run_metadata: 59267
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 59267 | SRR11785628 | SRX8337988 | SRS6656487 | SRP261473 | PRJNA632595 | Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways | GSE150498 | Transcriptome Analysis | Crohn's disease CD is a chronic inflammatory intestinal disease often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature and propose new precision therapeutic approaches involving gp130 blockade for select CD patients to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish | pubmed:33789339 | SNJCZ2 | GSM4551416 | source name:Intestinal dissection|tissue:Intestine|status:DSS treated | SNJCZ2 | FASTQ were demultiplexed using Cell Ranger v2.0 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 | Intestinal dissection | 6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours in a 37C incubator | post 24 hours of DSS treatment zebrafish larval intestines were dissected from untreated and DSS 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 chemistry kit. 10X chromium | zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed | tissue:Intestine|status:DSS treated | GSM4551416 | GSM4551416: SNJCZ2; Danio rerio; RNA Seq | GSM4551416 | 1 | post 24 hours of DSS treatment zebrafish larval intestines were dissected from untreated and DSS 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 chemistry kit. 10X chromium | GEO Accession:GSM4551416 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP261473 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=SNJCZ2 S2 L004 I1 001.fastq.gz read2PairFiles=SNJCZ2 S2 L004 R1 001.fastq.gz read3PairFiles=SNJCZ2 S2 L004 R2 001.fastq.gz | SNJCZ2_S2_L004_R2_001.fastq.gz SNJCZ2_S2_L004_R1_001.fastq.gz SNJCZ2_S2_L004_I1_001.fastq.gz | fastq fastq fastq | 1502275233.0 | 16879497.0 | GSM4551416 r4 | 0:8 1:26 2:55 | A:418327578;C:359123038;G:361317639;T:363357288;N:149690 | 8 | 26 | 55 | 418327578 | 359123038 | 361317639 | 363357288 | 149690 | SRX8337988 | SRS6656487 | SRA1075199 | GEO | Cho lab, Institute of Personalized medicine, Mount Sinai hospital | 1 | 0.95529 | 0.06072 | 0.87523 | 0.65804 | 55 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-05-13 | Larval | Larval | Gut | Digestive System |