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Series GSE161009 Query DataSets for GSE161009
Status Public on Oct 05, 2021
Title Chromatin accessibility changes in experimentally-induced basal to squamous cell carcinoma transition (BST)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Basal cell carcinoma may undergo BST spontaneously or upon Hedgehog targeting therapy. We identified that modulation of Ras/MAPK or TGFb signaling drive BST. Here, we induce Ras/MAPK and/or abrogate TGFb signaling to induce BST. Alternatively we drive c-FOS to induce BST. In these various experimentally-induced model of BST, we analyze chromatin accessibility profiles upon Ras/MAPK activation and/or TGFb signaling abrogation. We also analyze chromatin accessibility profiles upon c-FOS activation.
 
Overall design RasV12-expressing and/or TGFbR1-kd ASZcells were processed for ATAC-seq. Two biological replicates were sequenced per treatment group.
ATACseq profiles of ASZ transfected with doxycycline-inducible empty vector (ctrl) or c-FOS containing vector (c-FOS) upon Dox treatment, were generated by deep sequencing, in duplicate, using Illumina NextSeq. The sequence reads that passed quality filters were analyzed using bowtie for alignment and macs2 for peak calling.
 
Contributor(s) Kuonen F, Gaddam S
Citation(s) 34610301
Submission date Nov 06, 2020
Last update date Oct 19, 2021
Contact name Anthony Oro
Organization name Stanford University
Department Dermatology
Street address 269 Campus Drvie
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (16)
GSM4887760 ASZ_control_rep1
GSM4887761 ASZ_control_rep2
GSM4887762 ASZ_RasV12_rep1
This SubSeries is part of SuperSeries:
GSE168376 C-FOS-driven basal to squamous cell transition
Relations
BioProject PRJNA675105
SRA SRP291459

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
GSE161009_RAW.tar 3.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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