|
| Status |
Public on Dec 31, 2012 |
| Title |
Znf335a_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
lateral telencephalon
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E14.5
strain: C57BL/6
antibody: NIF1
antibody vendor: Bethyl
antibody catalog#: A300-797A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and Znf335-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. 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 |
| |
|
| Data processing |
Base calls performed using ELAND
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with default parameters
peaks were called using MACS with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using the SPP package (Karchenko et al, doi:10.1038/nbt.1508)
|
| |
|
| Submission date |
Mar 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher A Walsh |
| Organization name |
Children's Hospital Boston
|
| Department |
Genetics
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE36385 |
ZNF335 regulates stem cell proliferation and neuronal differentiation via Trithorax complex and REST/NRSF [ChIP-Seq] |
| GSE36386 |
ZNF335 regulates stem cell proliferation and neuronal differentiation via Trithorax complex and REST/NRSF |
|
| Relations |
| SRA |
SRX145997 |
| BioSample |
SAMN00990950 |
