|
| Status |
Public on Nov 22, 2017 |
| Title |
3T9 OHT DOX rep2 |
| Sample type |
SRA |
| |
|
| Source name |
3T9 OHT DOX rep2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 3T9
genotype: 3T9MycER
cell type: immortalized embryonic fibroblasts
|
| Treatment protocol |
MycER was activated by the addition of 400nM 4-hydroxytamoxifen, while YAPS127A was induced by 2 µg/ml doxycycline
|
| Growth protocol |
3T9MycER murine fibroblast were grown in DMEM medium supplemented with 10% tetracyclin-free serum, penicillin/streptomycin and 2mM L-Gln
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy MinElute Spin columns from Qiagen according to the manufacturer and eluted in 14µl of RNase free water
Libraries for RNA-Seq were prepared with the TruSeq RNA Sample Preparation Kits v2 (Illumina) following manufacturer instruction (except for skipping the first step of mRNA purification with poly-T oligo-attached magnetic beads)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing differential expression results (DESeq2) and DEG status (Y/N)
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
stefano campaner |
| E-mail(s) |
[email protected]
|
| Organization name |
fondazione Istituto italiano di tecnologia
|
| Department |
Center for Genomic Science
|
| Lab |
Cancer Biology
|
| Street address |
via adamello 16
|
| City |
milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE83867 |
Myc and YAP roles in the control of the cell cycle [3T9 RNA-seq] |
| GSE83869 |
Myc and YAP roles in the control of the cell cycle |
|
| Relations |
| BioSample |
SAMN05325959 |
| SRA |
SRX1885846 |
