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Sample GSM2049161 Query DataSets for GSM2049161
Status Public on Jun 07, 2016
Title MDA-LM2-RPF-rep1
Sample type SRA
Source name MDA-LM2
Organism Homo sapiens
Characteristics cell line: MDA-LM2
rep: 1
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 NextSeq 500
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 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 27, 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 GPL18573
Series (2)
GSE77315 Ribosomal footprinting of MDA-Parental and MDA-LM2
GSE77401 Modulated expression of specific tRNA species drives cancer progression
BioSample SAMN04445131
SRA SRX1550088

Supplementary file Size Download File type/resource
GSM2049161_MDA-RPF-1_isoforms.fpkm_tracking.gz 1.3 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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