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Everything about ATAC-seq
Molecular biology technique
ATAC-seq is a laboratory technique used in molecular biology to assess genome-wide chromatin accessibility. The technique was introduced in 2013 by the labs of Will Greenleaf and Howard Chang at Stanford University as an alternative to MNase-seq, FAIRE-Seq and DNase-Seq with faster turnaround time, simpler protocol, and lower DNA input requirements. Wikipedia →
🧭 Start here: a 6-step reading path
- Read the overview: ATAC-seqA 5-minute orientation
- Skim a recent paper: ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq dataInfluential work since 2022
- Pick up a classic book: Novel ATAC-Seq Approach Reveals Lineage-specific Reinforcement of the Open Chromatin Landscape Via Cooperation Between BAF and P63The most-reprinted book on the subject
- Read the landmark paper: ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐WideCited 3,167 times
- Go sideways: ScGET-seqA closely related topic
- Go sideways: H3K9me3A closely related topic
📖 Definitions
No dictionary entry for this exact phrase.
🏆 Landmark papers (most cited)
ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
Chromatin accessibility profiling by ATAC-seq
Identification of transcription factor binding sites using ATAC-seq
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq
Transcript-indexed ATAC-seq for precision immune profiling
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq
🆕 Influential since 2022
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning
scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks
📚 Books worth reading
- 📕Novel ATAC-Seq Approach Reveals Lineage-specific Reinforcement of the Open Chromatin Landscape Via Cooperation Between BAF and P63Leeds Leeds Press · 2016
Ranked by number of editions on Open Library, a rough measure of how lasting a book is.
🔗 Related topics
- ScGET-seq Single-cell genome and epigenome by transposases sequencing (scGET-seq) is a DNA sequencing method for profiling open and closed chromatin. In contrast…
- H3K9me3 H3K9me3 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the tri-methylation at the 9th lysine residue…
- H3K79me2 H3K79me2 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the di-methylation at the 79th lysine residue…
- H3K36me2 H3K36me2 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the di-methylation at the 36th lysine residue…
- H3R2me2 H3R2me2 is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the di-methylation at the 2nd arginine residue…
- H3R17me2 H3R17me2 is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the di-methylation at the 17th arginine residue…
- H3K36me H3K36me is an epigenetic modification to the DNA packaging protein Histone H3, specifically, the mono-methylation at the 36th lysine residue of the histone…
- H4R3me2 H4R3me2 is an epigenetic modification to the DNA packaging protein histone H4. It is a mark that indicates the di-methylation at the 3rd arginine residue…