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Sample GSM2048211 Query DataSets for GSM2048211
Status Public on Jun 07, 2016
Title CN34-LM1a-TT-rep2
Sample type SRA
 
Source name CN34-LM1a
Organism Homo sapiens
Characteristics fraction: TT
rep: 2
cell line: CN34-LM1a
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 Library strategy: Ribo-seq
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)
GSE77292 Ribosomal footprinting of CN34-Parental and CN34-LM1a
GSE77401 Modulated expression of specific tRNA species drives cancer progression
Relations
BioSample SAMN04444434
SRA SRX1549428

Supplementary file Size Download File type/resource
GSM2048211_Lm1a-tt-2_isoforms.fpkm_tracking.gz 1.4 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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