|
| Status |
Public on Mar 14, 2012 |
| Title |
Input WCE ChIP-seq Prima2 T-ALL 2 |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL primagraft
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: None
antibody catalog number: None WCE
sample type: T-ALL primagraft 05-261
|
| Growth protocol |
Diagnostic T-ALL patient samples were obtained with informed consent and Institutional Review Board approval from children treated on Dana-Farber Cancer Institute study 05-01. Mononuclear cells were purified by Ficoll-Hypaque centrifugation prior to FACS analysis and viable cryopreservation in liquid nitrogen. 50,000 human CD34+ cells selected from above T-ALL samples with the aid of immunomagnetic beads (Miltenyi Biotec, Auburn, CA) or FACSAria were transplanted intrahepatically into RAG2-/-γc-/- neonatal mice within 48 hours of birth. Mice were sacrificed at 8 weeks after transplantation. Bone marrow (BM), spleen, thymus, liver and peripheral blood was collected for FACS analysis of human CD45, CD34, CD2, and CD7 expression. Serial transplantation was done by intrahepatically injecting 50,000 human CD34+ cells selected from the T-ALL primary engrafted BM or thymus into the neonatal RAG2-/-γc-/- mice. Human CD34+ cells used in TAL1 ChIP-seq analysis were isolated from the primary engraftments of T-ALL patients.
|
| 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 4500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing using Beckman SPRIworks fragment library system with adapters from the Illumina TruSeq DNA kit. DNA fragments were end repaired, ligated and size selected using SPRIworks. DNA was then subjected to 18 cycles of PCR using oligos provided by Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against WCE Input 5261 (6/15/11)
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
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.
hg18
|
| |
|
| Submission date |
Nov 21, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
[email protected]
|
| 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 |
GPL11154 |
| Series (2) |
| GSE29181 |
Core transcriptional regulatory circuit controlled by the TAL1 complex in human T-cell acute lymphoblastic leukemia |
| GSE33850 |
Core transcriptional regulatory circuit controlled by the tal1 complex in human t-cell acute lymphoblastic leukemia (Subseries) |
|
| Relations |
| SRA |
SRX107303 |
| BioSample |
SAMN00760394 |
