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| Status |
Public on Jul 05, 2016 |
| Title |
CD14+ monocyte |
| Sample type |
SRA |
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| Source name |
CD14+ monocyte
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD14+ monocyte
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| Growth protocol |
Peripheral blood was collected from a healthy male and the seven leukocyte types were isolated reiterativly using antibodies to cell type specific surface antigens bound to magnetic Dynabeads.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was purified from seven isolated cell types using DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA cat# 69506), according to the manufacturer’s instructions. TAB-seq libraries were constructed according to Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
TAB-seq
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| Data processing |
Data were mapped to the H. sapiens GRCh38 reference genome
TAB-seq analysis were performed as described in Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell.2012, 149, 1368-1380.
Genome_build: H. sapiens GRCh38
Supplementary_files_format_and_content: tab delimited text file
Supplementary_files_format_and_content: Column1: chromosome
Supplementary_files_format_and_content: Column2: cytosine position
Supplementary_files_format_and_content: Column3: strand
Supplementary_files_format_and_content: Column4: CNN (N = A, T, C, G)
Supplementary_files_format_and_content: Column5: methylated cytosines in this site
Supplementary_files_format_and_content: Column6: totally detected cytosines in this site
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| Submission date |
Jul 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE70519 |
DNA Cytosine Hydroxymethylation Levels Are Distinct Among Peripheral Blood Leukocytes |
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| Relations |
| BioSample |
SAMN03840163 |
| SRA |
SRX1081254 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1808330_Schmitz_allc_CD14_monocyte.tsv.gz |
793.8 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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