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Sample GSM2047040 Query DataSets for GSM2047040
Status Public on Jan 25, 2019
Title IUGR168
Sample type SRA
 
Source name IUGR_human CD3+ T-cell
Organism Homo sapiens
Characteristics subject status: Intrauterine Growth Restricted (IUGR) Newborns
maternal age (years): 23
weight at term (lbs): 200
bmi at term: 35.4
gestational age (weeks): 39.6
birth weight (g): 2755
tissue: cord blood
cell type: CD3+ T-cell
Extracted molecule genomic DNA
Extraction protocol High molecular weight genomic DNA was extracted fromCD3+ T-cell from human cord blood.
Custom adapters were created for HELP-tagging, referred to as AE and AS Index. As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence, and adapter AS contains index sequences for multiplexing . Adapter AS contains an Illumina sequencing primer sequence. Five micrograms of genomic DNA were digested with HpaII in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation. The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl). After AE ligation, the products were purified using AMpure XP (Agencort), then digested with EcoP15I (NEB). The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end. After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl). After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion). Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen). The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension. After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description HpaII test for HELP-tagging
CB168
Data processing Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (ELAND - 1.7.0). Initial data processing was performed using the default read length of 37 or 42 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence). The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser. We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome. For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions. To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Illumina Casava was used for basecalling.
After the sequence data was obtained from Illumina HiSeq 2500, we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again (ELAND - 1.7.0) on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the hg19 freeze of the human genome at the UCSC genome browser. We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome. For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: hg19
Supplementary_files_format_and_content: Format: wiggle track; content: methylation level for each CpG site
 
Submission date Jan 27, 2016
Last update date May 15, 2019
Contact name Maureen J Charron
Organization name Albert Einstein College of Medicine
Department Biochemistry
Street address 1300 Morris Park Ave
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL16791
Series (1)
GSE77268 DNA Hypermethylation at Loci Associated with Diabetes, Obesity and Cardiac Abnormalities in CD3+ Lymphocytes of Intrauterine Growth Restricted Newbors
Relations
BioSample SAMN04442294
SRA SRX1548316

Supplementary file Size Download File type/resource
GSM2047040_hg19.CB168.AD0H8UACXX.lane_2.wig.gz 10.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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