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| Status |
Public on Jun 07, 2023 |
| Title |
U937 cells with PMA, 1uM JTE-607 ChrRNA-seq |
| Sample type |
SRA |
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| Source name |
U937
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
treatment: 1uM JTE-607
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| Extracted molecule |
total RNA |
| Extraction protocol |
Chromatin RNA extraction was carried out as previously described (Chen et al., 2019) with some modifications. Briefly, cells were seeded in 15-cm dishes and were treated with JTE-607 when cell confluency reached 75-80%. Adherent cells were wash with 10 ml of ice-cold PBS twice, scraped from the dishes, and collected into a 10-ml tube. Suspended cells were collected into a 10-ml tube, centrifuged at 420x g at 4°C for 5 min, and then washed with 10 ml ice-cold PBS twice. After removal of PBS, cells were re-suspended in 4 ml of ice-cold HLB+N buffer, containing 10 mM Tris- HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2 and 0.5% (v/) NP-40, and were left on ice for 5 min. Cells were then underlaid with 1 ml of ice-cold HLB+NS buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% (v/v) NP-40 and 10% (wt/vol) sucrose), and were centrifuged at 420x g at 4°C for 5 min. After careful removal of the supernatant, nuclear pellets were re-suspended in 125 ml of ice-cold NUN1 buffer, containing 20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA, and 50% (v/v) glycerol, followed by addition of 1.2 ml of ice-cold NUN2 buffer, containing 20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% (v/v) NP-40, and 1 M urea. Samples were vortexed at the maximum speed, followed by incubation on ice for 5 min. Chromatin pellets were collected after centrifugation at 16,000x g at 4°C for 2 min and were re-suspended with 50 ul RNase-free water. The chromatin pellet was dispersed by using a 200 µl tip before chromatin RNA was extracted with 1 ml TRIzol.
Chromatin RNA was subject to ribosomal removal before cDNA library construction by using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina Sequencing were carried out on an Illumina HiSeq machine at Ademera Health (South Plainfield, NJ, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
chrRNA-seq reads were first trimmed by using the TrimGalore tool for removal of 5’ and 3’ adapter sequences. Trimmed reads were mapped to the human genome (hg19) using STAR-2.7.7a (Dobin et al., 2013). The number of reads mapped to each gene was calculated by using the featureCounts tool (Liao et al., 2014).
Assembly: hg19
Supplementary files format and content: tab-delimited text file including reads count for each pAs/gene
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| Submission date |
Nov 22, 2022 |
| Last update date |
Jun 12, 2023 |
| Contact name |
Bin Tian |
| E-mail(s) |
btian@wistar.org
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| Organization name |
The Wistar Institute
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| Street address |
3601 Spruce Street
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| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE218545 |
Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation [ChrRNA-seq] |
| GSE218557 |
Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation |
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| Relations |
| BioSample |
SAMN31836889 |
| SRA |
SRX18348560 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6751697_U937_PMA_JTE1.featurecounts.Rmatrix.txt.gz |
285.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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