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| Status |
Public on Nov 01, 2015 |
| Title |
CALL4 |
| Sample type |
SRA |
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| Source name |
MHH-CALL- 4 B-cell acute lymphocytic leukemia
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| Organism |
Homo sapiens |
| Characteristics |
cell line: CALL4
cell line source: MHH-CALL- 4 B-cell acute lymphocytic leukemia
cell type: B cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hundreds of millions of Hi-C paired-end sequence reads for three different human cells (RL follicular lymphoma cell line, primary tumor B-cells from an acute lymphoblastic leukemia patient, and MHH-CALL-4 B-cell acute lymphoblastic leukemia cell line) using the Hi-C technique.
Hi-C libraries were created for a case of primary human B-acute lymphoblastic leukemia (B-ALL), the MHH-CALL-4 B-ALL cell line (CALL4), and the follicular lymphoma cell-line (RL). These libraries were sequenced using an Illumina HiSeq 2000. High-quality paired-end reads of 39M, 79M, and 33M were obtained for these cells, respectively.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: Hi-C seq
These libraries were sequenced using an Illumina HiSeq 2000
Software Maq was used to map each read-pair to the reference human genomes (NCBI build 36.3), where parameter “sum of mismatching base qualities (-e)” controlling the tolerance of mismatches was set to 150 in most experiments.
Data were filtered using the following specifications…
Maq outputs the base pair positions in the reference genomes where each DNA read is mapped to. The mapped positions were analyzed by our method to generate chromosomal contacts
An in-house bioinformatics software pipeline was developed and applied to map sequence reads to the human reference genome, producing a large data set of high-quality and high-resolution chromosome contacts
Genome_build: NCBI build 36.3
Supplementary_files_format_and_content: The processed data file is tab delimited with five columns. The column headers are; Mapping ID, chromosome number 1, chromosome location 1, chromosome number 2, chromosome location 2. The Mapping ID is the key assigned during Mapping for each sequence. The chromosome number and location respectively correspond to the id and location of the chromosome being mapped.
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| Submission date |
Oct 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianlin Jack Cheng |
| E-mail(s) |
chengji@missouri.edu
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| Organization name |
University of Missouri,columbia
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| Department |
Computer Science Department
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| Lab |
Bioinformatics, Data Mining, and Machine Learning Lab
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| Street address |
Engineering Building West 109
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| City |
columbia |
| State/province |
MO |
| ZIP/Postal code |
65211-2060 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE73924 |
The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types |
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| Relations |
| SRA |
SRX1330145 |
| BioSample |
SAMN04160497 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1906334_contact_CALL4.txt.gz |
659.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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