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Molecular biology technique
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a laboratory technique used in molecular biology to assess genome-wide chromatin
ATAC-seq
Topics referred to by the same term
for Transposase-Accessible Chromatin (ATAC-seq), a DNA sequencing technique Atac, a French supermarket chain ATAC SpA (Azienda per i Trasporti Autoferrotranviari
ATAC
Method used to analyse protein interactions with DNA
accessibility. The other three techniques are DNase-seq, FAIRE-seq, and ATAC-seq. While MNase-seq is primarily used to sequence regions of DNA bound by
MNase-seq
American geneticist and biophysicist (born 1979)
gene regulation and chromatin structure. Greenleaf is a co-inventor of ATAC-seq, a widely-used epigenomic method developed in his lab. Greenleaf grew up
William Greenleaf (American scientist)
William_Greenleaf_(American_scientist)
Study of epigenomics in individual cells by single cell sequencing
whole-genome ChIP-sequencing to measure histone modifications, whole-genome ATAC-seq to measure chromatin accessibility and chromosome conformation capture
Single_cell_epigenomics
Examines sequence information from individual cells
preparation in scATAC-Seq are based on split-pool cellular indexing and microfluidics. Standard methods such as microarrays and bulk RNA-seq analyze the RNA
Single-cell_sequencing
Nucleosome occupancy and methylome technique
comparison to CHIP-seq)[citation needed] Greater depth regarding the position of nucleosomes (comparison to DNase-seq, FAIRE-seq, and ATAC-seq. Identifies information
NOMe-seq
Cell-free DNA profiling method
As EPIC-seq studies epigenetic markers to infer gene expression, one can study epigenetic sequencing methods like ChIP-seq, ATAC-seq, MeDIP-seq, and Bisulfite-Free
EPIC-Seq
Molecular biology sequencing technique
For example, ChIP-seq, CUT&RUN, and CUT&Tag rely on antibodies and generate short fragments, while ATAC-seq, DNase-seq, and MNase-seq depend on enzymatic
Fiber-Seq
DNA barcoding technique
provides microfluidic chips and reagent kits for applying DBiT-seq to spatial ATAC-seq, CUT&Tag, and related assays on fresh-frozen and formalin-fixed
Deterministic Barcoding in Tissue for Spatial Omics Sequencing
Deterministic_Barcoding_in_Tissue_for_Spatial_Omics_Sequencing
DNA to identify and sequence open chromatin. The subsequently developed ATAC-seq employs the Tn5 transposase, which inserts specified fragments or transposons
FAIRE-Seq
Single-cell sequencing technology
transposase-accessible chromatin with sequencing (scATAC-seq), which only targets active euchromatin, scGET-seq is also capable of probing inactive heterochromatin
ScGET-seq
Field of study
context-specific expression of genes. Assays such as MNase-seq, DNase-seq, ATAC-seq, or FAIRE-seq are routinely used to understand the accessible chromatin
Epigenomics
Compact and highly condensed form of chromatin
transcriptional silence, low expression, low chromatin accessibility as measured by ATAC-seq, and late replication timing. All human chromosomes 1, 9, 16, and the Y
Heterochromatin
Large-scale deep-learning system developed by DeepMind
concurrently: RNA-seq, CAGE and PRO-cap (gene expression), splice sites, splice site usage and splice junctions (splicing patterns), DNase, ATAC-seq, histone modifications
AlphaGenome
American physician-scientist (born 1972)
extrachromosomal DNA in cancer pathogenesis. Chang is a co-inventor of ATAC-seq, a widely-used epigenomic method introduced in 2013 in collaboration with
Howard_Y._Chang
Histone acetylation on the tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K27ac
Field of molecular biology
chromatin are candidate regulatory regions. These assays include ATAC-seq, DNase-Seq and FAIRE-Seq. Microarrays measure the amount of mRNA in a sample that corresponds
Functional_genomics
Measure the amount of a target entity
interactions of proteins with DNA include: ATAC-seq Chromatin immunoprecipitation ChIP-exo ChIP-on-chip ChIP-seq CUT&RUN CUT&TAG Chromosome conformation
Assay
Region of DNA in a eukaryotic chromosome
regions in areas of active transcription. Methods such as DNase-seq, FAIRE-seq, and ATAC-seq exploit this accessibility to identify active chromatin sequences
Active_chromatin_sequence
Epigenitic modification to the protein histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K27me3
Project to catalogue genetic mutations responsible for cancer
sequencing (ATAC-seq) to 410 TCGA tumor samples covering 23 primary cancers in order to gain insights into gene dysregulation in cancer. ATAC-seq is a low-cost
The_Cancer_Genome_Atlas
Chinese-American computational biologist
cross-platform integration of single-cell datasets including scRNA-seq, scATAC-seq, and spatial omics.; GSDensity, for pathway-centric analysis of single-cell
Ken Chen (computational biologist)
Ken_Chen_(computational_biologist)
Histone methylation on tail of histone H3 associated with gene bodies
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K9me3
Histone acetylation on tail of histone H2B
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H2BK5ac
Biological analysis approach
bisulfite sequencing to single cell RNA-Seq. Other techniques to query the epigenome, as single-cell ATAC-seq and single-cell Hi-C also exist. A different
Multiomics
Biological term
evaluated by different approaches, like scATAC-seq and sciATAC-seq, scCOOL-seq, scNOMe-seq and scDNase-seq. Stage-specific proximal and distal regions
Epigenome
Histone acetylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K9ac
single-cell and spatial multi-omics data, and scReadSim for single-cell RNA-seq and ATAC-seq read simulation. Besides, her group developed scImpute, an imputation
Jingyi_Jessica_Li
Histone methylation on tail of histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4K20me
Histone methylation on tail of histone H3 associated with enhancers
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K4me1
Histone methylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K79me2
Histone acetylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K56ac
American plant biologist
genes that are located long distances away in the genome. They combine ATAC-seq with fluorescence-activated nuclei sorting to identify the locations of
Robert_J._Schmitz
Histone methylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K4me3
Histone acetylation on tail of histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4K12ac
Histone methylation on tail of histone H3 associated with gene bodies
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K36me3
Method used to analyze protein interactions with DNA
antibodies. CUT&RUN: Uses protein A-Mnase ChIP-on-chip ChIP-Seq CUT&RUN ChIL-Seq ChIP-exo ATAC-seq "CUT&Tag: a higher resolution, lower cost way to map chromatin"
CUT&Tag_sequencing
Complex of DNA and protein in eukaryotic cells
separation method to extract nucleosome depleted regions from the genome. ATAC-seq (Assay for Transposable Accessible Chromatin sequencing) uses the Tn5 transposase
Chromatin
Histone acetylation on tail of histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4K8ac
Topics referred to by the same term
genetics at the Stanford University School of Medicine and co-inventor of ATAC-seq William Greenleaf (American novelist) (born 1948), author of 1980 sci-fi
William_Greenleaf
Histone acetylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K36ac
Histone acetylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K23ac
Enzyme that catalyzes movement of transposable elements
high G-C content. This means of library preparation is also used in the ATAC-seq technique. The Sleeping Beauty (SB) transposase is the recombinase that
Transposase
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3T11P
Histone acetylation on tail of histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4K16ac
Technology for examining cells
single-cell ATAC-seq. Following this technology boom, single-cell methylation studies have been produced; some of these are Q-RRBS, snmC-seq, and scMspJI
Spatial DNA methylation profiling
Spatial_DNA_methylation_profiling
Histone acetylation on tail of histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4K91ac
Hashimshony T, Wagner F, Sher N, Yanai I (September 2012). "CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification". Cell Reports. 2 (3): 666–73
List of single cell omics methods
List_of_single_cell_omics_methods
Histone methylation on tail of histone H3 associated with gene bodies
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K36me2
DNA sequence that binds activators to increase the likelihood of gene transcription
DNase-seq have enabled identification of nucleosome-depleted, or open chromatin regions, which can contain CRM. More recently techniques such as ATAC-seq have
Enhancer_(genetics)
Spatial distribution of chromatin within a cell nucleus
cis-regulatory elements. Sites of accessible DNA are typically probed by ATAC-seq or DNase-Seq experimental methods. A 30 nm fiber has long been proposed as the
Nuclear_organization
Histone acetylation on tail of histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4K5ac
Computational method used in analyzing DNA
(2021-01-27). "LanceOtron: a deep learning peak caller for ATAC-seq, ChIP-seq, and DNase-seq". bioRxiv 10.1101/2021.01.25.428108. Meers, Michael P.; Tenenbaum
Peak_calling
Epigenetic modification
enrichment of sequences. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look into regions that are nucleosome-free (open chromatin)
H3K36me
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3T45P
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3T3P
Chemical compound
AML cells and a significant delay in leukemia latency in mice. ChIP-seq and ATAC-seq analysis revealed that inhibition of the CBFβ-SMHHC–RUNX1 protein–protein
AI-10-49
German scientist (born 1953)
study gene circuitries of DC development and function using RNA-Seq, ChIP-seq, ATAC-seq, chromosome conformation capture (4C) and CRISPR/Cas9 gene editing
Martin_Zenke
Biotechnological procedure
single cell assay for transposase-accessible chromatin using sequencing (scATAC-seq). Droplet digital PCR (ddPCR) is a method of dPCR in which a 20-microliter
Digital polymerase chain reaction
Digital_polymerase_chain_reaction
Histone acetylation on tail of histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3K14ac
Epigenetic modification to the DNA packaging protein Histone H33
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3R42me
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3Y41P
Epigenetic modification to the DNA packaging protein Histone H33
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3R17me2
Epigenetic modification to the DNA packaging protein Histone H4
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H4R3me2
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3T6P
Epigenetic modification to the DNA packaging protein Histone H33
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3R26me2
Belgian bio-engineer and computational biologist
Stein (May 2019). "cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data". Nature Methods. 16 (5): 397–400. doi:10.1038/s41592-019-0367-1.
Stein_Aerts
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3S10P
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3R8me2
Epigenetic modification to the DNA packaging protein Histone H3
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3S28P
laboratory has conducted functional genomics research, integrating ATAC-seq, RNA-seq, and immune cell profiling to define how genetic risk variants influence
James_T._Elder
Epigenetic modification to the DNA packaging protein Histone H33
of sequences. 3. Assay for transposase accessible chromatin sequencing (ATAC-seq) is used to look in to regions that are nucleosome free (open chromatin)
H3R2me2
Carl J. Hezrog Professor at the Stanford University School of Medicine
has innovated a number of technologies, including single cell perturb-ATAC-seq, RNA protein interaction detection (RAPID), RNA-protein microarray hybridization
Paul_Khavari
Computational methods in biology
datasets. For example, scRNA-seq features are expressed on a continuous scale whereas chromatin accessibility data (ie. scATAC-seq) exists between 0-2 (two
Single-cell multi-omics integration
Single-cell_multi-omics_integration
Lab technique
accessible chromatin. This approach can be used as an alternative to ATAC-seq or DNAse-seq. When combined with cell-type specific DamID methods, expression
DNA adenine methyltransferase identification
DNA_adenine_methyltransferase_identification
Method used to analyze protein interactions with DNA
biased towards open chromatin like ATAC-Seq and similar techniques. A similar limitation exists for contemporary ChIP-Seq protocols where enzymatic or sonicated
ChIL-sequencing
Echinoderm genomic database
for RNA-seq and ATAC-seq data - Echinobase uses JBrowse BLAST - Users can BLAST against supported genomes, RNA, and protein sequences RNA-seq data visualization
Echinobase
Line of stem cells for research
approach to obtain meaningful scRNA seq and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data from brain organoids. The protocol
Myelinoid
Turkish developmental and systems biologist
genomic level, she then combined cell sorting with genomic techniques, like ATAC-Seq to delineate the regulatory chromatin landscape of human pancreatic cell
H._Efsun_Arda
rapid development of single cell sequencing methods, such as scRNA-seq or scATAC-seq. Although thymic mimetic cells exhibit transcriptional programmes
Thymic_mimetic_cells
gene is located next to an enhancer called LOC130068517, also known as ATAC-STARR-Seq Lymphoblastoid Active Region 29826. Expression is ubiquitous and high
FAM199X
Protein
factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila"
ZZZ3
Beechcraft Bonanza (1947) Boeing F2B (1926) Bradley BA-100 Aerobat Bradley BA-200 ATAC Cessna 150 Aerobat (1957) Cessna 152 Aerobat (1977) Christen Eagle II/Aviat
List_of_aerobatic_aircraft
Protein-coding gene in the species Homo sapiens
PMID 21746879. Wang YL, Faiola F, Xu M, Pan S, Martinez E (December 2008). "Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone
USP22
Protein-coding gene in humans
PMID 10924333. Wang YL, Faiola F, Xu M, Pan S, Martinez E (December 2008). "Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone
CSRP2BP
Protein-coding gene in the species Homo sapiens
PMID 10801849. Wang YL, Faiola F, Xu M, Pan S, Martinez E (2008). "Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone
POLE4
Protein-coding gene in the species Homo sapiens
PDB id codes 1J8I, 1J9O, 2HDM, 2JP1, 2NYZ, 2N54 Identifiers Aliases XCL1, ATAC, LPTN, LTN, SCM-1, SCM-1a, SCM1, SCM1A, SCYC1, X-C motif chemokine ligand
XCL1
ATAC SEQ
ATAC SEQ
Girl/Female
Biblical
A thorn.
Boy/Male
African Egyptian
Ghanian name given to the first-born twin.
Girl/Female
Maori
Image.
Boy/Male
Hindu
The soul
Boy/Male
Afghan, Arabic, Muslim
Gift
Biblical
a thorn
Male
Egyptian
, the son of lady Ata.
Boy/Male
Muslim
Gift, Present
Female
Egyptian
, princess.
Boy/Male
Arabic, Muslim
Gift of Allah
Boy/Male
Afghan, Arabic, Gujarati, Hindu, Indian, Kannada, Malayalam, Marathi, Muslim, Punjabi, Sikh, Sindhi, Telugu
Admiring; Immovable; Attractive; Immoveable; Stable; Unshakeable
Boy/Male
African, Arabic, Farsi, French, German, Ghana, Hindu, Indian, Muslim, Turkish
Gift; One of Twins; From Fante; Donation; To Give; Twin; Father; Abandon; Ancestor
Male
Egyptian
, prince.
Boy/Male
Afghan, Arabic, Australian, Indian, Muslim
Gift; Favour
Boy/Male
Hindu
Immoveable, Firm, Unshakeable, Constant
Boy/Male
Muslim/Islamic
Gift Present
Boy/Male
Muslim
Gift. Favor.
Boy/Male
Armenian, Indian, Punjabi, Sikh
Adam; Self; Spiritual
Boy/Male
Muslim
Gift of Allah
Male
Turkish
Turkish name ATA means "ancestor."
ATAC SEQ
ATAC SEQ
Boy/Male
Indian, Sanskrit
Unimpeded
Boy/Male
British, English
From Ever's Meadow
Boy/Male
Tamil
Shaktidhar | ஷகà¯à®¤à®¿à®¤à®°
Lord Shiva, The Lord Subramanian
Boy/Male
Hindu
Moon
Boy/Male
Australian, Farsi, Irish, Latin
Vain; He who Guards the Treasure; Curly-headed
Girl/Female
Arabic, Muslim
Strong
Girl/Female
Arabic, Muslim, Pashtun
When Light Spreads over the World
Male
Italian
Italian name derived from the word torello, THORELLO means "young bull."
Boy/Male
Latin Spanish
Christian.
Boy/Male
Hindu, Indian
Lord Shiva
ATAC SEQ
ATAC SEQ
ATAC SEQ
ATAC SEQ
ATAC SEQ
n.
One who sequesters property, or takes the possession of it for a time, to satisfy a demand out of its rents or profits.
n.
That which follows as a result; a sequence.
p. pr. & vb. n.
of Sequestrate
v. t.
To cause (one) to submit to the process of sequestration; to deprive (one) of one's estate, property, etc.
pl.
of Sequestrum
imp. & p. p.
of Sequestrate
n.
Sequestration; separation.
n.
An ornament to be placed in the center, as of a table, ceiling, atc.; a central article or figure.
n.
One to whom the keeping of sequestered property is committed.
imp. & p. p.
of Sequester
n.
Same as Sequestrum.
v. t.
To sequester.
a.
Capable of being sequestered; subject or liable to sequestration.
n.
A genus of coniferous trees, consisting of two species, Sequoia Washingtoniana, syn. S. gigantea, the "big tree" of California, and S. sempervirens, the redwood, both of which attain an immense height.
n.
All five cards, of a hand, in consecutive order as to value, but not necessarily of the same suit; when of one suit, it is called a sequence flush.
p. pr. & vb. n.
of Sequester
n.
A hydrocarbon (C13H10) obtained in white fluorescent crystals, in the distillation products of the needles of the California "big tree" (Sequoia gigantea).
n.
A kind of customary payment by a tenant; -- a word used in old records.
a.
Of or pertaining to a sequestrum.
n.
Simple succession, or the coming after in time, without asserting or implying causative energy; as, the reactions of chemical agents may be conceived as merely invariable sequences.