|
| Status |
Public on Sep 24, 2014 |
| Title |
Reh DNAse-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Pro-B lymphoblastic leukemia cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Reh
lymphoma type: non-Hodgkin's Lymphoma cell line
passages: 7
dnasei origin: Worthington
dnasei units (u/ml): 6
|
| Treatment protocol |
To perform DNaseI accessibility assays with HRS and NH cell lines, the optimal cell number and DNaseI (DPFF DNaseI, Worthington Biochemical Corporation) concentration was titrated for each cell line. The DNA digestion extent was comparable in all the generated samples as measured by RT-PCR (5). Briefly, nuclei were isolated from 1-5 x 106 cells by detergent lysis and immediately digested for 3 min at 33 °C with DNaseI at 1-10 U/ml in a 1 mM CaCl2 supplemented buffer. The nuclei were lysed, the nuclear proteins digested with 1 mg/ml Proteinase K overnight at 37 °C
|
| Growth protocol |
Cells lines from Hodgkin's lymphoma (L1236, L428 and L519), Pro-B lymphoblastic leukemia (Reh) and Burkitt's lymphoma (Namalwa) were grown in IMDM medium containint 10% FCS, penicillin 100 U/mL, and streptomycin 50 pg/mL and incubated at 37C in a humidified atmosphere containing 5% CO2, with cell densities kept under 5x105 per ml
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNaseI-Seq samples were generated from a size selection of DNaseI-digested DNA fragments comprised within a range of 100 to 600 bp and subjected to library preparation as per manufacturer´s instruction (Illumina)
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Base-calling (Illumina)
DNAse-seq reads were aligned to the hg18 genome assembly using Bowtie 1.00 to SAM output using standard parameters
Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011.
Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011
Peaks were called using CoCAS
Genome_build: hg18
Supplementary_files_format_and_content: Fragments were extended using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Fixed-step 10bp wig files were generated using an R pipeline described in Koch, Fenouil, Gut et al. 2011. Peaks were called using CoCAS
|
| |
|
| Submission date |
Oct 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pierre Daniel Cauchy |
| E-mail(s) |
cauchy@ie-freiburg.mpg.de
|
| Phone |
+49 (0)761 5108-730
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Department of Cellular and Molecular Immunology
|
| Lab |
Laboratory Rudolf Grosschedl
|
| Street address |
Stübeweg 51
|
| City |
Freiburg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE51726 |
Genome-wide Dnase-Seq profiles in Hodgkin's and non-Hodgkin's lymphoma |
| GSE51814 |
Genome-wide DNase-Seq and methylation profiles in Hodgkin's and non-Hodgkin's lymphoma |
|
| Relations |
| BioSample |
SAMN02384489 |
| SRA |
SRX367996 |
