|
Status |
Public on Nov 09, 2023 |
Title |
A549, AFos Knock-In, plus Dox, RNA-seq, rep2 |
Sample type |
SRA |
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|
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.
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|
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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
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|
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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 |