|
| Status |
Public on Nov 03, 2022 |
| Title |
RNAi2 [ATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Cultured trypanosomes
|
| Organism |
Trypanosoma brucei brucei |
| Characteristics |
strain: Bloodstream forms, S16 strain
treatment: trasfected with pGR70 (RNAi plasmid)
sample group: RNAi induced
|
| Treatment protocol |
± 1 µg/ml tetracycline for RNAi induction
|
| Growth protocol |
Grown in HMI-9 medium at 37ºC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed, permeabilized with 40 uM digitonin for 5 min at RT, and incubated with Tn5 transposase for 30 min at 37ºC. DNA was purified using Qiagen MinElute Kit
Amplification was carried out with 2× KAPA HiFi mix and 1.25 uM of Nextera primers
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NGS078-20-6_S6
|
| Data processing |
75-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using bowtie2 with options --no-unal --no-mixed -5 5 -3 5
Fragments corresponding to nucleosome-free regions were extracted from BAM files using alignmentSieve (deeptools) with options --minMappingQuality 30 --maxFragmentLength 100 --ATACshift --ignoreDuplicates -bl mito.bed
Peaks were called using MACS2 callpeak with options -g 3.5e7 --nomodel -f BAMPE -B --keep-dup all -c genomic_control
bedGraph files were generated using MACS2 bdgcmp with option -m ppois
Genome_build: 427 2018 version 4.9
Supplementary_files_format_and_content: bigWig files generated from bedGraph files using bedGraphToBigWig
|
| |
|
| Submission date |
Oct 26, 2021 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Antonio M Estevez |
| E-mail(s) |
aestevez@ipb.csic.es
|
| Organization name |
CSIC
|
| Department |
Lopez-Neyra
|
| Street address |
Avda. del Conocimiento 17
|
| City |
Armilla |
| State/province |
Granada |
| ZIP/Postal code |
18016 |
| Country |
Spain |
| |
|
| Platform ID |
GPL22141 |
| Series (2) |
| GSE186562 |
Effect of the depletion of RBP33 (Tb927.8.990) on chromatin accesibility in bloodstream Trypanosoma brucei [ATAC-seq] |
| GSE186570 |
The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes |
|
| Relations |
| BioSample |
SAMN22567528 |
| SRA |
SRX12775917 |
