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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 16, 2015 |
| Title |
RNA_TKO_CTRL_KD_1 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 159 (mixed 129-C57Bl/6)
genotype: DNMT TKO
growth condition: serum
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| Treatment protocol |
Negative control siRNA for 72h (Qiagen, AllStars Negative Control siRNA, SI03650318)
Negative control siRNA for 72h (Qiagen, AllStars Negative Control siRNA, SI03650318)
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| Growth protocol |
Mouse embryonic stem cells were cultivated without feeders on 0.2% gelatine-coated dishes in DMEM, supplemented with 15% fetal calf serum, 1× non-essential amino acids, 2 mM L-glutamine, LIF and 0.001% β-mercaptoethanol (37°C, 7% CO2).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the RNeasy Mini kit (Qiagen) with on-column DNA digestion. Two micrograms of total RNA were depleted from ribosomal RNA using the Ribo-Zero rRNA removal kit (Epicentre).
Library Construction Protocol: Strand-specific libraries for RNA-seq were prepared using the ScriptSeq v2 protocol (Epicentre). Quality of the libraries and size distribution was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single end) according to Illumina standards.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalling was performed with the Illumina RTA 1.17.21.3 software with default parameters
Fastq files were generated with the Illumina bcl2fastq-1.8.4 software with options --use-bases-mask Y50n,I6n --fastq-cluster-count 100000000 --no-eamss
Read mapping was performed using tophat version 1.3.1 with parameter --no-novel-juncs.
Bigwig files were generated by using split RNA-seq reads and calculating for each genomic position the read density normalized to one million reads in the library
Genome_build: mm9
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| Submission date |
Sep 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Anais Flore Bardet |
| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE67867 |
Competition between DNA methylation and transcription factors determines binding of NRF1 |
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| Relations |
| BioSample |
SAMN04103871 |
| SRA |
SRX1280428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1891635_RNA_TKO_CTRL_KD_1.bw |
160.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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