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Series GSE181338 Query DataSets for GSE181338
Status Public on Oct 18, 2023
Title Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)
Organisms Homo sapiens; synthetic construct
Experiment type Expression profiling by high throughput sequencing
Other
Summary Albeit majority of eukaryotic genome can be pervasively transcribed to a diverse population of lncRNAs and various subtypes of lncRNA have been discovered. However, the genome-wide study of miRNA-derived lncRNAs is still lacking. Here, we report that over 800 miRNA gene-originated lncRNAs (molncRNAs) generated from miRNA loci. One of them, molnc-301b from miR-301b and miR-130b, functions as an "RNA decoy" to facilitate dissociation of the chromatin remodeling protein SMARCA5 from chromatin and thereby sequester transcription and mRNA translation. Specifically, molnc-301b attenuates erythropoiesis via mitigating the transcription of erythropoietic and translation-associated genes, such as GATA1 and FOS. In addition, we have established a useful and powerful CRISPR screen platform to characterize the biological functions of molncRNAs at large-scale and single-cell level, and identified 26 functional molncRNAs in hematopoietic cells. Collectively, we focused on miRNA-derived lncRNAs, deciphered their landscape during normal hematopoiesis, and comprehensively evaluated their potential roles.
 
Overall design We designed 3 pooled gRNA libraries: library 1 (molncRNA(-) and internal control) contained more than 2 pairs of gRNAs for each of 12 internal controls (ICs) and the 361 miRNA loci, which were targeted by D1 and D2 gRNAs recognizing the 1-3 kb or 0.5-1 kb downstream region of miRNA precursor to specifically perturb molncRNAs' expression. Library 2 (molncRNA(-/-) and internal control) contained gRNAs for the same target genes as library 1, but recognized the 1-2 kb upstream or 1-3 kb downstream region of the miRNA precursors (U1 and D1 gRNAs) to knock out both molncRNAs and the cognate miRNAs). Library 3 (non-targeting control library) consisted of 2,456 pairs of non-targeting control (NTC) gRNAs. We have applied three replicates for library1 and library2. K562 cells were infected with a mix of lentiviruses expressing Cas9-mCherry at a multiplicity of infection (MOI) ~50 and gRNA-EGFP at a MOI ~4. Infected EGFP+/mCherry+ cells were sorted for 10x Genomics 3' scRNA-seq poly(A)-primed platform, and their corresponding gRNAs were further amplified using a specific amplification protocol(Hill et al., 2018).
 
Contributor(s) Li W, Huo Y, Ren Y, Wang F, Yu J
Citation(s) 37849233
Submission date Aug 02, 2021
Last update date Dec 08, 2023
Contact name Yue Huo
E-mail(s) yuehuo_hy@outlook.com
Organization name Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College
Department State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences
Lab Key Laboratory of RNA and Hematopoietic Regulation
Street address Dongcheng District, Dongdan 3 Tiao 5 Hao
City Beijing
State/province Beijing
ZIP/Postal code 100005
Country China
 
Platforms (3)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL26697 HiSeq X Ten (synthetic construct)
Samples (40)
GSM5494916 K562_library1_1
GSM5494917 K562_library1_2
GSM5494918 K562_library1_3
Relations
BioProject PRJNA751597
SRA SRP330888

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
GSE181338_RAW.tar 464.7 Mb (http)(custom) TAR (of H5)
GSE181338_library1_gRNA_whitelist.txt.gz 7.5 Kb (ftp)(http) TXT
GSE181338_library2_gRNA_whitelist.txt.gz 7.5 Kb (ftp)(http) TXT
GSE181338_library3_gRNA_whitelist.txt.gz 16.8 Kb (ftp)(http) TXT
GSE181338_rep2_D1D2_1_raw_feature_bc_matrix.h5.gz 138.5 Mb (ftp)(http) H5
GSE181338_rep2_D1D2_2_raw_feature_bc_matrix.h5.gz 133.3 Mb (ftp)(http) H5
GSE181338_rep2_D1D2_3_raw_feature_bc_matrix.h5.gz 123.3 Mb (ftp)(http) H5
GSE181338_rep2_D1D2_4_raw_feature_bc_matrix.h5.gz 104.2 Mb (ftp)(http) H5
GSE181338_rep2_U1D1_1_raw_feature_bc_matrix.h5.gz 124.6 Mb (ftp)(http) H5
GSE181338_rep2_U1D1_2_raw_feature_bc_matrix.h5.gz 88.8 Mb (ftp)(http) H5
GSE181338_rep2_U1D1_3_raw_feature_bc_matrix.h5.gz 113.2 Mb (ftp)(http) H5
GSE181338_rep2_U1D1_4_raw_feature_bc_matrix.h5.gz 119.4 Mb (ftp)(http) H5
GSE181338_rep3_D1D2_1_raw_feature_bc_matrix.h5.gz 136.8 Mb (ftp)(http) H5
GSE181338_rep3_D1D2_2_raw_feature_bc_matrix.h5.gz 133.1 Mb (ftp)(http) H5
GSE181338_rep3_D1D2_3_raw_feature_bc_matrix.h5.gz 139.4 Mb (ftp)(http) H5
GSE181338_rep3_U1D1_1_raw_feature_bc_matrix.h5.gz 140.3 Mb (ftp)(http) H5
GSE181338_rep3_U1D1_2_raw_feature_bc_matrix.h5.gz 139.6 Mb (ftp)(http) H5
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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