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| Status |
Public on Jan 01, 2014 |
| Title |
P13_rat_kidney_Hnf4a_ChIP |
| Sample type |
SRA |
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| Source name |
whole kidney
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: whole kidney
strain: Sprague Dawley
age: Postnatal day 13 (P13)
Sex: unsexed
chip antibody: Hnf4a (Santa Cruz, sc-8987)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly-isolated kidneys were immediately frozen in liquid nitrogen. To isolate the kidney cortex, a whole adult kidney was kept frozen within a ceramic mortar surrounded by dry ice while the outer ~1mm was shaved off with a razor. Whole kidneys or isolated cortex were thawed and minced in 1% formaldehyde in PBS on ice, followed by rotation for 15 minutes at room temperature. Fixation was quenched with glycine for 5 minutes. Fixed samples were then homogenized with a tissue grinder, washed twice with cold 0.5% IGEPAL CA-630 in PBS, and further disrupted using a type A glass dounce homogenizer. Nuclei were pelleted and sonicated on ice (three 5 minute cycles of 30 seconds on/30 seconds off). A mix of pre-blocked protein A/G beads was used to recover antibody-bound complexes, which were subsequently washed and eluted with SDS-containing buffer. The DNA was purified from the enriched and non-enriched samples by treatment with first RNAse and then Proteinase K, further de-crosslinking overnight at 65C, phenol extraction and ethanol precipitation.
The protocol provided with the ChIP-Seq DNA Sample Prep Kit (Illumina, IP-102-1001) was followed. 200-400bp fragments were selected for sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Default settings for the eland_extended algorithm in the Illumina Casava1.8 software were utilized for mapping.
All further analysis on aligned reds was performed using HOMERv3.13 software with default settings. Only one tag per base pair position was considered to remove clonal reads.
Genome_build: rn4
Supplementary_files_format_and_content: Peak files are in the default format generated by HOMERv3.13. Comments in the beginning of peak file contain various parameters of the analysis and column headers. First six columns contain a unique id, chromosome, start location, end location, strand and normalized tag count. Additional statistics are available in columns 7-15.
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| Submission date |
Sep 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gleb Martovetsky |
| E-mail(s) |
gmartove@ucsd.edu
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| Organization name |
UCSD
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE50815 |
Hepatocyte Nuclear Factors 4a and 1a (Hnf4a and Hnf1a) Regulate Kidney Developmental Expression of Drug-Metabolizing Enzymes and Drug Transporters |
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| Relations |
| BioSample |
SAMN02355991 |
| SRA |
SRX349431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1230268_P13_rat_kidney_Hnf4a_peaks.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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