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| Status |
Public on Mar 28, 2019 |
| Title |
PARN_L4_T0 |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa PARN CRISPR KO
4su pulse time: 1 hr 250 uM
4su chase time: 0
molecule subtype: nascent RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of RNA
Kapa hyper-prep (KK8502) of RACE amplicons using illumina TruSeq (RS-122-2001, RS-122-2002) barcodes. Briefly, RACE amplicons of different RNAs from the same sample were pooled into one index, and libraries were prepared according to manufacturer protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
Illumina MiSeq |
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| Description |
3' RACE: TERC, U2, E1, U68
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| Data processing |
Paired-end joining using fastq-join (Galaxy Version 1.1.2-806.1)
Isolated 3' sequence ends with custom python scripts ()
Binned 3' ends into categories with custom python scripts ()
Supplementary_files_format_and_content: csv files were generated using custom python scripts ()
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| Submission date |
Jul 12, 2018 |
| Last update date |
Mar 28, 2019 |
| Contact name |
Caitlin M Roake |
| E-mail(s) |
[email protected]
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| Phone |
6504004908
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| Organization name |
Stanford
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| Lab |
Artandi
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| Street address |
CCSR 1150, 269 Campus Drive
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE117054 |
Maturation of human telomerase RNA component from an extended precursor |
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| Relations |
| BioSample |
SAMN09652308 |
| SRA |
SRX4386960 |
| 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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