NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3905166 Query DataSets for GSM3905166
Status Public on Dec 31, 2019
Title Foreskin fibroblasts, RNA-seq senescence rep1
Sample type SRA
 
Source name foreskin fibroblast
Organism Homo sapiens
Characteristics cell line: human diploid BJ fibroblasts
cell state: senescence
Treatment protocol Cells was induced with bleomycin (40 μg/ml; Biorbyt) for 2 hours and then cultured for 12 days
Growth protocol Human diploid BJ fibroblasts purchased from American Type Culture Collection were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin and streptomycin.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted using TRIzol (Life Technologies) and mRNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation kit (New England Biolabs)
Reverse transcription was carried out and cDNA was fragmented, purified, ligated with adapters. PCR was performed using an End Repair/dA-tail ligated DNA template to include unique barcodes to identify each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description five_condtions.FPKM.txt.gz
five_conditions.Counts.txt.gz
RNAseq_S_rep1
Data processing Hi-C reads were processed using HiC-Pro 2.7.0, raw and normalized contact maps at various resoultions were obtained both in biological replicates and pooled condtions.
Fit-Hi-C were used to call significant contacts with raw contacts maps of 20kb resolution and biases files from HiC-Pro with noOfPasses of 1 and distUpThres of 2000000.
RNA-seq reads were mapped to hg19 genome assembly with Tophat 2.1.1,and transcript abundance (FPKM) and counts were calculated based on GENCODE annotation using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: *.raw_contact_map.txt and *.iced_contact_map.txt were the representation of sparse contact matrix, contact scores were stored as 'bin number 1/bin number 2/score'; Bed files showed the corresponding between bin numbers in contact map and genomic regions; *.FPKM.txt and *.Counts.txt showed the transcription abundance of genes and repeated elements in each sample
 
Submission date Jun 25, 2019
Last update date Dec 18, 2020
Contact name Xianglin Zhang
E-mail(s) xl-zhang15@mails.tsinghua.edu.cn
Phone 15101669184
Organization name Tsinghua University
Street address Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL16791
Series (1)
GSE133292 The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
Relations
BioSample SAMN12136813
SRA SRX6366356

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

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