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| Status |
Public on Oct 28, 2019 |
| Title |
SOX21_Input |
| Sample type |
SRA |
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| Source name |
Neural epithelial cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human ES-derived neural epithelial cells
genotype/variation: wild type
time point: Day 5
chip antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neural epithelial cell lysates were clarified from sonicated nuclei and SOX21 complexes or b-catenin-DNA complexes were immunoprecipitated with SOX21 antibody (R&D AF3538) or b-catenin antibody (BD Biosciences, 610154), respectively. Protein A and G Magnetic Dynabeads were used to capture antibody-bound protein-DNA complexes.
The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding “A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq X-ten platforms.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to hg19 genome assembly by bowtie2 (v2.3.2) by default parameters.
Peaks were called using MACS2 (v2.1.0) with setting: fdr-q (0.01).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files were generated by MACS2, the score represents number of bp fall into the single base pair region.
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| Submission date |
Feb 12, 2018 |
| Last update date |
Oct 28, 2019 |
| Contact name |
Zhuoqing Fang |
| Organization name |
Stanford
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE110505 |
Genome-wide map of SOX21 occupancy in human embryonic stem cell-derived neural progenitor cells [ChIP-seq] |
| GSE110506 |
SOX21 ensures rostral forebrain identity by suppression of WNT8B during neural regionalization of human embryonic stem cells |
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| Relations |
| BioSample |
SAMN08522246 |
| SRA |
SRX3686696 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2994928_SOX21_control_lambda.sorted.bw |
357.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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