|
| Status |
Public on Sep 11, 2022 |
| Title |
Non-Ad_IL-1b(+)_5 [02exp3X3HUMxsample44adNOADilPOSrp5-3NOADILPOS] |
| Sample type |
SRA |
| |
|
| Source name |
Non-transduced TC28a2 cells with IL-1b stimulation
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: TC28a2 cells
genotype/variation: Non-transduced
tag: with 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 |
02exp3X3HUMxsample44adNOADilPOSrp5-3NOADILPOS_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 |
SAMN21396323 |
| SRA |
SRX12144706 |
