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GSE217735

GSE GEO
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Epigenetics CRISPRi screen in mouse neuronal progenitor cells (NPCs)

Organism: Mus musculus
Platform: GPL21626
Samples: 6
Experiment Types:
Other
Submitted: Nov 10 2022
Last Updated: Feb 05 2025
Status: Public on Nov 06 2024
Contact: LU,,YANG (city of hope)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA900244

Summary

This dataset examined the epigenetic gene effect on mouse NPCs with Upf2 gene knockout (KO). The sgRNA sequencing results form the epigenetics CRISPRi screen sample are reported.

Overall Design

CRISPR sgRNA sequencing: dCas9-Krab-expressing NPCs were harvested from the Upf2(f/f) mice, and transduced with a lentiviral CRISPRi library targeting mouse epigenetics genes (Total 3630 sgRNAs). The integrated sgRNA were amplified from each sample using DCF01 5’-CTTGTGGAAAGGACGAAACACCG-3’ and DCR03 5’- CCTAGGAACAGCGGTTTAAAAAAGC-3’ for high-throughput sequencing (SE75, NextSeq550).

Analysis (2 steps)

View Data Processing
Processing steps for GSE217735
  1. Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
  2. Raw reads were mapped against sgRNA library and raw counts table of sgRNA was generated using MAGeCK v0.5.9.3

Supplementary Files (1)

GSE217735_NPC_Upf2KO_SZ20210524JZ.count.txt.gz Download
GEO Samples (6)
GSM6725602 GSM6725603 GSM6725604 GSM6725605 GSM6725606 GSM6725607

Dataset Citations (1)

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
PMID 38697111 · 2024 · Neuron
Lin Lin, Jingrong Zhao, Naoto Kubota, Zhelin Li, Yi-Li Lam, Lauren P Nguyen, Lu Yang, Sheela P Pokharel, Steven M Blue, Brian A Yee, Renee Chen, Gene W Yeo, Chun-Wei Chen, Liang Chen, Sika Zheng

SRA Experiments (6) and Runs (6)

Total: 653 MB
SRX18232061 SRP407231 OTHER SINGLE
GSM6725602: msEpiCRISPRi_NPC_Upf2KO_05_Cre; Mus musculus; OTHER
Sample: SRS15728131
BioProject: PRJNA900244
BioSample: SAMN31683873
Platform: ILLUMINA
Instrument: NextSeq 550
Organism: Mus musculus
Sample attributes
source_name: Neuronal progenitor cells (NPCs)
cell type: Neuronal progenitor cells (NPCs)
sequencing type: CRISPR sequencing
geo_loc_name: missing
collection_date: missing
Original files (1)
Neuronal progenitor cells (NPCs)
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22255538 5338731 400404825 141.06 SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_Cre_S51_L999_R1_001.fastq.gz,… SRA
SRX18232062 SRP407231 OTHER SINGLE
GSM6725603: msEpiCRISPRi_NPC_Upf2KO_05_GFP; Mus musculus; OTHER
Sample: SRS15728132
BioProject: PRJNA900244
BioSample: SAMN31683872
Platform: ILLUMINA
Instrument: NextSeq 550
Organism: Mus musculus
Sample attributes
source_name: Neuronal progenitor cells (NPCs)
cell type: Neuronal progenitor cells (NPCs)
sequencing type: CRISPR sequencing
geo_loc_name: missing
collection_date: missing
Original files (1)
Neuronal progenitor cells (NPCs)
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22255537 4068156 305111700 107.91 SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_GFP_S50_L999_R1_001.fastq.gz,… SRA
SRX18232063 SRP407231 OTHER SINGLE
GSM6725604: msEpiCRISPRi_NPC_Upf2KO_05_sgRNA; Mus musculus; OTHER
Sample: SRS15728133
BioProject: PRJNA900244
BioSample: SAMN31683871
Platform: ILLUMINA
Instrument: NextSeq 550
Organism: Mus musculus
Sample attributes
source_name: Neuronal progenitor cells (NPCs)
cell type: Neuronal progenitor cells (NPCs)
sequencing type: CRISPR sequencing
geo_loc_name: missing
collection_date: missing
Original files (1)
Neuronal progenitor cells (NPCs)
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22255536 3995945 299695875 106.23 SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_sgRNA_S49_L999_R1_001.fastq.g… SRA
SRX18232064 SRP407231 OTHER SINGLE
GSM6725605: msEpiCRISPRi_NPC_Upf2KO_50_Cre; Mus musculus; OTHER
Sample: SRS15728134
BioProject: PRJNA900244
BioSample: SAMN31683870
Platform: ILLUMINA
Instrument: NextSeq 550
Organism: Mus musculus
Sample attributes
source_name: Neuronal progenitor cells (NPCs)
cell type: Neuronal progenitor cells (NPCs)
sequencing type: CRISPR sequencing
geo_loc_name: missing
collection_date: missing
Original files (1)
Neuronal progenitor cells (NPCs)
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22255535 3830045 287253375 101.35 SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_Cre_S54_L999_R1_001.fastq.gz,… SRA
SRX18232065 SRP407231 OTHER SINGLE
GSM6725606: msEpiCRISPRi_NPC_Upf2KO_50_GFP; Mus musculus; OTHER
Sample: SRS15728135
BioProject: PRJNA900244
BioSample: SAMN31683869
Platform: ILLUMINA
Instrument: NextSeq 550
Organism: Mus musculus
Sample attributes
source_name: Neuronal progenitor cells (NPCs)
cell type: Neuronal progenitor cells (NPCs)
sequencing type: CRISPR sequencing
geo_loc_name: missing
collection_date: missing
Original files (1)
Neuronal progenitor cells (NPCs)
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22255534 3767406 282555450 99.96 SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_GFP_S53_L999_R1_001.fastq.gz,… SRA
SRX18232066 SRP407231 OTHER SINGLE
GSM6725607: msEpiCRISPRi_NPC_Upf2KO_50_sgRNA; Mus musculus; OTHER
Sample: SRS15728136
BioProject: PRJNA900244
BioSample: SAMN31683868
Platform: ILLUMINA
Instrument: NextSeq 550
Organism: Mus musculus
Sample attributes
source_name: Neuronal progenitor cells (NPCs)
cell type: Neuronal progenitor cells (NPCs)
sequencing type: CRISPR sequencing
geo_loc_name: missing
collection_date: missing
Original files (1)
Neuronal progenitor cells (NPCs)
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR22255533 3645574 273418050 96.77 SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_sgRNA_S52_L999_R1_001.fastq.g… SRA

Linked Publications (2)

Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron · 2024
Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size.
Neuron · 2024

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_Cre_S51_L999_R… OTHER 141.1 MB link
— SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_GFP_S50_L999_R… OTHER 107.9 MB link
— SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_sgRNA_S49_L999… OTHER 106.2 MB link
— SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_Cre_S54_L999_R… OTHER 101.3 MB link
— SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_GFP_S53_L999_R… OTHER 100.0 MB link
— SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_sgRNA_S52_L999… OTHER 96.8 MB link