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| Status |
Public on May 08, 2024 |
| Title |
ChIP-seq of TCF7L2 in human GPC |
| Sample type |
SRA |
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| Source name |
GPC induced from ESC
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| Organism |
Homo sapiens |
| Characteristics |
antibody: TCF7L2
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| Growth protocol |
GPCs were generated from human embryonic stem cells (ESCs) using our previously described protocol (Wang et al., 2013, Windrem et al., 2017).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was carried out following Pedersen et al, 2016 with minor modifications. Briefly, freshly sorted GPCs were cross-linked using 37°C pre-heated medium/1% formaldehyde. Fixation was carried out at room temperature for 10 minutes, and reaction was terminated with 0.125 M glycine, followed by two PBS washes. The cross‐linked cells were lysed in SDS lysis buffer containing protease inhibitors (PMSF, Aprotinin and Leupeptin). Nuclei were then pelleted and resuspended in ice-cold IP Buffer (2:1 SDS:Triton dilution buffer). DNA were sonicated using a Diagenode biorupter pico (30 min ON, 30 min OFF for 5 cycles) to an average length of 200–700 nucleotides. DNA was subsequently incubated overnight with the appropriate antibodies (OLIG2 or TCF7L2), and immunoprecipitated the next day with Protein-G. Three washes in low‐salt wash buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 2 mM EDTA, 20 mM Tris–HCl pH 8), and three washes in high‐salt wash buffer (500 mM NaCl, 1% Triton X‐100, 0.1% SDS, 2 mM EDTA, 20 mM Tris–HCl pH 8) were carried out, followed by de-crosslinking at 65°C for 8-16 hours with SDS buffer (1% SDS, 0.1 M NaHCO3). DNA was purified using the Qiagen PCR Purification kit. Libraries were prepared with the NEBNext Ultra II DNA library preparation kit (NEB#7645) following manufacturer’s protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ChIP-seq
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| Data processing |
The sequencing reads were pre-processed by trimming off adapter and low-quality bases using fastp (Chen et al., 2018). Reads were then aligned to the human genome assembly GRCh38 or the rat genome assembly Rnor6.0 using bowtie2 (Flicek et al., 2014; Langmead and Salzberg, 2012). Following alignment, reads with low alignment quality were filtered using samtools (Li et al., 2009). Aligned reads were then assessed for enrichment in specific genomic regions, where peaks were called with MACS2 (Zhang et al., 2008).
Genome_build: GRCh38
Supplementary_files_format_and_content: bw
Supplementary_files_format_and_content: .narrowPeak
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| Submission date |
Nov 10, 2021 |
| Last update date |
May 08, 2024 |
| Contact name |
Steven Goldman |
| Organization name |
University of Rochester Medical Center
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| Department |
Center for Translational Neuromedicine
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| Lab |
Goldman Lab
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| Street address |
601 Elmwood Ave
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE188559 |
Shared patterns of glial transcriptional dysregulation link Huntington's disease and schizophrenia |
| GSE188561 |
Shared patterns of glial transcriptional dysregulation link Huntington's disease and schizophrenia |
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| Relations |
| BioSample |
SAMN23036188 |
| SRA |
SRX13097292 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5685576_TCF7L2_peaks.narrowPeak.gz |
23.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM5685576_TCF7L2_treat_pileup.bw |
48.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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