|
| Status |
Public on May 31, 2017 |
| Title |
H3 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
T. brucei (BF) Wt
|
| Organism |
Trypanosoma brucei brucei |
| Characteristics |
strain background: LISTER
chip antibody: polyclonal H3 rabbit antiserum
chip antibody details: From Gassen et al., 2012 (PMID 22941659)
treated with: none
|
| Growth protocol |
T. brucei Wt and genetically modified strains were cultured at 37°C in HMI-11 medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
[MNase ChIP-seq] The cells were cross-linked with formaldehyde, permeabilized and treated with micrococcal nuclease (MNase). H2A.Z/H3-containing nucleosomes were immunoprecipitated using the respective antibody.
[RNA pol II ChIP-seq] The cells were cross-linked with formaldehyde, permeabilized and chromatin was fragmented via sonification. RNA pol II bound DNA was immunoprecipitated using BB2 antibody.
ChIP-seq libraries were constructed as described by in Wedel & Siegel, 2017.
[Small 3P-RNA-seq] Small total RNAs (<200 nt) were extracted and treated with Terminator exonuclease to enrich for primary transcripts (3P-RNA). One half of the sample was treated with Polyphosphatase and the other half was mock treated.
NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England BioLabs)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: MNase ChIP-seq
FastQ quality trimming using FastX (version 0.0.13) and a cut-off value of 20
Adaptor trimming using cutadapt version 1.10
Readmapping using Bowtie 2 version 2.1.0
sorting and indexing of BAM files using samtools version 0.1.9-4428cd
Wiggle fill generation with COVERnant version 0.1
Genome_build: Tb927v24 or Tb427v24 (see processed file names)
Tb427v24:
http://tritrypdb.org/common/downloads/release-24/TbruceiLister427/fasta/data/TriTrypDB-24_TbruceiLister427_Genome.fasta
Tb927v24:
http://tritrypdb.org/common/downloads/release-9.0/TbruceiTREU927/fasta/data/TriTrypDB-9.0_TbruceiTREU927_Genome.fasta
Supplementary_files_format_and_content: wiggle
|
| |
|
| Submission date |
Apr 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21682 |
| Series (1) |
| GSE98061 |
GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes |
|
| Relations |
| BioSample |
SAMN06808444 |
| SRA |
SRX2751960 |
