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Sample GSM7680917 Query DataSets for GSM7680917
Status Public on Dec 31, 2023
Title kidney, PND7, HNF1b ChIP
Sample type SRA
Source name kidney
Organism Mus musculus
Characteristics tissue: kidney
age: PND7
chip antibody: HNF1b (Invitrogen #720259)
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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
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)
Submission date Aug 04, 2023
Last update date Dec 31, 2023
Contact name Hong Soon Kang
Phone 984-287-3921
Organization name NIH/NIEHS
Department IIDL
Lab Cell Biology Group
Street address 111 T.W. Alexander Dr.
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL19057
Series (2)
GSE240072 Identification of GLIS3 and HNF1b target genes in kidney
GSE240074 GLIS3
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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