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| Status |
Public on Oct 28, 2020 |
| Title |
1hr infected |
| Sample type |
SRA |
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| Source name |
Epithelial cells (HEp2)
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Epithelial cells (HEp2)
condition: Infected
hours post infection: 1
chlamydial species: Chlamydia trachomatis - Serovar E
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| Treatment protocol |
Chlamydia trachomatis serovar E infections of HEp-2 cells and matched mock infections proceeded to 1, 12, 24, and 48 hours post-infection before application of the FAIRE protocol
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| Growth protocol |
HEp-2 cells (American Type Culture Collection, ATCC No. CCL-23) were grown as monolayers in 6 x 100mm TC dishes until 90% confluent. Fresh monolayers were infected with Chlamydia trachomatis serovar E in 3.5 mL SPG buffer for an MOI ~ 1, using centrifugation to synchronize infections. Infections and subsequent culture were performed in the absence of cycloheximide or DEAE dextran. A matching number of HEp-2 monolayers were also mock-infected using uninfected cell lysates. Each treatment was incubated at 25°C for 2h and subsequently washed twice with SPG to remove dead or non-viable EBs. 10 mL fresh medium (DMEM + 10% FBS, 25μg/ml gentamycin, 1.25μg/ml Fungizone) was added and cell monolayers incubated at 37°C with 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
FAIRE analysis of Chlamydia trachomatis-infected and mock-infected HEp-2 cells was performed according to the protocol published by Simon et al (Simon JM, Giresi PG, Davis IJ, Lieb JD: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc 2012, 7(2):256-267), including crosslinking with formaldehyde, cell lysis, phenol-chloroform extraction, reverse-crosslinking, and purification prior to library construction.
FAIRE-Seq libraries were prepared from 10-100ng crosslinked DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) as per the manufacturer's protocol
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| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base calls were performed using the bulit in Illumina basecaller
Sequenced reads were trimmed and quality checked using Trimmomatic, FastQC and FastQ-Screen
Trimmed reads were aligned to the human genome (GRCh 38.87) using Bowtie2 (2.3.2) with additional parametres of no mismatches and –very-sensitive-local. Duplicate reads and unmapped reads were removed using Picard Tools
Peak calling was performed using MACS2 (2.1.1) in paired-end mode, with additional parameters of –no-model –broad -q 0.05 and MACS2 predicted extension sizes. All infected and mock-infected replicates were passed separately, with significant peaks determined against software-predicted background signal . Any peaks that fell within the ENCODE blacklisted regions or were located on non-standard chromosomes such as (ChrMT and ChrUn) were removed.
Genome_build: Genome Reference Consortium Human Build 38 patch release 87 (GRCh38.p87)
Supplementary_files_format_and_content: Peak files were generated using MACS2 as outlined above
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| Submission date |
Jun 10, 2019 |
| Last update date |
Oct 30, 2020 |
| Contact name |
Regan Hayward |
| Organization name |
Helmholtz Institute for RNA-based Infection Research
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| Street address |
Josef-Schneider-Straße 2 / D15
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| City |
Wurzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE132448 |
Chromatin accessibility dynamics of Chlamydia-infected epithelial cells |
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| Relations |
| BioSample |
SAMN12001407 |
| SRA |
SRX6028123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3864954_1hr_infected_rep1_broadPeaks.bed.gz |
206.2 Kb |
(ftp)(http) |
BED |
| GSM3864954_1hr_infected_rep2_broadPeaks.bed.gz |
338.6 Kb |
(ftp)(http) |
BED |
| GSM3864954_1hr_infected_rep3_broadPeaks.bed.gz |
119.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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