Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing.

Indu Santhanagopalan, Antonia Netzl, Tanya Mathur, Alison Smith, Howard Griffiths, Andre Holzer

Open access · goldAbstract read

In one paragraph

Article in STAR protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact, top 99% of its field

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 1 institution in 2 countries.

Indu SanthanagopalanDepartment of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK. Electronic address: is438@cam.ac.uk.

Antonia NetzlDepartment of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.

Tanya MathurDepartment of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.

Alison SmithDepartment of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.

Howard GriffithsDepartment of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.

Andre HolzerDepartment of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Center for Bioinformatics and Department of Computer Science, Saarland University, 66123 Saarbrücken, Germany. Electronic address: andre.holzer.biotech@gmail.com.

University of Cambridge · GB

Funding

Biotechnology and Biological Sciences Research Council BB/I013164/1

6 · The paper itself

Abstract

The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.

Indexed as

Chlamydomonas reinhardtiiCell NucleusChromatinHigh-Throughput Nucleotide SequencingSequence Analysis, DNAChromatinEnvironmental sciencesGeneticsGenomicsModel OrganismsMolecular BiologyPlant sciencesSequencingSystems biology

Identifiers

PMID38236771

DOI10.1016/j.xpro.2023.102764

PMCPMC10828896

OpenAlexW4391036318

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.