|
| Status |
Public on Dec 01, 2017 |
| Title |
CSB_24h |
| Sample type |
SRA |
| |
|
| Source name |
CS1AN+CSBwt
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dermal fibroblasts, immortalized
treatment: UV-C, 12 J/m2
|
| Treatment protocol |
UV-C, 12 J/m2
|
| Growth protocol |
DMEM/HamF10 (1:1) + 10 % FCS and 40 mg/ml gentamycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested and isolated using a QIAGEN RNA purification kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
S16041_allres.xlsx
|
| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Tophat 2.0.10 and Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Quantiifcation of gene expression has been performed using HTSeq-0.6.1
Read counts have then been normalized across libraries with the method proposed by Anders and Huber
Genome_build: hg19
Supplementary_files_format_and_content: Excel table with raw expression, normalized expression values and foldchange values
|
| |
|
| Submission date |
Oct 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao YE |
| Organization name |
IGBMC (CNRS/INSERM/UDS)
|
| Street address |
1 rue Laurent Fries
|
| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE87540 |
Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (RNA-seq) |
| GSE87564 |
Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process |
|
| Relations |
| BioSample |
SAMN05859545 |
| SRA |
SRX2207914 |
