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Sample GSM3692898

Query DataSets for GSM3692898

Status

Public on Mar 30, 2019

Title

Sample_97L_1

Sample type

SRA

Source name

liver

Organism

Homo sapiens

Characteristics

cell type: hepatoma carcinoma cell
cell line: MHCC97L
tissue: liver
treatment: none

Treatment protocol

MHCC97L and Hep3B cells were grown in T25 flasks and treated with saracatinib (2 μmol/L and 1 μmol/L) followed by the addition of increasingly higher concentrations of saracatinib until the MHCC97L cells became stably resistant to 4 μmol/L saracatinib and the Hep3B cells became stably resistant to 2 μmol/L saracatinib. These resistant cells were re-named MHCC97L-SRC and Hep3B-SRC. Oxaliplatin-resistant HCC cell lines were generated as previously described. MHCC97L cells that were stably resistant to 2 μmol/L oxaliplatin were re-named MHCC97L-OXA, and Hep3B cells that were stably resistant to 1 μmol/L oxaliplatin were re-named Hep3B-OXA.

Growth protocol

All cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM; GIBCO, Grand Island, NY, USA) and supplemented with 10% fetal bovine serum (FBS; GIBCO) at 37°C in a humidified incubator with 5% CO2.

Extracted molecule

total RNA

Extraction protocol

Take an appropriate amount of cell sample, and RNA was harvested using mirVana™ miRNA ISOlation Kit and Ambion-1561. Illumina TruSeq Stranded mRNA LTSample Prep Kit was used with total RNA for the construction of sequencing libraries.
After extracting total RNA from the sample and digesting the DNA with DNase, enrich the eukaryotic mRNA with magnetic beads with Oligo (dT) (if the prokaryote, remove the rRNA by the kit to enrich the mRNA); add the interrupting reagent The mRNA was broken into short fragments, and the broken mRNA was used as a template. A six-base random primer was used to synthesize a strand cDNA, and then a two-stranded reaction system was synthesized to synthesize a double-stranded cDNA, and the double-stranded cDNA was purified using a kit; The double-stranded cDNA was further ligated to the end, the A tail was added and the sequencing linker was ligated, and then the fragment size was selected, and finally PCR amplification was performed. The constructed library was tested with the Agilent 2100 Bioanalyzer and the Illumina HiSeqTM 2500 or Illumina HiSeq X Ten was used. The sequencer is sequenced to generate double-ended data of 125 bp or 150 bp. After passing the quality test, sequencing was performed using an Illumina sequencer.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Data processing

Trimmomatic 0.36 software used for filtering.
Using the Trimmomatic software to control the quality and remove the linker. Based on this, the low-quality base and the N-base are filtered out, and finally high-quality clean reads are obtained.
Hisat2 2.2.1.0 software used for alignment.
The clean reads are compared to the reference genome of the species using hisat2, and the software parameters are default parameters, and the sample is evaluated by the genomic alignment ratio.
Genome_build: Homo sapiens (assembly GRCh38.p12)
Supplementary_files_format_and_content: Excel files include gene expression for each Sample

Submission date

Mar 29, 2019

Last update date

Mar 31, 2019

Contact name

Xia Liao

E-mail(s)

[email protected]

Phone

86-18092788761

Organization name

Department of nutrition