|
| Status |
Public on Sep 13, 2013 |
| Title |
ILC2_Gfi1_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
Innate type-2 lymphocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type/growth condition: ILC2s were sorted from the MLN of IL-25-treated mice
antibody: anti-Gfi1 (a custom rabbit polyclonal antibody raised against N- and C-terminal peptides)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
~3 x 10^7 cells were harvested, crosslinked with formaldehyde, sonicated, IPed with appropriate antibodies and reverse-crosslinked to obtain 300-500 bp DNA fragments.
Standard Illumina kit was used for library construction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Base calling was performed using Illumina software pipeline (Genome Analyzer)
Align to the mouse genome (mm10) using bowtie (version 0.12.8) allowing 1 mismatch and reporting only uniquely aligning hits.
Peak calling was perfomed using (QuEST) v2.4 with input chromatin as control.
Genome_build: mm10
Supplementary_files_format_and_content: Peaks listed with genomic coordinates and QuEST score
|
| |
|
| Submission date |
Sep 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Aly Azeem Khan |
| Organization name |
University of Chicago
|
| Street address |
6045 S. Kenwood Ave.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE50806 |
Specification of innate type-2 lymphocytes by the transcriptional determinant Gfi1 |
|
| Relations |
| BioSample |
SAMN02355912 |
| SRA |
SRX349376 |
