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| Status |
Public on Apr 04, 2016 |
| Title |
icSHAPE - 293T - DMSO rep1 |
| Sample type |
SRA |
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| Source name |
Embryonic Kidney cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 293T
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| Extracted molecule |
total RNA |
| Extraction protocol |
HEK293T cells were grown, treated with DMSO or NAI-N3, and RNA collected with TRIzol as previously described (PMID: 25799993). Protocol: icSHAPE
Deep sequencing libraries were prepared using 3'end RNA ligation, cDNA synthesis with SuperScript III, cDNA circularization, and subsequent PCR amplification
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
RNA secondary Structure
processed data file: HS_293T_icSHAPE_InVitro_BaseReactivities.txt,HS_293T_icSHAPE_InVivo_BaseReactivities.txt
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| Data processing |
Library strategy: icSHAPE
After demultiplexing, reads were stripped adaptors (PMID: 25411354) and mapped to the Homo Sapiens transcriptome - GRCh37.74 (hg19) using Bowtie2.
All samples have a 13nt barcode on the 5'end which needs to be trimmed before mapping to the transcriptome
icSHAPE reverse transcriptase (RT) stops were isolated as the first nucleotide after the 5'end barcode. RT stops were used to calculated icSHAPE reactivity scores
Genome_build: Homo sapiens - GRCh37.74 (hg19)
Supplementary_files_format_and_content: 2 Tables (one each for In Vitro and In Vivo modified samples) of icSHAPE reactivities across human transcripts measured. Format: Transcript ID, Transcript Length (in nucleotides), RPKM value, icSHAPE reactivity scores per base for the length of each transcript (NULL values denote bases not measured by the icSHAPE experiment)
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| Submission date |
Feb 29, 2016 |
| Last update date |
Sep 18, 2020 |
| Contact name |
Zhipeng Lu |
| E-mail(s) |
zhipengluchina@gmail.com
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| Organization name |
Stanford University
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| Department |
Department of Dermatology
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| Lab |
Howard Chang
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| Street address |
269 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE74353 |
RNA duplex map in living cells reveals higher order transcriptome structure |
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| Relations |
| Reanalyzed by |
GSE149767 |
| BioSample |
SAMN04521235 |
| SRA |
SRX1605089 |
| 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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