|
| Status |
Public on Dec 07, 2016 |
| Title |
Clone 12 day4 Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
hF x mESC fusion_day4
|
| Organism |
Homo sapiens x Mus musculus hybrid cell line |
| Characteristics |
cell type: human fibroblast clone (derived from TERT-immortalised NHDF17914) fused with mouse ESC (E14Tg2a:puroR)
time point: day 4 after fusion with mouse ESC
|
| Treatment protocol |
hF clones were fused with mESC by PEG (Roche)
|
| Growth protocol |
Human fibroblast (hF) clones were maintainedat 3% O2 in DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine and antibiotics (10 µg/ml penicillin and streptomycin). After hF x mESC fusion, heterokaryons and hybrids were cultured in mouse ESC medium (KO-DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine, 50μM β-mercaptoethanol, antibiotics (10 µg/ml penicillin and streptomycin) and LIF) and selected 12hrs after by adding puromycin (1.5 μg/ml) and HAT (20μM hypoxantine, 0.08 mM aminopterin, and 3.2 mM thymidine; Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was exacted by RNABee (Amsbio) accordingly to manifacturer instructions
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). Libraries were amplified 14 cycles before deep-sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Clone_12_day4_1
|
| Data processing |
Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 using Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene was counted using HTSeq and differentially expressed genes were identified using edgeR
FPKM values were estimated using R script
Genome_build: hg19; mm9
Supplementary_files_format_and_content: hg19 FPKM values
|
| |
|
| Submission date |
Aug 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Gopuraja Dharmalingam |
| Organization name |
MRC London Institute of Medical Sciences
|
| Department |
Epigenetics section
|
| Street address |
Faculty of Medicine, Imperial College, Hammersmith Hospital Campus
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19068 |
| Series (1) |
| GSE60308 |
Selective reactivation of human X-linked genes in female fibroblasts reprogrammed by cell fusion |
|
| Relations |
| BioSample |
SAMN02981708 |
| SRA |
SRX674535 |
