|
| Status |
Public on Jul 12, 2023 |
| Title |
WT_IP_rep_1a |
| Sample type |
SRA |
| |
|
| Source name |
BM Neutrophils
|
| Organism |
Mus musculus |
| Characteristics |
isoloation markers: CD11b+SiglecF-F4/80-Ly6G+
cell type source: BM Neutrophils
strain: C57BL/6J
developmental stage: Adult (4-6 weeks old)
tissue: Bone Marrow
genotype: Control (Runx1f/f)
antibody: 9D5 dsRNA rabbit IgG mAb(Ab00458-23.0)
|
| Treatment protocol |
Cells were harvested and were sorted on the same day as harvest
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Protein G Dynabeads and Protein A Dynabeads were washed and resuspended in NET-2 buffer. 9D5 dsRNA rabbit IgG mAb was bound to the beads for 1-2 hours. Cells were lysed in cytosolic lysis buffer. The cell lysate was centrifuged at 980 x g for 3 min at 4℃ (X3). The cytosolic supernatant was spun at 17,000 x g for 10 min. For IP, lysate was diluted to 1:4 with NET-2-TurboDNase buffer. 95D-Dynabeads were added to the lysate and end-to-end rotated for 2 hr at 4 °C. Following magnetic separation, beads were washed with high salt washing buffer and then NET-2 buffer. 95D-bound dsRNA was extracted with Trizol reagent and purified using Direct-zol™ RNA Miniprep Kit (Zymo Research). RNA samples were ribo-depleted with Ribominus™ Eukaryote v2 kit (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Libraries were sequenced on Illumina HiSeq 2500 sequencer in paired-end mode with read length of 75bp.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA pulled down from neutrophils with dsRNA-specific 9D5 dsRNA rabbit IgG mAb
DESeq2_TE_subFamily.txt
|
| Data processing |
Raw dsRNA-seq sequencing data (.bcl files) was converted into Fastq files and de-multiplexed using Bcl2Fastq v2.20 software. The data in fastq file format was processed with the toolkit SQuIRE. The raw reads were aligned to the mm10 reference genome and TEs were annotated using RepeatMasker. The SQuIRE call module was used to perform differential expression analysis of genes, or TE by family, or TE by sub-family between Control and Runx1ΔGMP cells.
Assembly: mm10
Supplementary files format and content: Txt file for RNA-seq samples is an output of the SQuIRE call module
|
| |
|
| Submission date |
Dec 20, 2022 |
| Last update date |
Jul 12, 2023 |
| Contact name |
Alexandra Zezulin |
| E-mail(s) |
Alexandra.zezulin@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Lab |
Speck Lab
|
| Street address |
421 Curie Blvd 544 BRB II/III
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE221426 |
Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils [dsRNA-seq] |
| GSE221427 |
Epigenetic and transcriptomic alterations in key inflammatory pathways are established in RUNX1 deficient hematopoietic progenitors and are propagated to neutrophils. |
|
| Relations |
| BioSample |
SAMN32331234 |
| SRA |
SRX18787901 |
