|
| Status |
Public on Sep 15, 2011 |
| Title |
BCL6_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
ChIPSeq, human CML cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: JURL_MK1
chip antibody: anti-BCL6 antibody (N3)
chip antibody vendor: Santa Cruz
chip antibody lot#: I2607
chip antibody catalog#: sc-858
|
| Treatment protocol |
No treatment
|
| Growth protocol |
JURL-MK1 cells were maintained in Roswell Park Memorial Institute medium (RPMI-1640, Invitrogen, Carlsbad, CA) with GlutaMAX containing 20% fetal bovine serum, 100 IU/ml penicillin and 100 μg/ml streptomycin at 37°C in a humidified incubator with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were purified from crosslinked sonicated nuclei and BCL6-DNA complexes were isolated with BCL6 antibody (N3,Santa Cruz). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 11257047). 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 (3' to 5' 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 15 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 IIx |
| |
|
| Description |
Chromatin IP against BCL6
|
| Data processing |
Alignment: 36bp sequence reads were obtained and mapped using ELAND to the human genome (hg18) by Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
|
| |
|
| Submission date |
Dec 15, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Katerina Hatzi |
| E-mail(s) |
kac2029@med.cornell.edu
|
| Organization name |
WCMC
|
| Department |
Hematology/Oncology
|
| Lab |
Ari Melnick
|
| Street address |
413 E 69th Street, BB-1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE26085 |
BCL6 is required for the initiation and maintenance of chronic myeloid leukemia |
|
| Relations |
| SRA |
SRX035160 |
| BioSample |
SAMN00149686 |
