|
| Status |
Public on Mar 24, 2016 |
| Title |
ES si- (2) |
| Sample type |
SRA |
| |
|
| Source name |
46C ES cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: 46C ES cells
knock in: Atad2 TAP-tag
si rna: si control
|
| Treatment protocol |
46C ES tag cells were treated with an active anti-Atad2 siRNA (si Atad2) and an inactive siRNA (si ctrl)
|
| Growth protocol |
ES cells expressing a TAP-tagged Atad2 were cultured according to a standard in DMEM medium containing LIF (ESG1107, Millipore), non essential aminoacids, antibiotics (Penicillin and streptomycin), beta-mercaptoethanol and supplemented with 15% fetal bovine serum (Invitrogen), on 0.1% gelatin-coated tissue culture dishes at 37°C in CO2 incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAeasy kit from Quiagen following the manufacturer´s instruction.
Approximately 500ng of total RNA were used for sequencing library preparation with the TruSeq RNA protocol from Illumina.
Four libraries were multiplexed in a single lane (10pm) and subsequently sequenced on a HiSeq1000 (Illumina) with the paired end protocol and 50 cycle each.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
ES cells transfected with scrambled siRNA ( replicate 2)
|
| Data processing |
RNA-seq reads were aligned to the mm9 genome assembly using tophat (Galaxy Tool Version 1.1.2)
Cuffdiff (Galaxy Tool Version 2.2.1.2) was used to find genes differentially expressed between the two conditions
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output files corresponding to gene and transcript differential expression
|
| |
|
| Submission date |
Jun 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sophie Rousseaux |
| Organization name |
INSERM-UGA
|
| Department |
IAB
|
| Lab |
U1209
|
| Street address |
Bd de la Chantourne
|
| City |
La Tronche |
| ZIP/Postal code |
38706 |
| Country |
France |
| |
|
| Platform ID |
GPL15103 |
| Series (2) |
| GSE70314 |
Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells [Atad2_ES_RNAseq_BI] |
| GSE70315 |
Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells |
|
| Relations |
| BioSample |
SAMN03797963 |
| SRA |
SRX1074421 |
