Transcriptomic analysis of gene expression in the nucleus accumbens somatostatin interneurons of male 8�12-week-old Sst-Cre mice or Sst-Cre x TLG498 (SST-TLG498) mice following repeated cocaine intake. Expression was measured via RNA-seq. Values presented are p-values. Data taken from Supplementary Data 1. Data can be accessed at GEO with accession number: GSE116484.A7
Authors:
Efrain A Ribeiro, Marine Salery, Joseph R Scarpa, Erin S Calipari, Peter J Hamilton, Stacy M Ku, Hope Kronman, Immanuel Purushothaman, Barbara Juarez, Mitra Heshmati, Marie Doyle, Casey Lardner, Dominicka Burek, Ana Strat, Stephen Pirpinias, Ezekiell Mouzon, Ming-Hu Han, Rachael L Neve, Rosemary C Bagot, Andrew Kasarskis, Ja Wook Koo, Eric J Nestler
Genes down-regulated in various immune cells cells present in blood from MIS-C patients compared to
healthy child donors. Genes from each tab (NaïveCD8, MemoryCD8, NKcell, NaïveCD4, MemoryCD4, Treg, NaïveB, MemoryB, Monocytes, Neutrophils, cDCs, pDCs) of s3-table-S6-mmc3.xlxs were assigned a category based on their cell type (indicated by the tab name) and whether they were up or down regulated (indicated by a positive or negative value in the "avg_logFC" column, e.g. either "NaïveCD8 up" or "NaïveCD8 down" for markers present in the "NaïveCD8" tab. Note that the cut-off for differentially expressed genes was greater than absolute value of 0.5, rather than greater than absolute value of 1. Genes which exhibited decreased gene expression in all cell types in which they exhibited a change in expression level were included in this set. 34 genes which had increased expression in some cell types and decreased expression in other cell types were excluded (HGNC:1130, HGNC:6727, HGNC:10488, HGNC:4938,
HGNC:4940, HGNC:4948, HGNC:4953, HGNC:10630, HGNC:3068, HGNC:3443, HGNC:6204, HGNC:1711, HGNC:347, HGNC:533, HGNC:537, HGNC:14130, HGNC:7082, HGNC:2771, HGNC:2479, HGNC:30239, HGNC:3288, HGNC:3796, HGNC:4638, HGNC:6153, HGNC:6175, HGNC:6408, HGNC:6860, HGNC:7406, HGNC:13880, HGNC:672, HGNC:10368, HGNC:11554, HGNC:2464, HGNC:17521). The text strings "3-Mar" and "6-Sep" present in one or more Marker columns were converted to "MAR3" and "SEPT6" respectively. Genes were entered as HGNC IDs. 13 Markers could not be mapped at HGNC (43893, 44075, AC004865.2, AC007952.4, AC020636.1, AC020656.1, AC119396.1, AC243960.1, AC245014.3, AL360270.1, AL445524.1). These IDs were not present in GeneWeaver: HGNC:13378 HGNC:6463.
Authors:
Anjali Ramaswamy, Nina N Brodsky, Tomokazu S Sumida, Michela Comi, Hiromitsu Asashima, Kenneth B Hoehn, Ningshan Li, Yunqing Liu, Aagam Shah, Neal G Ravindra, Jason Bishai, Alamzeb Khan, William Lau, Brian Sellers, Neha Bansal, Pamela Guerrerio, Avraham Unterman, Victoria Habet, Andrew J Rice, Jason Catanzaro, Harsha Chandnani, Merrick Lopez, Naftali Kaminski, Charles S Dela Cruz, John S Tsang, Zuoheng Wang, Xiting Yan, Steven H Kleinstein, David van Dijk, Richard W Pierce, David A Hafler, Carrie L Lucas
Hippocampus Gene Expression Correlates for COCA_TIME_COND_CHG measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The COCA_TIME_COND_CHG measures Cocaine CPP - difference in time spent relative to baseline drug exposure under the domain Cocaine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
Hippocampus Gene Expression Correlates for URINE measured in BXD RI Males obtained using GeneNetwork Hippocampus Consortium M430v2 (Jun06) RMA. The URINE measures Novel Open Field Number of urinations under the domain Morphine. The correlates were thresholded at a p-value of less than 0.001.
Authors:
Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ
cocaine related behavior 6 (Cocrb6) spans 68.726231 - 118.726231 Mbp (NCBI Build 37) on Chr 5. Obtained from MGI (http://www.informatics.jax.org) by searching for QTLs containing the keyword .
QTL for cocaine related behavior on Chr5 at D5Mit7 (103.64 Mbp , Build 37)
Description:
cocaine related behavior spans 78.64 - 128.64 Mbp (NCBI Build 37) on Chr5. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for differences in cocaine responsiveness on Chr5 at Cyp3 (108.78 Mbp , Build 37)
Description:
differences in cocaine responsiveness spans 83.78 - 133.78 Mbp (NCBI Build 37) on Chr5. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for METH responses for chewing on Chr5 at D5Mit10 (111.96 Mbp , Build 37)
Description:
METH responses for chewing spans 86.96 - 136.96 Mbp (NCBI Build 37) on Chr5. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
QTL for METH responses for climbing on Chr5 at D5Byu4 (129.78 Mbp , Build 37)
Description:
METH responses for climbing spans 104.78 - 154.78 Mbp (NCBI Build 37) on Chr5. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
None - Basal gene expression profiles between C57BL/6J, DBA/2J, 129P3/J, and SWR/J strains DNA microarray Change in gene expression Two-way analysis of variance (ANOVA). 3,457 probe sets (corresponded to 2,870 different transcripts) with significant inter-strain differences (differ by at least 1.2-fold) - False discovery rate [FDR] < 1%, , rank > 3. Such a large disparity in the mouse striatal transcriptome was estimated by comparing nine array replicates prepared per strain from all of the treatment groups. More than half of the identified probe sets exhibited markedly significant results (1,735 with rank > 7). (NIF Method ID 84.1)
Authors:
Korostynski M, Piechota M, Kaminska D, Solecki W, Przewlocki R
Genes associated with Homo sapiens that interact with the MeSH term 'Arsenic' (D001151). Incorporates data from 87 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'butyraldehyde' (C018475). Incorporates data from 7 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Lasalocid' (D007832). Incorporates data from 185 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'Nickel' (D009532). Incorporates data from 166 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Chloris chloris that interact with the MeSH term 'lipopolysaccharide, E coli O55-B5' (C482199). Incorporates data from 29 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
Genes associated with Homo sapiens that interact with the MeSH term 'nickel chloride' (C022838). Incorporates data from 7 publications curated by the Comparative Toxicogenomics Database (CTD). ODE Gene scores represent number of supporting publications per gene.
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