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Sample GSM4029476 Query DataSets for GSM4029476
Status Public on Jan 08, 2020
Title S41: CTCFKD1_singleCell
Sample type SRA
 
Source name EL4
Organism Mus musculus
Characteristics strain: C57BL/6
cell number: Single cell
genotype: CTCF knockdown
tissue: EL4 cells
Treatment protocol 293T cells were co-transfected with an envelope plasmid (pLP/VSVG) to generate lentiviral particles. The medium containing lentiviral particles was harvested after 48h transfection. EL4 cells were infected with the harvested shLuc and shCTCF retroviral particles packaged in GP2-293.
Growth protocol EL4 cells were cultured in DMEM (GIBCO Invitrogen) supplemented with 50 IU/mL penicillin, 50 mg/mL streptomycin (GIBCO Invitrogen) and 10% heat inactivated calf serum (Sigma, USA). Cultures were maintained by replacement of fresh medium every 3 days, and cell density was kept between 1 X 105 and 1 X 106 cells/mL.
Extracted molecule total RNA
Extraction protocol Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System
Single cell RNA libraries were prepared by Fluidigm C1 Single-Cell Autoprep System
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description RNA-seq
Data processing Basecalls performed using RTA 1.7 or Illumina Casava1.7
Reads were aligned to the mouse genome (Ensemble version GRCm38.89) utilizing STAR
We calculated the TPM of each gene in single cell RNA-seq
Genome_build: GRCm38.89
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
 
Submission date Aug 13, 2019
Last update date Jan 08, 2020
Contact name Wenfei Jin
E-mail(s) jinwf@sustech.edu.cn
Phone +8675588018478
Organization name Southern University of Science and Technology
Department Department of Biology
Lab Single Cell Precise Medicine
Street address 1088 Xueyuan Rd #faculty research building 1
City Shenzhen
State/province Guangdong
ZIP/Postal code 518055
Country China
 
Platform ID GPL21493
Series (1)
GSE135769 Single Cell RNA-Seq Reveals Changing Landscape of Cell-to-Cell Variation Induced by CTCF Knockdown
Relations
BioSample SAMN12566477
SRA SRX6708196

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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