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Series GSE225867 Query DataSets for GSE225867
Status Public on Mar 05, 2023
Title Transcription factor interactions explain the context-dependent activity of CRX binding sites
Organisms Mus musculus; synthetic construct
Experiment type Other
Summary We assessed how the effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory sequence (CRS) depend on the local sequence context. We constructed a library of synthetic CRSs composed of TFBSs enriched in mouse photoreceptors and assayed them by massively parallel reporter assay in live mouse retina. We used the resulting data to train neural network-based models that predict CRS activity from sequence.
 
Overall design A library of 6600 barcoded reporter gene plasmids were transfected into mouse retinas. Three replicates were performed. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.
 
Contributor(s) White MA, Loell KJ, Friedman RZ
Citation(s) 38227575
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM121755 DISCOVERY OF DNA DETERMINANTS OF TRANSCRIPTION FACTOR BINDING AND FUNCTION IN PHO WASHINGTON UNIVERSITY Michael Aaron White
Submission date Feb 22, 2023
Last update date Feb 06, 2024
Contact name Michael Aaron White
E-mail(s) mawhite@wustl.edu
Organization name Washington University in St. Louis School of Medicine
Department Genetics
Street address 660 South Euclid Ave
City Saint Louis
State/province MO
ZIP/Postal code 63144
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19424 Illumina NextSeq 500 (synthetic construct)
Samples (4)
GSM7058909 CDNRM RNA-seq replicate 1
GSM7058910 CDNRM RNA-seq replicate 2
GSM7058911 CDNRM RNA-seq replicate 3
Relations
BioProject PRJNA937735

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
GSE225867_cdnrm_barcode_sequences.fa.gz 63.2 Kb (ftp)(http) FA
GSE225867_cdnrm_mpra_library.txt.gz 86.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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