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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 14, 2016 |
| Title |
Control siRNA-1 RNA-seq |
| Sample type |
SRA |
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| Source name |
TT2
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6xCBA
cell line: TT2 embryonic stem cells
developmental stage: Preimplantation embryo
genotype/variation: Control siRNA
Sex: female
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| Treatment protocol |
Cells were transfected with 100 nM siRNAs when 70-80% confluent, seeded again at the same density and transfected a second time 24 hours later with the same siRNAs, except at 50 nM. Approximately 72 hours after the second transfection, cells were harvested for RNA extraction
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| Growth protocol |
ES cells were maintained under standard feeder-free conditions in serum-containing media with LIF
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the ES cells using the GenElute Total Mammalian RNA extraction kit.
Poly(A) RNA was selected. Adaptor ligation based library construction for paired-end Illumina sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
siCTRL-1
total RNA (rRNA depleted)
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| Data processing |
Alignment: Sequence reads were aligned to the mouse reference genome mm9 (NCBI 37) using BWA (Li and Durbin 2009), with annotated exon-exon junctions compiled from Ensembl, RefSeq and UCSC gene annotation sources, as described (Morin et al., 2010; Shah et al., 2009). Sequence reads that could be uniquely assigned a position in the transcript resource (exon-exon junctions) were computationally repositioned to the genomic mm9 coordinates and a single merged bam file (Li et al., 2009) generated for downstream analyses.
Wigs: The Samtools pileup utility (Li et al., 2009) and FindPeaks 3.1 (Fejes et al., 2008) was used to generate data tracks for visualization (wig and bigWig (Kent et al., 2010)) in the UCSC browser. Repbase (Jurka et al., 2005), a comprehensive database of repetitive elements, was used for alignment of reads to repetitive elements.
Gene expression: Reads Per Kilobase per Million mapped reads (RPKM) (Mortazavi et al., 2008; Pepke et al., 2009) was calculated for each Ensembl protein coding gene.
Genome_build: mm9
Supplementary_files_format_and_content: [.bw] BigWig files
Supplementary_files_format_and_content: [.txt] RPKMs for all protein coding ensembl genes.
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| Submission date |
Jul 14, 2016 |
| Last update date |
Nov 27, 2019 |
| Contact name |
Matthew Lorincz |
| Organization name |
University of British Columbia
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| Department |
Medical Genetics
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| Lab |
Lorincz
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| Street address |
2350 Health Sciences Mall
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T1Z3 |
| Country |
Canada |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE84386 |
hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells |
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| Relations |
| BioSample |
SAMN05390149 |
| SRA |
SRX1948233 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2232901_siCTRL-1.bw |
312.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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