|
| Status |
Public on Jan 04, 2020 |
| Title |
WT1_0h |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
tissue: colon
crispr-cas9 knock-in: Wild-type
treatment: untreated
|
| Treatment protocol |
For IFN-γ treatment, cells were seeded in 10 cm plates at a confluency of 70%. IFN-γ was added to a final concentration of 5 ng/ml. After 24 hours of IFN-γ treatment cells were washed twice with ice-cold PBS and collected into Trifast (peqLAB).
|
| Growth protocol |
HCT116 and HCT116 E33Q MED12 knock-in cell lines were maintained in McCoy’s 5A media supplemented with 10% fetal bovine serum (FBS). Cells were cultivated at 37°C in 5% CO2 humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 500,000 HCT116 cells using TriFast reagent (peqlab) according to manufacturer’s extraction. Small RNAs (< 200 nt) were discarded from total extracted RNA with Zymo-spin IC columns (RNA Clean and Concentrator-5, Zymo Research). Total RNA (1 µg) was subjected to rRNA depletion as described (Kim et.al, 2019, doi: https://doi.org/10.1101/670604 ).
RNA libraries from 1 µg of total RNA were constructed as described (Zhang et al., 2012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
rRNA depleted total RNA from HCT116 wild-type cell line, untreated
|
| Data processing |
RTA2 was used for base-calling on NextSeq 500
Following adapter trimming with Trimmomatic (Bolger et al., 2014)) and ribosomal RNA filtering with SortMeRNA (Kopylova et al., 2012), sequenced reads were assigned to full human transcriptome from Ensembl (GRCh38) in strand-specific mode using kallisto (Bray et al., 2016).
Genome_build: human transcriptome Ensembl GRCh38
Supplementary_files_format_and_content: abundance in estimated counts file was generated by assigning the sequenced reads to human transcriptome GRCh38 with kallisto (Bray et al., 2016).
|
| |
|
| Submission date |
Aug 06, 2019 |
| Last update date |
Jan 04, 2020 |
| Contact name |
Claus Kuhn |
| E-mail(s) |
claus.kuhn@uni-bayreuth.de
|
| Organization name |
University of Bayreuth
|
| Department |
BIOmac Research Center, NW I
|
| Street address |
Universitätsstr. 30
|
| City |
Bayreuth |
| ZIP/Postal code |
95447 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE135458 |
A precisely positioned MED12 activation helix stimulates CDK8 kinase activity |
|
| Relations |
| BioSample |
SAMN12504683 |
| SRA |
SRX6660344 |
