|
| Status |
Public on Jun 15, 2010 |
| Title |
ChIP-Seq for TBP in mES cells (B2) |
| Sample type |
SRA |
| |
|
| Source name |
Embyonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: TBP
antibody catalog number: Abcam AB818
cell type: V6.5 embryonic stem cells
|
| Growth protocol |
V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were 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 350bp (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 Genome Analyzer II |
| |
|
| Description |
Chromatin IP against TBP
03172010_614ATAAXX_B2
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build (mm8) using bowtie.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
(etc.)
The data from the BWT1 category is what is visualized in the uploaded WIG files
|
| |
|
| Submission date |
Jun 11, 2010 |
| 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 |
GPL9250 |
| Series (1) |
| GSE22303 |
ChIP-Seq of TBP in Mouse Embryonic Stem Cells |
|
| Relations |
| SRA |
SRX022047 |
| BioSample |
SAMN00015139 |
| Named Annotation |
GSM555160_03172010_614ATAAXX_B2.wig.gz |
