|
| Status |
Public on Jun 09, 2016 |
| Title |
CON ASCL2 WT replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
CON ASCL2 WT
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: Duke's type B adenocarcinoma of the colon
cell line: LS174T
cell type: Derivatives of Ls174 colon cancer cells
genotype/variation: inducible shRNAs against the WNTRLINC1
treated with: none
|
| Treatment protocol |
KD treated samples were grown for three days in conditions described above in the presence of doxycycline (final concentration of 1ug/ml). Control cells were grown as KD cells without doxycycline addition.
|
| Growth protocol |
Cells were grown for three days at 37 C, 5% CO2 in DMEM standard growth medium, 10% FBS reaching a maximum confluency of 50 % before harvesting
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
For RNA-Seq experiments, the isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA). Samples were processed on an OneTouch 2 instrument and enriched on a One Touch ES station. Templating was performed using the Ion PI™ Template OT2 200 Kit (Life Technologies, Carlsbad, CA, USA) and sequencing with the Ion PI™ Sequencing 200 Kit on Ion Proton PI™ chips (Life Technologies, Carlsbad, CA, USA) according to commercially available protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Colon epithelial adherent cells
|
| Data processing |
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were trimmed for adaptor sequence using cutadapt software and mapped to hg19 whole genome using tophat 2.0.9 with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html).
Tags overlapping the Ensembl GRCh37 human exons were counted and filtered for artifacts as follows: if an annotated gene had up to five exons, tag presence was required in at least two exons. If an annotated gene had E >5 exons, tag presence was required in at least E/5 exons. The final gene counts were calculated as the sums of their exon tags. The counts table was normalized and analyzed for differential expression using DESeq. The final list of differentially expressed genes was derived by the genes demonstrating a binomial test p-value less than 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene.
|
| |
|
| Submission date |
May 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Pantelis Hatzis |
| E-mail(s) |
hatzis@fleming.gr
|
| Organization name |
Biomedical Sciences Research Center 'Alexander Fleming'
|
| Department |
Molecular Biology and Genetics
|
| Street address |
34 Fleming Str
|
| City |
Vari |
| State/province |
Attiki |
| ZIP/Postal code |
16672 |
| Country |
Greece |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE69036 |
A positive regulatory loop between a Wnt-regulated non-coding RNA and ASCL2 controls intestinal stem cell fate |
|
| Relations |
| BioSample |
SAMN03701679 |
| SRA |
SRX1033046 |
