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| Status |
Public on Dec 03, 2017 |
| Title |
shCtrl_RNAseq_rep1 |
| Sample type |
SRA |
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| Source name |
shCtrl
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| Organism |
Mus musculus |
| Characteristics |
tissue: AML12 cells
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| Treatment protocol |
The shRNA lentiviruses were prepared as previously described (Fu et al., 2015). Then, 2.5×105 AML12 were infected with the viruses and selected puromycine for 3 days.
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| Growth protocol |
AML12 cell were kept in complete growth medium：a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, 90%; fetal bovine serum, 10%.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
We trimmed and mapped reads to the mouse mm9 reference assembly by the Tophat2 software.
We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
For differential gene expression analysis, we analyzed raw read counts for GENCODE M1 gene models using HTSeq (Anders et al., 2015), and then calculated statistics of differential expression via DESeq2 version 1.8.2 (Love et al., 2014) with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each replicate.
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| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
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| Organization name |
Fudan University
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| Department |
Institutes of Biomedical Sciences
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| Street address |
130 DongAn Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE95111 |
The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [RNA-Seq] |
| GSE95116 |
The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture |
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| Relations |
| BioSample |
SAMN06350716 |
| SRA |
SRX2578753 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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