|
| Status |
Public on Apr 24, 2018 |
| Title |
H3.1K27A rep2 |
| Sample type |
SRA |
| |
|
| Source name |
fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: fibroblast
genotype: lenti-virus mediated H3.1K27A overexpression
passages: 20
|
| Treatment protocol |
Total RNA were extracted using Trizol reagent and used for mRNA capture.
|
| Growth protocol |
HDFs were cultured in DMEM medium supplemented with 10% fetal bovine serum,100U/mL penicillin and 100μg/mL streptomycin at 37℃ in 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 2μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manual instructions and index codes were added to attribute sequences to each sample. RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer instruction, and were sequenced on an Illumina HiSeq X-10).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat v2.0.13 with default parameters
Differences in expression were determined using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Sun |
| E-mail(s) |
[email protected]
|
| Organization name |
Tongji University
|
| Department |
life science and technology
|
| Lab |
Jiang
|
| Street address |
siping1239
|
| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE98768 |
Histone H3.1K27 methylation promotes NHEJ by antagonizing FANCD2 on Chromatin |
|
| Relations |
| BioSample |
SAMN06927216 |
| SRA |
SRX2795421 |
