GSM3427849: HCT116-Hx8-sh2+dox-rep2_1; Homo sapiens; RNA-Seq - SRA

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SRX4882224: GSM3427849: HCT116-Hx8-sh2+dox-rep2_1; Homo sapiens; RNA-Seq
1 BGISEQ (BGISEQ-500) run: 24M spots, 1.2G bases, 656.7Mb downloads

Submitted by: NCBI (GEO)

Study: Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 [RNA-seq]

PRJNA496312 • SRP165671 • All experiments • All runs

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HOXB8 acts as a transcription facor, thus we knock down HOXB8 gene by doxycycline induced shRNA in colon cancer cells and profiled the change of transcriptome after knocking down HOXB8 Overall design: Two independent shRNAs targeting HOXB8 were stably transduced into HCT116 cells. The expression of these shRNAs is induced by the presence of doxycycline (dox). Therefore, the control group includes two independent repeats of two shRNAs respectively, while the HOXB8 knock-down group includes two independent repeats of two shRNAs treated with doxycline respectively.

Sample: HCT116-Hx8-sh2+dox-rep2_1

SAMN10238552 • SRS3931064 • All experiments • All runs

Organism: Homo sapiens

Library:

Instrument: BGISEQ-500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction 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.

Experiment attributes:

GEO Accession: GSM3427849

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 24M spots, 1.2G bases, 656.7Mb

Run	# of Spots	# of Bases	Size	Published
SRR8052594	23,976,228	1.2G	656.7Mb	2019-10-06

ID:: 6582663

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