|
| Status |
Public on May 10, 2016 |
| Title |
KP22_PD1 [ChIP-seq] |
| Sample type |
SRA |
| |
|
| Source name |
KP22_PD
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KP22
cell type: tumor-derived cell line
genotype/variation: Trp53-/-;Rb1-/-
nfib expression level: Nfib low
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: KP22_chip_peaks.bed, KP22_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 |
SAMN04965905 |
| SRA |
SRX1753577 |
