|
| Status |
Public on Jan 20, 2015 |
| Title |
H3K4me3_kidney |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Homo sapiens |
| Characteristics |
body site: kidney
tissue type: kidney
Sex: male
developmental stage: adult
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Refer to extraction protocols described in the individual sample inputs for each average track
Refer to library contruction protocols described in the individual sample inputs for each average track
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
H3K4me3, in adult kidney (average of 2 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000
|
| Data processing |
For each tissue type, input tracks were selected based on the following criteria. Experiments from the Roadmap Epigenomics datasets were pooled, based on body site, tissue or cell type. Donor age was weighed and sample data from adults was segregated from those of fetal or neonatal. Donor sex was not taken into account, so some cases the track average is generated from pooled male and female tissues. Each input track was normalized by scaling all values to achieve a constant genome-wide summed signal. In the final track, the value in each 20 bp window is the arithmetic mean of the scaled input values.
Genome_build: GRCh37
Supplementary_files_format_and_content: WIG files generated by track averaging
|
| |
|
| Submission date |
Jan 16, 2015 |
| Last update date |
Jun 10, 2015 |
| Contact name |
Ian Fingerman |
| E-mail(s) |
ian.fingerman@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
NCBI Epigenomics
|
| Street address |
45 Center Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE65049 |
Track normalization and averaging of H3K4me3 ChIP-seq data across various cell and tissue types. |
| GSE65050 |
Track normalization and averaging of epigenetic features across various cell and tissue types derived from Roadmap Epigenomic datasets |
|
| Relations |
| Reanalysis of |
GSM621648 |
| Reanalysis of |
GSM773005 |
| BioSample |
SAMN03287061 |
| Named Annotation |
GSM1586397_H3K4me3_kidney.wig.gz |
| Named Annotation |
GSM1586397_H3K4me3_kidney_GRCh38.wig.gz |
