|
| Status |
Public on Apr 06, 2016 |
| Title |
SD wt ESC, replicate 2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
SD wt ESC
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Setdb1 and Dnmt1 double (flox/flox) conditional alleles; CreERT2 transgene
time point: Without 4-OHT (day 0)
|
| Growth protocol |
Standard condition for ES cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Genomic DNA was isolated using QIAGEN All-prep kit
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina. Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
S05927
|
| Data processing |
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned on mouse genome (mm9) using tophat2 (version 2.1.0) with option "--no-coverage search".
Gene expression was estimated using cufflinks (version 2.1.0) with default options.
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.
|
| |
|
| Submission date |
Feb 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Takaho A. Endo |
| E-mail(s) |
takaho.endo@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Integrative Genomics
|
| Street address |
1-7-22 Suehiro, Tsurumi
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE77778 |
Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing [RNA-seq] |
| GSE77781 |
Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing |
|
| Relations |
| BioSample |
SAMN04485130 |
| SRA |
SRX1569963 |
