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Series GSE80321 Query DataSets for GSE80321
Status Public on Dec 07, 2016
Title A multi-step transcriptional and chromatin cascade underlies motor neuron programming (transcription factor ChIP-seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Direct programming via the overexpression of transcription factors (TFs) aims to control cell fate at a precision that will be instrumental for clinical applications. However, direct programming of terminal fates remains an obscure process. Taking advantage of the rapid and uniquely efficient programming of spinal motor neurons by overexpression of Ngn2, Isl1 and Lhx3, we have characterized gene expression, chromatin and transcription factor binding time-course dynamics during complete motor neuron programming. Our studies point to a surprisingly dynamic programming process. Promoter chromatin and expression analysis reveals at least three distinct phases of gene activation, while programming factor binding shifts from one set of targets to another, controlling regulatory region activity and gene expression. Furthermore, our evidence suggest that the enhancers and genes activated in the final stage of motor neuron processing are dependent on the combined activities of Isl1 and Lhx3 factors with Ebf and Onecut TFs that are themselves activated midway through the programming process. Our results suggest an unexpected multi-stage model of motor neuron programming in which the programming TFs require activation of a set of intermediate regulators before they complete the programming process.
 
Overall design Transcription factor binding was characterized during the direct programming of ES cells into motor neurons using over-expression of Ngn2-Isl1-Lhx3 programming factors. ChIP-seq experiments were performed targeting Lhx3 (FLAG epitope tag), Isl1, Ngn2, Oct4, Onecut2, and Ebf2 at various time-points during the programming process. Input sequencing at each time-point was performed as a control.
 
Contributor(s) Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Al-Sayegh MA, Hirsekorn A, Satija R, Ohler U, Mahony S, Mazzoni EO
Citation(s) 27939218
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 HD079682 Molecular mechanisms of direct neuronal programming NEW YORK UNIVERSITY Mazzoni
Submission date Apr 15, 2016
Last update date May 15, 2019
Contact name Shaun Mahony
E-mail(s) mahony@psu.edu
Phone 814-865-3008
Organization name Penn State University
Department Biochemistry & Molecular Biology
Lab Shaun Mahony
Street address 404 South Frear Bldg
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (58)
GSM2124208 ChIP-seq Oct4 in EB+12hrDox(iFlag.Ngn2) replicate 1
GSM2124209 Input-DNA in EB+12hrDox(iFlag.Ngn2) replicate 1
GSM2124210 ChIP-seq Ngn2 in EB+12hrDox(iFlag.Ngn2) replicate 1
This SubSeries is part of SuperSeries:
GSE80483 A multi-step transcriptional and chromatin cascade underlies motor neuron programming
Relations
BioProject PRJNA318580
SRA SRP073362

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
GSE80321_Ebf2_48h_iNIL.bed.gz 1014.1 Kb (ftp)(http) BED
GSE80321_Ebf2_48h_iNIL.events.txt.gz 2.4 Mb (ftp)(http) TXT
GSE80321_Isl1_12h_iNIL.bed.gz 221.8 Kb (ftp)(http) BED
GSE80321_Isl1_12h_iNIL.events.txt.gz 1.6 Mb (ftp)(http) TXT
GSE80321_Isl1_24h_iNIL.bed.gz 72.4 Kb (ftp)(http) BED
GSE80321_Isl1_24h_iNIL.events.txt.gz 538.0 Kb (ftp)(http) TXT
GSE80321_Isl1_48h_iNIL.bed.gz 157.2 Kb (ftp)(http) BED
GSE80321_Isl1_48h_iNIL.events.txt.gz 1.2 Mb (ftp)(http) TXT
GSE80321_Isl1_8h_iNIL.bed.gz 105.1 Kb (ftp)(http) BED
GSE80321_Isl1_8h_iNIL.events.txt.gz 809.9 Kb (ftp)(http) TXT
GSE80321_Lhx3_12h_iIL.bed.gz 21.2 Kb (ftp)(http) BED
GSE80321_Lhx3_12h_iIL.events.txt.gz 85.3 Kb (ftp)(http) TXT
GSE80321_Lhx3_12h_iILEO.bed.gz 45.4 Kb (ftp)(http) BED
GSE80321_Lhx3_12h_iILEO.events.txt.gz 388.3 Kb (ftp)(http) TXT
GSE80321_Lhx3_12h_iNIL.bed.gz 140.4 Kb (ftp)(http) BED
GSE80321_Lhx3_12h_iNIL.events.txt.gz 1.0 Mb (ftp)(http) TXT
GSE80321_Lhx3_12h_iNILEO.bed.gz 136.4 Kb (ftp)(http) BED
GSE80321_Lhx3_12h_iNILEO.events.txt.gz 1.2 Mb (ftp)(http) TXT
GSE80321_Lhx3_24h_iILEO.bed.gz 84.3 Kb (ftp)(http) BED
GSE80321_Lhx3_24h_iILEO.events.txt.gz 729.7 Kb (ftp)(http) TXT
GSE80321_Lhx3_24h_iNIL.bed.gz 212.9 Kb (ftp)(http) BED
GSE80321_Lhx3_24h_iNIL.events.txt.gz 1.6 Mb (ftp)(http) TXT
GSE80321_Lhx3_24h_iNILEO.bed.gz 112.3 Kb (ftp)(http) BED
GSE80321_Lhx3_24h_iNILEO.events.txt.gz 992.7 Kb (ftp)(http) TXT
GSE80321_Lhx3_36h_iILEO.bed.gz 81.4 Kb (ftp)(http) BED
GSE80321_Lhx3_36h_iILEO.events.txt.gz 715.2 Kb (ftp)(http) TXT
GSE80321_Lhx3_48h_iIL.bed.gz 20.1 Kb (ftp)(http) BED
GSE80321_Lhx3_48h_iIL.events.txt.gz 76.6 Kb (ftp)(http) TXT
GSE80321_Lhx3_48h_iILEO.bed.gz 6.9 Kb (ftp)(http) BED
GSE80321_Lhx3_48h_iILEO.events.txt.gz 59.6 Kb (ftp)(http) TXT
GSE80321_Lhx3_48h_iNIL.bed.gz 95.0 Kb (ftp)(http) BED
GSE80321_Lhx3_48h_iNIL.events.txt.gz 742.8 Kb (ftp)(http) TXT
GSE80321_Lhx3_8h_iNIL.bed.gz 24.7 Kb (ftp)(http) BED
GSE80321_Lhx3_8h_iNIL.events.txt.gz 182.3 Kb (ftp)(http) TXT
GSE80321_Ngn2_12h_iN.bed.gz 193.2 Kb (ftp)(http) BED
GSE80321_Ngn2_12h_iN.events.txt.gz 575.7 Kb (ftp)(http) TXT
GSE80321_Ngn2_12h_iNIL.bed.gz 118.3 Kb (ftp)(http) BED
GSE80321_Ngn2_12h_iNIL.events.txt.gz 348.1 Kb (ftp)(http) TXT
GSE80321_Oct4_0h_iNIL.bed.gz 53.8 Kb (ftp)(http) BED
GSE80321_Oct4_0h_iNIL.events.txt.gz 245.2 Kb (ftp)(http) TXT
GSE80321_Oct4_12h_iN.bed.gz 4.3 Kb (ftp)(http) BED
GSE80321_Oct4_12h_iN.events.txt.gz 16.1 Kb (ftp)(http) TXT
GSE80321_Oct4_12h_iNIL.bed.gz 2.6 Kb (ftp)(http) BED
GSE80321_Oct4_12h_iNIL.events.txt.gz 12.1 Kb (ftp)(http) TXT
GSE80321_Onecut2_48h_iNIL.bed.gz 786.0 Kb (ftp)(http) BED
GSE80321_Onecut2_48h_iNIL.events.txt.gz 1.7 Mb (ftp)(http) TXT
GSE80321_RAW.tar 18.0 Gb (http)(custom) TAR (of BW)
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Processed data are available on Series record
Raw data are available in SRA
Processed data provided as supplementary file
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