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Series GSE197060 Query DataSets for GSE197060
Status Public on Aug 25, 2023
Title Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes
Organisms Homo sapiens; Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary Investigation of translation in rare cell types or subcellular contexts is challenging due to large input requirements for standard approaches. Here, we present “nanoRibo-seq” an optimized approach using 102- to 103-fold less input material than bulk approaches. nanoRibo-seq exhibits rigorous quality control features consistent with quantification of ribosome protected fragments with as few as 1,000 cells. We compare translatomes of two closely related cortical neuron subtypes, callosal projection neurons (CPN) and subcerebral projection neurons (SCPN), during their early postnatal development. We find that, while translational efficiency is highly correlated between CPN and SCPN, several dozen mRNAs are differentially translated. We further examine upstream open reading frame (uORF) translation and identify that mRNAs involved in synapse organization and axon development are highly enriched for uORF translation in both subtypes. nanoRibo-seq enables investigation of translational regulation of rare cell types in vivo and offers a flexible approach for globally quantifying translation from limited input material.
 
Overall design nanoRibo-seq: low input ribosome profiling
Web link https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01006-9
 
Contributor(s) Froberg JE
Citation(s) 37624698
Submission date Feb 20, 2022
Last update date Nov 13, 2023
Contact name John Edward Froberg
E-mail(s) jfroberg@fas.harvard.edu
Phone 8479770174
Organization name Harvard University
Department Stem Cell & Regenerative Biology
Lab Macklis Lab
Street address 7 Divinity Avenue
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platforms (3)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (45)
GSM5907715 forebrain, 30ng_equiv
GSM5907716 forebrain, bulk_RP
GSM5907717 forebrain, in_vitro_G>R
Relations
BioProject PRJNA808741

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
GSE197060_BulkVs30ng_CDS_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_BulkVs30ng_five_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_BulkVs30ng_lengthDistro.csv.gz 14.5 Kb (ftp)(http) CSV
GSE197060_BulkVs30ng_three_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_CPN_RiboCode_ORFs_collapsed.bed.gz 1.7 Mb (ftp)(http) BED
GSE197060_CPN_RiboCode_ORFs_collapsed.txt.gz 6.5 Mb (ftp)(http) TXT
GSE197060_CPN_SCN_FC_3pUTR_summary.txt.gz 957.5 Kb (ftp)(http) TXT
GSE197060_CPN_SCN_FC_5pUTR_summary.txt.gz 882.1 Kb (ftp)(http) TXT
GSE197060_CPN_SCN_FC_CDS_summary.txt.gz 2.5 Mb (ftp)(http) TXT
GSE197060_CPN_SCPN_DESeq2_counts_matrix.csv.gz 206.1 Kb (ftp)(http) CSV
GSE197060_CPN_SCPN_lengthDistroTidy.txt.gz 16.9 Kb (ftp)(http) TXT
GSE197060_CPN_hemispheres_CDS_FC_matrix.csv.gz 2.2 Mb (ftp)(http) CSV
GSE197060_CPN_hemispheres_five_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_CPN_hemispheres_lengthDistro.csv.gz 29.3 Kb (ftp)(http) CSV
GSE197060_CPN_hemispheres_three_utr_FC_matrix.csv.gz 2.2 Mb (ftp)(http) CSV
GSE197060_HEK_TPMs.csv.gz 1013.6 Kb (ftp)(http) CSV
GSE197060_RiboCode_ORFs_collapsed.bed.gz 1.6 Mb (ftp)(http) BED
GSE197060_RiboCode_ORFs_collapsed.txt.gz 6.3 Mb (ftp)(http) TXT
GSE197060_RnaseTitration_CDS_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_RnaseTitration_five_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_RnaseTitration_lengthDistro.csv.gz 25.4 Kb (ftp)(http) CSV
GSE197060_RnaseTitration_three_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_SCPN_RiboCode_ORFs_collapsed.bed.gz 1.8 Mb (ftp)(http) BED
GSE197060_SCPN_RiboCode_ORFs_collapsed.txt.gz 6.9 Mb (ftp)(http) TXT
GSE197060_sorted_neurons_CDS_FC_matrix.csv.gz 2.2 Mb (ftp)(http) CSV
GSE197060_sorted_neurons_five_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
GSE197060_sorted_neurons_lengthDistro.csv.gz 16.5 Kb (ftp)(http) CSV
GSE197060_sorted_neurons_three_utr_FC_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
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