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| Status |
Public on Nov 17, 2020 |
| Title |
H3K4me3-AB2-hNSC-H7-WT |
| Sample type |
SRA |
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| Source name |
Cell Line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Neural Stem Cells H7
chip antibody: H3K4me3(Diagenode,C15410003-50)
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| Treatment protocol |
On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation (STEMCELL Technologies, #08500) started from day 11 to day 16. On day 17, cells were treated with Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium (STEMCELL Technologies, #08510) till days 22–24.
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| Growth protocol |
H7/WA07 (WiCell) and H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies, #85850) at 37°C and 5% CO2. For neural differentiation, ES cells were seeded onto AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested in PBS. Cytoplasmic fractions were extracted using buffer A with 1× protease inhibitors and 1 mM DTT. Nuclear pellets were cross-linked by 1.1% formaldehyde in buffer B with 1× protease inhibitors and 1 mM DTT; washed; and lysed in lysis buffer 3 with 1× protease inhibitors, 1 mM DTT, and 1 mM PMSF. The fixed and lysed nuclear extract was sonicated with Bioruptor® Pico (Diagenode) 10 times for 15 s each, with 45-s intervals. Chromatin was added to Dynabeads™ (Life Technologies) prebound with 4 μg of antibodies. For UTX chromatin immunoprecipitation (ChIP), chromatin and antibodies were incubated overnight, followed by 4 h of recapture with Dynabeads™ the next day.
After incubation, beads were washed and immunoprecipitates were eluted. DNA from eluates was recovered by the GeneJET FFPE DNA purification kit (ThermoFisher Scientific, #K0882).Libraries are prepared and sequenced at the St. Jude Hartwell Center.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
H3K4me3-AB2-hNSC-H7-WT.hg19.narrowPeak.gz
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| Data processing |
Basecalls performed using CASAVA
Single-end reads of 50bp were mapped human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with Picard(version 2.6.0-SNAPSHOT) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. For peak calling of H3K27ac, H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are reproducible between biological replicates.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: Peaks
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| Submission date |
Feb 28, 2019 |
| Last update date |
Nov 17, 2020 |
| Contact name |
Beisi Xu |
| E-mail(s) |
[email protected]
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| Organization name |
St Jude Children's Research Hosipital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE127512 |
UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells[ChIP-seq] |
| GSE127515 |
UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells |
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| Relations |
| BioSample |
SAMN11037919 |
| SRA |
SRX5444547 |
| 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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