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Sample GSM782158 Query DataSets for GSM782158
Status Public on Oct 06, 2011
Title BL41_CTCF
Sample type SRA
 
Source name B cells
Organism Homo sapiens
Characteristics cell line: Cell line derived from Burkitt's lymphoma
passage: Multiple
chip antibody: CTCF
chip antibody vendor: Millipore
chip antibody catalog#: 07-729
chip antibody lot#: DAM1772428
Treatment protocol No treatment was performed.
Growth protocol Cells were maintained in RPMI with 10% FBS and 1% L-glutatmine.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and chromatin complexes were isolated with antibody to CTCF (Millipore 07-729) or normal Rabbit Ig control (Cell signaling Technology 2729). Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq sample preparation kit (Part#11257047 Rev.A). 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, size selection was performed by excising a band of 200±25 bp from an agarose gel to remove excess adapters. The gel purified DNA was PCR amplified with Illumina primers for 15 cycles and purified by MinElute PCR purification kit according to manufacturer's instruction. 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 CTCF
Data processing Illumina software pipeline (Basecalls were done by using Illumina RTA 1.8 for GAIIx run. Alignment was done by using Illumina CASAVA_v1.7.0 pipelines) read length -> 36 bps for Chip-Seq data. The bed files are the MACS peaks and they are generated as follows: Illumina FastQ files were mapped to the human genome (hg19) using Bowtie (Langmead et al. Genome Biol 2009) requiring a unique match (using the '-m 1' flag). The aligned reads in SAM format were analzyed using the MACS peak caller (Zhang et a.l. Genome Biol 2008). MACS peak calling was run using the respective Rabbit Ig control sequencing data as background files for BJAB and BL41 CTCF ChIP-Seq data.
 
Submission date Aug 18, 2011
Last update date May 15, 2019
Contact name Shalini Oberdoerffer
E-mail(s) shalini.oberdoerffer@nih.gov
Phone 301-846-7104
Organization name National Cancer Institute
Street address 1050 Boyles Street
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platform ID GPL10999
Series (2)
GSE31278 CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing
GSE31485 CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [ChIP-Seq]
Relations
SRA SRX092416
BioSample SAMN00710362
Named Annotation GSM782158_BL41_CTCF_MACS_summits.bed.gz

Supplementary file Size Download File type/resource
GSM782158_BL41_CTCF_MACS_summits.bed.gz 393.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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