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Series GSE210779 Query DataSets for GSE210779
Status Public on Jan 18, 2023
Title EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary EKLF/Klf1 is a Zinc-finger transcription activator essential for erythroid lineage commitment and terminal differentiation. Using ChIP-Seq, we investigate EKLF DNA binding and transcription activation mechanisms during mouse embryonic erythropoiesis. Our study focuses on global EKLF binding dynamics during embryonic erythropoiesis in primary WT and Nan/+ mouse fetal liver, and its correlation with chromatin accessibility, CBP occupancy, histone acetylation, and finally its effect on RNA Polymerase II pausing and elongation. Our goal is to elucidate the mechanisms of transcription activation by EKLF/Klf1 during embryonic erythropoiesis in vivo and in the context of RNA pol II pause-release control. Additionally, we aim to understand the unusually severe effects of conservative E to D change in Nan-EKLF and the molecular mechanisms leading to dominant anemia through global gene dysregulation.
 
Overall design Chromatin Immunoprecipitation and NGS (ChIP-seq) for EKLF/Klf1, CBP, H3K27ac, RNA Polymerase II C-terminal domain phospho-Serine5, RNA Polymerase II C-terminal domain phospho-Serine2, ATAC-Seq in mouse E13.5 fetal liver from WT and Nan/+ embryos. All ChIPs except RNA Pol II are biological triplicates from littermate fetal livers. RNA Pol II was performed in duplicate for each experiment. ATAC-Seq was performed in biological duplicates
Web link http://10.1016/j.celrep.2022.111830
 
Contributor(s) Mukherjee K, Bieker J
Citation(s) 36543143
Submission date Aug 08, 2022
Last update date Jan 23, 2023
Contact name Kaustav Mukherjee
E-mail(s) kaustav.mukherjee@mssm.edu
Phone 2122414143
Organization name Icahn School of Medicine at Mount Sinai
Department Cell, Developmental and Regenerative Biology
Lab Dr. James Bieker
Street address 1 Gustave Levy Place
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (43)
GSM6437118 FL_wt_eklf_chip_rep1
GSM6437119 FL_wt_eklf_chip_rep2
GSM6437120 FL_wt_eklf_chip_rep3
Relations
BioProject PRJNA867412

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE210779_CBP_nan_norm_rpkm.bw 242.9 Mb (ftp)(http) BW
GSE210779_CBP_wt_norm_rpkm.bw 283.6 Mb (ftp)(http) BW
GSE210779_EKLF_nan_norm_rpkm.bw 400.1 Mb (ftp)(http) BW
GSE210779_EKLF_wt_norm_rpkm.bw 396.9 Mb (ftp)(http) BW
GSE210779_RAW.tar 56.9 Gb (http)(custom) TAR (of BAM, BW)
GSE210779_atac_nan_combined.bw 195.8 Mb (ftp)(http) BW
GSE210779_atac_wt_combined.bw 244.5 Mb (ftp)(http) BW
GSE210779_h3k27ac_nan_norm.bw 383.4 Mb (ftp)(http) BW
GSE210779_h3k27ac_wt_norm.bw 394.4 Mb (ftp)(http) BW
GSE210779_n_peaks_125_250_sig_fold.bed.gz 212.3 Kb (ftp)(http) BED
GSE210779_nan_S2_norm.bw 282.9 Mb (ftp)(http) BW
GSE210779_nan_S5_norm.bw 229.4 Mb (ftp)(http) BW
GSE210779_w_peaks_125_250_sig_fold.bed.gz 127.1 Kb (ftp)(http) BED
GSE210779_wt_S2_norm.bw 299.3 Mb (ftp)(http) BW
GSE210779_wt_S5_norm.bw 224.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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