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Sample GSM2147635 Query DataSets for GSM2147635
Status Public on May 10, 2016
Title KP1-PD1 [ChIP-seq]
Sample type SRA
 
Source name KP1-PD1
Organism Mus musculus
Characteristics cell line: KP1
cell type: tumor-derived cell line
genotype/variation: Trp53-/-;Rb1-/-
nfib expression level: Nfib high
sample type: Nfib pulldown
chip antibody: Nfib antibody (Sigma, #HPA003956)
Treatment protocol Chromatin immunoprecipitation (ChIP) for Nfib was performed as described by the Farnham laboratory (http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf
Growth protocol All murine and human SCLC cell lines used in this study grow as floating spheres and were cultured in RPMI with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Nuclei were lysed and sonicated, genomic DNA was isolated with antibody and purified with RNAse and Proteinase K before being purified with QIAquick PCR purification kit (Qiagen).
Library was generated following Clontech low input with 1ng of ChIP product. 12 samples were pooled for Illumina Hiseq.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description processed data file: KP1_chip_peaks.bed, KP1_chip_FE.s20.w150.bw, merged_peaks.deseq_results.all.csv
Data processing Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag. Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30
peak calling was done for each cell lines, using the input reads as controls, using MACS2 (callpeak -t 16T_PD1.st.all.rmdup.bam 16T_PD2/16T_PD2.st.all.rmdup.bam -c 16T_input1.st.all.rmdup.bam 16T_input2.st.all.rmdup.bam -B --SPMR -g mm
fold enrichment over input was found using MACS2
differential counts were found using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: *bed files are the peak calls for each cell line
Supplementary_files_format_and_content: *bw files are bigwig files containing the fold enrichment of pull down above input per base pair, smoothed over 150 bp windows (20bp step size). Sample replicates are merged.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)
 
Submission date May 09, 2016
Last update date May 15, 2019
Contact name William Greenleaf
E-mail(s) wjg@stanford.edu
Organization name Stanford University
Street address 279 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL17021
Series (2)
GSE81256 Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility [ChIP-seq]
GSE81258 Nfib promotes Metastasis through a Widespread Increase in Chromatin Accessibility
Relations
BioSample SAMN04965901
SRA SRX1753573

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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