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| Status |
Public on Dec 31, 2023 |
| Title |
kidney, PND7, HNF1b ChIP |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
age: PND7
chip antibody: HNF1b (Invitrogen #720259)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Immunoprecipitated chromatin was washed and ChIPed-DNA was eluted, reverse cross-linked, and DNA fragments purified using PCR purification kit form Qiagen.
NEXTflex DNA-Seq kit from PerkinElmer was used.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were filtered to remove any with mean base quality score < 20.
Adapters were removed by Cutadapt v1.12 and filtered to retain only those with length at least 30nt.
Filtered and trimmed reads were mapped via Bowtie v1.2 with parameter "-m 1".
Alignment files were combined via MergeSamFiles.jar (Picard tools v1.110) for samples with multiple sequencing runs.
Duplicate mapped reads were removed via MarkDuplicates.jar (Picard tools v1.110) with flag "REMOVE_DUPLICATES=TRUE".
Peak calls were made by HOMER (v4.10.3) with parameters “-style factor” then re-sized to 300bp centered on the called peak midpoints.
For visualization purposes, uniquely-mapped non-duplicate reads were extended to the 200bp estimated fragment size via BEDTools v2.29.2 "slop -s -r 125 -l 0", converted to bedGraph via BEDTools v2.29.2 "genomecov -bg", scaled to 10 million fragments per sample, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: peak calls (BED)
Supplementary files format and content: normalized depth tracks (bigWig)
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| Submission date |
Aug 04, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Hong Soon Kang |
| E-mail(s) |
kang1@niehs.nih.gov
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| Phone |
984-287-3921
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| Organization name |
NIH/NIEHS
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| Department |
IIDL
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| Lab |
Cell Biology Group
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| Street address |
111 T.W. Alexander Dr.
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
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| Relations |
| BioSample |
SAMN36839269 |
| SRA |
SRX21250304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7680917_HNF1b.peaks.bed.gz |
120.3 Kb |
(ftp)(http) |
BED |
| GSM7680917_HNF1b_IP.normalized_depth.bigWig |
296.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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