|
| Status |
Public on Mar 07, 2015 |
| Title |
CSS68 Input sample |
| Sample type |
SRA |
| |
|
| Source name |
Total DNA control (Input)
|
| Organism |
Nostoc sp. PCC 7120 = FACHB-418 |
| Characteristics |
strain: CSS68
antibody used: none
genotype/variation: TAP-tag under the all3953 promoter
|
| Treatment protocol |
Cells were treated with formaldehyde (1 %, 15 min) and glycine (125 mM, 5 min), and collected. The cells were broken, the DNA was sheared by sonication, and a sample was taken for the control (Input). The extract was incubated with IgG-conjugated dynabeads, and the immunoprecipitated material was eluted at 65 ºC. Crosslinking reversion was carried out at 65ºC for 5h and proteins were eliminated using Proteinase K at 55ºC for 2h.
|
| Growth protocol |
Cells of strains CSS57 (All3953-TAP) and CSS68 (control) grown in BG110+NH4+10 mM bicarbonate and bubbled with 1% CO2-containing air were filtered, washed, and resuspended in the same medium without bicarbonate and incubated for 3h with aeration with air (no CO2).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using phenol:chloroform extraction followed by ethanol precipitation with ammonium acetate and glycogen. DNA was dissolved in DNAse-free purified water.
ChIP DNA Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Total DNA
|
| Data processing |
Libraries were loaded at 8pM concentration into the flow cell using the Cluster Station running recipe v7 with the Single-Read Cluster Generation Kit v4 (all Illumina).
The flow cell was loaded into the Genome Analyzer II and samples were sequenced for 120 nucleotides from a single end using the Sequencing Kit v5 and recipe v8 (all Illumina). Manufacturer’s recommendations were strictly followed.
Illumina sequencing data were pre-processed with the standard Illumina pipeline version 1.5 and sequences were aligned to the Anabaena sp. PCC 7120 genome with the Bowtie software 0.12.5. (Langmead et al., 2009)
The Triform algorithm method (Kornacker et al., 2012) was used to the identify peak regions found in the ChIP sample with respect to the control.To identify the specific peaks found in strain CSS57, the CSS68 (control strain) ChIP data was used as the background for analysis of the CSS57 ChIP data.
A cysfinder analysis was carried out to find a primary motif using the sequences of all the peaks.
Genome_build: Anabaena sp. PCC 7120 genome (http://wiki.annotation.jp/Kazusa:CyanoBase:Anabaena_sp._PCC_7120)
Supplementary_files_format_and_content: Processed data files are in tab-delimited text format. Trifrom.PCC7120.bed contains the location in the chromosome of PCC 7120 of the 142 identified peaks. To view the alignment between peaks and genes, upload the contents of the Triform.PCC7120.bed sheet into a custom track using the "Nostoc sp" browser, available via http://microbes.ucsc.edu. Triform.PCC7120.peaks.txt contains all the information about each of the peak, including the Q-values and the raw coverage of the peaks. Primary motif matches.txt shows the information about the peaks containing sequences which match the consensus sequence found (ATAAN2TTTN2TTAT) in the analysis.
|
| |
|
| Submission date |
Jun 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Picossi |
| E-mail(s) |
silvia.picossi@ibvf.csic.es
|
| Organization name |
CSIC
|
| Department |
Instituto de Bioquímica Vegetal y Fotosíntesis
|
| Street address |
Avda. Americo Vespucio 49
|
| City |
Sevilla |
| ZIP/Postal code |
41092 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11645 |
| Series (1) |
| GSE58861 |
Identification of the global transcriptional regulator All3953 (RbcR) in the cyanobacterium Anabaena sp. PCC 7120 by ChIP-Seq analysis |
|
| Relations |
| BioSample |
SAMN02887298 |
| SRA |
SRX627425 |
