Human TF ChEC-seq profile in budding yeast


title: SOX13 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX13_1
Human TF ChEC-seq profile in budding yeast


title: POU3F1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: POU3F1_3
Human TF ChEC-seq profile in budding yeast


title: POU3F1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: POU3F1_2
Human TF ChEC-seq profile in budding yeast


title: SOX7-nonDBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX7_nonDBD_only_1
Human TF ChEC-seq profile in budding yeast


title: POU3F1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: POU3F1_1
Human TF ChEC-seq profile in budding yeast


title: POU2F3 (fused to YFP, MNase, NLS), rep 2

description:
Library name: POU2F3_2
Human TF ChEC-seq profile in budding yeast


title: POU2F3 (fused to YFP, MNase, NLS), rep 1

description:
Library name: POU2F3_1
Human TF ChEC-seq profile in budding yeast


title: POU2F3 (fused to YFP, MNase, NLS), rep 3

description:
Library name: POU2F3_3
Human TF ChEC-seq profile in budding yeast


title: NFATC4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: NFATC4_3
Human TF ChEC-seq profile in budding yeast


title: NFATC4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: NFATC4_2
Human TF ChEC-seq profile in budding yeast


title: SOX7 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX7_1
Human TF ChEC-seq profile in budding yeast


title: NFATC4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: NFATC4_1
Human TF ChEC-seq profile in budding yeast


title: NFATC3 (fused to YFP, MNase, NLS), rep 3

description:
Library name: NFATC3_3
Human TF ChEC-seq profile in budding yeast


title: NFATC3 (fused to YFP, MNase, NLS), rep 2

description:
Library name: NFATC3_2
Human TF ChEC-seq profile in budding yeast


title: NFATC3 (fused to YFP, MNase, NLS), rep 1

description:
Library name: NFATC3_1
Human TF ChEC-seq profile in budding yeast


title: MXD4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: MXD4_3
Human TF ChEC-seq profile in budding yeast


title: SOX6-DBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX6_DBD_only_2
Human TF ChEC-seq profile in budding yeast


title: MXD4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: MXD4_2
Human TF ChEC-seq profile in budding yeast


title: SOX5-nonDBD-only (fused to YFP, MNase, NLS), rep 2

description:
Library name: SOX5_nonDBD_only_2
Human TF ChEC-seq profile in budding yeast


title: MXD4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: MXD4_1
Human TF ChEC-seq profile in budding yeast


title: MNT (fused to YFP, MNase, NLS), rep 3

description:
Library name: MNT_3
Human TF ChEC-seq profile in budding yeast

value: MNT


title: MLX (fused to YFP, MNase, NLS), rep 2

description:
Library name: MLX_2
Human TF ChEC-seq profile in budding yeast

value: MLX


title: SOX5-DBD-only (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX5_DBD_only_1
Human TF ChEC-seq profile in budding yeast


title: MNT (fused to YFP, MNase, NLS), rep 2

description:
Library name: MNT_2
Human TF ChEC-seq profile in budding yeast


title: MLXIPL (fused to YFP, MNase, NLS), rep 3

description:
Library name: MLXIPL_3
Human TF ChEC-seq profile in budding yeast

value: MLXIPL


title: MLX (fused to YFP, MNase, NLS), rep 1

description:
Library name: MLX_1
Human TF ChEC-seq profile in budding yeast


title: MNT (fused to YFP, MNase, NLS), rep 1

description:
Library name: MNT_1
Human TF ChEC-seq profile in budding yeast


title: MLXIPL (fused to YFP, MNase, NLS), rep 2

description:
Library name: MLXIPL_2
Human TF ChEC-seq profile in budding yeast


title: MLXIPL (fused to YFP, MNase, NLS), rep 1

description:
Library name: MLXIPL_1
Human TF ChEC-seq profile in budding yeast


title: SOX5 (fused to YFP, MNase, NLS), rep 1

description:
Library name: SOX5_1
Human TF ChEC-seq profile in budding yeast


title: SOX5 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX5_3
Human TF ChEC-seq profile in budding yeast


title: HOXD9 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXD9_3
Human TF ChEC-seq profile in budding yeast


title: HOXD9 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXD9_2
Human TF ChEC-seq profile in budding yeast


title: HOXC9 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXC9_3
Human TF ChEC-seq profile in budding yeast


title: HOXC9 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXC9_1
Human TF ChEC-seq profile in budding yeast


title: HOXD9 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXD9_1
Human TF ChEC-seq profile in budding yeast


title: HOXC13 (fused to YFP, MNase, NLS), rep 4

description:
Library name: HOXC13_4
Human TF ChEC-seq profile in budding yeast


title: HOXC13 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXC13_2
Human TF ChEC-seq profile in budding yeast


title: HOXC13 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXC13_1
Human TF ChEC-seq profile in budding yeast


title: HOXC13 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXC13_3
Human TF ChEC-seq profile in budding yeast


title: HOXC10 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXC10_3
Human TF ChEC-seq profile in budding yeast


title: HOXC10 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXC10_2
Human TF ChEC-seq profile in budding yeast


title: HOXB9 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXB9_3
Human TF ChEC-seq profile in budding yeast


title: SOX30 (fused to YFP, MNase, NLS), rep 5

description:
Library name: SOX30_5
Human TF ChEC-seq profile in budding yeast


title: HOXA9 (fused to YFP, MNase, NLS), rep 5

description:
Library name: HOXA9_5
Human TF ChEC-seq profile in budding yeast


title: HOXB9 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXB9_2
Human TF ChEC-seq profile in budding yeast


title: HOXB9 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXB9_1
Human TF ChEC-seq profile in budding yeast


title: HOXA9 (fused to YFP, MNase, NLS), rep 4

description:
Library name: HOXA9_4
Human TF ChEC-seq profile in budding yeast


title: HOXA9 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXA9_3
Human TF ChEC-seq profile in budding yeast


title: HOXA9 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXA9_2
Human TF ChEC-seq profile in budding yeast


title: HOXA11 (fused to YFP, MNase, NLS), rep 4

description:
Library name: HOXA11_4
Human TF ChEC-seq profile in budding yeast


title: HOXA11 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXA11_2
Human TF ChEC-seq profile in budding yeast


title: HOXA11 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXA11_1
Human TF ChEC-seq profile in budding yeast


title: HOXA9 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXA9_1
Human TF ChEC-seq profile in budding yeast


title: HOXA11 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXA11_3
Human TF ChEC-seq profile in budding yeast


title: HOXA10 (fused to YFP, MNase, NLS), rep 5

description:
Library name: HOXA10_5
Human TF ChEC-seq profile in budding yeast


title: HOXA10 (fused to YFP, MNase, NLS), rep 4

description:
Library name: HOXA10_4
Human TF ChEC-seq profile in budding yeast


title: HOXA10 (fused to YFP, MNase, NLS), rep 3

description:
Library name: HOXA10_3
Human TF ChEC-seq profile in budding yeast


title: HOXA10 (fused to YFP, MNase, NLS), rep 1

description:
Library name: HOXA10_1
Human TF ChEC-seq profile in budding yeast


title: GATA6 (fused to YFP, MNase, NLS), rep 3

description:
Library name: GATA6_3
Human TF ChEC-seq profile in budding yeast


title: HOXA10 (fused to YFP, MNase, NLS), rep 2

description:
Library name: HOXA10_2
Human TF ChEC-seq profile in budding yeast


title: GATA6 (fused to YFP, MNase, NLS), rep 2

description:
Library name: GATA6_2
Human TF ChEC-seq profile in budding yeast


title: GATA6 (fused to YFP, MNase, NLS), rep 1

description:
Library name: GATA6_1
Human TF ChEC-seq profile in budding yeast


title: GATA5 (fused to YFP, MNase, NLS), rep 5

description:
Library name: GATA5_5
Human TF ChEC-seq profile in budding yeast


title: GATA5 (fused to YFP, MNase, NLS), rep 3

description:
Library name: GATA5_3
Human TF ChEC-seq profile in budding yeast


title: GATA5 (fused to YFP, MNase, NLS), rep 2

description:
Library name: GATA5_2
Human TF ChEC-seq profile in budding yeast


title: GATA5 (fused to YFP, MNase, NLS), rep 1

description:
Library name: GATA5_1
Human TF ChEC-seq profile in budding yeast


title: GATA5 (fused to YFP, MNase, NLS), rep 4

description:
Library name: GATA5_4
Human TF ChEC-seq profile in budding yeast


title: GATA4 (fused to YFP, MNase, NLS), rep 4

description:
Library name: GATA4_4
Human TF ChEC-seq profile in budding yeast


title: GATA4 (fused to YFP, MNase, NLS), rep 5

description:
Library name: GATA4_5
Human TF ChEC-seq profile in budding yeast


title: GATA4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: GATA4_3
Human TF ChEC-seq profile in budding yeast


title: GATA4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: GATA4_2
Human TF ChEC-seq profile in budding yeast


title: GATA4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: GATA4_1
Human TF ChEC-seq profile in budding yeast


title: GATA3 (fused to YFP, MNase, NLS), rep 3

description:
Library name: GATA3_3
Human TF ChEC-seq profile in budding yeast


title: GATA3 (fused to YFP, MNase, NLS), rep 2

description:
Library name: GATA3_2
Human TF ChEC-seq profile in budding yeast


title: GATA3 (fused to YFP, MNase, NLS), rep 1

description:
Library name: GATA3_1
Human TF ChEC-seq profile in budding yeast


title: SOX15 (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX15_3
Human TF ChEC-seq profile in budding yeast


title: GATA2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: GATA2_2
Human TF ChEC-seq profile in budding yeast


title: GATA2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: GATA2_3
Human TF ChEC-seq profile in budding yeast


title: GATA2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: GATA2_1
Human TF ChEC-seq profile in budding yeast


title: FOXP3 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXP3_3
Human TF ChEC-seq profile in budding yeast


title: FOXP3 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXP3_2
Human TF ChEC-seq profile in budding yeast


title: FOXP3 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXP3_1
Human TF ChEC-seq profile in budding yeast


title: FOXP2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXP2_2
Human TF ChEC-seq profile in budding yeast


title: FOXP2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXP2_3
Human TF ChEC-seq profile in budding yeast


title: FOXP2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXP2_1
Human TF ChEC-seq profile in budding yeast


title: FOXP1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXP1_3
Human TF ChEC-seq profile in budding yeast


title: FOXP1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXP1_2
Human TF ChEC-seq profile in budding yeast


title: FOXO3 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXO3_3
Human TF ChEC-seq profile in budding yeast


title: SOX13-DBD-only (fused to YFP, MNase, NLS), rep 3

description:
Library name: SOX13_DBD_only_3
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP3-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_DBD_FOXP3_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: FOXL2-DBD-FOXP3-nonDBD fusion


title: FOXO3 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXO3_2
Human TF ChEC-seq profile in budding yeast


title: FOXP1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXP1_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP2-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_DBD_FOXP2_nonDBD_1
Human TF ChEC-seq profile in budding yeast

value: FOXL2-DBD-FOXP2-nonDBD fusion


title: FOXL2-DBD-FOXP3-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_DBD_FOXP3_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP2-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_DBD_FOXP2_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP3-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_DBD_FOXP3_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: FOXO3 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXO3_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP2-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_DBD_FOXP2_nonDBD_3
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_DBD_FOXP1_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: FOXL2-DBD-FOXP1-nonDBD fusion


title: FOXL2-DBD-FOXP1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_DBD_FOXP1_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXP1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_DBD_FOXP1_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXO3-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_DBD_FOXO3_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: FOXL2-DBD-FOXO3-nonDBD fusion


title: FOXL2-DBD-FOXO3-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_DBD_FOXO3_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXF1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_DBD_FOXF1_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: FOXL2-DBD-FOXF1-nonDBD fusion


title: FOXL2-DBD-FOXO3-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_DBD_FOXO3_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXF1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_DBD_FOXF1_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXA2-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_DBD_FOXA2_nonDBD_2
Human TF ChEC-seq profile in budding yeast

value: FOXL2-DBD-FOXA2-nonDBD fusion


title: FOXL2-DBD-FOXA2-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_DBD_FOXA2_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2 (fused to YFP, MNase, NLS), rep 4

description:
Library name: FOXL2_4
Human TF ChEC-seq profile in budding yeast


title: FOXL2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_3
Human TF ChEC-seq profile in budding yeast


title: FOXL2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL2_2
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXA2-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL2_DBD_FOXA2_nonDBD_3
Human TF ChEC-seq profile in budding yeast


title: FOXL2-DBD-FOXF1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_DBD_FOXF1_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: FOXL2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL2_1
Human TF ChEC-seq profile in budding yeast


title: FOXL1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXL1_2
Human TF ChEC-seq profile in budding yeast


title: FOXL1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXL1_3
Human TF ChEC-seq profile in budding yeast


title: FOXL1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXL1_1
Human TF ChEC-seq profile in budding yeast


title: FOXJ2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXJ2_2
Human TF ChEC-seq profile in budding yeast


title: FOXJ2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXJ2_1
Human TF ChEC-seq profile in budding yeast


title: FOXF1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXF1_3
Human TF ChEC-seq profile in budding yeast


title: FOXF1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXF1_1
Human TF ChEC-seq profile in budding yeast


title: FOXF1 (fused to YFP, MNase, NLS), rep 4

description:
Library name: FOXF1_4
Human TF ChEC-seq profile in budding yeast


title: FOXA2 (fused to YFP, MNase, NLS), rep 4

description:
Library name: FOXA2_4
Human TF ChEC-seq profile in budding yeast


title: FOXA2 (fused to YFP, MNase, NLS), rep 5

description:
Library name: FOXA2_5
Human TF ChEC-seq profile in budding yeast


title: FOXA2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOXA2_3
Human TF ChEC-seq profile in budding yeast


title: FOXA2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOXA2_2
Human TF ChEC-seq profile in budding yeast


title: FOS (fused to YFP, MNase, NLS), rep 4

description:
Library name: FOS_4
Human TF ChEC-seq profile in budding yeast

value: FOS


title: FOXA2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOXA2_1
Human TF ChEC-seq profile in budding yeast


title: FOS (fused to YFP, MNase, NLS), rep 2

description:
Library name: FOS_2
Human TF ChEC-seq profile in budding yeast


title: FOXL2 (fused to YFP, MNase, NLS), rep 5

description:
Library name: FOXL2_5
Human TF ChEC-seq profile in budding yeast


title: FOS (fused to YFP, MNase, NLS), rep 3

description:
Library name: FOS_3
Human TF ChEC-seq profile in budding yeast


title: FOS (fused to YFP, MNase, NLS), rep 5

description:
Library name: FOS_5
Human TF ChEC-seq profile in budding yeast


title: FOS (fused to YFP, MNase, NLS), rep 1

description:
Library name: FOS_1
Human TF ChEC-seq profile in budding yeast


title: FLI1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: FLI1_3
Human TF ChEC-seq profile in budding yeast


title: FLI1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: FLI1_2
Human TF ChEC-seq profile in budding yeast


title: FLI1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: FLI1_1
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-FLI1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_DBD_FLI1_nonDBD_2
Human TF ChEC-seq profile in budding yeast

value: ERG-DBD-FLI1-nonDBD fusion


title: ERG-DBD-FLI1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_DBD_FLI1_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: Saccharomyces cerevisiae cells


title: ERG-DBD-FLI1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_DBD_FLI1_nonDBD_1
Human TF ChEC-seq profile in budding yeast

value: HO


title: ERG-DBD-ERF-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_DBD_ERF_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ERG-DBD-ERF-nonDBD fusion


title: ERG-DBD-ERF-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_DBD_ERF_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELK4-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_DBD_ELK4_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ERG-DBD-ELK4-nonDBD fusion


title: ERG-DBD-ELK4-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_DBD_ELK4_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELK4-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_DBD_ELK4_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELK1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_DBD_ELK1_nonDBD_1
Human TF ChEC-seq profile in budding yeast

value: ERG-DBD-ELK1-nonDBD fusion


title: ERG-DBD-ELK1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_DBD_ELK1_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELK1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_DBD_ELK1_nonDBD_3
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ERF-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_DBD_ERF_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELF2-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_DBD_ELF2_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ERG-DBD-ELF2-nonDBD fusion


title: ERG-DBD-ELF2-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_DBD_ELF2_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELF2-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_DBD_ELF2_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELF1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_DBD_ELF1_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ERG-DBD-ELF1-nonDBD fusion


title: ERG (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_2
Human TF ChEC-seq profile in budding yeast

value: ERG


title: ERG (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERG_3
Human TF ChEC-seq profile in budding yeast


title: ERG-DBD-ELF1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERG_DBD_ELF1_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ERF (fused to YFP, MNase, NLS), rep 3

description:
Library name: ERF_3
Human TF ChEC-seq profile in budding yeast

value: ERF


title: ERG-DBD-ELF1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_DBD_ELF1_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ERF (fused to YFP, MNase, NLS), rep 2

description:
Library name: ERF_2
Human TF ChEC-seq profile in budding yeast


title: ELK4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELK4_3
Human TF ChEC-seq profile in budding yeast


title: ERG (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERG_1
Human TF ChEC-seq profile in budding yeast


title: ELK4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELK4_2
Human TF ChEC-seq profile in budding yeast


title: ELK4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELK4_1
Human TF ChEC-seq profile in budding yeast


title: ERF (fused to YFP, MNase, NLS), rep 1

description:
Library name: ERF_1
Human TF ChEC-seq profile in budding yeast


title: ELK1 (fused to YFP, MNase, NLS), rep 6

description:
Library name: ELK1_6
Human TF ChEC-seq profile in budding yeast


title: ELK1 (fused to YFP, MNase, NLS), rep 5

description:
Library name: ELK1_5
Human TF ChEC-seq profile in budding yeast


title: ELK1 (fused to YFP, MNase, NLS), rep 4

description:
Library name: ELK1_4
Human TF ChEC-seq profile in budding yeast


title: ELK1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELK1_3
Human TF ChEC-seq profile in budding yeast


title: ELK1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELK1_1
Human TF ChEC-seq profile in budding yeast


title: ELF2 (fused to YFP, MNase, NLS), rep 5

description:
Library name: ELF2_5
Human TF ChEC-seq profile in budding yeast


title: ELF2 (fused to YFP, MNase, NLS), rep 4

description:
Library name: ELF2_4
Human TF ChEC-seq profile in budding yeast


title: ELF2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF2_3
Human TF ChEC-seq profile in budding yeast


title: ELF2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF2_2
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-FLI1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_DBD_FLI1_nonDBD_1
Human TF ChEC-seq profile in budding yeast

value: ELF1-DBD-FLI1-nonDBD fusion


title: ELF1-DBD-ERG-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_DBD_ERG_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ELF1-DBD-ERG-nonDBD fusion


title: ELF1-DBD-FLI1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_DBD_FLI1_nonDBD_3
Human TF ChEC-seq profile in budding yeast


title: ELF2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF2_1
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-FLI1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_DBD_FLI1_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ERG-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_DBD_ERG_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ERF-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_DBD_ERF_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ELF1-DBD-ERF-nonDBD fusion


title: ELF1-DBD-ERG-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_DBD_ERG_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ERF-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_DBD_ERF_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ELK1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELK1_2
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ERF-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_DBD_ERF_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ELK4-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_DBD_ELK4_nonDBD_3
Human TF ChEC-seq profile in budding yeast

value: ELF1-DBD-ELK4-nonDBD fusion


title: ELF1-DBD-ELK4-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_DBD_ELK4_nonDBD_2
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ELK4-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_DBD_ELK4_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ELK1-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_DBD_ELK1_nonDBD_2
Human TF ChEC-seq profile in budding yeast

value: ELF1-DBD-ELK1-nonDBD fusion


title: ELF1-DBD-ELK1-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_DBD_ELK1_nonDBD_3
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ELF2-nonDBD fusion (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_DBD_ELF2_nonDBD_2
Human TF ChEC-seq profile in budding yeast

value: ELF1-DBD-ELF2-nonDBD fusion


title: ELF1-DBD-ELF2-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_DBD_ELF2_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ELK1-nonDBD fusion (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_DBD_ELK1_nonDBD_1
Human TF ChEC-seq profile in budding yeast


title: ELF1-DBD-ELF2-nonDBD fusion (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_DBD_ELF2_nonDBD_3
Human TF ChEC-seq profile in budding yeast


title: ELF1 (fused to YFP, MNase, NLS), rep 4

description:
Library name: ELF1_4
Human TF ChEC-seq profile in budding yeast


title: ELF1 (fused to YFP, MNase, NLS), rep 3

description:
Library name: ELF1_3
Human TF ChEC-seq profile in budding yeast


title: ELF1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ELF1_1
Human TF ChEC-seq profile in budding yeast


title: ELF1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ELF1_2
Human TF ChEC-seq profile in budding yeast


title: CREB5 (fused to YFP, MNase, NLS), rep 5

description:
Library name: CREB5_5
Human TF ChEC-seq profile in budding yeast


title: CREB5 (fused to YFP, MNase, NLS), rep 3

description:
Library name: CREB5_3
Human TF ChEC-seq profile in budding yeast


title: CREB5 (fused to YFP, MNase, NLS), rep 4

description:
Library name: CREB5_4
Human TF ChEC-seq profile in budding yeast


title: CREB5 (fused to YFP, MNase, NLS), rep 1

description:
Library name: CREB5_1
Human TF ChEC-seq profile in budding yeast


title: CREB5 (fused to YFP, MNase, NLS), rep 2

description:
Library name: CREB5_2
Human TF ChEC-seq profile in budding yeast


title: CREB1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: CREB1_1
Human TF ChEC-seq profile in budding yeast


title: CREB1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: CREB1_2
Human TF ChEC-seq profile in budding yeast


title: CDX4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: CDX4_3
Human TF ChEC-seq profile in budding yeast


title: CDX4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: CDX4_2
Human TF ChEC-seq profile in budding yeast


title: CDX2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: CDX2_3
Human TF ChEC-seq profile in budding yeast


title: CDX4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: CDX4_1
Human TF ChEC-seq profile in budding yeast


title: CDX2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: CDX2_2
Human TF ChEC-seq profile in budding yeast


title: CDX2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: CDX2_1
Human TF ChEC-seq profile in budding yeast


title: ATF4 (fused to YFP, MNase, NLS), rep 5

description:
Library name: ATF4_5
Human TF ChEC-seq profile in budding yeast


title: ATF4 (fused to YFP, MNase, NLS), rep 4

description:
Library name: ATF4_4
Human TF ChEC-seq profile in budding yeast


title: ATF4 (fused to YFP, MNase, NLS), rep 3

description:
Library name: ATF4_3
Human TF ChEC-seq profile in budding yeast


title: ATF4 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ATF4_2
Human TF ChEC-seq profile in budding yeast


title: ATF2 (fused to YFP, MNase, NLS), rep 3

description:
Library name: ATF2_3
Human TF ChEC-seq profile in budding yeast


title: ATF4 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ATF4_1
Human TF ChEC-seq profile in budding yeast


title: ATF2 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ATF2_1
Human TF ChEC-seq profile in budding yeast


title: ATF2 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ATF2_2
Human TF ChEC-seq profile in budding yeast


title: ATF1 (fused to YFP, MNase, NLS), rep 1

description:
Library name: ATF1_1
Human TF ChEC-seq profile in budding yeast

data_processing:
After demultiplexing using bcl2fastq (Illumina), reads were filtered using cutadapt with the following parameters: ‘--pair-filter=any -m 15 --action=trim’.
Alignment to the S. cerevisiae genome R64-1-1 was done using Bowtie2 (‘--very-sensitive --trim-to 30 --dovetail’).
genomeCoverageBed (‘-5 -fs 1 -d’) was used to achieve single bp resolution of MNase cut sites.
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content:
*.out file contains genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
*.bam.bw file contains normalized genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria). Normalization: ribosomal locus (chr12: 450,000-490,001), CUP1 and CUP2 sites (chr8: 212,408-215,118), and partial GAL11 promoter (chr15: 234,421 - 234,548) were filtered out
Library strategy: ChEC-seq


title: ATF1 (fused to YFP, MNase, NLS), rep 2

description:
Library name: ATF1_2
Human TF ChEC-seq profile in budding yeast