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Sample GSM7889192 Query DataSets for GSM7889192
Status Public on Nov 09, 2023
Title A549, AFos Knock-In, plus Dox, RNA-seq, rep2
Sample type SRA
 
Source name A549
Organism Homo sapiens
Characteristics cell line: A549
cell type: Human lung carcinoma
genotype: A-Fos integrated into genome with piggyBac
treatment: Doxycycline (1 μg/mL)
Treatment protocol For doxycyline treated cells, doxycyline was added to cell medium a final concentration of 1 μg/mL.
Growth protocol Ham's F-12K (Kaighn's), 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
Extracted molecule polyA RNA
Extraction protocol Cells were lysed by Trizol, extracted by 0.2 volume of chloroform, followed by adding equal volume of 100% ethanol. RNeasy kit was then used to purify the RNA. 3 µg of purified RNA was treated with 2 U of RNase-free DNase I, and purified again with RNeasy kit.
Sequencing library was constructed by the Illumina Stranded mRNA Prep kit. 30 million paired-end 50bp reads were obtained for each RNA-seq sample using a NextSeq 2000 instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using Cutadapt (Version 4.0) according to default settings.
Filtered reads were aligned to the human reference genome (hg38) using gapped-read mapper RNA STAR (Version 2.7.10b).
Read counts were generated for genomic features from the BAM alignment files using featureCounts (Version 2.0.3).
Differential expression analysis was performed using DESeq2 (Version 2.11.40.7).
Assembly: hg38
Supplementary files format and content: tabular file for featureCounts
 
Submission date Nov 09, 2023
Last update date Nov 09, 2023
Contact name Lu Bai
E-mail(s) lub15@psu.edu
Organization name Penn State University
Street address 406 South Frear Building
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL30173
Series (2)
GSE247414 Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 [RNA-seq]
GSE247432 Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1
Relations
BioSample SAMN38193620
SRA SRX22478054

Supplementary file Size Download File type/resource
GSM7889192_A549_AFos_plusDox_RNA_rep2_featureCounts.tabular.txt.gz 249.3 Kb (ftp)(http) TXT
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Raw data are available in SRA

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