|
| Status |
Public on Jan 03, 2022 |
| Title |
E281A-1 |
| Sample type |
SRA |
| |
|
| Source name |
MGAS2221
|
| Organism |
Streptococcus pyogenes |
| Characteristics |
replicate: Replicate 1
growth condition: in vitro
genotype: CovS-E281A
chip antibody: CovR-specific antibody
|
| Treatment protocol |
No treatments
|
| Growth protocol |
GAS cells were grown in rich medium (Todd-Hewitt, 0.2% yeast extract) to an OD of 0.5 (mid-exponential phase)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bacterial cell lysates were purified using a CovR-specific antibody
Illumina compatible indexed libraries were prepared from 2-10ng of sheared ChIP or input DNA using the KAPA Hyper Library Preparation Kit (KAPA Biosystems, Inc.)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
processed data file: M1-E281A_GEO-chip_12-2021.xlsx
|
| Data processing |
Base calls onboard Illumina NextSeq500
Raw data files processed using CLC Genomics Workbench v 21
Reads mapped to reference genome MGAS2221 (CP043530.1) using CLC Genomics Workbench v 21
Peak calls using CLC Genomics Workbench v 21 ChIP-seq analysis tool
Individual peaks enumeratied and normalized [(total reads mapped to peak)/(peak length in bp)*100; reads per kilobase length - RPKL]
Genome_build: MGAS2221 (CP043530.1)
Supplementary_files_format_and_content: Excel tables with peak calls and RPKL
|
| |
|
| Submission date |
Dec 30, 2021 |
| Last update date |
Jan 03, 2022 |
| Contact name |
Anthony Flores |
| E-mail(s) |
anthony.r.flores@uth.tmc.edu
|
| Phone |
7135006626
|
| Organization name |
UTHSC/McGovern Medical School
|
| Street address |
6431 Fannin St., MSB 3.130
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL31155 |
| Series (1) |
| GSE192795 |
CovS Inactivation Reduces CovR Promoter Binding at Diverse Virulence Factor Encoding Genes in Group A Streptococcus |
|
| Relations |
| BioSample |
SAMN24518855 |
| SRA |
SRX13556842 |
