title: ps-bZIP53..ph-bZIP9_Col..h-B_o

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B_o-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B_o-nuc1_GPS_events.narrowPeak

tag: replicate code

tag: control sample 3


title: C2C12 Cells SATB2 ChIP-seq 4 single-end

status: Public on Apr 06 2023

type: SRA

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

description: ChIP-seq Pull down - single End

library_source: genomic

data_processing:
Data was mapped using bowtie2, and peaks were called for ChIP-seq using combined MACS2 peak calling with q-value cutoff of 0.05. Gene Ontology (GO) term annotation was performed using GREAT v3.0.0 available online from the Bejerano lab at Stanford University.
Data was mapped using bowtie2, and peaks were called for ChIP-seq using combined MACS2 peak calling with q-value cutoff of 0.05.
For RNA-seq, data was mapped to reference mm10 genome using TopHat2. Transcripts were identified using CuffLinks. Differential expression was calculated using CuffDiff.

molecule: genomic DNA

organism: Mus musculus

source_name: muscle myoblast

growth_protocol: Cells of the immortalized mouse cell line, C2C12, were grown on non-collagen coated cell culture plates in Dulbecco’s Modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (growth medium). When confluent, cells were differentiated in DMEM supplemented with 2% horse serum and 1% penicillin/streptomycin (differentiation medium).

extract_protocol:
Twenty million cells per time point were used for each ChIP sample. Cells were fixed for 10 min using 1% formaldehyde in DMEM. Cell fixation was quenched by removing the fixation solution, rinsing the plates with PBS, and then pouring a solution of 0.125 M glycine in PBS onto the cells and incubating for 5 min. Subsequently, plates were washed 2× with PBS and then cells were scraped from the plates, pelleted, and stored at -80 °C until used.  Given that SATB2 is a nuclear matrix attachment protein, it required an alternative protocol for chromatin shearing than standard preparations. First, a commercial hypotonic solution (Active Motif) was used to lyse cellular membranes but retain intact nuclear membranes. We subsequently performed additional lysis using a hand held glass Dounce homogenizer. After centrifugation, the supernatant was discarded and the pelleted nuclei were treated with Active Motif’s Pro-enzymatic Digestion Nuclear Extraction Solution. After incubation at 37 °C for 5 min, we supplemented the reaction with 1 U micrococcal nuclease (New England Biolabs) and allowed it to incubate for 10 min. We then supplemented the reaction with SDS to a final volume 2% SDS-chromatin solution. We proceeded to the second stage of shearing using sonication via a Covaris M220 Focused-Ultrasonicator instrument, setting the parameters to produce sheared DNA of 200 bp. After sonication, we performed a final centrifugation at 16 000 × g at 4 °C for 20 min and collected the supernatant containing the sheared chromatin.   We performed immunoprecipitations with 5 μg 1°Ab (Target: SATB2, Abcam, positive control: RNA pol II, Active Motif, negative control: mouse IgG, Santa Cruz) using magnetic beads (Active Motif) diluted in commercial ChIP-buffer (Active Motif) overnight at 4 °C. Captured chromatin was isolated using magnetic stands to pulldown the beads. Bound DNA was subsequently eluted with commercial elution, reverse cross-linking, protein digestion, and RNA digestion solutions (Active Motif). The resulting samples of DNA were further purified using phenol:chloroform extraction procedures. Final DNA was quantified using a NanoDrop spectrophotometer, with a 25 μL final   volume having concentrations of 75–100 ng/μL.
For genome-wide analysis, immunoprecipitated DNA was amplified and 75 bp single read sequencing was performed on an Illumina HiSeq 2500 at the Next-Generation  Sequencing Facility at The Centre for Applied Genomics in The Hospital for Sick Children (Toronto, Ontario, Canada).

tag: cell type

value: C2C12 muscle myoblasts

tag: strain


title: C2C12 Cells SATB2 ChIP-seq 2

description: ChIP-seq using mouse SATB2 for the pulldown


title: NSPCs, Control 1, 24h

city: Guangzhou

first: Li

last: Xu

address: TianHe road 600#

country: China

institute: the third affiliated hospital of SYSU

library_source: transcriptomic

data_processing: Comparative gene expression profiling analysis of RNA-seq data for PTN groups and control groups.

molecule: total RNA

source_name: neural stem progenitor cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: neural stem progenitor cells

tag: genotype

value: WT

tag: treatment

value: PBS

tag: time


title: ps-bZIP53..ph-bZIP9_Col..h-B_n

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

department: Biology

country: USA

institute: New York University

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B_n-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP9_Col..h-B_n-nuc1_GPS_events.narrowPeak

data_processing:
library strategy: DAP-seq
Base calling was done with RTA 2.4.11 and FASTQ files were generated by Picard tools IlluminaBasecallsToFastq v2.17.11.
Raw reads were trimmed using TrimGalore 0.6.6 wrapper for Cutadapt 3.1 with the following parameter: "-q 20".
Trimmed reads were aligned by bowtie2 version 2.3.2 with default parameters against the Arabidopsis thaliana genome assembly TAIR10. Aligned reads were filtered by MAPQ score of at least 30.
Peak calling was done by the GEM peak caller version 3.3 with the default read distribution, Arabidopsis thaliana genome TAIR10 nuclear chromosome sequences, and parameters "--f SAM ---t 1 --k_min 5 --k_max 14 --k_seqs 2000 --k_neg_dinu_shuffle --outNP --outBED --outMEME --outJASPAR --outHOMER --print_bound_seqs --print_aligned_seqs".  Peaks were called for each replicate individually or by merging the two replicates using GEM's multi-replicate mode, with samples from experiments of empty vector pIXHALO and/or pIXSBP as control (indicated by the "control sample" characteristics of the sample).
Assembly: TAIR10
Supplementary files format and content: Binding events determined by GEM and GPS (part of GEM) in narrowPeak format.

organism: Arabidopsis thaliana

source_name: rosette leaf

growth_protocol: Arabidopsis thaliana reference accession Col-0 CS70000 was grown in 16h light/8h dark cycle for three weeks. Leaf materials was collected between 9am and 11am.

extract_protocol:
Genomic DNA extracted method and DAP-seq experiment was performed as described in Li et al., 2022 (Li M., Huang SS.C. DNA Affinity Purification Sequencing (DAP-Seq) for Mapping Genome-Wide Transcription Factor Binding Sites in Plants. In: Bilichak A., Laurie J.D. (eds) Accelerated Breeding of Cereal Crops. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1526-3_15) and Bartlett et al., 2017 (Bartlett, A., O'Malley, RC., Huang, SC. et al. Mapping genome-wide transcription-factorbinding sites using DAP-seq. Nat Protoc 12:1659-1672 (2017). https://doi.org/10.1038/nprot.2017.055).  The DAP-seq DNA library was prepared from fragmented genomic DNA ligated with a short DNA sequence (20bp) encoding a truncated Illumina TruSeq adapter.  In DAP-seq, a protein expression construct containing HALO-tagged transcription factors are translated by in vitro (rabbit reticulocyte) expression system in single DAP experiment to form homodimers. In double DAP-seq, one construct containing Halo-tagged transcription factor and one containing SBP-tagged transcription factor were co-expressed by in vitro  (rabbit reticulocyte) expression system to form heterodimers. The affinity-tagged proteins are immobilized on the Halo ligand magnetic beads.  The DNA affinity purification step begins by combining the DNA library with the immobilized transcription factor. After the wash steps remove the unbound DNA, the bound DNA fraction is eluted.
The DNA fragments bound to in vitro expressed proteins (homodimers or heterodimers) were eluted from affinity beads, PCR amplified with a full-length indexed TruSeq primer and directly sequenced on Illumina NextSeq 500.

treatment_protocol: Leaf material was collected and flash frozen with liquid nitrogen prior to genomic DNA isolation.

tag: cultivar

tag: protein complex

tag: protein1 gene id tair

tag: protein2 gene id tair

tag: protein1 family

value: bZIP

tag: protein2 family

tag: protein1 affinity tag

value: SBP

tag: protein2 affinity tag

value: HALO

tag: dna affinity purification tag

tag: expression system

value: rabbit reticulocyte lysate

tag: protein source

value: Arabidopsis thaliana

tag: dna source

value: n

tag: replicate

tag: control sample 1

tag: control sample 2


title: ps-vec..ph-bZIP53_Col..h-B_q

description:
merged replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP53_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP53_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP53_Col..h-B_q-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP53_Col..h-B_q-nuc1_GPS_events.narrowPeak

value: ps-pIXSBP

value: control

tag: replicate code

value: q


title: C2C12 Cells SATB2 ChIP-seq 1

tag: cell type

tag: strain


title: ps-vec..ph-bZIP10_Col..h-B_o2

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-control..bZIP_rr-ps-vec..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak

tag: cultivar

tag: protein complex


title: ps-bZIP53..ph-bZIP25_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP25_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP25_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP25_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP25_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein1 gene id tair

tag: protein2 gene id tair

tag: control sample 3


title: ps-bZIP53..ph-bZIP10_Col..h-B_o

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B_o-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B_o-nuc1_GPS_events.narrowPeak

tag: protein1 family

tag: protein2 family

tag: protein1 affinity tag

value: o


title: ps-bZIP44..ph-bZIP9_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein2 affinity tag

tag: dna affinity purification tag

tag: expression system


title: C2C12 Cells IgG ChIP-seq 1

description: ChIP-seq using mouse IgG for the pulldown (control for the SATB2 pulldown)


title: C2C12 SATB2 Knockdown cells RNA-seq 3

description: These samples were from C2C12 cells that were treated with Satb2 siRNA

data_processing:
For RNA-seq, data was mapped to reference mm10 genome using TopHat2. Transcripts were identified using CuffLinks. Differential expression was calculated using CuffDiff.
Data was mapped using bowtie2, and peaks were called for ChIP-seq using combined MACS2 peak calling with q-value cutoff of 0.05.
For RNA-seq, data was mapped to reference mm10 genome using TopHat2. Transcripts were identified using CuffLinks. Differential expression was calculated using CuffDiff.

extract_protocol:
Total RNA was isolated using an RNeasy Kit (QIAGEN) using an on-column DNase digestion (RNase-Free DNase Set, QIAGEN) to avoid genomic DNA contamination.
Library preparation and 126-bp paired-end RNA-seq was performed by the Next-Generation Sequencing Facility at The Centre for Applied Genomics in The Hospital for Sick Children. RNA integrity was assessed using the Bioanalyzer platform (Agilent Technologies, Inc.). Sequencing was performed using standard procedures for  the Illumina HiSeq 2500 platform.

treatment_protocol: siRNA duplexes were used to suppress SATB2 gene expression in C2C12 cells. C2C12 cells were transfected at 25% confluence with 10 nM siRNA (siSATB2 or siControl) and the Lipofectamine RNAiMAX reagent, as directed by the manufacturer’s protocol (Invitrogen). After an overnight incubation, fresh media was added onto the cells and the cells were re-transfected. This continued until the cells reached 100% confluence.

tag: knockdown


title: C2C12 SATB2 Knockdown cells RNA-seq 2


title: ps-bZIP44..ph-bZIP9_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP9_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein source

tag: dna source

tag: replicate

tag: control sample 1


title: ps-bZIP44..ph-bZIP63_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: replicate code

tag: control sample 2

tag: control sample 4

tag: control sample 5


title: ps-bZIP44..ph-bZIP25_Col..h-B_p2

description: weak bZIP25 heterodimer; low/no peaks

tag: cultivar

tag: protein complex

tag: protein1 gene id tair

tag: protein2 gene id tair


title: ps-bZIP44..ph-bZIP63_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP63_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein1 family

tag: protein2 family

tag: protein1 affinity tag

tag: control sample 3


title: ps-bZIP44..ph-bZIP10_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein2 affinity tag

tag: dna affinity purification tag

tag: expression system


title: ps-bZIP44..ph-bZIP25_Col..h-B_p1

description: weak bZIP25 heterodimer; low/no peaks

tag: protein source

tag: dna source

tag: replicate


title: C2C12 SATB2 Knockdown cells RNA-seq 1

tag: cell type

tag: strain

tag: knockdown


title: ps-bZIP2..ph-vec_Col..h-B_p

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP2..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP2..ph-vec_Col..h-B_p-nuc1_GPS_events.narrowPeak

tag: cultivar

value: ph-pIXHALO

tag: replicate code

value: p

tag: control sample 1

tag: control sample 2


title: ps-bZIP44..ph-bZIP10_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP44..ph-bZIP10_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein complex

tag: protein1 gene id tair

tag: protein2 gene id tair

tag: protein1 family


title: C2C12 Cells IgG ChIP-seq 3


title: C2C12 Control Cells RNA-seq 2

description: These samples were from C2C12 cells that were treated with control siRNA

value: control siRNA


title: ps-bZIP53..ph-bZIP63_Col..h-B_m

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B_m-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B_m-nuc1_GPS_events.narrowPeak

tag: protein2 family

tag: protein1 affinity tag

tag: protein2 affinity tag

value: m

tag: control sample 3

tag: control sample 4

tag: control sample 5


title: ps-bZIP2..ph-bZIP9_Col..h-B_r2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B_r2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B_r2-nuc1_GPS_events.narrowPeak

tag: dna affinity purification tag

tag: expression system

tag: protein source

tag: dna source

tag: replicate


title: C2C12 Control Cells RNA-seq 3

tag: cell type

value: C2C12 muscle myoblasts

tag: strain

tag: knockdown


title: ps-bZIP2..ph-bZIP9_Col..h-B_r1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B_r1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP9_Col..h-B_r1-nuc1_GPS_events.narrowPeak

tag: cultivar

tag: protein complex

tag: protein1 gene id tair

tag: replicate code

tag: control sample 1

tag: control sample 2


title: C2C12 Control Cells RNA-seq 1


title: ps-bZIP2..ph-bZIP63_Col..h-B_r2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B_r2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B_r2-nuc1_GPS_events.narrowPeak

tag: protein2 gene id tair

tag: protein1 family

tag: protein2 family

tag: protein1 affinity tag

tag: protein2 affinity tag

tag: control sample 3


title: ps-bZIP53..ph-bZIP63_Col..h-B_n

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B_n-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP63_Col..h-B_n-nuc1_GPS_events.narrowPeak

tag: dna affinity purification tag

tag: expression system

tag: protein source

tag: dna source

tag: control sample 4

tag: control sample 5


title: ps-bZIP53..ph-bZIP10_Col..h-B_n

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B_n-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP53..ph-bZIP10_Col..h-B_n-nuc1_GPS_events.narrowPeak

tag: cultivar

tag: protein complex

tag: replicate


title: ps-bZIP2..ph-bZIP25_Col..h-B_p2

description: weak bZIP25 heterodimer; low/no peaks

tag: protein1 gene id tair

tag: replicate code

tag: control sample 1


title: ps-bZIP2..ph-bZIP25_Col..h-B_p1

description: weak bZIP25 heterodimer; low/no peaks

tag: protein2 gene id tair

tag: protein1 family

tag: control sample 2


title: ps-bZIP44..ph-vec_Col..h-B_p

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP44..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP44..ph-vec_Col..h-B_p-nuc1_GPS_events.narrowPeak

tag: protein2 family

tag: protein1 affinity tag

tag: protein2 affinity tag


title: ps-bZIP2..ph-bZIP10_Col..h-B_r2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B_r2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B_r2-nuc1_GPS_events.narrowPeak

tag: dna affinity purification tag

tag: expression system

tag: control sample 3


title: ps-bZIP11..ph-vec_Col..h-B_p

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP11..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP11..ph-vec_Col..h-B_p-nuc1_GPS_events.narrowPeak

tag: protein source

tag: dna source


title: ps-bZIP2..ph-bZIP10_Col..h-B_r1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B_r1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP10_Col..h-B_r1-nuc1_GPS_events.narrowPeak

tag: cultivar


title: ps-bZIP11..ph-bZIP9_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein complex


title: ps-bZIP11..ph-bZIP9_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP9_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: replicate


title: ps-bZIP11..ph-bZIP63_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein1 gene id tair

tag: control sample 4

tag: control sample 5


title: ps-bZIP25..ph-vec_Col..h-B_q

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP25..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP25..ph-vec_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: replicate code

tag: control sample 1


title: ps-bZIP11..ph-bZIP25_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein2 gene id tair

tag: protein1 family

tag: control sample 2


title: ps-bZIP11..ph-bZIP63_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP63_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein2 family

tag: protein1 affinity tag

tag: protein2 affinity tag


title: ps-bZIP11..ph-bZIP25_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP25_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: dna affinity purification tag

tag: expression system

tag: control sample 3


title: ps-bZIP11..ph-bZIP10_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: cultivar

tag: protein source

tag: dna source


title: ps-bZIP10..ph-vec_Col..h-B_q

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP10..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP10..ph-vec_Col..h-B_q-nuc1_GPS_events.narrowPeak

tag: protein complex

tag: protein1 gene id tair

tag: replicate


title: ps-bZIP11..ph-bZIP10_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP11..ph-bZIP10_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: replicate code


title: ps-bZIP1..ph-vec_Col..h-B_p

description:
double DAP-seq empty vector control; no peaks expected
merged replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP1..ph-vec_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..control_rr-ps-bZIP1..ph-vec_Col..h-B_p-nuc1_GPS_events.narrowPeak

tag: control sample 1


title: ps-bZIP1..ph-bZIP9_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein2 gene id tair


title: ps-bZIP1..ph-bZIP9_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP9_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein1 family


title: ps-bZIP1..ph-bZIP63_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: control sample 2

tag: control sample 4

tag: control sample 5


title: ps-bZIP1..ph-bZIP25_Col..h-B_p2

description: weak bZIP25 heterodimer; low/no peaks

tag: protein2 family

tag: protein1 affinity tag

tag: protein2 affinity tag


title: ps-bZIP1..ph-bZIP25_Col..h-B_p1

description: weak bZIP25 heterodimer; low/no peaks

tag: dna affinity purification tag

tag: expression system

tag: control sample 3


title: pIXHALO_Col-B_r

description: DAP-seq empty vector control; no peaks expected

tag: cultivar

value: pIXHALO

tag: protein source

tag: dna source

value: Col-B

value: r


title: ps-bZIP1..ph-bZIP10_Col..h-B_p2

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B_p2-nuc1_GPS_events.narrowPeak

tag: protein complex

tag: protein1 gene id tair

value: bZIP

value: SBP

tag: replicate


title: ps-bZIP2..ph-bZIP63_Col..h-B_r1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B_r1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP2..ph-bZIP63_Col..h-B_r1-nuc1_GPS_events.narrowPeak

tag: protein2 gene id tair

value: HALO

value: rabbit reticulocyte lysate

tag: replicate code

tag: control sample 1


title: pIXHALO_Col-B_b

tag: protein1 family

value: Arabidopsis thaliana

value: b

tag: control sample 2


title: ps-bZIP1..ph-bZIP10_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP10_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein2 family


title: ps-bZIP1..ph-bZIP63_Col..h-B_p1

description:
merged replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP..bZIP_rr-ps-bZIP1..ph-bZIP63_Col..h-B_p1-nuc1_GPS_events.narrowPeak

tag: protein1 affinity tag

tag: control sample 4

tag: control sample 5


title: bZIP9_Col-B_o2

description:
DAP-seq bZIP C bZIP; no peaks expected
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP9_Col-B-nuc1_GPS_events.narrowPeak

tag: dna affinity purification tag

tag: expression system


title: bZIP63_Col-B_r

description:
DAP-seq bZIP C bZIP; no peaks expected
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B_r-nuc1_GPS_events.narrowPeak

tag: cultivar


title: bZIP9_Col-B_o1

tag: protein source


title: bZIP63_Col-B_q

description:
DAP-seq bZIP C bZIP; no peaks expected
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B-nuc1_GPS_events.narrowPeak

tag: dna source


title: pIXSBP_Col-B_n

tag: protein complex

value: pIXSBP

value: control

value: n


title: bZIP63_Col-B_p

description:
DAP-seq bZIP C bZIP; no peaks expected
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B_p-nuc1_GPS_events.narrowPeak

tag: protein1 gene id tair


title: bZIP63_Col-B_k

description:
DAP-seq bZIP C bZIP; no peaks expected
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B-nuc1_GPS_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP63_Col-B_k-nuc1_GPS_events.narrowPeak

value: k

tag: replicate


title: bZIP53_Col-B_p1

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP53_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP53_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP53_Col-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP53_Col-B_p1-nuc1_GPS_events.narrowPeak


title: bZIP53_Col-B_p2

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP53_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP53_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP53_Col-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP53_Col-B_p2-nuc1_GPS_events.narrowPeak


title: bZIP25_Col-B_o2

description: DAP-seq bZIP C bZIP; no peaks expected


title: bZIP44_Col-B_p1

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP44_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP44_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP44_Col-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP44_Col-B_p1-nuc1_GPS_events.narrowPeak


title: bZIP25_Col-B_o1

description: DAP-seq bZIP C bZIP; no peaks expected


title: bZIP2_Col-B_p2

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP2_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP2_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP2_Col-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP2_Col-B_p2-nuc1_GPS_events.narrowPeak


title: bZIP10_Col-B_o2

description: DAP-seq bZIP C bZIP; no peaks expected


title: bZIP2_Col-B_p1

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP2_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP2_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP2_Col-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP2_Col-B_p1-nuc1_GPS_events.narrowPeak


title: bZIP11_Col-B_p1

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP11_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP11_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP11_Col-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP11_Col-B_p1-nuc1_GPS_events.narrowPeak


title: bZIP11_Col-B_p2

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP11_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP11_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP11_Col-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP11_Col-B_p2-nuc1_GPS_events.narrowPeak


title: bZIP1_Col-B_p1

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP1_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP1_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP1_Col-B_p1-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP1_Col-B_p1-nuc1_GPS_events.narrowPeak


title: bZIP1_Col-B_p2

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP1_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP1_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP1_Col-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP1_Col-B_p2-nuc1_GPS_events.narrowPeak


title: Lenti CAR-T replicate2

city: Chongqing

first: Jintao

last: Zou

state: China

address: Gaotanyanstreet

institute: Army Medical University

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt(v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis.
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: hg38
Supplementary files format and content: xlsx files include RPKM and read count values for each Sample

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system(Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina)

tag: tissue

value: Blood

tag: cell line

value: T cell

tag: treatment

value: transfection using Lentivirus


title: Lenti CAR-T replicate1


title: Lenti CAR-T replicate3


title: PB CAR-T replicate1

value: electroporation with PiggyBac Transposon Vector System


title: Control T cells replicate2

value: without transfection


title: PB CAR-T replicate2


title: Control T cells replicate1


title: bZIP44_Col-B_p2

description:
DAP-seq bZIP S1; peaks expected
merged replicate GEM events: DAPSeq-bZIP_rr-bZIP44_Col-B-nuc1_GEM_events.narrowPeak
merged replicate GPS events: DAPSeq-bZIP_rr-bZIP44_Col-B-nuc1_GPS_events.narrowPeak
replicate GEM events: DAPSeq-bZIP_rr-bZIP44_Col-B_p2-nuc1_GEM_events.narrowPeak
replicate GPS events: DAPSeq-bZIP_rr-bZIP44_Col-B_p2-nuc1_GPS_events.narrowPeak

tag: protein1 family

value: Col-B

tag: replicate code

tag: control sample 1


title: bZIP10_Col-B_o1

description: DAP-seq bZIP C bZIP; no peaks expected

tag: protein1 affinity tag

tag: control sample 2


title: Control T cells replicate3


title: Don3_d6_LPS_IL4

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq.txt pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Genome_build: hg19
Supplementary_files_format_and_content: .gene.mmseq.txt files contain counts per gene

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Trained immunity was induced by exposing cells to BCG vaccines for 24 hours, while a tolerance control was induced by LPS for 24 hours.

extract_protocol:
Total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

tag: individual

tag: cell type

value: Monocyte

value: IL4 and LPS co-exposed for 24 hours, rested in media alone for 5 days


title: Don3_d6_IL4_Restim

value: IL4 exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: Don3_d6_LPS_IL4_Restim

value: IL4 and LPS co-exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: Don3_d6_LPS_Restim

value: LPS exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: Don3_d6_IL4

value: IL4 exposed for 24 hours, rested in media alone for 5 days


title: Don3_d6_RPMI

value: RPMI media only, collected at 6 days post culture


title: Don3_4hr_LPS

value: LPS exposed, collected at 4 hours post exposure


title: Don3_4hr_IL4

value: IL4 exposed, collected at 4 hours post exposure


title: Don3_4hr_LPS_IL4

value: IL4 and LPS co-exposed, collected at 4 hours post exposure


title: Don3_d6_RPMI_Restim

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: Don3_4hr_RPMI

value: RPMI media only, collected at 4 hours post culture


title: PB CAR-T replicate3

value: Blood

value: T cell


title: Don2_d6_LPS_IL4_Restim


title: Don3_d0

value: Baseline monocyte, attached to dish for 1  hour


title: Don2_d6_IL4_Restim


title: Don2_d6_LPS_Restim


title: Don2_d6_LPS_IL4


title: Don2_d6_IL4


title: Don2_d6_RPMI_Restim


title: Don2_d6_LPS

value: LPS exposed for 24 hours, rested in media alone for 5 days


title: Don2_d6_RPMI


title: Don3_d6_LPS


title: Don2_4hr_LPS


title: Don2_4hr_IL4


title: Don2_4hr_RPMI


title: Don2_4hr_LPS_IL4


title: Don1_d6_LPS_IL4_Restim


title: Don1_d6_IL4_Restim


title: Don1_d6_RPMI_Restim


title: Don2_d0


title: Don1_d6_IL4


title: Don1_d6_LPS_IL4


title: Don1_4hr_RPMI


title: Don1_4hr_LPS_IL4


title: Don1_d6_RPMI


title: Don1_4hr_IL4


title: Don1_d0


title: Don1_4hr_LPS


title: Healthy_MCSF_SiCu_MDM rep 4

city: Biberach

first: karim

last: el kasmi

address: Birkendorferstr 65

department: Immunology & Respiratory

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & CO. KG

data_processing:
Basecalling has been done with bcl2fastq v2.20.0.422.
Alignment has been performed with STAR v2.5.2 using hg38 genome reference.
Read counts has been obtained with featureCounts v1.5.1.
Demultiplexing was performed using bcl2fastq v2.20.0.422 from Illumina (https://emea.support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html).  Sequencing reads from the RNA-seq experiment were processed with a pipeline building upon the implementation of the ENCODE “Long RNA-seq” pipeline (also described in (Schlager et al., 2020)): filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner (Dobin et al., 2013) allowing for soft clipping of adapter sequences.   For quantification, we used transcript annotation files from Ensembl version 86, which corresponds to GENCODE 25 for human. Gene expression levels were quantified with the above annotations, using RSEM (v1.3.0) (Li and Dewey, 2011) and featureCounts (v1.5.1) (Liao, Smyth and Shi, 2014). Quality controls were implemented using FastQC (v0.11.5) [ Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ], picardmetrics (v0.2.4) [ Slowikowski K. (2016): Available online at: https://github.com/slowkow/picardmetrics ] and dupRadar (v1.0.0) (Sayols, Scherzinger and Klein, 2016) at the respective steps.
Genome_build: ENSEMBL hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Human monocyte derived macrophages

growth_protocol: Human MDMs were generated from PBMCs from human volunteer donors. All experiments with blood from human volunteer donors were approved by the blood donation service from Boehringer Ingelheim Pharma GmbH and Co KG following ethical standards and local regulation. For the indirect co-culture we used 12-well plates with cell culture inserts (Fisher Scientific GmbH; #10061051) and plated  5*10^5 MDMs directly in the well and 25*10^3 normal human lung fibroblasts (NHLF) obtained from LONZA into the insert.

extract_protocol:
RNA was isolated isolation using MagMax (biosystems #AM1830) following the manufactures procedure. Final elution 50uL. Total RNA was quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively.
RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). At total RNA input of 250ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 upstream and the NEXNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) for double-stranded cDNA purification, instead of the recommended SPRIselect Beads. Final sequencing libraries were quantified by the High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). mRNA libraries were also assessed for size distribution and adapter dimer presence (<0.5%) by the High Sensitivity Small Fragment DNF-477 Kit on a 48-channel Fragment Analyzer (Agilent). All sequencing libraries were then normalized on the MicroLab STAR (Hamilton), pooled and spiked in with PhiX Control v3 (Illumina).

treatment_protocol: Monocytes were differentiated into MDMs over 7 days with rhM-CSF (50 ng/mL). For the experiment, MDMs were stimulated for 24 hours with rhM-CSF (10 ng/mL) in combination with the treatment group, rhIL-4 (10 ng/mL),  rhIL-13 (10 ng/mL), rhTNFα (10 ng/mL) and/or Nintedanib (100 nM).

value: MCSF

tag: culture conditions


title: Healthy_MCSF_SiCu_MDM rep 5


title: Healthy_MCSF_SiCu_MDM rep 1


title: Healthy_MCSF_SiCu_MDM rep 2


title: Healthy_MCSF_SiCu_MDM rep 3


title: Healthy_MCSF_SiCu_MDM rep 6


title: Healthy_MCSF_NTB_SiCu_MDM rep 5


title: Healthy_MCSF_NTB_SiCu_MDM rep 4


title: Healthy_MCSF_NTB_SiCu_MDM rep 1


title: Healthy_MCSF_NTB_CoCu_MDM_Fibs rep 6

source_name: Human monocyte derived macrophages which had been cultured in indirect co-culture with human lung fibroblasts


title: Don1_d6_LPS

value: Monocyte


title: Healthy_MCSF_NTB_SiCu_MDM rep 2


title: Don1_d6_LPS_Restim


title: Healthy_MCSF_NTB_SiCu_MDM rep 6


title: Healthy_MCSF_NTB_CoCu_MDM_Fibs rep 2


title: Healthy_MCSF_NTB_CoCu_MDM_Fibs rep 3


title: Healthy_MCSF_NTB_SiCu_MDM rep 3


title: Healthy_MCSF_NTB_CoCu_MDM_Fibs rep 4


title: Healthy_MCSF_IL4_IL13_TNFa_SiCu_MDM rep 6


title: Healthy_MCSF_NTB_CoCu_MDM_Fibs rep 5


title: Healthy_MCSF_IL4_IL13_TNFa_SiCu_MDM rep 2


title: Healthy_MCSF_NTB_CoCu_MDM_Fibs rep 1


title: Healthy_MCSF_IL4_IL13_TNFa_SiCu_MDM rep 3


title: Healthy_MCSF_IL4_IL13_TNFa_SiCu_MDM rep 4


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_SiCu_MDM rep 6


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_SiCu_MDM rep 4


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_SiCu_MDM rep 2


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_SiCu_MDM rep 3


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_SiCu_MDM rep 1


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_CoCu_MDM_Fibs rep 4


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_CoCu_MDM_Fibs rep 6


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_CoCu_MDM_Fibs rep 2


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_CoCu_MDM_Fibs rep 3


title: Healthy_MCSF_IL4_IL13_TNFa_SiCu_MDM rep 5


title: Healthy_MCSF_IL4_IL13_TNFa_CoCu_MDM_Fibs rep 3


title: Healthy_MCSF_IL4_IL13_TNFa_CoCu_MDM_Fibs rep 1


title: Healthy_MCSF_IL4_IL13_TNFa_CoCu_MDM_Fibs rep 2


title: Healthy_MCSF_IL4_IL13_TNFa_CoCu_MDM_Fibs rep 6


title: Healthy_MCSF_IL4_IL13_TNFa_CoCu_MDM_Fibs rep 4


title: Healthy_MCSF_CoCu_MDM_Fibs rep 5


title: Healthy_MCSF_CoCu_MDM_Fibs rep 3


title: Healthy_MCSF_IL4_IL13_TNFa_SiCu_MDM rep 1


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_SiCu_MDM rep 5


title: Healthy_MCSF_CoCu_MDM_Fibs rep 2


title: Healthy_MCSF_IL4_IL13_TNFa_CoCu_MDM_Fibs rep 5


title: CB-IMR5-DHX9_si3-R01-R2

city: Berlin

first: Steffen

last: Fuchs

address: Augustenburger Platz 1

department: Pediatric Oncology

institute: Charité - Universitätsmedizin Berlin

data_processing:
Reads were aligned to GRCh38 using the GENCODE (v30) annotation and the STAR aligner (v2.7.1a) with the following non-standard parameters --sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 --outSAMattributes NH NM MD AS XS nM HI.
Feature counting  was done using featureCounts (v1.5.1) with the following non-standard parameters when counting at the gene level -t exon -g gene_id -C -M --fraction -p -s 2 -O -B -Q 4 and the following non-standard parameters when counting at the exon level -t exon -f -J -g gene_id -C -M --fraction -p -s 2 -O -B -Q 4.
Genome_build: GRCh38 using the GENCODE (v30)
Supplementary_files_format_and_content: Table reporting the read counts

source_name: Neuroblastoma cell line

growth_protocol: IMR-05 cells were routinely cultured with RPMI medium supplemented with 10% FCS, 1% penicillin and streptomycin

extract_protocol:
Cells were harvested and RNA was isolated with Trizol.
Depletion of ribosomal RNA was performed by enzymatic digestion. The ribodepletion was validated by qRT-PCR and a depletion of 95-99% was regularly reached. The ribodepleted RNA was used for generation of total RNA sequencing libraries with the TrueSeq Stranded mRNA kit (Illumina San Diego, USA) according to the manufacturer. The final libraries were stored at -20°C until sequencing. Libraries were sequenced on a NovoSeq6000 (Illumina, San Diego, USA) with a paired-end read length of 2 × 150 nucleotides. On average 100 Mio read pairs were generated per sample.

treatment_protocol: Knockdown with 2 different siRNAs and scrambled control was performed by lipofection for 3 days.

tag: cancer type

value: Neuroblastoma

tag: knockdown

value: SiRNA 3


title: Hepatic endothelial cells - Control No5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

source_name: Hepatic endothelial cells

extract_protocol:
Non-parenchymal liver cells were separated by a 19.3 % Nycodenz (1002424, Axis-Shield, Alere Technologies) gradient. Then, magnetic-activated cell sorting (MACS) was used with anti-CD146 MicroBeads (ME-9F1, 130-092-007, Miltenyi Biotech) to purify endothelial cells. RNA from hepatic endothelial cells was isolated using the innuPREP RNA Mini Kit 2.0 (845-KS-2040250, Analytik Jena).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols.

tag: genotype

value: WT


title: Healthy_MCSF_CoCu_MDM_Fibs rep 1


title: Healthy_MCSF_CoCu_MDM_Fibs rep 4


title: Hepatic endothelial cells - Alk1-HEC-KO No5

value: KO


title: CB-IMR5-DHX9_si3-R01-R1


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_CoCu_MDM_Fibs rep 5


title: Hepatic endothelial cells - Control No4


title: Hepatic endothelial cells - Alk1-HEC-KO No4


title: CB-IMR5-DHX9_si2-R01-R2

value: SiRNA 2


title: CB-IMR5-DHX9_si2-R01-R1


title: Healthy_MCSF_IL4_IL13_TNFa_NTB_CoCu_MDM_Fibs rep 1


title: Hepatic endothelial cells - Alk1-HEC-KO No3


title: Healthy_MCSF_CoCu_MDM_Fibs rep 6


title: CB-IMR5-DHX9_scr-R01-R3

value: Scramble


title: CB-IMR5-DHX9_si3-R01-R3


title: Hepatic endothelial cells - Alk1-HEC-KO No2


title: nrf2 28 rep3

city: Bristol

first: Eugenia

last: Piddini

address: Biomedical Sciences Building, University walk

department: CMM

country: United Kingdom

institute: University of Bristol

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with FastQC v0.11.5 and Exonerate
reads mapped to dme.BDGP6 using Bowtie
Genome_build: dme.BDGP6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: wing discs

extract_protocol:
Total RNA extracted using RNAeasy kit with standard protocol using 500ng for each library
Libraries were prepared with Illumina TruSeq standard protocol

value: wing discs

value: CncC overexpression


title: Hepatic endothelial cells - Control No1


title: C2C12 Cells IgG ChIP-seq 2

description: ChIP-seq using mouse IgG for the pulldown (control for the SATB2 pulldown)

value: C2C12 muscle myoblasts

tag: strain


title: Hepatic endothelial cells - Alk1-HEC-KO No1


title: CB-IMR5-DHX9_scr-R01-R1


title: nrf2 28 rep2


title: Whole liver cells - Alk1-HEC-KO No5

source_name: Whole liver cells

extract_protocol:
Frozen whole liver tissue was homogenized (Precellys 24 tissue homogenizer, P000669-PR240-A, Bertin-Instruments) in lysis buffer (845-KS-2040250, Analytik Jena). Then RNA was isolated using the innuPREP RNA Mini Kit 2.0 (845-KS-2040250, Analytik Jena).
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols


title: yw 28 rep2

value: wild type


title: CB-IMR5-DHX9_scr-R01-R2


title: yw 28 rep3


title: hTNFtg, Amisulpride treatment, rep1

city: Vari

first: George

last: Kollias

state: Attica

address: 34 Fleming Street

department: Institute for Bioinnovation/ Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/ National and Kapodistrian University of Athens

data_processing:
The RNA-Seq FASTQ files obtained after Ion Proton sequencing were mapped using TopHat2 [Kim2013], with default settings and using additional transcript annotation data for the mm10 genome from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). According to the Ion Proton manufacturers recommendation, the reads which remained unmapped were submitted to a second round of mapping using Bowtie2 [Langmead2012] against the mm10 genome with the --very-sensitive switch turned on and merged with the initial mappings.
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges.
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq.
All the above were performed through the Bioconductor package metaseqr.
Assembly: mm10
Supplementary files format and content: txt (tab separated) files containing all the results from metaseqr analysis including normalized expression per replicate, fold change compared to control and p-values.

source_name: ankle joints

extract_protocol:
Total RNA was extracted using RNAeasy Mini kit (QIAGEN), according to the manufacturer's instructions.
The quantity and quality of RNA samples from sorted cells were analyzed using the bioanalyzer form Agilent in combination with the Agilent RNA 6000 Nano. RNA samples with RNA Integrity Number (RIN) > 7 were further used for library preparation using the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN™) according to manufacturer’s instructions. The quantity and quality of libraries were assessed using the DNA High Sensitivity Kit in the bioanalyzer, according to the manufacturer’s instructions (Agilent Technologies). Libraries were subsequently pooled and templated using the Ion PI IC200 Chef Kit (ThermoFisher Scientific) on an Ion Proton Chef instrument or Ion OneTouch System. Sequencing was performed using the Ion PI™ Sequencing 200 V3 Kit and Ion Proton PI™ V2 chips (ThermoFisher Scientific) on an Ion Proton™ System, according to the manufacturer's instructions.

value: ankle joints

value: Synovial fibroblasts

value: hTNFtg

value: Amisulpride 500μΜ 48h


title: CB-IMR5-DHX9_si2-R01-R3


title: Hepatic endothelial cells - Control No2


title: hTNFtg, Amisulpride treatment, rep2


title: T3 hTNFtg, rep3

value: no treatment


title: nrf2 28 rep1


title: yw 28 rep1


title: T2 hTNFtg, rep2


title: Hepatic endothelial cells - Control No3


title: Whole liver cells - Alk1-HEC-KO No4


title: hTNFtg, Amisulpride treatment, rep3


title: Whole liver cells - Alk1-HEC-KO No3


title: Whole liver cells - Alk1-HEC-KO No2


title: T1 hTNFtg, rep1


title: Whole liver cells - Alk1-HEC-KO No1


title: hTNFtg, Infliximab (Remicade) treatment, rep3

description:
metaseqr_all_out_TU_vs_TR.txt
GK3R107_TR3

value: Infliximab 1μg/ml 48h


title: hTNFtg, Infliximab (Remicade) treatment, rep2

description:
metaseqr_all_out_TU_vs_TR.txt
GK3R106_TR2


title: HeLa cell, pCMV-Myc-4

city: Beijing

first: Xiaomei

last: Yuan

state: Beijing

address: Three No. 5, Dongdan, Dongcheng District, Beijing

department: Department of Pathogen Biology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, PUMC

data_processing:
HISAT v2.0.4
HISAT(Kim D, et al. 2015) was used to compare clean reads and reference genome (Parameter: -phred33-sensitive-no-discordant-no-mixed-I 1-X 1000)
Bowtie2 v2.2.6, RSEM v1.2.12
Read count extraction and normalization were performed using Bowtie2 and RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cervix

extract_protocol:
the integrity and concentration of the total RNA was determined by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA) and NanoDrop (Thermo Fisher Scientific, Inc., Waltham, MA, USA)
Illumina HiSeq platform based on 150 bp pair-end strategy.
the sequencing libraries were constructed according to the manufacturer’s instruction, and the final libraries was qualified with Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System.

value: cervix

value: HeLa

value: cervical cancer

value: over-expression of pCMV-Myc

value: transfection


title: HeLa cell, pCMV-Myc-6


title: Whole liver cells - Control No5

value: Ctrl


title: HeLa cell, Myc-IL-23R-3

value: over-expression of Myc-IL-23R


title: hTNFtg, Infliximab (Remicade) treatment, rep1

description:
metaseqr_all_out_TU_vs_TR.txt
GK3R105_TR1


title: Whole liver cells - Control No4


title: HeLa cell, Myc-IL-23R-2


title: Whole liver cells - Control No3


title: Whole liver cells - Control No2


title: HeLa cell, Myc-IL-23R-1


title: hTNFtg, rep3

description:
metaseqr_all_out_WU_vs_TU.txt
metaseqr_all_out_TU_vs_TR.txt
GK3R101_TU3


title: hTNFtg, rep1

description:
metaseqr_all_out_WU_vs_TU.txt
metaseqr_all_out_TU_vs_TR.txt
GK3R99_TU1


title: Whole liver cells - Control No1


title: hTNFtg, rep2

description:
metaseqr_all_out_WU_vs_TU.txt
metaseqr_all_out_TU_vs_TR.txt
GK3R100_TU2


title: Oxr c10  Attach 5 days

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgssonsgate 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Faculty of Medicine and Health Sciences,NTNU

data_processing:
Sequence reads were checked for adaptor sequence/low-quality sequence
Sequence reads were mapped to GRCh38/hg38 using hisat2
Read count extraction was performed using featureCounts
Downstream DEGs analysis was performed with DESeq2 in R
Pathway and GO analysis was performed with GSEA
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file including raw counts of sequencing reads for the features of interest and for all samples in the same matrix

source_name: Oxr1 C10

growth_protocol: The iPSCs were continuously cultured and expanded on Geltrex coated 6-well plates with Essential 8 medium (ThermoFisher Scientific, Cat#A1517001).

extract_protocol:
Total RNA was isolated from patient and control samples using the RNeasy Kit (Qiagen) following the manufacture’s protocol. The quality of purified RNA was estimated on an Epoch Microplate Spectrophotometer (Bio-Tek).
Total RNA was isolated from patient and control samples using the RNeasy Kit (Qiagen) following the manufacture’s protocol. The quality of purified RNA was estimated on an Epoch Microplate Spectrophotometer (Bio-Tek).

treatment_protocol: Differentiation of hiPSC towards neural lineage was performed.Briefly, iPSCs were pretreated with 50 μM Y-27632 (Stemcell Technologies) for 1 h. Then the cells were dissociated with Accutase (Stemcell Technologies) and plated onto low attachment V-type 96-well plate at 20 000 cells per well or AggreWell800 plate (Stemcell Technologies) to form aggregates. The culture was maintained in neural induction medium consisting of DMEM/F12 supplemented with 2% B27 supplement without vitamin A, 1% N2 supplement, 200 nM Noggin (R&D Systems) and 10 μM Y-27632 for 48 h. Formed aggregates were then transferred onto low attachment 6-well plates and continued culture for another 4 days. To induce neural rosette formation, the aggregates were transferred onto Geltrex coated 6-well plate and cultured for 4 days in neural induction medium supplemented with 200 ng/mL Noggin, 200 ng/mL DKK1 (R&D Systems), and 20 ng/mL bFGF (Life Technologies). Neural rosettes were manually picked and transferred onto low attachment 6-well plate in neural induction medium supplemented with 10 ng/mL bFGF and 10 ng/mL EGF to allow neuroepithelial sphere formation. Five days later, two procedures were performed to directly neural differentiation. First, the neural aggregates were placed onto Geltrex coated plates and treated with neural differentiation medium consisting of Neurobasal A medium supplemented with 10 ng/mL BDNF, 10 ng/mL GDNF, 200 μM ascorbic acid, 500 μM cyclic AMP. Second, the neural aggregates were dissociated into single cells with Accutase and replated onto poly-D-lysine/laminin coated 24 or 48-well plates for further differentiation with neural differentiation medium supplemented with 10 ng/mL BDNF, 10 ng/mL GDNF, 200 μM ascorbic acid, 500 μM cyclic AMP.

value: Oxr1 C10

value: Neuron

value: OXR1 mutation

value: Neural differentiation


title: Oxr c3 Attach for 5 days

source_name: Oxr1 C3

value: Oxr1 C3


title: Oxr c11 Attach 5 days

source_name: Oxr1 C11

value: Oxr1 C11


title: Wild type, rep2

description:
metaseqr_all_out_WU_vs_TU.txt
GK3R109_WU2

value: ankle joints

value: Synovial fibroblasts

value: wild type


title: Wild type, rep3

description:
metaseqr_all_out_WU_vs_TU.txt
GK3R110_WU3

value: no treatment


title: AG c15 Attach 5 days


title: Wild type, rep1

description:
metaseqr_all_out_WU_vs_TU.txt
GK3R108_WU1


title: HeLa cell, pCMV-Myc-5

value: cervix


title: 7096

type: genomic

city: Honolulu

first: Rafael

middle: Aniu

last: Peres-David

state: Hawaii

address: 1800 East-West road

department: Anatomy

institute: University Of Hawaii

description: Normal self-esteem monocyte DNA

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IlluminaInfinium MethylationEPIC v2.0 BeadChip Kit using standard Illumina protocol

scan_protocol: Arrays were imaged using illumina iScan Reader using standard recommended Illumina scanner setting

data_processing: Raw IDAT files were analyzed using R statistical software (v4.1.2) via the RnBeads package (v2.12.2)

label: Cy5 and Cy3

source_name: genomic monocyte DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen Allprep DNA/RNA/miRNA Universal Kit according to standard instructions

tag: age

tag: self-esteem category

value: Normal

value: monocytes


title: AG c1  Attach 5 days


title: AG Attach for 5 days


title: HET : 4 : 1215 [PLS_vinican 32347]

type: RNA

city: RIVERSIDE

first: Declan

last: McCole

state: CA

address: 3401 Watkins Drive

department: Biomedical Sciences

institute: University of California Riverside

description: 50ug of total RNA was used for each sample. WT samples were used as reference samples for comparison in analysis.

hyb_protocol: 50 ng of total RNA was used in the hybridization from each sample following manufacturer's guidelines (18 hours at 65°C). Samples were loaded into a PanCancer Pathways Nanostring panel with the addition of 30 custom targets screening for intestinal epithelial cell markers/function (PLS_vinican 32347).

scan_protocol: Scanning of the panels was performed by nCounter SPRINT Profiler and data analysis by nSolver Analysis Software 4.0.

data_processing: Results from each panel were normalized in nSolver software 4.0. using the advanced analysis 2.0 function which relies on the gNorm algorithm. nSolver-generated principal component analysis and heat maps were used to evaluate specific sample clustering and to identify covariants. Principal component analysis identified that at least of set of littermates (co-housing) clustered together, hence data analysis was normalized taking into account littermate effect as a covariate. The same analysis was performed to identify sex differences but none was found. Then, the normalized data from each intestinal segment was consolidated using the MultiRLF function and used for differential expression between genotypes to identify specific targets that exhibit significantly increased or decreased gene expression. p-value was set at 0.05. Benjamini-Yekutieli test was used to calculate the false discovery rate for multiple comparisons analysis. Q-value was set at 0.1.

label: codeset probes

source_name: Isolated Ileal IECs

label_protocol: Samples were labelled with panel-specific codesets, or barcodes, probes designed by Nanostring.

extract_protocol: Distal ileum sections were cut opened longitudinally and immersed in 500uL of Cell Recovery Solution (Corning, Cat. No. 354253) for two hours on ice, and then shaken with forceps to release the intestinal crypts/villi into the solution. Samples were centrifuged at 1.5xG for 10 minutes at 4°C. The supernatant was aspirated and IECs washed with ice-cold PBS (x2). Samples were stored in RNA later and frozen at -80°C until day of experiment. RNA later was removed and cells lysed with syringe and needle (22G). Total RNA was isolated using QIAGEN RNeasy mini kit. RNA estimation was done using Qubit 2.0. Sample purity was assessed by NanoDrop absorbance 260/280 ratio.

value: HET

tag: littermate group

tag: mouse number

tag: Sex

value: Female


title: KO : 4 : 1214 [PLS_vinican 32347]

value: KO


title: WT : 4 : 1216 [PLS_vinican 32347]

value: WT


title: 7090

description: Normal self-esteem monocyte DNA


title: 7092

description: Low self-esteem monocyte DNA

value: Low


title: 7089

description: Low self-esteem monocyte DNA


title: Oxr c2 NE 48h

source_name: Oxr C2

tag: cell line

value: Oxr C2

value: NE

tag: treatment


title: Oxr  c10 NE 48 h

source_name: Oxr c10

value: Oxr c10

value: OXR1 mutation

value: Neural differentiation


title: 7088

description: Low self-esteem monocyte DNA


title: Oxr c3  NE 48 h

value: Oxr1 C3


title: HET : 3 : 1245 [PLS_vinican 32347]


title: 7085

description: Normal self-esteem monocyte DNA


title: WT : 2 : 957 [PLS_vinican 32347]

value: Male


title: KO : 3 : 1243 [PLS_vinican 32347]


title: 7084

description: Normal self-esteem monocyte DNA


title: AG c10  NE 48 h

value: Ctrl


title: KO : 2 : 954 [PLS_vinican 32347]


title: AG c15 NE 48 h


title: KO : 4 : 1218 [PLS_vinican 32347]


title: 7081

description: Low self-esteem monocyte DNA


title: Human Oxr1 C3 p27

value: iPS

value: non


title: HET : 2 : 950 [PLS_vinican 32347]


title: AG c1 NE 48 h


title: WT : 1 : 810 [PLS_vinican 32347]


title: Human Oxr1 C11 p26

value: Oxr1 C11


title: HET : 1 : 811 [PLS_vinican 32347]


title: 7072

description: Normal self-esteem monocyte DNA

value: Normal

value: monocytes


title: BMSC_RNAseq_O_rep3

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Bowtie2 or STAR.
We eliminated the reads mapped to mitochondrial DNA, duplicated and unkown by Sambamba and only unique reads were analysed.
We performed peak calling using MACS2, summarized the read counts by FeatureCounts and obtained the differential peaks by DiffBind (DESeq2. model). Differentially expressed genes were caculated by DESeq2 for RNA-seq.
Enriched motifs in differential peaks between different samples using HOMER.
ClusterProfiler (R package) and DAVID for pathway enrichment.
Assembly: mm10
Supplementary files format and content: bw files and narrowPeak files for ATAC-seq and tab-delimited text files include CPM values for each RNA-seq Sample.

source_name: CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells

extract_protocol:
Td-tomato+Pdgfra+ BMSCs were sorted for Lepr-Cre;Td-tomato mice.
ATAC-seq libraries were prepared according to TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01), and sequenced on a HiSeq X Ten system (Illumina) as paired-end 150-bp reads. RNA-seq libraries were prepared according to modified SMART-seq2 protocols.

value: Lepr-Cre;td-Tomato

value: 22-24 months


title: 7071

description: Normal self-esteem monocyte DNA


title: 7070

description: Normal self-esteem monocyte DNA


title: Human Oxr1 C10 p25

value: Oxr1 C10


title: BMSC_RNAseq_O_rep2

value: CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells

value: WT


title: Human AG05836B C1 p22


title: BMSC_RNAseq_O_rep1


title: 7069

description: Normal self-esteem monocyte DNA


title: BMSC_RNAseq_M_rep3

value: 12 months


title: Human AG05836B C10 p20


title: 7065

description: Normal self-esteem monocyte DNA


title: BMSC_RNAseq_M_rep2


title: Human AG05836B C15 p21


title: 7064

description: Low self-esteem monocyte DNA

value: Low


title: Blastoid_4CL_IVC, scRNAseq

first: yuan

middle: qing

last: zhu

address: Zhongguancun north street

institute: Tsinghua University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10X Genomics single-cell data were processed with common Cell Ranger pipeline (v.6.1.2) to generate the expression matrix. The number of single cells in the assay was determined by the Cell Ranger pipeline with the expecting cell number parameter (8000 cells). The reference and gene annotations Macaca fascicularis genome (Macaca_fascicularis_5.0) were prepared as Cell Ranger pipeline.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Comma-separated values files and matrix files

organism: Macaca fascicularis

source_name: Monkey blastoids

extract_protocol:
Monkey blastoids were picked up manually by mouth pipette. Then blastoids were washed with PBS containing 0.05% BSA and dissociated with trypsin-EDTA (0.25%) (Gibco) at 37 °C in 5% CO2 for 10 min. The dissociation was terminated by PBS with 15% FBS and centrifuged the sample at 300g for 5 min. Cell pellets were resuspended in PBS containing 0.05% BSA, filtered through a 40-μm cell strainer and counted.
Single-cell suspensions were loaded into a 10X Genomics Chromium Chip following the manufacturer’s instructions 48 (10X Genomics, Chromium Next GEM Single Cell 3ʹ GEM, Library and Gel Bead Kit v.3.1).

value: Monkey blastoids


title: BMSC_RNAseq_M_rep1


title: 7059

description: Low self-esteem monocyte DNA


title: 7056

description: Normal self-esteem monocyte DNA


title: 7061

description: Normal self-esteem monocyte DNA


title: BMSC_RNAseq_Y_rep1

value: 8 weeks


title: met1-3_methyltransferase_mutants_MNase_rep1

city: Ann Arbor

first: Shriya

last: Sethuraman

state: MI

address: 5164 Biological Sciences Building, 1105 N. University Ave.

department: Bioinformatics

institute: University of Michigan

description:
processed data file:
met13_MNase_readCount_met1_CG_DMR.csv
met13_MNase_readCount_met1_CHG_DMR.csv
met13_MNase_readCount_met1_CHH_DMR.csv

data_processing:
library strategy: Mnase-H3-ChIP-Seq
The fastq reads were mapped using Bowtie2.
The mapped reads were deduplicated using PICARD and filtered by fragment length between 120-170 bp and MAPQ value >=2.
Differential nucleosomes were identified using DANPOS2.
The WGBS reads were mapped using Bismark allowing no mismatches. The methylation information was extracted using bismark_methylation_extractor
DMRs were identified using methylKit R package.
Genome_build: TAIR10
Supplementary_files_format_and_content:
PolV_stabilized_nucleosomes.bed: the locations of the identified Pol V stabilized nucleosomes
SWI3B_stabilized_nucleosomes.bed: the locations of the identified SWI3B stabilized nucleosomes
PolV_stabilized_Col-0_methylation.csv: the Col-0 average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
PolV_stabilized_nrpe1_methylation.csv: the nrpe1 average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
PolV_stabilized_swi3b_methylation.csv: the swi3b average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
SWI3B_stabilized_Col-0_methylation.csv: the Col-0 average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
SWI3B_stabilized_nrpe1_methylation.csv: the nrpe1 average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
SWI3B_stabilized_swi3b_methylation.csv: the swi3b average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
Col-0_MNase_readCount_drm2_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CG-DMRs
Col-0_MNase_readCount_drm2_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CHG-DMRs
Col-0_MNase_readCount_drm2_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CHH-DMRs
Col-0_MNase_readCount_met1_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CG-DMRs
Col-0_MNase_readCount_met1_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CHG-DMRs
Col-0_MNase_readCount_met1_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CHH-DMRs
Col-0_MNase_readCount_cmt3_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CG-DMRs
Col-0_MNase_readCount_cmt3_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHG-DMRs
Col-0_MNase_readCount_cmt3_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHH-DMRs
drm2_MNase_readCount_drm2_CG_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CG-DMRs
drm2_MNase_readCount_drm2_CHG_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CHG-DMRs
drm2_MNase_readCount_drm2_CHH_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CHH-DMRs
met13_MNase_readCount_met1_CG_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CG-DMRs
met13_MNase_readCount_met1_CHG_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CHG-DMRs
met13_MNase_readCount_met1_CHH_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CHH-DMRs
cmt3_MNase_readCount_cmt3_CG_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CG-DMRs
cmt3_MNase_readCount_cmt3_CHG_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHG-DMRs
cmt3_MNase_readCount_cmt3_CHH_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHH-DMRs

growth_protocol: Arabidopsis thaliana plants were grown at 22ºC under white fluorescent light in 16h/8h day/dark cycle for 3.5 weeks

extract_protocol:
Mnase samples: Mature leaf tissues from the 3.5-week old plants were digested with Micrococcal Nuclease. MNase-digested chromatin was immunoprecipitated with anti-histone H3 antibody.
WGBS samples: Genomic DNA was extracted from 3.5-week old Arabidopsis leaves using Dneasy Plant Mini Kit.
The Mnase-ChIP-seq samples were sequenced by 50 bp paired-end sequencing. The DNA extracted for WGBS were processed with bisulfite treatment followed by 100 bp paired-end sequencing.

tag: ecotype background

value: Columbia

tag: genotype/variation

tag: developmental stage/tissue

value: 3.5 week old leaves

tag: chip antibody

value: anti-histone H3 antibody


title: BMSC_RNAseq_Y_rep2

tag: cell type


title: 7054

description: Low self-esteem monocyte DNA


title: 7050

description: Normal self-esteem monocyte DNA


title: KO : 1 : 809 [PLS_vinican 32347]

value: KO

value: Female


title: drm2_methyltransferase_mutants_MNase_rep1

description:
processed data file:
drm2_MNase_readCount_drm2_CG_DMR.csv
drm2_MNase_readCount_drm2_CHG_DMR.csv
drm2_MNase_readCount_drm2_CHH_DMR.csv


title: cmt3_methyltransferase_mutants_MNase_rep1

description:
processed data file:
cmt3_MNase_readCount_cmt3_CG_DMR.csv
cmt3_MNase_readCount_cmt3_CHG_DMR.csv
cmt3_MNase_readCount_cmt3_CHH_DMR.csv


title: Ezh2_Y726D_ESC_SUZ12

city: Dublin

first: Cheng

last: Wang

address: College Green

department: Genetics

country: Ireland

institute: Smurfit Institute of Genetics, Trinity College Dublin

description: no spike in

data_processing:
ChIP-seq reads quality was confirmed by fastqc, then high-quality reads aligned to reference mouse genome (mm10) by bowtie2. PCR duplicate reads were removed by Picard.
The duplicates-removed spike-in bam files mapped reads number was counted and used for generating the normalization factor (a). Generally, normalization factor (a) was calculated by a fix number N divide the spike-in genome bam file reads count. (Orlando, et al 2014)
For UCSC genome browser visualization, bigwigs were generated by BamCoverage with extending to 200 bp and RPGC normalization. ChIP-Rx bigwig files  were generated by BamCoverage with  Rx normalization factor.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Mouse Embryonic stem cells E14

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatinized culture dishes in GMEM (Sigma) supplemented with 20% FBS (Gibco), 100U/mL Penicillin-Streptomycin (Gibco), 50 μM β-mercaptoethanol (Sigma), 1:100 GlutaMax, 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 1:500 homemade leukaemia inhibitory factor (LIF), and 2i components; 3 μM GSK inhibitor CHIRON99021 (Cayman) and 1 μM MEK inhibitor PD0325901 (Cayman).The ESCs were spited and changed medium every 2 days.For EpiLC differentiation experiments, the dishes were coated with 16 μl/ml fibronectin for 2~3 hours. 2 million ESCs were washed three times with PBS and seeded on the fibronectin coated dished in NDiff227 medium (Takara) supplemented with 20 ng/ml Activin A (Peprotech), 12 ng/ml bFGF (Gibco) and 1% Knockout Serum Replacement (KSR, Thermo) for 2 days. The EpiLC culture medium were changed daily.

extract_protocol: ChIP-seq library preparation was performed using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) according to the manufacturer’s protocol.

treatment_protocol: No treatment/stimulations for this project.

value: Ezh2-Y726D Mouse Embryonic stem cells (ESC)

value: SUZ12 (Cell Signaling,D39F6)


title: Col-0_methyltransferase_mutants_MNase_rep1

description:
processed data file:
Col-0_MNase_readCount_drm2_CG_DMR.csv
Col-0_MNase_readCount_drm2_CHG_DMR.csv
Col-0_MNase_readCount_drm2_CHH_DMR.csv
Col-0_MNase_readCount_met1_CG_DMR.csv
Col-0_MNase_readCount_met1_CHG_DMR.csv
Col-0_MNase_readCount_met1_CHH_DMR.csv
Col-0_MNase_readCount_cmt3_CG_DMR.csv
Col-0_MNase_readCount_cmt3_CHG_DMR.csv
Col-0_MNase_readCount_cmt3_CHH_DMR.csv

value: Col-0 (wild-type)


title: 7047

description: Normal self-esteem monocyte DNA

value: Normal

value: monocytes


title: Ezh1_2_dKO_ESC_SUZ12

description: no spike in

value: Ezh1/2 double KO Mouse Embryonic stem cells (ESC)


title: swi3b_SWISNF_mutants_WGBS_rep2

description:
processed data file:
PolV_stabilized_swi3b_methylation.csv
SWI3B_stabilized_swi3b_methylation.csv

data_processing:
The fastq reads were mapped using Bowtie2.
The mapped reads were deduplicated using PICARD and filtered by fragment length between 120-170 bp and MAPQ value >=2.
Differential nucleosomes were identified using DANPOS2.
The WGBS reads were mapped using Bismark allowing no mismatches. The methylation information was extracted using bismark_methylation_extractor
DMRs were identified using methylKit R package.
Genome_build: TAIR10
Supplementary_files_format_and_content:
PolV_stabilized_nucleosomes.bed: the locations of the identified Pol V stabilized nucleosomes
SWI3B_stabilized_nucleosomes.bed: the locations of the identified SWI3B stabilized nucleosomes
PolV_stabilized_Col-0_methylation.csv: the Col-0 average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
PolV_stabilized_nrpe1_methylation.csv: the nrpe1 average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
PolV_stabilized_swi3b_methylation.csv: the swi3b average methylation levels at every nucleotide 500bps around the Pol V stabilized nucleosomes
SWI3B_stabilized_Col-0_methylation.csv: the Col-0 average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
SWI3B_stabilized_nrpe1_methylation.csv: the nrpe1 average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
SWI3B_stabilized_swi3b_methylation.csv: the swi3b average methylation levels at every nucleotide 500bps around the SWI3B stabilized nucleosomes
Col-0_MNase_readCount_drm2_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CG-DMRs
Col-0_MNase_readCount_drm2_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CHG-DMRs
Col-0_MNase_readCount_drm2_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around drm2 CHH-DMRs
Col-0_MNase_readCount_met1_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CG-DMRs
Col-0_MNase_readCount_met1_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CHG-DMRs
Col-0_MNase_readCount_met1_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around met1 CHH-DMRs
Col-0_MNase_readCount_cmt3_CG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CG-DMRs
Col-0_MNase_readCount_cmt3_CHG_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHG-DMRs
Col-0_MNase_readCount_cmt3_CHH_DMR.csv: Col-0 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHH-DMRs
drm2_MNase_readCount_drm2_CG_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CG-DMRs
drm2_MNase_readCount_drm2_CHG_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CHG-DMRs
drm2_MNase_readCount_drm2_CHH_DMR.csv: drm2 MNase H3-ChIP-Seq read counts 500bps around drm2 CHH-DMRs
met13_MNase_readCount_met1_CG_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CG-DMRs
met13_MNase_readCount_met1_CHG_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CHG-DMRs
met13_MNase_readCount_met1_CHH_DMR.csv: met1-3 MNase H3-ChIP-Seq read counts 500bps around met1 CHH-DMRs
cmt3_MNase_readCount_cmt3_CG_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CG-DMRs
cmt3_MNase_readCount_cmt3_CHG_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHG-DMRs
cmt3_MNase_readCount_cmt3_CHH_DMR.csv: cmt3 MNase H3-ChIP-Seq read counts 500bps around cmt3 CHH-DMRs


title: E14WT_ESC_SUZ12

description: no spike in

value: E14 Mouse Embryonic stem cells (ESC)


title: Ezh2_Y726D_ESC_JARID2

description: no spike in

value: JARID2 (Cell Signaling, D6M9X)


title: nrpe1_SWISNF_mutants_WGBS_rep2

description:
processed data file:
PolV_stabilized_nrpe1_methylation.csv
SWI3B_stabilized_nrpe1_methylation.csv


title: Ezh1_2_dKO_ESC_JARID2

description: no spike in


title: Blastoid_4CL, scRNAseq

description: 10x Genomics


title: 7043

description: Normal self-esteem monocyte DNA


title: BMSC_RNAseq_Y_rep3

value: Lepr-Cre;td-Tomato

value: CD45-Ter119-CD31-Pdgfra+td-Tomato+ bone marrow stromal cells

value: WT


title: 7042

description: Low self-esteem monocyte DNA

value: Low


title: 7041

description: Normal self-esteem monocyte DNA


title: 7037

description: Low self-esteem monocyte DNA


title: E14WT_ESC_JARID2

description: no spike in


title: 7033

description: Low self-esteem monocyte DNA


title: Ezh1_2_dKO_ESC_CBX7

description: no spike in

value: CBX7 (Abcam, Ab21873)


title: nrpe1_SWISNF_mutants_WGBS_rep1

value: Columbia

value: 3.5 week old leaves


title: Col-0_SWISNF_mutants_WGBS_rep1

description:
processed data file:
PolV_stabilized_Col-0_methylation.csv
SWI3B_stabilized_Col-0_methylation.csv


title: 7032

description: Low self-esteem monocyte DNA


title: 7029

description: Normal self-esteem monocyte DNA


title: swi3b_SWISNF_mutants_MNase_rep2

description:
processed data file:
SWI3B_stabilized_nucleosomes.bed

value: anti-histone H3 antibody


title: E14WT_ESC_CBX7

description: no spike in


title: 7027

description: Normal self-esteem monocyte DNA


title: nrpe1_SWISNF_mutants_MNase_rep2

description:
processed data file:
PolV_stabilized_nucleosomes.bed


title: Col-0_SWISNF_mutants_MNase_rep2

description:
processed data file:
PolV_stabilized_nucleosomes.bed
SWI3B_stabilized_nucleosomes.bed


title: 7017

description: Normal self-esteem monocyte DNA


title: swi3b_SWISNF_mutants_MNase_rep1


title: Col-0_SWISNF_mutants_WGBS_rep2


title: CD4 T cell - αCD3/CD28+TRAIL, rep1 [a_CD3_CD28_TRA_1]

city: Taipei

first: I-Tsu

last: Chyuan

state: Outside of the US

address: No. 280, Sec. 4, Renai Rd.

department: Internal Medicine

country: Taiwan

institute: Cathay General Hospital

description: CD4+ T cells were cultured in RPMI-1640 medium containing 10% fetal calf serum plus penicillin (10 units/ml) and streptomycin (10 µg/ml), then the cells were stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies in the presence of TRAIL (10 µg/ml) for 24 hours.

data_processing:
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases (LEADING:20 TRAILING:13 SLIDINGWINDOW:5:20 MINLEN:30).
Trimmed reads were aligned to the reference genome sequence (GRCh38) using HISAT2 v2.1.0 to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Read count extraction and normalization were performed using StringTie v2.1.2.
Differential expression analysis was performed using DESeq2 (for replicate samples) R package v1.28.1 to test for differential expression for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each gene of each Sample

source_name: spleen

growth_protocol: CD4+ T cells were isolated from murine spleens using negative selection kits, EasySep™ Mouse CD4+ T Cell Isolation Kit (StemCell Technologies), and were cultured in RPMI-1640 medium (Invitrogen) containing 10% fetal calf serum (Invitrogen) plus penicillin (10 units/ml) and streptomycin (10 µg/ml) (Invitrogen).

extract_protocol:
Total RNA extraction was performed using TRIzol (Invitrogen) following the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent SureSelect XT HS2 mRNA Library Prep Kit following manufacturer's instructions.

treatment_protocol: The CD4+ T cells stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies (BioLegend) in the presence or absence of TRAIL (10 µg/ml)(GenScript) for 24 hours.

tag: tissue

value: spleen

value: wild type


title: CD4 T cell - αCD3/CD28+TRAIL, rep3 [a_CD3_CD28_TRA_3]

value: stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies in the presence of TRAIL (10 µg/ml) for 24 hours


title: CD4 T cell - αCD3/CD28, rep3 [a_CD3_CD28_3]

description: CD4+ T cells were cultured in RPMI-1640 medium containing 10% fetal calf serum plus penicillin (10 units/ml) and streptomycin (10 µg/ml), then the cells were stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies in the absence of TRAIL for 24 hours.

value: stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies in the absence of TRAIL (10 µg/ml) for 24 hours


title: nrpe1_SWISNF_mutants_MNase_rep1


title: Ezh2_Y726D_ESC_CBX7

description: no spike in

value: Ezh2-Y726D Mouse Embryonic stem cells (ESC)


title: CD4 T cell - αCD3/CD28, rep2 [a_CD3_CD28_2]


title: swi3b_SWISNF_mutants_WGBS_rep1


title: Col-0_SWISNF_mutants_MNase_rep1

value: Col-0 (wild-type)


title: CD4 T cell - αCD3/CD28, rep1 [a_CD3_CD28_1]


title: 7014

description: Normal self-esteem monocyte DNA

value: Normal

value: monocytes


title: 7010

description: Normal self-esteem monocyte DNA


title: BPA Female

city: Bangkok

first: Tewarit

last: Sarachana

address: 154 Rama 1 Rd. Wangmai Pathumwan

country: Thailand

institute: Chulalongkorn University

data_processing:
The library is sequenced using Illumina HiSeq 4000.
Raw reads were filtered by removing the adaptors, sequences with more than 5% of unknown bases(N), and low quality reads to get clean reads. The clean reads were used to perform genome mapping with rn6 genome using HISAT version: v0.1.6-beta with parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
The clean reads were mapped to reference genome using  Bowtie2, version: v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200, and then calculate gene expression level with software package RSEM version: v1.2.12.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: frontal cortex

extract_protocol:
Neonatal rat frontal cortex tissues were quickly removed in cold buffer and collected in RNAlater until use. RNA was extracted using mirVana miRNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
To isolate mRNA, total RNA was treated with DNase I, and Oligo(dT) was used. The mRNA was then mixed with a fragmentation buffer, resulting in the fragmentation of the mRNA. cDNA was synthesized using the mRNA fragments as templates, and the resulting short fragments were purified and resolved with an EB buffer for end reparation and the addition of a single nucleotide A (adenine). The short fragments were then connected with adapters, and suitable fragments were selected for PCR amplification. During the quality control (QC) steps, the sample library was quantified and qualified using the Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System.

treatment_protocol: Pregnant female rat at gestation day 1 (GD1) were daily treated with 5,000 microgram/kilogram of maternal body weight or vehicle control until parturition.

value: Wistar

value: female

value: prenatally exposed to BPA

value: postnatal day 1

value: frontal cortex


title: BPA Male

value: male


title: 7007

description: Normal self-esteem monocyte DNA


title: CD4 T cell - medium, rep2 [medium_CD4_2]

description: CD4+ T cells were cultured in RPMI-1640 medium containing 10% fetal calf serum plus penicillin (10 units/ml) and streptomycin (10 µg/ml) only.


title: 7008

description: Normal self-esteem monocyte DNA


title: Vehicle control Male

value: prenatally exposed to vehicle (control)


title: 7006

description: Low self-esteem monocyte DNA

value: Low


title: CD4 T cell - medium, rep1 [medium_CD4_1]


title: 7022

description: Normal self-esteem monocyte DNA


title: 3D cultured middle aged hematopoietic stem and progenitor cells

description: cultured-M

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The filtering, normalization, scaling, integrating,dimension reduce, clustering and finding markers were processed the seurat (v4.0.4).
The trajecory inference was processed with slingshot based on the coordinate which was reduced by Diffusion Map.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 3D co-cultured

extract_protocol:
After 3D co-cultured, all cells was collected by dissociating with collegen type I and neutral protease, and Lin- cells was sorted by FACS. About 20000 Lin- cells was used to constructe the scRNA-seq libraries.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hematopoietic stem and progenitor cells

value: 3D co-cultured

value: WT

value: 12 months


title: CD4 T cell - αCD3/CD28+TRAIL, rep2 [a_CD3_CD28_TRA_2]

value: spleen

value: wild type

value: stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies in the presence of TRAIL (10 µg/ml) for 24 hours


title: Placenta, Control, CTL13-575

city: New York

first: Corina

last: Lesseur

state: New York

address: 1428 Madison Ave

department: Environmental Medicine & Public Health

institute: Icahn School of Medicine at Mount Sinai

description: MGI Tech

data_processing:
CLC Genomics Workbench v 11.0.1
RNA-seq reads in the fastq files were characterized with FastQC, MultiQC, the reads were quality‐filtered (90% of bases quality score >20), aligned and quantified using STAR v2.7.5b. Transcript level counts were summarized to the gene level using featureCounts.
Assembly: Gencode release M20; GRCm38.p6
Supplementary files format and content: tab-delimited text files with gene counts aligned wih STAR and summarized with featureCounts

source_name: Placenta

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. 1 ug was used for RNA-seq libraries)
Libraries were prepared with the RNAse H protocol for rRNA depletion (New England Biolabs (NEB), Ipswich, MA, USA).

value: Placenta

value: Gestational day 17

value: Control


title: 7015

description: Normal self-esteem monocyte DNA

value: Normal

value: monocytes


title: Fetal Brain, Deltamethrin, DM-8-512

description: MGI Tech

source_name: Fetal Brain

value: Fetal Brain

value: Deltamethrin


title: 7004

description: Low self-esteem monocyte DNA


title: 3D cultured young hematopoietic stem and progenitor cells

description: cultured-Y

value: 8 weeks


title: Placenta, Control, CTL-3-520

description: MGI Tech


title: 7003

description: Low self-esteem monocyte DNA


title: 7002

description: Normal self-esteem monocyte DNA


title: Fetal Brain, Control, CTL16-550

description: MGI Tech