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Sample GSM7880340

Query DataSets for GSM7880340

Status

Public on Nov 01, 2024

Title

HCT 116 Cas9 Luc B

Sample type

SRA

Source name

HCT116

Organism

Homo sapiens

Characteristics

cell line: HCT116
cell type: colon cancer
genotype: control

Extracted molecule

total RNA

Extraction protocol

Total RNA from cell lines was isolated using RNAeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the Stranded mRNA Prep, Ligation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, mRNA was purified from 1 µg total RNA using oligo(dT) beads, poly(A)+ RNA was fragmented to 150 bp and converted into cDNA, and cDNA fragments were end-repaired, adenylated on the 3’ end, adapter-ligated, and amplified with 12 cycles of PCR. The final libraries were validated using a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer 2100 system. All barcoded libraries were pooled and sequenced 2x75bp paired-end on an Illumina NextSeq550 platform to obtain a minimum of 10 Mio reads per sample.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

NextSeq 550

Data processing

Quality control assessment of raw reads was performed using FastQC, followed by Trimmomatic trimming to remove low-quality sequences. The trimmed reads were then aligned to the reference genome using STAR version 2.7.9a. To facilitate the mapping process, a genome reference index was constructed using either GRCh37.fa (hg19) or GRCh38.108.gtf (hg38) as the reference.
Supplementary files format and content: Excel file includes unfiltered normalized raw counts for all genes for each Sample

Submission date

Nov 02, 2023

Last update date

Nov 01, 2024

Contact name

Alexander Arthur Wurm

E-mail(s)

[email protected]

Organization name

NCT Dresden

Street address

Fetscherstrasse 74