Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TAL1

Cell type

Cell type Class
Blood
Cell type
Hematopoietic Stem Cells
MeSH Description
Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Attributes by original data submitter

Sample

source_name
Hematopoietic Stem & Progenitor Cells
chip antibody
TAL1
antibody catalog number
Santa Cruz SC-12984
cell type
CD133+ expanded UCB
cell number
1 million
library prep protocol
Illumina ChIP-seq
replicate
1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified. Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.  Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
19580904
Reads aligned (%)
10.7
Duplicates removed (%)
51.4
Number of peaks
39 (qval < 1E-05)

hg38

Number of total reads
19580904
Reads aligned (%)
11.1
Duplicates removed (%)
50.2
Number of peaks
33 (qval < 1E-05)

Base call quality data from DBCLS SRA