Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Bisulfite-Seq
Antigen
Bisulfite-Seq

Cell type

Cell type Class
Placenta
Cell type
Placental villi
NA
NA

Attributes by original data submitter

Sample

source_name
placental villi
tissue
placental villi
developmental stage
3rd trimester
genotype
Control

Sequenced DNA Library

library_strategy
Bisulfite-Seq
library_source
GENOMIC
library_selection
RANDOM
library_construction_protocol
submitter states "custom" (no meaningful entry) DNeasy Blood and Tissue Kit DNA extraction Parallel PCR reactions to assay 151 imprinted differentially methylated domains (Supplementary material in manuscript) with a final concentration of 1xHotStar PCR buffer, 0.2mM dNTPs, 1U HotStar taq and 0.4uM each primer pair and 2ng DNA were performed in a 15uL reaction volume in 384-well plates. The plates were prepared on the Agilent Bravo Workstation. The cycling conditions included a 15 minute 95°C denaturation, followed by 30 cycles of 95°C for 30 seconds, 50°C for 30 seconds, 72°C for 90 seconds, with a 5 minute final extension at 72°C and were performed on the C1000 Touch Thermal Cycler. PCR products were pooled for each sample and SPRI-purified using Sera-Mag carboxylate-modified Magnetic SpeedBeads as per manufacturer’s recommendations. A-overhang addition was done using 1x NEB buffer 2, 0.2mM dATP, 12.5U Klenow fragment (3’->5’ exo-) in a 25uL reaction incubated at 37°C for 30 minutes. Following SPRI purification, Illumina adapters were ligated using the Quick ligation kit in a 40uL reaction. Following another SPRI purification, libraries were amplified (11 cycles) and barcoded using the Sanger 8-base index in a 50uL reaction containing: 1x High Fidelity buffer, 1U Phusion High Fidelity taq, 0.2mM dNTPs, 0.1uM each primer . Final libraries were SPRI purified and concentration and quality were assessed by the 2100 Bioanalyzer system and Kapa library quantification. The 48 barcoded libraries were pooled and multiplexed.

Sequencing Platform

instrument_model
Illumina MiSeq

hg38

Number of total reads
233600
Reads aligned (%)
6.1
Coverage rate (×)
0.0
Number of hyper MRs
126 (qval < 1E-05)

hg19

Number of total reads
233600
Reads aligned (%)
6.1
Coverage rate (×)
0.0
Number of hyper MRs
129 (qval < 1E-05)

Base call quality data from DBCLS SRA