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Series GSE241353 Query DataSets for GSE241353
Status Public on Sep 01, 2023
Title Active learning of enhancer and silencer regulatory grammar in photoreceptors
Organisms Escherichia coli; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We performed iterative rounds of massively parallel reporter assay experiments in ex vivo retinas to generate training data for machine learning models of the photoreceptor cis-regulatory grammar.
Overall design A series of libraries of barcoded reporter gene plasmids were transfected into mouse retinas in triplicate. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.
Contributor(s) White MA, Friedman RZ, Cohen BA
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Submission date Aug 21, 2023
Last update date Sep 02, 2023
Contact name Michael Aaron White
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 (4)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21222 Illumina NextSeq 500 (Escherichia coli)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (42)
GSM7727567 Library3 RNA-seq rep1
GSM7727568 Library3 RNA-seq rep3
GSM7727569 Library3 RNA-seq rep4
BioProject PRJNA1007735

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
GSE241353_RAW.tar 22.6 Mb (http)(custom) TAR (of COUNTS)
GSE241353_library3.fasta.gz 324.8 Kb (ftp)(http) FASTA
GSE241353_library4.fasta.gz 601.6 Kb (ftp)(http) FASTA
GSE241353_library5.fasta.gz 601.3 Kb (ftp)(http) FASTA
GSE241353_library6.fasta.gz 338.4 Kb (ftp)(http) FASTA
GSE241353_library7.fasta.gz 337.1 Kb (ftp)(http) FASTA
GSE241353_library8a.fasta.gz 2.4 Mb (ftp)(http) FASTA
GSE241353_library8b.fasta.gz 2.4 Mb (ftp)(http) FASTA
GSE241353_library8c.fasta.gz 2.4 Mb (ftp)(http) FASTA
GSE241353_library9a.fasta.gz 555.1 Kb (ftp)(http) FASTA
GSE241353_library9b.fasta.gz 554.3 Kb (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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