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| Status |
Public on May 11, 2015 |
| Title |
dgcr8-/-_RNAseq |
| Sample type |
SRA |
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| Source name |
mESCs
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| Organism |
Mus musculus |
| Characteristics |
cell type: dgcr8-/- mESCs
strain: V6.5
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| Growth protocol |
Mouse ESCs (V6.5, Dgcr8-/- and Dicer-/-) were cultured in DMEM with ESGRO (1000 units/mL), supplemented with 15% (v/v) FBS and antibiotics
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNAs were extracted using Trizol reagent
200 ng polyA(+) RNA isolated as described above was used for mRNA-seq. Sample preparation was with the TruSeq Stranded mRNA Sample Prep Kits (Illumina).10ug total RNAs was used for small RNA libraries preparaion fellowing small RNA Sample Prep Kits (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Data processing |
bowtie softare is used to map reads to mRNA with two mismatches permitted, and self-developed perl scripts were used to coculate the reads of each genes
For small RNA sequencing, after removal of the adaptor sequences, bowtie software was used to mapping the small RNAs into mature miRNA sequences (miRBase).
Genome_build: mm9
Supplementary_files_format_and_content: RNAseq.txt provided a matrix table, which contained five columns including the gene's name, cDNA's name, reads number in WT, DGCR8 and Dicer samples; small RNA seq.txt provided the reads number for each miRNAs.
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| Submission date |
May 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peng Du |
| E-mail(s) |
Peng.Du@childrens.harvard.edu
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| Organization name |
Boston Children’s Hospital, Harvard Medical School
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| Lab |
Richard Gregory
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| Street address |
1 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE68699 |
A biogenesis step upstream of Microprocessor controls miR-17~92 expression |
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| Relations |
| BioSample |
SAMN03649544 |
| SRA |
SRX1022480 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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