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Table 2 ATAC-seq datasets used for the ATACseqQC case studies. The four datasets chosen for detailed quality control are highlighted in bold

From: ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

SRA Run Accession

Condition

Comment

Study Description

Reference

SRR891269

EBV-transformed lymphoblastoid cell line

GM12878, 50 k cells

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

[4]

SRR891270

EBV-transformed lymphoblastoid cell line

GM12878, 50 k cells

SRR891271

EBV-transformed lymphoblastoid cell line

GM12878, 50 k cells

SRR891272

EBV-transformed lymphoblastoid cell line

GM12878, 500 cells

SRR891274

EBV-transformed lymphoblastoid cell line

GM12878, 500 cells

SRR891275

CD4+ T-cells purified using negative selection

CD4+ T cells, day 1

SRR891276

CD4+ T-cells purified using negative selection

CD4+ T cells, day 1

SRR891277

CD4+ T-cells purified using negative selection

CD4+ T cells, day 2

SRR891278

CD4+ T-cells purified using negative selection

CD4+ T cells, day 2

SRR3295017

Uninfected

HFF_uninfected

Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells

[30]

SRR3295018

HFF cells, uninfected

HFF_uninfected

SRR3295019

HFF cells, uninfected

HFF_uninfected

SRR3295020

HFF cells infected with T. gondii

HFF_infected

SRR3295021

HFF cells infected with T. gondii

HFF_infected

SRR3295022

HFF cells infected with T. gondii

HFF_infected

SRR5720369

J-Lat A72 cells treated with DMSO

Replicate 1

The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin Remodeling Complexes

[29]

SRR5720370

J-Lat A72 cells treated with JQ1

Replicate 1

SRR5720371

J-Lat A72 cells treated with DMSO

Replicate 2

SRR5720372

J-Lat A72 cells treated withJQ1

Replicate 2

SRR5800797

Breast cancer cell line T47D, multiH1sh Control

Replicate 1, 75 k cells

Analysis of the DNA accessibility upon knocking-down multiple histone H1 variants by ATAC-seq

Vallés AJ and Izquierd-Bouldstridge A., unpublished

SRR5800798

Breast cancer cell line T47D, multiH1sh Control

Replicate 2, 75 k cells

SRR5800799

Breast cancer cell line T47D, multiH1sh Dox

Replicate 1, 75 k cells

SRR5800800

Breast cancer cell line T47D, multiH1sh Dox

Replicate 2, 75 k cells

SRR5800801

Breast cancer cell line T47D, RDsh control

Replicate 1, 75 k cells

SRR5800802

Breast cancer cell line T47D, RDsh Dox Control

Replicate 1, 75 k cells