NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2075717 Query DataSets for GSM2075717
Status Public on Apr 04, 2016
Title icSHAPE - 293T - NAI-N3 In Vitro rep2
Sample type SRA
 
Source name Embryonic Kidney cells
Organism Homo sapiens
Characteristics cell line: 293T
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
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description RNA secondary Structure
processed data file: HS_293T_icSHAPE_InVitro_BaseReactivities.txt
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)
 
Submission date Feb 29, 2016
Last update date May 03, 2020
Contact name Zhipeng Lu
E-mail(s) zhipengluchina@gmail.com
Organization name Stanford University
Department Department of Dermatology
Lab Howard Chang
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL20301
Series (1)
GSE74353 RNA duplex map in living cells reveals higher order transcriptome structure
Relations
Reanalyzed by GSE149767
BioSample SAMN04521238
SRA SRX1605092

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap