Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Bisulfite-Seq
Antigen
Bisulfite-Seq

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
A single colony forming unit grown from human bone marrow aspirate donation
donor number
23
donorid
BMA02
donor age
42
cell type
hematiopoietic progenitor
hmlh1 expression
1
barcode
GTACTCATG

Sequenced DNA Library

library_strategy
Bisulfite-Seq
library_source
GENOMIC
library_selection
RANDOM
library_construction_protocol
DNA from individual CFU, CD34+, or RKO cells was harvested by Qiagen genomic DNA kit. DNA was next bisulfite modified and PCR amplified with forward oligonucleotides MLH1-AF (5' [Linker/spacer][barcode]actcaaaatcctctaccttataatatc 3'), MLH1-BF (5' [Linker/spacer][barcode]acaaaccaaacacaaaaccccat 3'), MLH1-CF (5' [Linker/spacer][barcode] tcacctcaacaaaaacacacaaac 3') when [linker/spacer]= (5' CGTATCGCCTCCCTCGCGCCATCAG 3') and [barcode] was sample specific. Negative oligonucleotides used were: MLH1-AR (5'[Linker/spacer][barcode]ttaaaagaagtaagatggaag 3'), MLH1-BR (5' [Linker/spacer][barcode]tttagttaataggagtagagatg 3'), MLH1-CR (5' [Linker/spacer][barcode]GTTAAATTTTTTAATTTTGTGGGTTGTTGGG 3') when [linker/spacer]= (5' CTATGCGCCTTGCCAGCCCGCTCAG 3') and [barcode] was sample specific. Amplified products were run on an 1.5% agarose gel and appropriate sized bands excized. DNA fragments were purified from gel fragments and submitted for 454 sequencing. In parallel 1/2 of each sample was processed for RNA extracts. Total RNA was generated for each sample and used as the template for cDNA synthesis by a single cycle of reverse transcriptase activity followed by RNA digestion. Expression of the human gene hMLH1 (in parallel with human beta actin as a control) was next assessed for each cDNA sample generated by QRT-PCR on an Applied biosystems RT-PCR 7500 fast machine. Threshold values were automatically generated according to the manufacturers protocol. Gene expression for hMLH1 (scored as 1) was considered observed if amplification products broke threshold for both hMLH1 and beta actin. However, loss of hMLH1 (scored as 0) gene expression was defined as the observation of detectable amplification products for beta actin but not hMLH1

Sequencing Platform

instrument_model
454 GS FLX

hg38

Number of total reads
9330
Reads aligned (%)
96.2
Coverage rate (×)
0.0
Number of hyper MRs
1 (qval < 1E-05)

hg19

Number of total reads
9330
Reads aligned (%)
96.2
Coverage rate (×)
0.0
Number of hyper MRs
2 (qval < 1E-05)

Base call quality data from DBCLS SRA