|
| Status |
Public on Apr 28, 2022 |
| Title |
90 min after-deflagellation rep2 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 |
SAMN14829509 |
| SRA |
SRX8246165 |
