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Sample GSM1906332 Query DataSets for GSM1906332
Status Public on Nov 01, 2015
Title RL
Sample type SRA
 
Source name B-cell Follicular Lymphoma
Organism Homo sapiens
Characteristics cell line: RL
cell line source: B-cell Follicular Lymphoma
cell type: B cells
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
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.
 
Submission date Oct 12, 2015
Last update date Nov 01, 2015
Contact name Jianlin Jack Cheng
E-mail chengji@missouri.edu
Organization name University of Missouri,columbia
Department Computer Science Department
Lab Bioinformatics, Data Mining, and Machine Learning Lab
Street address Engineering Building West 109
City columbia
State/province MO
ZIP/Postal code 65211-2060
Country USA
 
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
Relations
SRA SRX1330143
BioSample SAMN04160495

Supplementary file Size Download File type/resource
GSM1906332_contact_RL.txt.gz 369.9 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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