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| Status |
Public on Aug 28, 2024 |
| Title |
Lx891, SMARCA4, ChIP |
| Sample type |
SRA |
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| Source name |
PDX
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PDX
chip antibody: SMARCA4 #ab110641
cell type: SCLC
genotype: WT
treatment: none
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| Treatment protocol |
none
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| Growth protocol |
Flash frozen PDXs
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In house protocol (Active Motif)
In house protocol (Active Motif). ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara). Adapter sequences were not trimmed during demultiplexing
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing reads were trimmed with Trim Galore (v0.4.4). Reads were aligned to human assembly hg38 using bowtie2 v2.3.4 with the default settings
Enriched binding regions were called against the input using MACS2 with p value less than 0.001. The bigwig format for each sample was created using the BEDTools suite (https://bedtools.readthedocs.io) with the normalization factor 10 million
ChIP density profiles were created with deeptools v3.4.0
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak (except for Input sample)
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| Submission date |
Feb 22, 2024 |
| Last update date |
Aug 28, 2024 |
| Contact name |
Yingqian Ada Zhan |
| E-mail(s) |
zhany@mskcc.org
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| Organization name |
MSKCC
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| Department |
EPIGENETICS RESEARCH CENTER
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| Street address |
430 East 67th Street
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE256346 |
SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [ChIP-seq] |
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| Relations |
| BioSample |
SAMN40033999 |
| SRA |
SRX23698971 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8094132_LX891_BRG1_hs_i40.hg38.sorted.RmDup.10mNorm.bw |
233.6 Mb |
(ftp)(http) |
BW |
| GSM8094132_MACS2_vsMatchedInput_LX891_BRG1_hs_i40.hg38.sorted.RmDup_peaks.narrowPeak.gz |
1.7 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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