|
| Status |
Public on Jan 10, 2021 |
| Title |
HCT15 shKSR1 Poly Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Colorectal Cancer Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT15
condition: stable expression of KSR1 shRNA
|
| Treatment protocol |
Cell Treated with 100 µg/mL cycloheximide prior to extraction in polysome lysis buffer (10 mM HEPES, 100 mM KCL, 5 mM MgCl2, 100 µg/mL cycloheximide, 2 mM DTT, 1% Triton-X100, 2.5 µl RNaseOUT).
|
| Growth protocol |
DMEM 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA and RNA pooled from the polysome fraction (fractions 6-9) was isolated using RNAzol. RNA sequencing libraries were prepared using 500 ng of RNA using Truseq mRNA protocol kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
polysomal RNA
|
| Data processing |
The reads were mapped to the Homo sapiens (human) genome assembly GRCh38 (hg38) using STAR v2.7 alignment and --quantMode GeneCounts option in STAR 2.7 to obtain the HTSeq counts per gene.
Gencode v22 was used for the transcript/gene annotations.
Translational efficiency was calculated using the R Bioconductor anota2Seq package
HTSeq counts by first removing genes that did not contain expression values in more than 10% of the samples.
Significant genes were obtained using anota2seqDataSetFromMatrix and anota2seqRun function
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Matrix table withHTSeq gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with anota2Seq output for significant gene and every sample
|
| |
|
| Submission date |
Jan 09, 2021 |
| Last update date |
Jan 11, 2021 |
| Contact name |
Chaitra Rao |
| E-mail(s) |
chaitra.rao@unmc.edu
|
| Phone |
4025598271
|
| Organization name |
University of Nebraska Medical Centre
|
| Department |
Eppley Institute
|
| Lab |
Robert E Lewis
|
| Street address |
505 S 45th St
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE164492 |
Next generation sequencing analysis of control and KSR1 knockdown CRC cell line translatomes. |
|
| Relations |
| BioSample |
SAMN17268925 |
| SRA |
SRX9813106 |
