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| Status |
Public on Jun 30, 2023 |
| Title |
IVT_3hr_4_S34 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
time point: 3hr
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| Treatment protocol |
the aqueous layer was transferred to a new tube containing 1µL of glycogen and equal volume isopropanol added
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| Growth protocol |
RNA was isolated from samples collected in TRIzol using a chloroform-isopropanol protocol. 200µL chloroform was added to 1mL TRIzol samples, transferred to a heavy phase-lock gel tube (QuantaBio), and spun in a microcentrifuge at 12,000xg for 15 minutes at 4°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
After 10 minutes of incubation at room temperature, sample was spun at 20,000xg for 20 minutes at 4°C, then RNA pellet washed with fresh 75% ethanol before drying and resuspending in 40µL water.
isolated mRNA was DNase treated using Turbo DNase in reactions consisting of 11µL (~15µg) RNA and 1.5µL Turbo DNase according to manufacturer’s protocol. DNase-treated RNA was purified using lithium chloride precipitation as described in mMESSAGE mMACHINE T7 ULTRA Transcription Kit (Invitrogen). 2µg RNA per sample was reverse transcribed into cDNA using SuperScript III First-Strand Synthesis System (Invitrogen) and MPRA RNA-specific primer (Table **, primer #22).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
3 hr rep4
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| Data processing |
Sequencing was performed using an NextSeq 2000in Rapid Run mode and employed a Paired end, 150 base read length sequencing strategy.
Files were aligned to guides using bowtie2 for each sample. Next, the barcodes for WT and mutant were segregated for each sample.
log2 CPM values for each barcode using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 cpm values for each Sample.
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| Submission date |
Nov 08, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
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| Organization name |
FHCRC
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| Street address |
1100 Fairview Ave N,
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE200304 |
A genome-wide functional study of 3’UTR mutations in advanced prostate cancer |
| GSE217530 |
A genome-wide functional study of 3’UTR mutations in advanced prostate cancer [RNA-seq] |
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| Relations |
| BioSample |
SAMN31657569 |
| SRA |
SRX18206498 |
| 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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