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Title: Transcriptomic Profiles of Sepsis in the Human Brain Open Access Deposited

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Methodology
  • RNA was isolated from human post-mortem parietal cortex tissue samples. RNAseq was performed by the University of Michigan Advanced Genomics core, data was QC'd and initially analysed by the University of Michigan Bioinformatics core using standardized methods. The secondary analyses was performed using R.
Description
  • This study was conducted to detect and analyze modules, or clusters of genes, associated with sepsis, using RNAseq data obtained from 12 participants who died of sepsis and 12 participants who died of non-infectious critical illness while hospitalized. This deposit contains the input data and parameters needed to reproduce the weighted gene co-expression network analysis (WGCNA) and gene enrichment analysis performed on this data. This analysis requires the R packages "WGCNA" version 1.68 and "DESeq2" version 1.22.2 available for download from bioconductor ( http://bioconductor.org). The external bioinformatics tool DAVID version 6.8 ( https://david.ncifcrf.gov/) was used as an additional gene enrichment analysis. Please see the supplemental methods document within this deposit and published research letter for more detailed information.
Creator
Depositor
  • asovinsk@umich.edu
Contact information
Discipline
Funding agency
  • National Institutes of Health (NIH)
Keyword
Citations to related material
  • Bustamante, A.C., Opron, K., Ehlenbach, W.J., Larson, E.B., Crane, P.K., Keene, C.D., Standiford, T.J., Singer, B.H., 2020. Transcriptomic Profiles of Sepsis in the Human Brain. Am J Respir Crit Care Med. https://doi.org/10.1164/rccm.201909-1713LE
Resource type
Last modified
  • 11/18/2022
Published
  • 11/26/2019
Language
DOI
  • https://doi.org/10.7302/6fv8-bv53
License
To Cite this Work:
Bustamante, A. C., Opron, K., Ehlenbach, W. J., Crane, P. K., Keene, D., Standiford, T. J., Singer, B. H. (2019). Transcriptomic Profiles of Sepsis in the Human Brain [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/6fv8-bv53

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Files (Count: 43; Size: 7.79 MB)

Thumbnaildsfsdfsdf Title Original Upload Last Modified File Size Access Actions
File_Manifest.rtf 2019-11-25 2019-11-26 18.7 KB Open Access
Resub_Supplemental_Methods_Trans....docx 2019-11-25 2019-11-25 36.5 KB Open Access
Heatmap_bicor_TuxedoFix_p7_ds3cu...r.pdf 2019-11-25 2019-11-25 16.8 KB Open Access
iPathways_Export_DE_results.csv 2019-11-25 2019-11-25 552 KB Open Access
vst_filtered_TuxedoRAWCount_FIXE...r.txt 2019-11-25 2019-11-25 6.48 MB Open Access
GeneInfoModuleMembership.ACTRNAs....xlsx 2019-11-25 2019-11-25 493 KB Open Access
GENESYMBOL-SEPSIS_4.10.19_darkorange.txt 2019-11-25 2019-11-25 719 Bytes Open Access
GENESYMBOL-SEPSIS_4.10.19_lightgreen.txt 2019-11-25 2019-11-25 1.99 KB Open Access
GENESYMBOL-SEPSIS_4.10.19_grey60.txt 2019-11-25 2019-11-25 2.2 KB Open Access
GENESYMBOL-SEPSIS_4.10.19_midnig...e.txt 2019-11-25 2019-11-25 2.52 KB Open Access
GENESYMBOL-SEPSIS_4.10.19_paletu...e.txt 2019-11-25 2019-11-25 458 Bytes Open Access
GENESYMBOL-SEPSIS_4.10.19_skyblue.txt 2019-11-25 2019-11-25 528 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_black.txt 2019-11-25 2019-11-25 7.47 KB Open Access
GENESYMBOL-WGCNA_4.10.19_blue.txt 2019-11-25 2019-11-25 17.4 KB Open Access
GENESYMBOL-WGCNA_4.10.19_brown.txt 2019-11-25 2019-11-25 16.5 KB Open Access
GENESYMBOL-WGCNA_4.10.19_cyan.txt 2019-11-25 2019-11-25 2.7 KB Open Access
GENESYMBOL-WGCNA_4.10.19_darkgreen.txt 2019-11-25 2019-11-25 1.16 KB Open Access
GENESYMBOL-WGCNA_4.10.19_darkgrey.txt 2019-11-25 2019-11-25 968 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_darkmagenta.txt 2019-11-25 2019-11-25 371 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_darkoli...n.txt 2019-11-25 2019-11-25 435 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_darkred.txt 2019-11-25 2019-11-25 1.22 KB Open Access
GENESYMBOL-WGCNA_4.10.19_darktur...e.txt 2019-11-25 2019-11-25 1021 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_green.txt 2019-11-25 2019-11-25 13 KB Open Access
GENESYMBOL-WGCNA_4.10.19_greenyellow.txt 2019-11-25 2019-11-25 4.25 KB Open Access
GENESYMBOL-WGCNA_4.10.19_grey.txt 2019-11-25 2019-11-25 44.2 KB Open Access
GENESYMBOL-WGCNA_4.10.19_lightcyan.txt 2019-11-25 2019-11-25 2.4 KB Open Access
GENESYMBOL-WGCNA_4.10.19_lightyellow.txt 2019-11-25 2019-11-25 1.29 KB Open Access
GENESYMBOL-WGCNA_4.10.19_magenta.txt 2019-11-25 2019-11-25 4.93 KB Open Access
GENESYMBOL-WGCNA_4.10.19_orange.txt 2019-11-25 2019-11-25 774 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_pink.txt 2019-11-25 2019-11-25 6.13 KB Open Access
GENESYMBOL-WGCNA_4.10.19_purple.txt 2019-11-25 2019-11-25 5.28 KB Open Access
GENESYMBOL-WGCNA_4.10.19_red.txt 2019-11-25 2019-11-25 12.2 KB Open Access
GENESYMBOL-WGCNA_4.10.19_royalblue.txt 2019-11-25 2019-11-25 1.24 KB Open Access
GENESYMBOL-WGCNA_4.10.19_saddlebrown.txt 2019-11-25 2019-11-25 572 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_salmon.txt 2019-11-25 2019-11-25 2.54 KB Open Access
GENESYMBOL-WGCNA_4.10.19_sienna3.txt 2019-11-25 2019-11-25 340 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_steelblue.txt 2019-11-25 2019-11-25 486 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_tan.txt 2019-11-25 2019-11-25 3.71 KB Open Access
GENESYMBOL-WGCNA_4.10.19_turquoise.txt 2019-11-25 2019-11-25 27.8 KB Open Access
GENESYMBOL-WGCNA_4.10.19_violet.txt 2019-11-25 2019-11-25 465 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_white.txt 2019-11-25 2019-11-25 612 Bytes Open Access
GENESYMBOL-WGCNA_4.10.19_yellow.txt 2019-11-25 2019-11-25 13.7 KB Open Access
Table_S1_cause_of_death.docx 2019-11-25 2019-11-25 14.6 KB Open Access

"ABCB10"
"ABCE1"
"ABHD10"
"ACP1"
"ACTB"
"ACTR3"
"ADD1"
"ADPRM"
"ADSS"
"AFG3L2"
"AGGF1"
"AHR"
"AKAP3"
"ANK3"
"ANKRD12"
"ANKRD28"
"ANXA7"
"AP1AR"
"AP1G1"
"AP1S2"
"API5"
"APLP1"
"APOO"
"APP"
"APPBP2"
"ARCN1"
"ARF4"
"ARMC8"
"ARV1"
"ATP11B"
"ATP8A1"
"BCHE"
"BCL2L2-PABPN1"
"BCLAF1"
"BECN1"
"BET1"
"BLOC1S1"
"BNIP3L"
"BOD1L1"
"BRIX1"
"BRWD1"
"BTF3L4"
"C10orf128"
"C11orf58"
"C12orf45"
"C1QBP"
"C21orf91-OT1"
"C3orf14"
"C9orf78"
"CALM2"
"CAPNS1"
"CAPZB"
"CASD1"
"CATSPERB"
"CBX3"
"CCDC112"
"CCDC43"
"CCDC47"
"CCSER2"
"CD164"
"CDC42BPA"
"CDC42BPB"
"CDC42SE2"
"CEBPZ"
"CEP120"
"CEP170"
"CFDP1"
"CHD8"
"CHMP2A"
"CHMP2B"
"CHRDL2"
"CIR1"
"CKAP5"
"CLASP2"
"CLCN3"
"CLPX"
"CLTA"
"COMMD1"
"COPB2"
"COPG1"
"COX17"
"CPSF3"
"CPXM2"
"CREG1"
"CRHBP"
"CRYZL1"
"CSDE1"
"CSE1L"
"CSNK2A1"
"CSNK2B"
"CSRP2BP"
"CSTF2T"
"CTDSPL2"
"CUL3"
"CUL4B"
"CUL5"
"CWC22"
"CXorf31"
"CXorf40B"
"CXorf58"
"DCAF13"
"DCAF17"
"DCTN6"
"DDHD2"
"DDX1"
"DDX18"
"DDX52"
"DHX32"
"DHX40"
"DLAT"
"DLD"
"DLG2"
"DNAJC10"
"DNAJC13"
"DNAJC19"
"DNAJC21"
"DNAJC6"
"DNAJC7"
"DNAJC8"
"DNM3"
"DTD1"
"DUSP22"
"EBNA1BP2"
"EDARADD"
"EDEM3"
"EEA1"
"EEF1E1"
"EFCAB11"
"EFTUD1"
"EID1"
"EIF2S1"
"EIF4G3"
"EIF4H"
"ELMO1"
"ENOPH1"
"EPB41L3"
"EPRS"
"EPS15"
"ERI1"
"ERLEC1"
"FAF1"
"FAM111B"
"FAM133DP"
"FAM135A"
"FAM174A"
"FAM179B"
"FAM192A"
"FAM49B"
"FAM69A"
"FARSB"
"FBXO25"
"FBXO38"
"FBXO43"
"FGF7"
"FH"
"FIGNL1"
"FMR1"
"FTO"
"GALNT8"
"GATAD2B"
"GDI2"
"GGNBP2"
"GK2"
"GLTSCR1L"
"GNAI1"
"GOLPH3"
"GOLT1A"
"GORAB"
"GORASP2"
"GPATCH11"
"GPR15"
"GSG1"
"GTF2H1"
"GUSBP10"
"GYG2"
"HBS1L"
"HDHD2"
"HDLBP"
"HECTD1"
"HECW2"
"HNRNPA3"
"HNRNPD"
"HNRNPK"
"HNRNPR"
"HNRNPUL2-BSCL2"
"HOOK3"
"HSF2"
"HTATSF1"
"IARS2"
"IDH3A"
"IFITM5"
"IFT80"
"IMPAD1"
"ING3"
"IRX3"
"ISL2"
"ITFG1"
"KAL1"
"KAZN"
"KBTBD3"
"KCNS3"
"KCTD13"
"KHSRP"
"KIAA0368"
"KIAA1468"
"KIDINS220"
"KIRREL3"
"KLHL20"
"KPNA1"
"KPNB1"
"KRIT1"
"LANCL1"
"LARP4B"
"LDLRAD4"
"LEO1"
"LGI3"
"LIN54"
"LMBRD1"
"LOC100127983"
"LOC100131320"
"LOC100132146"
"LOC144486"
"LOC643037"
"LOC645752"
"LOC646719"
"LOC729177"
"LPGAT1"
"LSM3"
"LTN1"
"LURAP1"
"MAGEF1"
"MAK16"
"MARCH6"
"MASTL"
"MCM4"
"MEA1"
"MED4"
"METAP1"
"METTL22"
"METTL4"
"MIR135A1"
"MIR3064"
"MIR4691"
"MIR663B"
"MIR762"
"MIS18BP1"
"MRGPRE"
"MSLN"
"MTHFD1"
"MTIF2"
"MTMR6"
"MTMR7"
"MYL12B"
"NAE1"
"NAP1L1"
"NARS"
"NBN"
"NBR1"
"NCAM2"
"NCOA7"
"NDST4"
"NDUFA5"
"NDUFV2"
"NIPAL3"
"NKAP"
"NOLC1"
"NPAT"
"NPM1"
"NRD1"
"NSA2"
"NUB1"
"NUCKS1"
"NUP153"
"OCIAD1"
"OMG"
"OSBPL1A"
"OTOR"
"PA2G4"
"PABPC4"
"PADI1"
"PAIP1"
"PAIP2"
"PAPSS1"
"PARN"
"PARP2"
"PDCD10"
"PDCD11"
"PDCD4"
"PDCD6"
"PDCD6IP"
"PDZD8"
"PELI1"
"PEMT"
"PEX11B"
"POLR2B"
"PPIE"
"PPP1CB"
"PPP2R2A"
"PRKAR1A"
"PRPF6"
"PSMA5"
"PSMB2"
"PSMC1"
"PSMC2"
"PSMC3"
"PSMC5"
"PSMD14"
"PSMD7"
"PSMF1"
"PSORS1C1"
"PSPN"
"PTPLB"
"PTPRD"
"PTPRE"
"RAB5A"
"RABEP1"
"RABGGTB"
"RAC1"
"RAD17"
"RAD21"
"RALA"
"RALBP1"
"RANBP1"
"RAP1GDS1"
"RASA1"
"RASGEF1B"
"RBBP8"
"RBM27"
"RCAN1"
"RLN2"
"RNASEH1"
"RNASEK"
"RRM2B"
"RSBN1L"
"RSRC1"
"RTCA"
"RTFDC1"
"RTN4"
"RUFY2"
"RUFY3"
"RWDD1"
"SARNP"
"SBDS"
"SCARA5"
"SCARB2"
"SDHA"
"SEC62"
"SEC63"
"SEL1L"
"SEMA6D"
"SENP2"
"SERTAD4"
"SESTD1"
"SETX"
"SF3A3"
"SH3BP5"
"SHBG"
"SHOX2"
"SIAH1"
"SKA2"
"SLC20A1"
"SLC24A2"
"SLC25A27"
"SLC35A5"
"SLN"
"SMARCA5"
"SMC2"
"SMIM14"
"SMIM15"
"SNRPC"
"SNRPD1"
"SNRPF"
"SNW1"
"SNX2"
"SNX24"
"SNX25"
"SPCS2"
"SPOCK1"
"SPRR2G"
"SREK1IP1"
"SRP54"
"SRPK2"
"ST6GALNAC3"
"STAM"
"STK4"
"STRN"
"STX7"
"SUPT16H"
"SURF2"
"SUZ12"
"TAF9"
"TAOK1"
"TAP2"
"TARDBP"
"TATDN1"
"TCEAL8"
"TCP11"
"THG1L"
"TM9SF3"
"TMC3"
"TMED2"
"TMED5"
"TMEM106B"
"TMEM230"
"TMEM55A"
"TMEM59"
"TMF1"
"TMX3"
"TMX4"
"TOP2B"
"TOPORS"
"TOX3"
"TRIM2"
"TRIM35"
"TSN"
"TSNAX"
"TTC1"
"TTC13"
"UBA2"
"UBA3"
"UBE2R2"
"UBE4A"
"UBLCP1"
"UBR3"
"UCHL5"
"USO1"
"USP16"
"USP32"
"USP47"
"USP5"
"USP7"
"VCPIP1"
"VRK1"
"WBP11"
"WBP4"
"WFDC11"
"XCR1"
"XPO4"
"XRCC5"
"XRCC6"
"XRN2"
"YTHDF2"
"ZC3H6"
"ZCRB1"
"ZDHHC6"
"ZFP91"
"ZMYM2"
"ZNF10"
"ZNF141"
"ZNF174"
"ZNF180"
"ZNF207"
"ZNF23"
"ZNF330"
"ZNF451"
"ZNF611"
"ZNF675"

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