DnA Lab

Resources | our software, datasets, genomes, and more...

      Software   Datasets

      Datasets

We and our collaborators have generated many short-read sequencing datasets using many different protocols, including PRO-seq, GRO-seq, ATAC-seq, ChIP-seq, RNA-seq, and more. All datasets are listed in specific publications and are available through NCBI.

ATAC-seq, RNA-seq, and single-cell RNA-seq of hair follicle stem cells

Dataset available for download: GSE133648
Originally published in:

Single cell analysis of transcriptome and open chromatin reveals the dynamics of hair follicle stem cell aging
C. Zhang, D. Wang, R. Dowell, R. Yi
Frontiers in Aging Volume 4 (2023)

PRO-seq and ATAC-seq of small airway epithelial cells

Dataset available for download: GSE201152
Originally published in:

Integrated genomics approaches identify mediators of transcriptional and epigenetic responses to Afghan desert particulate matter in human small airway epithelial cells
A. Gupta, S.K. Sasse, R. Berman, M.A. Gruca, R.D. Dowell, H.W. Chu, G.P. Downey, A.N. Gerber
Physiological Genomics 54(10):389-401 (2022)

PRO-seq and ATAC-seq of BEAS-2B cells

Dataset available for download: GSE167372
Originally published in:

Deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid aryl hydrocarbon receptor signaling dynamics
A. Gupta, S.K. Sasse, M.A. Gruca, L. Sanford, R.D. Dowell, A.N. Gerber
J. of Biol. Chemistry 297(4):101147 (2021)

ATAC-seq, RNA-seq, and CUT&RUN sequencing of mesenchymal stem cells

Dataset available for download: GSE147703
Originally published in:

The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation
C.B. Levandowski, T. Jones, M. Gruca, S. Ramamoorthy, R.D. Dowell#, D.J. Taatjes#
PLoS Biology 19(8): e3001364 (2021)

GRO-seq and PRO-seq of HCT116 and MCF10A cells

Dataset available for download: PRJNA722106
Originally published in:

Protocol Variations in Run-On Transcription Dataset Preparation Produce Detectable Signatures in Sequencing Libraries
S. Hunter, R. Sigauke, J. Stanley, M. Allen, R.D. Dowell
BMC Genomics 23, 187 (2022)

Pol II Ser5 (3E8) ChIP-seq from HCT116 cells

Dataset available for download: GSE193418
Originally published in:

Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide
B.L. Allen*, K. Quach*, T. Jones*, C.B. Levandowski, C.C. Ebmeier, J.D. Rubin, T. Read, R.D. Dowell, A. Schepartz, D.J. Taatjes
Cell Rep. 39(1):110630 (2022)

RNA-seq of HCT116 cells

Dataset available for download: GSE135870
Originally published in:

Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide
B.L. Allen*, K. Quach*, T. Jones*, C.B. Levandowski, C.C. Ebmeier, J.D. Rubin, T. Read, R.D. Dowell, A. Schepartz, D.J. Taatjes
Cell Rep. 39(1):110630 (2022)