|
| Status |
Public on Jun 17, 2020 |
| Title |
50 ug/mL H2A (Replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
growth phase: Mid-exponential culture
treatment: H2A, 50 ug/mL
|
| Treatment protocol |
Samples were untreated or treated with H2A, and harvested after 30 minutes. Experiments performed in biological triplicate.
|
| Growth protocol |
MG1655 cultured to mid-exponential phase in minimal medium A at 37 degrees C in shaker at 225 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol
DNase, Illumina RiboZero, NEBNext Ultra Directional Library kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA
exp20
processed data file: hist3-counted.xlsx
|
| Data processing |
Custom script - barcode identification.
Custom script - remove primer adapters.
Bowtie2 alignment using MG1655 genome U00096.3.
Custom script - count reads.
Custom script - normalizing and averaging.
Genome_build: MG1655 genome U00096.3
Supplementary_files_format_and_content: hist3-counted.xlsx: RAW counts for each experiment, averaged counts from triplicate experiments.
|
| |
|
| Submission date |
Dec 30, 2019 |
| Last update date |
Jun 17, 2020 |
| Contact name |
Albert Siryaporn |
| Organization name |
University of California Irvine
|
| Street address |
4129 Reines Hall
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL18956 |
| Series (1) |
| GSE142755 |
E. coli transcriptional response to mammalian histone H2A |
|
| Relations |
| BioSample |
SAMN13700482 |
| SRA |
SRX7478980 |
