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| Status |
Public on Jun 07, 2023 |
| Title |
U937/iFIP1, Dox+, DMSO, QuantSeq-Pool, read 1 |
| Sample type |
SRA |
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| Source name |
U937
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| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
treatment: Dox-FIP1-on, DMSO
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| Extracted molecule |
total RNA |
| Extraction protocol |
Library preparation of total RNA was carried out by using the Lexogen 3’ mRNA-Seq QuantSeq FWD or QuantSeq-Pool kit according to manufacturer’s instructions. Library preparation, quality control, and sequencing were carried out by Ademera Health (South Plainfield, NJ, USA). cDNA libraries were sequenced on an Illumina HiSeq machine (2x150 nt) at Ademera Health.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
QuantSeq-Pool read1
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| Data processing |
QuantSeq FWD or QuantSeq-Pool data were processed according to manufacturer’s recommendation. Briefly, For QuantSeq FWD data, read 1 data were first trimmed by using the BBtools 64 and then mapped to the human genome (hg19) using STAR-2.7.7a 65. The number of reads mapped to each gene was counted by using featureCounts 66. For QuantSeq-Pool data, raw pooled data were first demultiplexed by using the idemux tool, and the read 1 data were then used. The Umi_tools package was used to remove read duplicates based on the location of the alignment and the UMI information. The number of reads mapped to each gene was calculated by using the featureCounts tool
Assembly: hg19
Supplementary files format and content: tab-delimited text file including reads count for each pAs/gene
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| Submission date |
May 02, 2023 |
| 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) |
| GSE218557 |
Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation |
| GSE231527 |
Elevated pre-mRNA 3' end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation [QuantSeq-Pool] |
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| Relations |
| BioSample |
SAMN34543015 |
| SRA |
SRX20204428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7287689_U937_DpJn_R1.featurecounts.Rmatrix.txt.gz |
260.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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