|
| Status |
Public on Aug 03, 2014 |
| Title |
Sox2GFP_WCE_ChipSeq |
| Sample type |
SRA |
| |
|
| Source name |
Neural Progenitors
|
| Organism |
Mus musculus |
| Characteristics |
chip-seq antibody: None
antibody catalog number: None WCE
cll type: Sox2-GFP primary
|
| Growth protocol |
Jaenisch lab- John Cassady
|
| 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 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 |
| |
|
| Description |
Chromatin IP against Sox2GFP_WCE
04252013_D24CWACXX_2.TTAGGC
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For samples MEF_WCE_ChipSeq, MEF_K27Ac_ChipSeq, 13F_WCE_ChipSeq, Sox2GFP_WCE_ChipSeq, 13F-K27Ac_ChipSeq, and Sox2GFP_K27Ac_ChipSeq reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
For samples AD-12-Med1-Skeletal_ChipSeq and AD-1-WCE-astrocytes_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 (human); mm8 (mouse)
Supplementary_files_format_and_content: WIG files: 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.
|
| |
|
| Submission date |
Aug 01, 2014 |
| 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) |
| GSE60026 |
ChIP-seq of enhancer-associated transcription factors and histone modifications |
|
| Relations |
| BioSample |
SAMN02950415 |
| SRA |
SRX668239 |
