|
| Status |
Public on Dec 05, 2014 |
| Title |
Spleen_K4Me1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen red pulp macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
cell type: Spleen red pulp macrophages
chip antibody: anti-H3K4me1
chip antibody vendor/cat.#: Abcam ab8895 and Millipore 07-436 mixed ratio 1:1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was eluted from the beads, then treated with RNase (Roche) for 30 min at 37°c and with Proteinase K (NEB) for 2 hrs at 37°c. Reverse cross-linking was performed at 65°c overnight. DNA was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter) at 2.3x ratio. Sequential steps of end-repair, A-base addition, adapter-ligation and amplification were performed, with DNA purification with SPRI beads after each step. Following the amplification step, DNA concentration was measured, and equivalent amounts of barcoded ChIPed DNA from each sample were pooled together. An additional size-selection step was performed
Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
Nat Protoc. 2013 Mar;8(3):539-54. doi: 10.1038/nprot.2013.023. PMID: 23429716
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
alignment using bowtie 0.12 using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Nov 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ido Amit |
| E-mail(s) |
[email protected]
|
| Phone |
972-8-9343338
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Immunology
|
| Street address |
234 Herzl st.
|
| City |
Rehovot |
| ZIP/Postal code |
760001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE63339 |
Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ChIP-seq] |
| GSE63341 |
Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment |
|
| Relations |
| BioSample |
SAMN03196791 |
| SRA |
SRX760587 |
| Named Annotation |
GSM1546002_merged_Spleen_K4Me1_2.bigWig |
