NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6774451 Query DataSets for GSM6774451
Status Public on Dec 01, 2023
Title RCCD1_replication_3
Sample type SRA
 
Source name MCF-7 cells
Organism Homo sapiens
Characteristics cell line: MCF-7 cells
cell type: mammary adenocarcinoma cells
genotype: RCCD1-overexpressed
Treatment protocol The mammary adenocarcinoma MCF-7 cells were infected with lentivirus carrying FLAG-RCCD1 construction or control vector.
Growth protocol Mammary adenocarcinoma MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from MCF-7 cells using the TRIzol reagent (Invitrogen)
The sequencing libraries were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Raw sequencing data were preprocessed through fastp version 0.23.0 for adapter and low-quality reads removal
The clean reads were aligned to the GRCh38/hg38 reference genome by using Spliced Transcripts Alignment to a Reference (STAR) version2.7.10A
Sequencing was performed with biologically triplicate of each group of MCF-7 cells.
Read count extraction and normalization were performed using CLC genomic benchwork
Expression abundance estimation was performed through HTSeq version 1.99.2and differential expression gene identification were done using DESeq2 R package, with |log2FC| > 0.5 and p value < 0.05 deemed significant differential expression between the two groups.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
 
Submission date Dec 01, 2022
Last update date Dec 01, 2023
Contact name Yani Peng
E-mail(s) pengyn@bjmu.edu.cn
Phone 18870421072
Organization name Peking University
Street address Xueyuan load number 38
City Beijing
State/province State...
ZIP/Postal code oncomine1996
Country China
 
Platform ID GPL16791
Series (1)
GSE219134 RCCD1 also Resides in Mitochondria to Regulate mtDNA Dynamics and Mitochondrial Homeostasis
Relations
BioSample SAMN31956378
SRA SRX18443258

Supplementary file Size Download File type/resource
GSM6774451_R1_rep3.csv.gz 201.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap