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| Status |
Public on Nov 03, 2015 |
| Title |
rad21_mut_input_rep2 |
| Sample type |
SRA |
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| Source name |
TF-1-RAD21 Q592* (Input #2)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: TF-1
cell type: Erythroleukemia Cell Line
transduction: TF-1-RAD21 Q592* (Input #2)
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| Treatment protocol |
TF-1 RAD21 Q592* and TF-1 RAD21 WT were induced with DOX for 6 days.
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| Growth protocol |
Cells from obtained from New York Blood Center and grown in HPGM Medium supplemented with cytokines
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
~100,000,000 cells were were crosslinked in 1% formaldehyde for 10 minutes at room temperature. Typically, 5 million cells were used for each ChIP experiment and chromatin was sheared on a Bioruptor (Diagenode) to an average of 200-400bp. The following antibodies were used for ChIP studies: SMC3 (clone: ab9263, Abcam), GATA2 (Clone: sc-9008, Santa Cruz Biotechnology) and RUNX1 (Clone: sc-365644, Santa Cruz Biotechnology)
After specific recovery of chromatin bound proteins via immunoprecipitation, samples were reverse crosslinked at 65°C overnight and DNA was purified for subsequent library preparation. ChIP-seq libraries were prepared according to the NEBNext protocol and sequenced using Illumina NextSeq.
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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 trimmed for adaptor sequence, then mapped to UCSC hg19 using Bowtie2, duplicate fragments were then removed using Picard. Peaks were called using MACS2.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab separated format, which includes the following columns: chromosome, start, stop, name, score, strand, signalValue, pValue, qValue, peak
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| Submission date |
Sep 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Chang |
| Organization name |
Stanford University
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| Street address |
269 Campus Dr. Stanford, CA
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE73207 |
ChIP-Seq on Cohesin mutant TF-1 Cell Line |
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| Relations |
| BioSample |
SAMN04096375 |
| SRA |
SRX1261515 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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