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| Status |
Public on Jan 31, 2020 |
| Title |
RNA-seq 6 day timecourse for K562 cells grown in hypoxia/normoxia (21%, 5%, 1% oxygen) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
K562 cells were grown at different oxygen levels (21%, 5%, 1%) and samples were collected at 6hr, 24hr, 3day, and 6day time points (triplicate per time point).
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| Overall design |
RNA-seq was performed for K562 cells grown in 3 oxygen levels (21%, 5%, 1%) at 4 time points (6hr, 24hr, 3day, 6day) for each of 3 replicates. K562 cells were seeded at a density of 1e5/ml in 3ml of DMEM media per well of 6-well plate. Plates were maintained in 1%, 5% or 21% O2 incubators and passaged at 3d of growth. At each time point, cells were pelleted, rinsed with PBS and then stored at -80C. RNA extraction was performed using the Qiagen RNAeasy kit. The RNASeq libraries were generated as described (Picelli et al., 2014; Trapnell et al., 2012). RNA was isolated using RNASPRI beads. Following reverse transcription, cDNA was fragmented and barcoded. Samples were subjected to paired-end sequencing of 2x25bp. RNASeq data was processed using the Cufflinks suite (tophat, cuffquant, cuffnorm) as previously described (Trapnell et al., 2012).
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| Contributor(s) |
Jain IH, Calvo SE, Mootha VK |
| Citation(s) |
32259488 |
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| Submission date |
Jan 30, 2020 |
| Last update date |
Apr 21, 2020 |
| Contact name |
Sarah E Calvo |
| E-mail(s) |
scalvo@broadinstitute.org
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| Organization name |
Broad Institute
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| Street address |
415 Main St
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02141 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA603962 |
| SRA |
SRP246093 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE144527_gene.fpkm.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSE144527_transcript.fpkm.txt.gz |
4.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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