|
| Status |
Public on Apr 21, 2016 |
| Title |
input_DNA_LPS |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW264.7
s. typhosa lps (minutes): 120
sodium crotonate (mm): 0
antibody: none
|
| Treatment protocol |
For LPS stimulation, 100ng/mL of LPS from Salmonella typhosa (Sigma L2387) was added to full media for 2hrs. For Crotonate pre-treatment, 10mM sodium crotonate (pH 7.4) was added to full media for 16 hours prior to LPS stimulation.
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10% FBS, 1% Pen/Strep and 1x Glutamax
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were fixed on plate with 1% formaldehyde, nuclei were isolated and then sonicated by bath ultrasonicator (Covaris). Lysates were clarified and DNA-histone complexes were isolated by either anti-AF9 (Sigman HPA001824) or anti-FLAG (Sigma F1804) immobilized by protein G dynabeads (Life).
For ChIP-seq, purified DNA was prepared for sequencing with the TruSeq ChIP sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on either HiSeq2000 (Illumina) with 50bp single reads or NextSeq500 with 75bp single reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
crosslinked chromatin
|
| Data processing |
For ChIP-seq, data was aligned using bowtie (version 1.0.1) to the mouse mm9 genome reporting only unique reads in the best stratum, with up to 2 mismatches (bowtie -p 8 -S -q -v 2 -m 1 -k 1 --best –strata).
Samtools (version 0.1.19) was used to convert files to bam and sort
TDF files were generated by IGVtools (2.3.7) count function with processed bam files as input
Genome_build: mm9
Supplementary_files_format_and_content: TDF files contained tag density data for all ChIPseq samples
|
| |
|
| Submission date |
Jan 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Sabari |
| E-mail(s) |
Benjamin.Sabari@UTSouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE76539 |
AF9/MLLT3 ChIP-Seq in LPS-stimulated RAW264.7 cells |
|
| Relations |
| BioSample |
SAMN04384542 |
| SRA |
SRX1517426 |
