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Sample GSM1921005 Query DataSets for GSM1921005
Status Public on Nov 12, 2015
Title Ctrli_rep2_RNAseq
Sample type SRA
Source name human keratinoctyes with control siRNA
Organism Homo sapiens
Characteristics cell type: primary human neonatal keratinocytes
genotype/variation: control knockdown
Treatment protocol To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 1nM of siRNA for each target were nucleofected (Lonza to keratinocytes)
Growth protocol neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium
Extracted molecule total RNA
Extraction protocol For ATAC-seq, around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition. For ChIP-seq, a mininum of 2 million cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipiated with antibodies recognizing Brg1/Brm (J1), H3K27Ac, H3K27me3, H3K4me1, p300, pol II, and p63. For RNA-seq, RNA were extracted using RNeasy Plus (Qiagen), rRNA were removed using using Ribo-Zero rRNA Removal Kit (Illumina).
For ATAC-seq, sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit. For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina was used for library construction. For RNA-seq, NEBNext Ultra RNA Library Prep Kit was used for library construction.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.ATACseq peaks were called using the MACS2 algorithm,ChIPseq peaks were called using MACS14.
Number of Raw reads in each peak (or each gene for RNAseq) was calculated using in house generated script, and data matrix was normalized using R. For RNAseq, data normalization of significant analysis was performend using Deseq.
Genome_build: hg19
Supplementary_files_format_and_content: normalized read counts for each gene (RNA-seq) is in a text file.
Submission date Oct 28, 2015
Last update date Oct 11, 2022
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL16791
Series (1)
GSE67382 BAF controls genome accessibility
BioSample SAMN04223656
SRA SRX1396668

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

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