|
| Status |
Public on Mar 15, 2018 |
| Title |
BA40_1503_input |
| Sample type |
SRA |
| |
|
| Source name |
Brodmann area 40
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Frozen brain tissue
line: --
Sex: M
age: 60
|
| Treatment protocol |
6μg of rabbit αCLOCK (ab3517, Abcam, lot #GR222742-4) was used for CLOCK ChIP and 6μg of normal rabbit αIgG (#2729, Cell Signaling) was used as a negative control. Please refer to manuscript for detailed ChIP protocol, adapted from Koike et. al. 2012 (PMID: 22936566).
|
| Growth protocol |
Differentiated human neural progenitor cells and adult human BA10 and BA40 neocortex was used
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using Qiagen Qiaquick PCR purification kit, assayed for quality by Bioanalyzer (Agilent), and quantified using a Qubit Fluorometer according to the manufacturer’s instructions.
Libraries were prepared using previously published methods (PMID: 25662462)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Single-end reads were aligned in a staged manner. Reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC)
ChIP-seq data were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to a reference sequence comprised of mitochondrial DNA (hg38 from UCSC).
ChIP-seq was analyzed using MACS2 with following parameter "--bw 300 --tsize 50 --nomodel --keep-dup all --extsize 300 -q 0.05 –nolambda".
ChIP-seq was analyzed using MACS2 with default parameter and "--nolambda --shift 75".
bed-files including coordinates of the detected peaks from ChIP-Seq.
Genome_build: Human hg38
|
| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Genevieve Konopka |
| E-mail(s) |
gena@alum.mit.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Neuroscience
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE96659 |
Novel transcriptional networks regulated by CLOCK in human neurons |
|
| Relations |
| BioSample |
SAMN06604891 |
| SRA |
SRX2642656 |
