|
| Status |
Public on Oct 04, 2019 |
| Title |
HCT116-Hx8-sh1+dox-rep2_1 |
| Sample type |
SRA |
| |
|
| Source name |
shRNAs targeting HOXB8 stably transduced into HCT116 and induced with dox
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Colon cancer cell line
cell line: HCT116
genotype/variation: HOXB8 knock-down
|
| Treatment protocol |
HCT116 cells stably expressing shRNAs targeting HOXB8 were treated with or without 1 ug/ml doxycycline for 72 hours. After 72h of treatment, cells were harvested and total RNA was extracted.
|
| Growth protocol |
HCT116 cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from HCT116 cells using RNeasy kit from Qiagen according to manufacturer's instructions
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers are used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
After QC of library by Agilent 2100 Bioanalyzer, sequencing was performed on BGISEQ-500 platform.
Primary sequencing data, called as raw reads, is subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences. Briefly, the single-end 50bp sequence tags from BGISEQ-500 sequencer were subjected to data cleaning by SOAPnuke first, which includes getting rid of the low quality tags and several kinds of contaminants. We then used Hisat and Bowtie2 to align the clean data after filtering to reference genome (hg19) and gene respectively.
We used FPKM method to calculate expression level of genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 14, 2018 |
| Last update date |
Oct 04, 2019 |
| Contact name |
Xingsheng Shu |
| E-mail(s) |
shuxingsheng@gmail.com
|
| Organization name |
Shenzhen University
|
| Department |
Health Science Center
|
| Street address |
No 3688, Nanhai Avenue
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE121207 |
Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 [RNA-seq] |
| GSE121209 |
Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 |
|
| Relations |
| BioSample |
SAMN10238556 |
| SRA |
SRX4882219 |
