|
| Status |
Public on Feb 08, 2021 |
| Title |
SCI_input |
| Sample type |
SRA |
| |
|
| Source name |
Spinal cord dissociated cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Spinal cord dissociated cells
strain: C57BL/6
chip antibody: None
treatment: Thoracic (T9) moderate contusion injury for 7 days
|
| Treatment protocol |
The mice were conducted with moderate contusive injury with Infinite Horizons impactor (Precision Systems and Instrumentation) at T9 level of the exposed spinal cord (60 kdyn) and mentained for 7 days.
|
| Growth protocol |
Epicenter spinal cord tissue was harvested at respective time points and dissociated using a mixed digestion solution of 0.01% papain (LS003126, Worthington Biochemical,), 0.025% trypsin-EDTA (25200056, Gibco), 0.01% DNase I (LS002138, Worthington Biochemical) and 0.01% L-Cysteine (2430-100GM, Calbiochem) for 15 min at 37 ℃ with gentle shaking (70 rpm). The cells were separated from undigested pellet by triturating with wide-tipped, fire-polished glass Pasteur pipette for 8 times. After repeating 2 times of digestion and separation, cell suspension was filtered by 40 μm cell strainer and DMEM with 4% high BSA by centrifugation to obtain the single-cell suspension.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (IP) was performed using STAT3 antibody (sc-482x, Santa Cruz Biotechnology). IP DNA and input DNA were extracted using phenol:chloroform as described in our previous study
Libraries were constructed with the DNA SMART ChIP-Seq Kit (634865, Clontech) by following the manufacturer’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
All reads were mapped to the mm10 reference genome using Bowtie2, and only unique mapped reads were used for subsequent analysis.
STAT3 ChIP-Seq data were analyzed using the transcription factor pipeline from ENCODE. Peaks for STAT3 were called using SPP and filtered to exclude regions blacklisted by ENCODE, and peaks with FDR > 0.05 and fold-enrichment < 5.
Genome_build: Mm10
Supplementary_files_format_and_content: peak files
|
| |
|
| Submission date |
Jun 23, 2020 |
| Last update date |
Feb 08, 2021 |
| Contact name |
Haichao Wei |
| E-mail(s) |
haichaowei1985@gmail.com
|
| Phone |
3462479690
|
| Organization name |
UTHealth
|
| Street address |
1825 Pressler St., SRB 637.C
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE153085 |
Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis [ChIP-Seq] |
| GSE153721 |
Systematic analysis of purified astrocytes after spinal cord injury unveils lncRNA Zeb2os as a novel molecular target for astrogliosis |
|
| Relations |
| BioSample |
SAMN15352430 |
| SRA |
SRX8603494 |
