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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.
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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.
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Contributor(s) |
White MA, Friedman RZ, Cohen BA |
Citation missing |
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Submission date |
Aug 21, 2023 |
Last update date |
Sep 02, 2023 |
Contact name |
Michael Aaron White |
E-mail(s) |
mawhite@wustl.edu
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Organization name |
Washington University in St. Louis School of Medicine
|
Department |
Genetics
|
Street address |
660 South Euclid Ave
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City |
Saint Louis |
State/province |
MO |
ZIP/Postal code |
63144 |
Country |
USA |
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Platforms (4)
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GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
GPL25368 |
Illumina NovaSeq 6000 (Escherichia coli) |
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Samples (42)
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Relations |
BioProject |
PRJNA1007735 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |