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Sample GSM4514153 Query DataSets for GSM4514153
Status Public on Apr 28, 2022
Title 30 min after-deflagellation rep1 Ribo-Seq
Sample type SRA
 
Source name CC125
Organism Chlamydomonas reinhardtii
Characteristics strain: CC125
Extracted molecule total RNA
Extraction protocol Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion
Libraries were performed as Ingolia et al. 2012 published protocol described.
Chlamydomonas cells were flash-frozen and stored in liquid nitrogen. The sample pellets were crushed into powder in a motar filled with liquid nitrogen prior to the experiments. RPF was harvested using RNase I digestion
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Ribosome protected mRNA fragment
C_reinhardtii_allSamples_Riboseq_edgR_normalized_CPM.txt
C_reinhardtii_allSamples_Riboseq_genes_CDS_counts.txt
Data processing Tophat (v2.1.1) was used to align all reads from individual samples to Chlamydomonas v5.5 genome, parameters are the following: splice-mismatches 0; max-multihits 20; segment-mismatches 2; segment length 25; -no-novel-juncs.
HTseq-count with default setting was used to calculate exon or CDS abundance (--type) using bam files generated by Tophat with gene annotation from Chlamydomonas v5.3.1 genome.
Counts normalization and differential expession analysis by edgR.
For the riboseq data,the length range of the RPF reads and the P-site location was selected through interpretation of the metaplots drawing the distance between 5' end and start codon by RiboCode.
Chlamydomonas v5.5 genome
Tab-delimited text files include raw counts values for all sample;
Tab-delimited text files include normalized counts (CPM) for all sample;
CPM normalized bigwig converted from bam file by bamCoverage with the following setting: --binSize 5 --normalizeUsing CPM
 
Submission date May 04, 2020
Last update date Apr 28, 2022
Contact name Jingying Huang
E-mail(s) huang-jy18@mails.tsinghua.edu.cn
Organization name Tsinghua University
Department School of Life Sciences
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL15922
Series (1)
GSE149844 Global Analysis of Translational Reprogramming during Flagellar Regeneration Reveals the Role of Sphingolipid Metabolism in Ciliogenesis and Ciliopathies
Relations
BioSample SAMN14829514
SRA SRX8246160

Supplementary file Size Download File type/resource
GSM4514153_RiboSeq_30min_rep1.bw 3.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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