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| Status |
Public on Sep 27, 2013 |
| Title |
141 KO (clone #10, set 2) |
| Sample type |
SRA |
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| Source name |
SK-BR-3 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-BR-3
genotype: mir-141 knockout
experimental set: set 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol, and DNase I was treated.
mRNA was enriched from total RNA by Oligo(dT)-Dynabead. The enriched mRNA was randomly fragmented in the Magnesium ion-containing buffer. The mRNA fragments ranging 70-90nt were fractionated, ligated to adaptors at both 5' and 3' ends, and reverse-transcribed for PCR amplification. The final PCR products were sequenced by HiSeq 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sequencing result of mir-141 knockout cells, clone #10 (exp. set 2)
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| Data processing |
FASTQ sequences from the sequencer were aligned into human reference genome by Tophat2.
After the calculation of RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each isoform, representative isoforms for each gene with the highest RPKM were identified.
Based on this data, reference genome was rebuilt, and RPKM was re-calculated with Tophat2.
Fold change was calculated after the quantile normalization against RPKM, and LOWESS smoothing was applied for fold change.
Genome_build: human reference genome (GRCh37.p10)
Supplementary_files_format_and_content: Log2(fold change) of transcripts in each knockout cells compared to wild type cells (parental cells for knockout) was calculated.
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| Submission date |
Sep 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Young-Kook Kim |
| E-mail(s) |
ykkim.bio@gmail.com
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| Organization name |
Chonnam National University Medical School
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| Department |
Department of Biochemistry
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| Street address |
264, Seoyang-ro
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| City |
Hwasun, Jeollanam-do |
| ZIP/Postal code |
58128 |
| Country |
South Korea |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE51217 |
TALEN-based knockout of mir-141 and mir-200c in SK-BR-3 cells |
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| Relations |
| BioSample |
SAMN02364269 |
| SRA |
SRX360460 |
| 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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