|
| Status |
Public on Feb 09, 2018 |
| Title |
HCT116_H2B_GFP_3.3.c11_1_miRNA |
| Sample type |
SRA |
| |
|
| Source name |
Human colorectal cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell line origin: Human colon carcinoma
aneuploidy: trisomy of chromosome 3
stable expression: H2B tagged with GFP
|
| Growth protocol |
Cells were maintained in 10 cm dishes in Dulbecco’s Modified Eagle Medium (DMEM) at 37°C and 5% CO2. Culture medium was supplemented with growth factors from 5% Fetal Calf Serum (FCS) and 1% Penicillin/ Streptavidin to avoid bacterial growth and contamination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA, including small RNAs from 18 nucleotides upwards, was extracted using miRNeasy Mini Kit (QIAGEN).
TruSeq small RNA library preparation were performed by the Max Planck-Genome-Center Cologne, Germany.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
small RNA
normalized to HCT116_H2B_GFP_1/HCT116_H2B_GFP_2/ HCT116_H2B_GFP_3
processed data file:
HCT116_H2B_3.3c11.txt
|
| Data processing |
If necessary, raw sequencing read ends were trimmed for low quality base calls using the FASTQ quality trimmer with the following parameters: “-Q33 -t 20 -l 17“ (28,33).
Sequencing adapters were removed with cutadapt.
Mapping to the human genome hg19 and miRNA identification was performed using mirdeep2 (v2.0.0.8) (33) with the following commands: “mapper.pl -e -h -i -j -l 18 -m -p hg19 ‑q” and “miRDeep2.pl reads.fa hg19.fa genome.arf human_mature_rmspace.fa others_mature_rmspace.fa human_hairpin_rmspace.fa -d -t Human”.
The three biological replicates of aneuploid and the corresponding parental cell line were analyzed within the same analysis run. For subsequent normalization and differential expression analysis miRNA_expressed_all_samples.csv was used as an input for DESeq2.
To account for sequencing batch effects, paired replicate information in addition to condition information was input to the DESeq2 analysis for HCT116 5/4, RPE1 5/3 12/3 and RPE1* 21/3 and corresponding parental cell lines.
Genome_build: hg19
Supplementary_files_format_and_content: Tab- delimited text file containing the DeSeq2 normalized, log2 texpression fold changes of the aneuploid cell line to the control cell line (log2FoldChange). baseMean=mean of normalized counts for all samples; lfcSE=standard error: condition treated vs untreated stat=Wald statistic: aneuploidy vs control; pvalue=Wald test p-value: aneuploidy vs control; padj="Benjamini-Hochberg adjusted p-values
|
| |
|
| Submission date |
Aug 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Milena Dürrbaum |
| Organization name |
Max Planck Institute of Biochemistry
|
| Department |
Maintenance of Genome Stability
|
| Street address |
Am Klopferspitz 18
|
| City |
Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE102854 |
The deregulated microRNAome contributes to the cellular response to aneuploidy [miRNA] |
| GSE102855 |
The deregulated microRNAome contributes to the cellular response to aneuploidy |
|
| Relations |
| BioSample |
SAMN07522711 |
| SRA |
SRX3110457 |
