NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1932923 Query DataSets for GSM1932923
Status Public on Oct 23, 2018
Title siCTRL_3T3-L1_rep2BS
Sample type SRA
 
Source name Mouse 3T3-L1 cells
Organism Mus musculus
Characteristics cell line: 3T3-L1
transfection: siCTRL
tissue: adipose tissue
Extracted molecule polyA RNA
Extraction protocol mRNAs of siCTRL 3T3-L1 cell were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA) and performed sequencing on HiSeq2000 (Illumina) in pair-end mode, creating reads with a length of 101 bp.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description mRNA m5C profiles in normal 3T3-L1 cells rep2
Data processing Raw Reads were stripped of adaptor sequences and low quality bases were removed using Trimmomatic. Filtered paired-end RNA-BisSeq reads were mapped against mouse (mm10) reference genome by Bismark (version 0.13.0). The m5C sites calling was performed using Bismark (version 0.13.0).
Genome_build: mm10
Supplementary_files_format_and_content: txt format. Information of m5C positions and modified gene types (mm10).
 
Submission date Nov 06, 2015
Last update date May 15, 2019
Contact name Bao-Fa Sun
E-mail(s) sunbf@big.ac.cn
Organization name Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)
Street address Da-Tun Road
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL13112
Series (1)
GSE74771 Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome
Relations
BioSample SAMN04247337
SRA SRX1422959

Supplementary file Size Download File type/resource
GSM1932923_siCTRL_3T3-L1_rep2BS.txt.gz 22.5 Kb (ftp)(http) TXT
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