|
| Status |
Public on Mar 05, 2021 |
| Title |
SNJM09 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal dissection
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Intestine
treatment: 2X DSS
genotype/variation: nod2-/-
10x chemistry: V3
|
| Treatment protocol |
6dpf zebrafish larvae were single- treated with 0.075% Dextran Sodium Sulphate (DSS) or co-treated with DSS+ 10uM Bazedoxifene (BZA) in egg water for 24 hours, in a 37C incubator
|
| Growth protocol |
zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 24 hours of DSS/BZA treatment, zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly, cells were dissociated and digested using standard collagenase and DNAse protocols, and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads
Library construction was performed as per 10X Genomics v2 and v3 chemistry kits (see descriptors for applications).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
extracted cell-barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger
Genome_build: danRer11
|
| |
|
| Submission date |
Nov 03, 2020 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Mamta Giri |
| E-mail(s) |
mamta.giri@mssm.edu
|
| Organization name |
Mount Sinai hospital
|
| Department |
Institute of Personalized medicine
|
| Lab |
Cho lab
|
| Street address |
1470 madison ave
|
| City |
new york |
| State/province |
new york |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE150498 |
Myeloid-stromal subtypes reveal NOD2-mediated Crohn's and rescue pathways |
|
| Relations |
| BioSample |
SAMN16644510 |
| SRA |
SRX9426453 |
