Supplementary Table 2. Overall results of WGCNA combined with differential expression between people with a history of alcohol use and controls BLA: basolateral amygdala
Authors:
Ponomarev I, Wang S, Zhang L, Harris RA, Mayfield RD
Differential gene expression of RNA-Seq data for alcohol dependence. Gene Symbol and p-value (unadjusted). Samples were from twenty-three hippocampi from eight people with a history of alcohol user, seven people with a history of cocaine uses, and eight matched control subjects.
545 genes differentially expressed in human subjects in the opioid abuse cohort, some of which are overlapping with genes previously shown to be differentially expressed in relation to cocaine use. The opioid use and control cohorts were "matched in terms of gender, race, age, brain pH, and RIN [RNA integrity number]." Post-mortem ventral midbrain specimens were collected and analyzed via RNA-seq. The full raw sequencing data can be found at NCBI Sequence Read Archive with accession number PRJNA492904. Data taken from Supplementary Table S2. Values presented are p-adjusted values.
Authors:
Manal H Saad, Matthew Rumschlag, Michael H Guerra, Candace L Savonen, Alaina M Jaster, Philip D Olson, Adnan Alazizi, Francesca Luca, Roger Pique-Regi, Carl J Schmidt, Michael J Bannon
170 differentially expressed in the nucleus accumbens of Long-Evans rats reared in limited bedding and nesting (LBN) conditions. The effect of LBN on morhpine self-administration was investigated. Bilateral NAc specimens were analyzed for gene expression using RNA-seq. Data available at GEO (accession number GSE160495). Data presented are p-values.
Authors:
Evelyn Ordoñes Sanchez, Charlotte C Bavley, Andre U Deutschmann, Rachel Carpenter, Drew R Peterson, Reza Karbalaei, James Flowers, Charleanne M Rogers, Miranda G Langrehr, Cory S Ardekani, Sydney T Famularo, Angela R Bongiovanni, Melissa C Knouse, Stan B Floresco, Lisa A Briand, Mathieu E Wimmer, Debra A Bangasser
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
534 differentially expressed genes in the prefrontal cortex of adult male C57BL/6J mice within 7 d of withdrawal from chronic cocaine. Gene expression was evaluated using RNA-seq, and validation of DEGs was performed using RT-qPCR. Data taken from Supplemental Table S4. Values presented are log2 fold change. Data can be accessed from GEO with accession # GSE89572.
Authors:
Mingzhen Li, Peng Xu, Yanhua Xu, Huajing Teng, Weiping Tian, Quansheng Du, Mei Zhao
Genes that have regions with differential 5-hydroxymethylcytosine (5hmC) levels in response to cocaine in adult (8-10 week) male C57BL/6J mice. 5hmC levels were measured via 5hmC-seq. Data taken from Supplementary Table 2. Values presented are p-values. Data available at GEO with accession number GSE63749.
This set describes genes whose transcription is upregulated in the whole blood of severe COVID-19 patients versus healthy donors. Genes listed in table S2 were entered using ENSEMBL Gene identifiers. Values are the reported log2 fold-change.
Authors:
Anna C Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna D Gemünd, Nikoletta Rovina, Shobhit Agrawal, Kilian Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon Rieke, Valentina Talevi, Dirk Skowasch, N Ahmad Aziz, Peter Pickkers, Frank L van de Veerdonk, Mihai G Netea, Joachim L Schultze, Matthijs Kox, Monique M B Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J Giamarellos-Bourboulis, Thomas Ulas,
Differentially expressed genes in male Sprague-Dawley rats (300-375 g or 250-300 g) following cocaine administration. Some animals expressed the H3.3 Q5A vector, which led to down-regulation of histone H3 glutamine 5 dopaminylation (H3Q5dop), which is involved in midbrain plasticity in response to cocaine. Gene expression was evaluated via RNA-seq. Data taken from Supplemental Table S3 (associated with Fig 2. E, G, and I). Values presented are p-values. Data available at GEO with accession number GSE124055.
Authors:
Ashley E Lepack, Craig T Werner, Andrew F Stewart, Sasha L Fulton, Ping Zhong, Lorna A Farrelly, Alexander C W Smith, Aarthi Ramakrishnan, Yang Lyu, Ryan M Bastle, Jennifer A Martin, Swarup Mitra, Richard M O'Connor, Zi-Jun Wang, Henrik Molina, Gustavo Turecki, Li Shen, Zhen Yan, Erin S Calipari, David M Dietz, Paul J Kenny, Ian Maze
Differentially expressed genes in male Sprague-Dawley rats (300-375 g or 250-300 g) following cocaine administration. Some animals expressed the H3.3 Q5A vector, which led to down-regulation of histone H3 glutamine 5 dopaminylation (H3Q5dop), which is involved in midbrain plasticity in response to cocaine. Gene expression was evaluated via RNA-seq. Data taken from Supplemental Table S4 (associated with Fig 2. E, G, and I). Values presented are p-values. Data available at GEO with accession number GSE124055.
Authors:
Ashley E Lepack, Craig T Werner, Andrew F Stewart, Sasha L Fulton, Ping Zhong, Lorna A Farrelly, Alexander C W Smith, Aarthi Ramakrishnan, Yang Lyu, Ryan M Bastle, Jennifer A Martin, Swarup Mitra, Richard M O'Connor, Zi-Jun Wang, Henrik Molina, Gustavo Turecki, Li Shen, Zhen Yan, Erin S Calipari, David M Dietz, Paul J Kenny, Ian Maze
The total transcriptome including genes that are differentially expressed in cocaine addicts compared to control subjects. Post-mortem brain samples were collected from the dorsolateral prefrontal cortex (dlPFC) of the cocaine addict group and the control group. To assess gene expression, RNA-seq was performed. Data taken from Supplementary Table 2. Values presented are k.diff values. Data available from GEO with accession number GSE99349."
Authors:
Efrain A Ribeiro, Joseph R Scarpa, Susanna P Garamszegi, Andrew Kasarskis, Deborah C Mash, Eric J Nestler
Genes that are upregulated in adult male C57BL/6J mice given chronic cocaine vs. chronic saline. Tissue was collected from the ventral tegmental area (VTA) of the brain. Gene expression was evaluated via RNA-seq, and differential gene expression was determined via the Bayesian-regulated t-test (BayT). Values presented are p-values. Data taken from Supplementary Table 1. Data available from GEO with accession number GSE155313."""
Authors:
Rianne R Campbell, Siwei Chen, Joy H Beardwood, Alberto J López, Lilyana V Pham, Ashley M Keiser, Jessica E Childs, Dina P Matheos, Vivek Swarup, Pierre Baldi, Marcelo A Wood
Genes that are differentially expressed in adult male C57BL/6J mice given cocaine conditioning vs. saline conditioning. Tissue was collected from the ventral tegmental area (VTA) of the brain. Gene expression was evaluated via RNA-seq, and differential gene expression was determined via linear regression (LR). Values presented are p-values. Data taken from Supplementary Table 1. Data available from GEO with accession number GSE155313."""
Authors:
Rianne R Campbell, Siwei Chen, Joy H Beardwood, Alberto J López, Lilyana V Pham, Ashley M Keiser, Jessica E Childs, Dina P Matheos, Vivek Swarup, Pierre Baldi, Marcelo A Wood
Differentially expressed geens in the central amygdala (CeA) of male Sprague-Dawley rats (300-350 g prior to surgery, 325-375 g at start of self-administration) on day 2 following methamphetamine withdrawal. Gene Expression was evaluated via RNA-seq. Data taken from Supplementary Table S2. Values presented are adjusted p-values. Data available from GEO with accession number GSE111243."
Authors:
Hannah M Cates, Xuan Li, Immanuel Purushothaman, Pamela J Kennedy, Li Shen, Yavin Shaham, Eric J Nestler
Differentially expressed geens in the central amygdala (CeA) of male Sprague-Dawley rats (300-350 g prior to surgery, 325-375 g at start of self-administration) on day 35 following methamphetamine withdrawal. Gene Expression was evaluated via RNA-seq. Data taken from Supplementary Table S2. Values presented are adjusted p-values. Data available from GEO with accession number GSE111243."
Authors:
Hannah M Cates, Xuan Li, Immanuel Purushothaman, Pamela J Kennedy, Li Shen, Yavin Shaham, Eric J Nestler
RNA-Seq was performed to discover gene expression
changes in the hippocampus of rats in withdrawal from
chronic alcohol exposure. RNA-Seq was performed on the
hippocampus from control, ethanol (no withdrawal), and
ethanol plus withdrawal (24 h) groups. The largest number
of differentially expressed (DE) genes were in the
control vs. withdrawal comparison (925 out of 18,118
detected; q < 0.1)
Authors:
Wei-Yang Chen, Hu Chen, Kana Hamada, Eleonora Gatta, Ying Chen, Huaibo Zhang, Jenny Drnevich, Harish R Krishnan, Mark Maienschein-Cline, Dennis R Grayson, Subhash C Pandey, Amy W Lasek
Striatum Gene Expression Correlates for ACTI05_ETHA measured in BXD RI Females obtained using GeneNetwork Striatum M430V2 (Apr05) RMA. The ACTI05_ETHA measures Distance traveled (cm) during the first five minutes after ethanol under the domain Ethanol. 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
A list of genes whose transcript abundance in the PFC changed significantly 4 hours after an acute dose of ethanol (1.8 g/kg). This list was generated using Fisher's Combined Probability test to analyze saline vs ethanol S-scores across B6 and D2 inbred strains (n=3) and 27 BXD RI lines (n=1). Statistical significance was determined using 1,000 permutations of S-score data and selecting for probe-sets with q-values < 0.05. Aaron Wolen 5-26-10.
Authors:
Wolen AR, Phillips CA, Langston MA, Putman AH, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF
These genes are a 1 class SAM significant (1% FDR) in nucleus accumbens (core + shell) for saline treated ("basal") control vs. Fyn KO mice. The list was filtered for an average Sscore >2.0 or <-2.0. Data from Farris and Miles, PLoS One, 2013.
from Lewohl et al., 2000; from case group one (identical to case group used in PCR-differential display experiments reported by Fan et al., 1999); includes three uncomplicated alcoholics, one alcoholic with cirrhosis, and one alcoholic with concomitant Wernicke encephalopathy
Authors:
Lewohl JM, Wang L, Miles MF, Zhang L, Dodd PR, Harris RA
QTL for high-dose ethanol actions on Chr14 at D14Mit1 (5.65 Mbp , Build 37)
Description:
high-dose ethanol actions spans 0.00 - 30.65 Mbp (NCBI Build 37) on Chr14. This interval was obtained by using an interval width of 25 Mbp around the peak marker (Build 37, MGI, http://informatics.jax.org).
Authors:
Erwin VG, Markel PD, Johnson TE, Gehle VM, Jones BC
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