|
| Status |
Public on Oct 09, 2015 |
| Title |
shLuc_Input_r2_batch4 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BirA
purification target: None
bead manufacturer: N/A
young_id: 20150820_4057
|
| Treatment protocol |
shLuciferase
|
| Growth protocol |
Cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with streptavidin beads.
The chromatin extracts containing DNA fragments with an average size of 500 bp were affinity purified using streptavidin beads. Purified DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
Genome_build: mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Oct 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE68195 |
Transcription factor trapping by RNA in gene regulatory elements (ChIP-Seq) |
|
| Relations |
| BioSample |
SAMN04156761 |
| SRA |
SRX1318185 |
