|
| Status |
Public on Oct 23, 2023 |
| Title |
Sylvio_MNase_35U_Replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
Sylvio-X10
|
| Organism |
Trypanosoma cruzi |
| Characteristics |
strain: Sylvio-X10
life stage: exponentially growing epimastigotes
mnase amount: 35U
|
| Treatment protocol |
no pre treatment
|
| Growth protocol |
Sylvio-X10 and CL Brener epimastigotes were grown at 28 °C in liver infusion tryptose (LIT) medium. Cell density was maintained between 1x106 and 1x108 cells.ml-1 by sub-culturing parasites every 6-7 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Late exponentially growing epimastigotes of the Sylvio-X10 and CL Brener strains were collected and permeabilized as previously described with modifications (Leandro de Jesus et al., 2017). Chromatin was digested with different amounts of MNase (units given in filenames)
The DNA was repaired using the DNA PreCR kit from New England Biolabs. Paired-end libraries were constructed and indexed using Illumina kits from NEB (E7370 and E7335). Agencourt AMPure XP beads (Beckman, A63880) were used to purify the DNA after adaptor ligation and PCR products before sequencing
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Biological replicate 2
|
| Data processing |
Sequences were aligned to Sylvio-X10 genome version 64 or CL Brener_all genome version 46 respectively using Bowtie2 with default settings.
Reads were size selected, and we kept all reads with the lengths between 120 and 180bp.
Genome-wide coverage profiles were computed with R, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks containing normalized nucleosome occupancy for reads from 120-180bp (bw files) were generated with R.
Assembly: Sylvio-X10 genome version 64 and Cl Brener _all, made from the combination Esmeraldo like haplotype reference genome (TriTrypDB-46_TcruziCLBrenerEsmeraldo-like_Genome.fasta), non Esmeraldo like haplotype reference genome(TriTrypDB-46_TcruziCLBrenerNon-Esmeraldo-like_Genome.fasta) and CL Brener genome (not included in the annotated haplotypes(TriTrypDB-46_TcruziCLBrener_Genome.fasta)
Supplementary files format and content: bw files containing the normalized occupancy profiles, for the IGV browser
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Oct 23, 2023 |
| Contact name |
Josefina Ocampo |
| E-mail(s) |
jocampo@dna.uba.ar, josefinaoca@gmail.com
|
| Organization name |
INGEBI-CONICET
|
| Lab |
Chromatin structure and function
|
| Street address |
Vuelta de Obligado 2490
|
| City |
Buenos Aires |
| ZIP/Postal code |
C1428 ADN |
| Country |
Argentina |
| |
|
| Platform ID |
GPL30239 |
| Series (1) |
| GSE176341 |
Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi |
|
| Relations |
| BioSample |
SAMN37004537 |
| SRA |
SRX21381684 |
