|
| Status |
Public on Oct 07, 2011 |
| Title |
H3K4me1 ChIP-seq K562 BIO |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me1_K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
chip antibody: H3K4me1
chip antibody vendor: Santa Cruz
chip antibody cat. #: SC-265
|
| 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 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Truseq Genomic DNA protocol. Fragmented DNA were ligated to Illumina Truseq adapters and size selected between 200 and 400bp using the SPRIWorks system and subjected to 18 cycles of PCR using oligos provided by Illumina. Amplified libraries were purified using Ampure XP beads to remove linker prior to sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H3K4me1 ChIP-seq in K562 cells treated with BIO
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using Eland.
For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 10bp bins. Counts were normalized to reads per million, and bins with at least 0.5-1 reads per million are shown.
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Teresa Venezia Bowman |
| Organization name |
Children's Hospital Boston
|
| Lab |
Zon Laboratory
|
| Street address |
One Blackfan Circle, 7th floor
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE29195 |
Genome-wide location analysis of WNT (Tcf7l2) and BMP (SMAD1) in human hematopoeitic cell lines co-occupied with lineage specific regulators (GATA1, GATA2, CEBPA) |
| GSE29196 |
Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration |
|
| Relations |
| SRA |
SRX097111 |
| BioSample |
SAMN00717443 |
