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Sample GSM6928207 Query DataSets for GSM6928207
Status Public on Sep 07, 2023
Title L31419_K562_endogenous_RNA_Dex_replicate2
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics cell line: K562
cell type: Lymphoblast cells
genotype: wildtype
treatment: Dex
Treatment protocol In this data set, 6 replicate flasks of K562 cells were treated for 6 hours with each of the following treatments: dexamethasone (1 uM), IFNA2b (2,000U/ml), or vehicle control (media). Cells were then collected for mRNA-Seq to assess the endogenous gene expression response of K562 cells to treatment.
Growth protocol We made 18 replicate T75 flasks, each containing 12 million K562s. 42 hours later, K562s were stimulated with treatment, and cells were collected 6 hours post-treatment.
Extracted molecule polyA RNA
Extraction protocol We extracted RNA from the separately aliquoted cells using the Qiagen RNEasy kit.
We prepared RNA-Seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description L31419
Data processing Reads were trimmed with Trim Galore (Trim Galore version 0.6.4_dev; Cutadapt version 2.3) to remove basepairs with a Phred score less than 20, and end sequences that matched at least two basepairs of the adapter sequence. Only trimmed reads longer than 25 basepairs were retained.
We used the STAR package (version 2.5.0) (Dobin et al., 2013) two-pass mapping to map the filtered reads to the hg38 genome. We retained uniquely mapped reads by filtering the output SAM file to keep reads with MAPQ = 255.
We then used htseq (version 0.6.0) (Anders et al., 2014) to quantify read counts per gene.
We only retained genes that had TPM > 3 in at least 3 of 6 samples in at least one of the three conditions (baseline, IFNA, or dex).
Only protein-coding genes were retained for final analysis, resulting in a total of 10,676 testable genes.
Assembly: hg38
Supplementary files format and content: Tab delimited text file with data matrix of raw read counts mapping to a gene, where each row represents a gene, and each column represents a biological replicate (i.e., library). Only protein-coding genes that had transcripts per million > 3 in at least 3 of 6 samples in at least 1 of the 3 conditions (baseline, IFNA, or dex) are included.
 
Submission date Jan 11, 2023
Last update date Sep 07, 2023
Contact name Rachel A Johnston
E-mail(s) racheljohnston7@gmail.com
Organization name Duke University
Department Evolutionary Anthropology
Lab Jenny Tung
Street address 130 Science Dr, Rm 108 Biological Sciences
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL24676
Series (1)
GSE222643 DNA methylation-environment interactions in the human genome
Relations
BioSample SAMN32677790
SRA SRX19003511

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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