|
| Status |
Public on Jan 01, 2016 |
| Title |
IRP2 immunoprecipitation from cells treated with DFO, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
human bronchial epithelial cells (Beas2B cells)
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: Irp2 (7H6: sc-33682, Santa Cruz)
treatment: DFO
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
Beas2B cells were treated with 10 μM DFO (16 h) (15 cm2 dishes) and were washed with ice cold PBS and collected into 2 ml eppendorfs by scraping.
|
| Growth protocol |
Beas2B cells were seeded into 15cm2 dishes and left overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Samples were prepared for RNA-Seq using the TruSeq RNA-Seq Lib Prep Reagent (Illumina)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DFO12vsCTRL12_Peaks_LowFilter.txt (peak calls comparing IRP2 immunoprecipitation in DFO versus CTL treatments)
SC2_DFO_12_Peaks_LowFilter.txt (peak calls comparing IRP2 and IGG immunoprecipitation)
|
| Data processing |
Sequenced readswere aligned to the human hg19 known transcriptome using bowtie2-2.0.6 and tophat-2.0.7.Linux_x84_64. Any unmapped reads were then allowed to map to the hg19 genome.
Aligned reads from replicates were combined using the 'merge' function in samtools-0.1.18, creating one bam file each for CONTROL, CONTROL IGG, DFO and DFO IGG
the 'findPeaks' function in homer v4.4 (style=factor) was used to to call peaks with a two-fold tag enrichment in a given 'samples' relative to a given 'control' and a Poisson p-value less than 0.1
Peaks common between multiple comparisons were identified with the 'mergePeaks' function in homer v4.4
Peaks were mapped to hg19 genes using the 'annotatePeaks' function in homer v4.4.
Peaks with a homer "peak-score" greater than 5 were retained for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: txt (homer findPeaks output) includes the locations of peaks called by HOMER and statistical scores associated with these peaks
Supplementary_files_format_and_content: txt (homer annotatePeaks output) includes information included in the "homer findPeaks output" as well as additional information about the genomic features related to the peak regions
Supplementary_files_format_and_content: SC1_CONTROL_12_Peaks_LowFilter.txt: peak calls comparing CONTROL to CONTROL-IGG
Supplementary_files_format_and_content: SC2_DFO_12_Peaks_LowFilter.txt: peak calls comparing DFO to DFO-IGG
Supplementary_files_format_and_content: CTRL12vsDFO12_Peaks_LowFilter.txt: peak calls comparing CONTROL to DFO
Supplementary_files_format_and_content: DFO12vsCTRL12_Peaks_LowFilter.txt: peak calls comparing DFO to CONTROL
Supplementary_files_format_and_content: CTRL__Both.txt_Annotated.txt: annotated peaks common to CONTROL/CONTROL-IGG and CONTROL/DFO peaks calls
Supplementary_files_format_and_content: DFO__Both.txt_Annotated.txt: annotated peaks common to DFO/DFO-IGG and DFO/CONTROL peaks calls
Supplementary_files_format_and_content: IREB__Both.txt_Annotated.txt: annotated peaks common to CONTROL/CONTROL-IGG and DFO/DFO-IGG peaks calls
|
| |
|
| Submission date |
Apr 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Augustine MK Choi |
| Organization name |
Weill Cornell Medical College
|
| Department |
Department of Medicine
|
| Street address |
525 East 68th Street, Room M-522, Box 130
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE57073 |
Irp2 mediates cigarette smoke-induced bronchitis and emphysema via regulation of cytochrome c oxidase and mitochondrial iron loading |
|
| Relations |
| BioSample |
SAMN02737203 |
| SRA |
SRX527296 |
