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Sample GSM5574870 Query DataSets for GSM5574870
Status Public on Sep 11, 2022
Title Ad-KLF4_IL-1b(-)_1 [02exp3X3HUMxsample33adKLF4ilNEGrp1-2KLF4ILNEG]
Sample type SRA
 
Source name Ad-KLF4-transduced TC28a2 cells without IL-1b stimulation
Organism Homo sapiens
Characteristics cell type: TC28a2 cells
genotype/variation: Ad-KLF4-transduced
tag: without IL-1b stimulation
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Direct-zol RNA MicroPrep kit (Zymo Research) according to manufacturer’s protocol.
Libraries were constructed using an early access High Throughput RNAseq Prep kit (Twist Bioscience).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description 02exp3X3HUMxsample33adKLF4ilNEGrp1-2KLF4ILNEG_S0
Data processing library strategy: DRUG-seq
High-throughput RNAseq library was sequenced on 100 cycle P2 flowcells with an Illumina NextSeq2000 sequencing instrument using paired-end sequencing (read1: 26 bases, read2: 94 bases, i5 and i8 indexes used 8 base reads).
A two-step demultiplexing was carried out: pooled libraries were demultiplexed using dual-index 8-base Illumina barcodes; then the individual samples from the pooled libraries were separated using 5'-end 10-base and 8-base inline barcodes on read1 and read2 respectively (BBTools; https://sourceforge.net/projects/bbmap/). The 3'-end 12-base UMI sequences from read1 were extracted using UMI-tools (Smith et al 2017, PMID: 28100584) and incorporated in read2 fastq as part of sequence ID.
The alignment ready, inline-barcode trimmed read2 fastq files (from the pre-deduplictated dataset) for 42 samples (made available as raw data files) were analyzed using nf-core/RNA-seq pipeline (v1.4.2 Ewels et al 2020, PMID: 32055031) written in the Nextflow domain specific language.
Adapter trimmed read2 were aligned to the reference genome using STAR v2.6.1d and gene abundance was estimated using featureCounts v1.6.4. Raw gene counts were then used to get differentially expressed genes using Bioconductor R package DESeq2 v1.20.0. Genes with BH- adjusted P-value <0.05 found by DESeq2 were assigned as significantly differentially expressed genes.
Genome_build: Ensembl GRCh38 release98
Supplementary_files_format_and_content: raw gene counts, Transcripts per million per sample; differentially expressed genes from DESeq2
 
Submission date Sep 11, 2021
Last update date Sep 11, 2022
Contact name Padma Natarajan
E-mail(s) ccbb@scripps.edu
Organization name The Scripps Research Institute
Department CCBB
Street address 10550 N.Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL30173
Series (2)
GSE183954 Krüppel-like factors-4 and -2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis [DRUG-seq]
GSE183956 Krüppel-like factors-4 and -2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis
Relations
BioSample SAMN21396351
SRA SRX12144737

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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