|
| Status |
Public on Dec 31, 2019 |
| Title |
Foreskin fibroblasts, RNA-seq quiescence rep1 |
| Sample type |
SRA |
| |
|
| Source name |
foreskin fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human diploid BJ fibroblasts
cell state: quiescence
|
| Treatment protocol |
Cells were induced by 0.1% FBS for 4 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_Q_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 |
SAMN12136815 |
| SRA |
SRX6366354 |
