NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1499402 Query DataSets for GSM1499402
Status Public on Oct 01, 2014
Title ASCL1_1755_1
Sample type SRA
 
Source name Tumor
Organism Homo sapiens
Characteristics classification: NE-NSCLC
ascl1 expression: ASCL1(+)
antibody: mouse anti-ASCL1,BD Pharmigen, cat# 556604
Treatment protocol No treatment performed
Growth protocol Cells were grown in RPMI 1640 supplemented with 10% FBS
Extracted molecule genomic DNA
Extraction protocol For full ChIP protocol see Borromeo et al. Development. 2014. For extraction, nuclei were liberated from cells by dounce homogenization in PBS and then fixed in 1% formaldehyde for 10 minutes at room. temperature. Fixation was terminated by adding glycine to a final concentration of 0.125M. Chromatin was sheared by using a Diagenode Bioruptor for 30 minutes on high power with 30s:30s on:off cycles. 100 μg chromatin was immunoprecipitated with 5 μg affinity-purified mouse anti-ASCL1 antibody (BD Biosciences) followed by anti-mouse Dyna beads (Invitrogen).
All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description H1755.wig
Data processing All samples were ran on a Illumina GAIIX and basecalls were performed using CASAVA
Mapping using bowtie with parameters "-S -n 2 -e 70 -l 20 -m 3 --time -p 12 --chunkmbs 512"
Replicates were mapped individually and pooled together. Multi-mapped reads were removed in order to reduce ambiguity
Peaks called with MACS1.4.0 with parameters "-f 'SAM' -g 'hs' --keep-dup=1 --nomodel -wig -S". Reads from H524 and H526 cell lines were pooled as control. The shift size for H1184 is 74, H128 86, H1755 89, H2107 89 and HCC4018 71.
Called peaks are screened by a fold change cutoff between 11 and 19 that is specific for each dataset and chosen by manual inspection.
A hierarchical clustering algorithm is used to identify consensus peaks in the ASCL1(+) cell lines
Genome_build: hg19
Supplementary_files_format_and_content: The wiggle files are generated with span=10bp by MACS1.4.0 using parameters "-wig -S"
 
Submission date Sep 08, 2014
Last update date May 15, 2019
Contact name Yang Xie
E-mail(s) yang.xie@utsouthwestern.edu
Organization name UT Southwestern Medical Center
Street address 5323 Harry Hines Boulevard
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL10999
Series (1)
GSE61197 ASCL1 is a lineage oncogene providing therapeutic targets for high-grade neuroendocrine lung cancers
Relations
BioSample SAMN03023763
SRA SRX695883

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap