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Sample GSM2049900 Query DataSets for GSM2049900
Status Public on Jun 07, 2016
Title MDA-ctrl-RPF-rep2-readlane1
Sample type SRA
Source name MDA-parental
Organism Homo sapiens
Characteristics cell line: MDA-parental
rep: 2
fraction: RPF
Treatment protocol Cells were treated 0.1mg/ml cycloheximide
Growth protocol Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep
Extracted molecule total RNA
Extraction protocol RNA was extracted post treatment per manufacturer's instructions
Samples were prepared for sequencing per manufacturer's instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description ribosome footprinting
Data processing FASTQ reads were quality trimmed and subjected to adapter removal (cutadapt). The trimmed sequences were then mapped against contaminating RNAs (i.e. rRNA and tRNA sequences) using Bowtie2. Unaligned reads were then combined across the technical replicates and were aligned to the human transcriptome using Tophat2.
Cufflinks and cuffdiff were used to normalize ribosome protected fragments (RPF) to total RNA (TT) prepared in parallel.
The difference between RPF to TT log fold-change for each sample was used as a measure of ribosome occupancy.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms
Submission date Jan 28, 2016
Last update date May 15, 2019
Contact name Hani Goodarzi
Organization name UCSF
Department Biochemistry and Biophysics
Street address 600 16th St, GH S312D
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL11154
Series (2)
GSE77347 Ribosomal footprinting of MDA_Ctrl and MDA_Glu overexpression cell lines
GSE77401 Modulated expression of specific tRNA species drives cancer progression
BioSample SAMN04446351
SRA SRX1550668

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

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