|
| Status |
Public on Apr 21, 2021 |
| Title |
H2_S3: epimastigotes rep2, supplemented with haemoglobin |
| Sample type |
SRA |
| |
|
| Source name |
Trypanosoma cruzi epimastigotes
|
| Organism |
Trypanosoma cruzi |
| Characteristics |
tissue: epimastigote
|
| Treatment protocol |
20 mM heme stock solution was freshly prepared by dissolving in 0.1 N NaOH, and after it was buffered in PBS (100 mM sodium phosphate buffer and 150 mM NaCl at pH 7.4). The stock solution was diluted immediately before use to 5 mM in the same PBS buffer or in culture medium.
|
| Growth protocol |
Epimastigote forms of Trypanosoma cruzi, clone CL Brener were grown in 50 mL medium BHI with 10% FCS in the presence of 30 μMheme to 28˚C for 7 days in culture bottle cells with 25 cm2 surface area
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples of epimastigotes incubated with or without heme were extracted from samples by using TRIzol method. Total RNA was measured using Qubit RNA assay kit (Life technologies, USA). The mRNA enrichment was performed in a NEBNext Poly(A) mRNA Magnetic Isolation Module
cDNA libraries were synthesized by Illumina
TruSeq RNA Sample Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H2_S3
|
| Data processing |
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality trimmed by sickle (v1.33) using default settings.
Trimmed reads were directionally separately aligned to the haploid genome of T. cruzi strain CL Brener Esmeraldo and Nonesmeraldo-like available at triTrypDB using bowtie2 (version 2.3.5) with -very-sensitive-local option.
Uniquely and correctly mapped reads were extracted for the downstream analysis. featureCounts was used to count the number of reads aligned to each gene.
Gene expression level was calculated and normalised by Fragments Per Kilobase Per Million (FPKM). Genes with FPKM < 10 on both conditions were removed from the posterior analysis.
Genome_build: T. cruzi strain CL Brener Esmeraldo and Nonesmeraldo-like available at triTrypDB
|
| |
|
| Submission date |
Apr 20, 2021 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Fei Sang |
| E-mail(s) |
mbzfs1@exmail.nottingham.ac.uk
|
| Organization name |
University of Nottingham
|
| Department |
School of Life Sciences
|
| Lab |
DeepSeq
|
| Street address |
QMC
|
| City |
Nottingham |
| ZIP/Postal code |
NG72UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL27740 |
| Series (1) |
| GSE172452 |
Gene expression profiling of Trypanosoma cruzi in the presence of heme points to glycosomal metabolic adaptation of epimastigotes inside the vector |
|
| Relations |
| BioSample |
SAMN18813200 |
| SRA |
SRX10646611 |
