|
| Status |
Public on Aug 07, 2014 |
| Title |
Granta519-IgG Run1 |
| Sample type |
SRA |
| |
|
| Source name |
MCL Cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Granta-519
passages: Less than 15 passages
chip antibody: IgG (Cell Signaling, 2729)
|
| Treatment protocol |
Granta-519 cell line was transfected with 100uM SOX11 specific siRNA or control scarmble siRNA uisng Amaxa program G16, Kit T (Lonza). Cells were harvested 42-46 hours after transfection.
|
| Growth protocol |
Granta-519 was grown in a humidified incubator at 37°C and 5% CO2 with RPMI 1640 medium (Cellgro, Herndon, VA) supplemented with 10% fetal bovine serum (FBS; Gemini Bio-Products, Woodland, CA), 2 mM L-glutamine, 100 units/mL of penicillin G and 100 µg/mL of streptomycin (Cellgro, Herndon, VA).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-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 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 |
| |
|
| Data processing |
Sequence data (base call files or bcl files) generated from the sequencer are converted to fastq files using the Illumina CASAVA 1.8.2 pipeline
The sequence data are aligned to genomes Human genome hg18 via Illumina's iGenome using Gerald (Illumina’s ELAND aligner) via the CASAVA 1.8.2 pipeline. Only raw reads that pass Illumina's purity filter are aligned.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: hg18
Supplementary_files_format_and_content: The processed data is supplied in bigBed file format.
|
| |
|
| Submission date |
Nov 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Samir Parekh |
| E-mail(s) |
[email protected]
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Hematology and Medical Oncology
|
| Street address |
1470 Madison Ave, 5th FL, Room 114
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE52146 |
High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (ChIP-Seq) |
| GSE52149 |
High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma |
|
| Relations |
| BioSample |
SAMN02399594 |
| SRA |
SRX373875 |
