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Sample GSM1917756 Query DataSets for GSM1917756
Status Public on Apr 04, 2016
Title HEK293T_2
Sample type SRA
Source name human HEK293T cells
Organism Homo sapiens
Characteristics cell line: HEK293T
Treatment protocol HEK293T Cells were induced for 8 hours with 1 μg/ml Doxycycline before AMT crosslinking.
Growth protocol HeLa-S3 cells were cultured in DMEM+ 10% FBS + Pen/Strep at 37ºC with 5% CO2. Flp-In HEK293T-REx cells express doxycycline inducible 3XFLAG-DDX3X at a level comparable to endogenous DDX3X. The 293T cells were cultured with DMEM + 10% Tetracycline-free FBS (Clontech, Tet System Approved FBS, 631106) + Pen/Strep + 2mM Glutamax (Gibco). J1 mouse ES cells (male) were cultured on gelatin coated plates at 37ºC with mES media: 500ml Knockout DMEM (Gibco), 90ml FBS, 6ml non-essential amino acid (MEM NEAA, 100x, Gibco), 6ml glutamine or glutamax (200mM stock solution), 6ml Pen/Strep, 1ml BME and 60ul LIF (Millipore, ESG1106).
Extracted molecule total RNA
Extraction protocol Cells were digested with S1 nuclease, proteinase K and RNA was extracted using TRIzol.
See previous publication for the protocol (PMID: 25799993)
Library strategy OTHER
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing remove 5' and 3' adapters using trimmomatic-0.32.jar SE -threads 16 -phred33
removed PCR duplicates using splitFastqLibrary (in the icSHAPE pipeline)
mapped reads using STAR, version 2.4, with the following parameters: --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --runThreadN 16
secondary mappings were removed using samtools
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: read count was calculated using bedtools v2.22.0
Submission date Oct 26, 2015
Last update date May 15, 2019
Contact name Zhipeng Lu
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 GPL18573
Series (1)
GSE74353 RNA duplex map in living cells reveals higher order transcriptome structure
BioSample SAMN04215497
SRA SRX1382447

Supplementary file Size Download File type/resource
GSM1917756_HEK293T_2_count.txt.gz 282.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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