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| Status |
Public on Aug 02, 2021 |
| Title |
5CAPture-seq: a method for enriching full-length cDNA and identifying 5′ capped nucleotides |
| Organism |
Plasmodium falciparum |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Current transcriptomic methods for mapping 5′-ends of eukaryotic RNA employ only 5′-end enriched samples. The absence of a matched unenriched control limits the ability to distinguish genuine 5′ ends from incomplete cDNAs. We developed a transcriptomic method based on sequencing of cDNA enriched for full-length fragments and an unenriched control. From the mapped sequence reads, enrichment scores are calculated for all transcribed nucleotides and a statistical model of the enrichment constructed. We tested the method in the human malaria parasite Plasmodium falciparum. Data were obtained from ring, trophozoite and schizont stages of the parasite intra-erythrocytic development cycle. Two groups of 5′ capped nucleotides were assigned by unsupervised clustering. The first group contains sites located mostly outside of annotated protein-coding exons in regions of high local nucleosomal occupancy, but low occupancies of ribosome and elongating RNA polymerase II. The majority of sites in the second group are intra-exonic and show different patterns, most notably a peak of ribosome occupancy centered on the 5′ end position and a biased representation among codons possibly prone to ribosome stalling. Our method can be used to annotate 5′ capped nucleotides, including intra-exonic nucleotides that can be distinguished from incomplete cDNA artifacts.
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| Overall design |
Total RNA was extracted from synchrononous cultures of Plasmodium falciparum. Parasites were harvested at ring, trophozoite and schizont stages. Two independent cultures were performed. cDNA from each RNA sample was synthesized and split into two pools. One pool was enriched for full-length cDNA, whereas another was processed as an unenriched control sample. Enriched and unenriched cDNAs were converted to Illumina sequencing libraries for transcriptomic sequencing.
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| Contributor(s) |
Shaw PJ, Piriyapongsa J, Kaewprommal P, Wongsombat C, Chaosrikul C, Teeravajanadet K, Boonbangyang M, Uthaipibull C, Kamchonwongpaisan S, Tongsima S |
| Citation(s) |
34527439 |
| Submission date |
Aug 24, 2017 |
| Last update date |
Sep 21, 2021 |
| Contact name |
Pavita Kaewprommal |
| E-mail(s) |
pavita.kae@nstda.or.th
|
| Organization name |
NSTDA
|
| Department |
NBT
|
| Lab |
DATA
|
| Street address |
113
|
| City |
Khlong Nung |
| State/province |
Pathum Thani |
| ZIP/Postal code |
12120 |
| Country |
Thailand |
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| Platforms (2) |
| GPL16607 |
Illumina HiSeq 2000 (Plasmodium falciparum) |
| GPL19269 |
Illumina MiSeq (Plasmodium falciparum) |
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| Samples (24)
|
| GSM2752830 |
MiSeq_Method1 ring parasites unenriched |
| GSM2752831 |
MiSeq_Method1 ring parasites enriched |
| GSM2752832 |
MiSeq_Method1 trophozoite parasites unenriched |
| GSM2752833 |
MiSeq_Method1 trophozoite parasites enriched |
| GSM2752834 |
MiSeq_Method1 schizont parasites unenriched |
| GSM2752835 |
MiSeq_Method1 schizont parasites enriched |
| GSM2752836 |
MiSeq_Method2 ring parasites unenriched |
| GSM2752837 |
MiSeq_Method2 ring parasites enriched |
| GSM2752838 |
MiSeq_Method2 trophozoite parasites unenriched |
| GSM2752839 |
MiSeq_Method2 trophozoite parasites enriched |
| GSM2752840 |
MiSeq_Method2 schizont parasites unenriched |
| GSM2752841 |
MiSeq_Method2 schizont parasites enriched |
| GSM4712775 |
HiSeq_Method1 ring parasites unenriched |
| GSM4712776 |
HiSeq_Method1 ring parasites enriched |
| GSM4712777 |
HiSeq_Method1 trophozoite parasites unenriched |
| GSM4712778 |
HiSeq_Method1 trophozoite parasites enriched |
| GSM4712779 |
HiSeq_Method1 schizont parasites unenriched |
| GSM4712780 |
HiSeq_Method1 schizont parasites enriched |
| GSM4712781 |
HiSeq_Method2 ring parasites unenriched |
| GSM4712782 |
HiSeq_Method2 ring parasites enriched |
| GSM4712783 |
HiSeq_Method2 trophozoite parasites unenriched |
| GSM4712784 |
HiSeq_Method2 trophozoite parasites enriched |
| GSM4712785 |
HiSeq_Method2 schizont parasites unenriched |
| GSM4712786 |
HiSeq_Method2 schizont parasites enriched |
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| Relations |
| BioProject |
PRJNA399851 |
| SRA |
SRP116088 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE103036_Ring_method1_Hiseq_enrichment_score.txt.gz |
23.4 Mb |
(ftp)(http) |
TXT |
| GSE103036_Ring_method1_Miseq_enrichment_score.txt.gz |
6.5 Mb |
(ftp)(http) |
TXT |
| GSE103036_Ring_method2_Hiseq_enrichment_score.txt.gz |
14.3 Mb |
(ftp)(http) |
TXT |
| GSE103036_Ring_method2_Miseq_enrichment_score.txt.gz |
5.1 Mb |
(ftp)(http) |
TXT |
| GSE103036_Schiz_method1_Hiseq_enrichment_score.txt.gz |
28.1 Mb |
(ftp)(http) |
TXT |
| GSE103036_Schiz_method1_Miseq_enrichment_score.txt.gz |
6.9 Mb |
(ftp)(http) |
TXT |
| GSE103036_Schiz_method2_Hiseq_enrichment_score.txt.gz |
12.3 Mb |
(ftp)(http) |
TXT |
| GSE103036_Schiz_method2_Miseq_enrichment_score.txt.gz |
5.3 Mb |
(ftp)(http) |
TXT |
| GSE103036_Troph_method1_Hiseq_enrichment_score.txt.gz |
33.5 Mb |
(ftp)(http) |
TXT |
| GSE103036_Troph_method1_Miseq_enrichment_score.txt.gz |
6.3 Mb |
(ftp)(http) |
TXT |
| GSE103036_Troph_method2_Hiseq_enrichment_score.txt.gz |
9.4 Mb |
(ftp)(http) |
TXT |
| GSE103036_Troph_method2_Miseq_enrichment_score.txt.gz |
12.1 Mb |
(ftp)(http) |
TXT |
| GSE103036_combine_enrichment_score.txt.gz |
339.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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