|
| Status |
Public on Apr 08, 2010 |
| Title |
KLF1_ChIPSeq, 3.0 |
| Sample type |
SRA |
| |
|
| Source name |
E14.5 fetal liver, ChIP
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell type: erythroid
age: E14.5
developmental stage: fetal
strain: Balb/c Klf3 -/-
gender: female
passages: primary tissue
antibody: rabbit polyclonal to KLF1
|
| Growth protocol |
4 x Klf3 -/- fetal livers were collected at E14.5 from timed mated female mice, homogenized using a 23G needle, then strained through a 40 micron cell strainer and pooled.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The SOLiD System 2.0 workflow for Lower Input/Lower Complexity DNA fragment library preparation (Applied Biosystems) was followed to prepare libraries containing 80-130bp of ChIP DNA (or Input DNA) flanked by the appropriate adaptors. A detailed description of the method is provided in the Supplemental Experimental Procedures of the publication.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
ChIP against KLF1.
|
| Data processing |
Alignment: Sequencing reads were mapped to the mm9 mouse genome using the mapreads algorithm (Applied Biosystems). In order to maximize the number of mappable reads, we removed the final 5 nucleotides for unmapped reads in a recursive strategy until the reads reached 25 nucleotides in length.
Peaks: We employed the same method used by Chen et al. (2008, Cell 133, 1106-1117) in order to declare a set of KLF1-bound regions for downstream analysis. When generating the tag intensity profile used in peak declaration, we added a count of 1 to each position up to 100bp 3' from the start of each tag. To be declared a peak, a genomic position must pass both a tag intensity threshold and a fold-change threshold. We applied a false discovery rate (FDR) threshold of 1%, which resulted in a tag intensity profile threshold of 9. We applied negative control tag library fold-change threshold of 5.0 at the centre of each declared peak, yielding the final set of 945 declared peaks.
|
| |
|
| Submission date |
Apr 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew C Perkins |
| E-mail(s) |
a.perkins@imb.uq.edu.au
|
| Phone |
+61733462077
|
| Fax |
+61733462101
|
| Organization name |
The University of Queensland
|
| Department |
Institute for Molecular Bioscience
|
| Street address |
Institute for Molecular Bioscience
|
| City |
The University of Queensland, St Lucia, Brisbane |
| State/province |
QLD |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL9318 |
| Series (1) |
| GSE20478 |
KLF1/EKLF regulatory networks in primary erythroid cells |
|
| Relations |
| SRA |
SRX018750 |
| BioSample |
SAMN00010887 |
