|
| Status |
Public on Jan 21, 2020 |
| Title |
HCT116_Auxin6hr_PolyA_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116-OsTIR1-MED26AID
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Auxin
spike-in: Drosophila melanogaster
cell line: HCT116 expressing F-box protein (OsTIR1) and Auxin-inducible degron (AID) tagged endogenous MED26
protocol: PolyA Selected RNA-seq
|
| Treatment protocol |
Cells were seeded at a density of 5x10e5 cells on a 6-well plate and culture overnight. Auxin treatment was started by replacing cultured media to fresh completed media supplemented with Auxin final 500uM. Mock treatment (NT) was performed same as Auxin treatment by using completed media mock supplemented with no auxin solvent (water). After incubated for 6 hrs in 37oC with 5% CO2, RNA was extracted for analysis.
|
| Growth protocol |
HCT116-OsTIR1-MED26AID cells were cultured in McCoy's-5A media supplemented with 10% (v/v) fetal bovine serum, 1x MEM non-essential amino acids, 100mcg/ml Hygromycin, 1mcg/ml Puromycin and 100U/ml Penicillin- 100mcg/ml Streptomycin at 37oC with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the Maxwell simplyRNA cells kit (Promega) on a Maxwell RSC instrument according to the manufacture's instructions.
Standard protocol using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-zero Gold (Ribodep), or TruSeq Stranded mRNA Preparation Kit (PolyA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAseqTPM.csv
|
| Data processing |
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome hg38 from UCSC using STAR aligner
TPM was generated using RSEM
Genome_build: UCSC genome hg38, ensembl 87 gene model
Supplementary_files_format_and_content: RNA-seq TPM in csv file
|
| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
Jan 21, 2020 |
| Contact name |
Shiyuan (Cynthia) Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Stowers Institute for Medical Research
|
| Department |
Computational Biology
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE121024 |
The role of Mediator and Little Elongation Complex in transcription termination |
|
| Relations |
| BioSample |
SAMN13836810 |
| SRA |
SRX7546961 |
