|
| Status |
Public on Jan 28, 2014 |
| Title |
ChIP sample |
| Sample type |
SRA |
| |
|
| Source name |
Cells of Anabaena
|
| Organism |
Anabaena |
| Characteristics |
type of sample: ChIP sample
chip antibody: anti-NtcA
strain: PCC 7120
|
| 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 affinity-purified anti-NtcA, and the immunoprecipitated material was pulled down using Protein G. 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 Anabaena sp. PCC 7120 growing in ammonium-containing medium were filtered, washed, and resuspended in the same medium without ammonium and incubated for 3 h with aeration.
|
| 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 |
Immunoprecipitated 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.
The processed data files include 3 files per genome location (chromosome, plasmid alpha, beta, delta, epsilon and gamma) where the peaks have been found. They can be visualized using the Integrative Genome Viewer (Broad Institute) (Thorvaldsdotti et al., 2012)
Genome_build: Anabaena sp. PCC 7120 genome (http://wiki.annotation.jp/Kazusa:CyanoBase:Anabaena_sp._PCC_7120)
Supplementary_files_format_and_content: There are 3 files per chromosome/plasmid to be visualized with the Integrative Genome Viewer (Broad Institute). First, the genome sequence (.seq) is imported along with the .bed file. Then, the .igv file is the one containing the information of the obtained peaks.
|
| |
|
| Submission date |
Oct 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Picossi |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17858 |
| Series (1) |
| GSE51865 |
ChIP analysis unravels an exceptionally wide distribution of binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium. |
|
| Relations |
| BioSample |
SAMN02388140 |
| SRA |
SRX370338 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1254240_PCC7120_alpha.bed.gz |
4.1 Kb |
(ftp)(http) |
BED |
| GSM1254240_PCC7120_alpha.seq.txt.gz |
123.3 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_alpha_peaks.igv.txt.gz |
4.0 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_beta.bed.gz |
1.9 Kb |
(ftp)(http) |
BED |
| GSM1254240_PCC7120_beta.seq.txt.gz |
57.1 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_beta_peaks.igv.txt.gz |
2.4 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_chromo.bed.gz |
57.8 Kb |
(ftp)(http) |
BED |
| GSM1254240_PCC7120_chromo.seq.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_chromo_peaks.igv.txt.gz |
55.5 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_delta.bed.gz |
746 b |
(ftp)(http) |
BED |
| GSM1254240_PCC7120_delta.seq.txt.gz |
17.1 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_delta_peaks.igv.txt.gz |
470 b |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_epsilon.bed.gz |
396 b |
(ftp)(http) |
BED |
| GSM1254240_PCC7120_epsilon.seq.txt.gz |
12.6 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_epsilon_peaks.igv.txt.gz |
414 b |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_gamma.bed.gz |
999 b |
(ftp)(http) |
BED |
| GSM1254240_PCC7120_gamma.seq.txt.gz |
30.8 Kb |
(ftp)(http) |
TXT |
| GSM1254240_PCC7120_gamma_peaks.igv.txt.gz |
877 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
