NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE141705 Query DataSets for GSE141705
Status Public on Dec 15, 2020
Title LFY is pioneer transcription factor [MNase-seq]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary This study identified LEAFY (LFY) as a pioneer transcription factor. We made use of 35S:LFY-GR, an inducible version of the LFY protein fused to the rat glucocorticoid hormone binding domain. In root explants, steroid activated LFY-GR triggers synchronous and abundant flower induction (PMID: 15225291). We combined LFY ChIP-seq, MNase-seq before and after LFY binding and time-course RNA-seq in 35S:LFY-GR root explants to characterize the role of LFY as a pioneer transcription factor.
 
Overall design MNase seq of 35S:LFY-GR root explants. Tissues were treated with dexamethasone (after LFY binding) or mock (before LFY binding) solution. Two MNase concentrations were used: low MNase treatment, which preserve fragile nucleosomes and standard (high) MNase treatment, in which fragile nucleosomes are lost. Two biological replicates were sequenced for each condition.
Web link https://doi.org/10.1101/2020.03.16.994418
 
Contributor(s) Klasfeld S, Jin R, Wagner D
Citation(s) 33504790
Submission date Dec 09, 2019
Last update date Oct 05, 2021
Contact name Doris Wagner
E-mail(s) wagnerdo@sas.upenn.edu
Phone 2158980483
Organization name University of Pennsylvania
Department Department of Biology
Lab Wagner Lab
Street address 103G Carolyn Lynch Laboratory
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (8)
GSM4962682 1hrMock_LowDigest_1 MNase-seq
GSM4962683 1hrMock_LowDigest_2 MNase-seq
GSM4962684 1hrDex_LowDigest_1 MNase-seq
This SubSeries is part of SuperSeries:
GSE141706 LFY is pioneer transcription factor
Relations
BioProject PRJNA594411
SRA SRP235378

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
GSE141705_MNase_HD_pooled.bed.gz 4.4 Mb (ftp)(http) BED
GSE141705_MNase_HD_pooled.bigwig 26.0 Mb (ftp)(http) BIGWIG
GSE141705_MNase_HM_pooled.bed.gz 5.8 Mb (ftp)(http) BED
GSE141705_MNase_HM_pooled.bigwig 29.4 Mb (ftp)(http) BIGWIG
GSE141705_MNase_LD_pooled.bed.gz 1.9 Mb (ftp)(http) BED
GSE141705_MNase_LD_pooled.bigwig 10.3 Mb (ftp)(http) BIGWIG
GSE141705_MNase_LM_pooled.bed.gz 3.4 Mb (ftp)(http) BED
GSE141705_MNase_LM_pooled.bigwig 21.5 Mb (ftp)(http) BIGWIG
GSE141705_RAW.tar 92.0 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap