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Status |
Public on May 04, 2024 |
Title |
THP-1_DMSO_48_rep3 |
Sample type |
SRA |
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Source name |
THP1 human AML cells
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Organism |
Homo sapiens |
Characteristics |
treatment: DMSO 0.05% treatment duration: 48h genome build: hg38
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Growth protocol |
Cells were grown in RPMI (Corning, 15-040-CV) with 10% dialyzed fetal bovine serum (Sigma, F0392), 4mM glutamine, and 1% penicillin/streptomycin (Corning, 45000-652).
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Extracted molecule |
total RNA |
Extraction protocol |
1 million live cells were sorted using a BD FACSAria and placed on ice. Immediately following the sort, cells were centrifuged, pelleted, and flash frozen in liquid nitrogen and placed at -80C. Pellets were processed in groups of 24 using the Zymo RNA Miniprep Kit and quantified using the Invitrogen Quant-it RNA kit. RNA was then diluted to a concentration of 2 ng/ul and 5ul of each sample was transferred to a 96 well plate. Poly-A enrichment and cDNA synthesis were performed in parallel as described in Soumilion et al. 2014, followed by library preparation using the Nextera XT kit and paired-end sequencing on an Illumina NextSeq 500.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
THP-1_DMSO_48_rep3
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Data processing |
Mouse and human data were mapped to mm10 and hg38 genomes, respectively, using STAR v2.7.8a and default parameters. Reads that mapped to transcripts were counted using featureCounts v2.0.1 (with parameters -M -O --fraction --primary). Supplementary files format and content: A tab-delimited file containing raw counts generated from featureCounts.
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Submission date |
Aug 11, 2022 |
Last update date |
May 04, 2024 |
Contact name |
Brian Do |
E-mail(s) |
bdo311@gmail.com
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Organization name |
MIT
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Department |
Biology
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Lab |
Vander Heiden
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Street address |
500 Main St
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02139 |
Country |
USA |
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Platform ID |
GPL18573 |
Series (2) |
GSE172333 |
A myeloid maturation program initiated by nucleotide depletion during S phase [RNA-Seq] |
GSE172335 |
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress |
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Relations |
BioSample |
SAMN30266386 |
SRA |
SRX17035526 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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