|
| Status |
Public on Nov 23, 2010 |
| Title |
YY1 ChIPSeq in Neural Progenitor cells |
| Sample type |
SRA |
| |
|
| Source name |
Neural Progenitor Cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: YY1
chip antibody vendor: Santa Cruz
chip antibody catalog number: sc-1703
cell type: ES-derived Neural Progenitor cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-600 bp using Branson Sonifer. After IP and adapter ligation library fragments of ~250 bp were isolated. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ES cells were differentiated into adherent neural cultures and plated on uncoated flasks in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).
|
| Data processing |
Bed files: Reads were aligned to the mm8 assembly using MAQ (version 0.7.1) with default parameters. The MAQ output (http://maq.sourceforge.net/maq-manpage.shtml) was converted to BAM (http://samtools.sourceforge.net/SAM1.pdf). All duplicate reads (reads mapping to the exact same genomic coordinates) were collapsed to one. The BAM was converted to BED format as specified in the UCSC documentation (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). The bed score field was calculated as (n/90)*1000, where n is the mapping quality score assigned by MAQ. Any score calculated to be above 1000 was given a value of 1000. The 'name' bed field was populated with the read name assigned by the sequencer.
WIG files: WIG files were produced from BAM using the igvtools count command (http://www.broadinstitute.org/igv/node/173), using the -e parameter to extend the reads to 200 bp. Default values were used for all other parameters.
|
| |
|
| Submission date |
Nov 22, 2010 |
| Last update date |
Nov 19, 2022 |
| Contact name |
Kevin Dong |
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
360 Longwood Ave
|
| City |
Boston |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE25197 |
GC-rich Sequence Elements Recruit Polycomb Repressive Complex 2 (PRC2) in ES cells |
|
| Relations |
| SRA |
SRX031664 |
| BioSample |
SAMN00138273 |
