title: US-1674394_colon_DIO

value: DIO


title: Man_C

status: Public on Oct 13 2021

type: SRA

city: Merelbeke

first: Yu

last: Wang

address: Salisburylaan 133, D5

country: Belgium

institute: Ghent University

library_source: transcriptomic

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Quantification: Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GCA_002006685.1
Supplementary_files_format_and_content: readcount_genename.txt

molecule: total RNA

organism: Batrachochytrium salamandrivorans

source_name: Batrachochytrium salamandrivorans (AMFP 13/01)

growth_protocol: Bsal type strain (AMFP 13/01) (Martel et al., 2013) was grown in tryptone-gelatin hydrolysate-lactose (TGhL) broth and incubated for 5-7 days at 15 °C. Zoospores were harvested from 175 cm2 cell culture flasks by replacing the TGhL broth with distilled water, which was filtered using a sterile mesh filter with pore size 10 µm (Pluristrainer, PluriSelect).

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen). The RNA was treated with Turbo™ DNase (Ambion), following the manufacturer's instructions. RNA degradation and contamination was monitored on 1% agarose gels. The RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). Finally, the RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologie, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six independent pools containing 4 x 10e7 zoospores were obtained (biological replicates). Per pool, the spores were divided in 4 eppendorfs (107 zoospores/eppendorf) which were treated for 1 hour at 15°C with H2O (control), 50 mM α-D-galactose, 50 mM α-D-glucose or 50 mM α-D-mannose. After 1 hour, the zoospores were centrifuged for 5 min at 3000 rpm at 15°C to remove the supernatant, after which RNA was extracted.

tag: strain

tag: sample type

value: zoospores

tag: zoospore pool/biological replicate

value: pool C

tag: treatment

value: Mannose treated (50 mM)

tag: duration treatment

value: 1 hour


title: US-1675285_colon__lean

city: Seattle

first: Sara

middle: A

last: Murray

state: WA

address: 530 Fairview Ave N

department: Obesity Research Group

country: USA

institute: Novo Nordisk Research Center Seattle, Inc.

data_processing:
fastqc sequencing quality assessment
STAR alignment of sequenced reads
HTseq read counting
QC using DESeq2 guidelines: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
Low expression filter: genes that had a total count of >= 10 across all samples within a tissue type were included in the analysis
Count normalization with 'normTransform' (DESeq2)
Differential gene expression between DIO and Lean mice within each tissue type was run with DESeq2 'results'
Genome_build: Mmusculus_GRCm38r90
Supplementary_files_format_and_content: Normalized read counts

organism: Mus musculus

source_name: Colon

growth_protocol: Adult wild-type male C57BL/6J mice aged 6-12 weeks were obtained from Jackson Laboratories (Stock # 000664). Mice were housed 4-8 per cage with ad libitum access to water and food (Type IV Scanbur Cages; 1800 cm2 floor area). Mice were acclimated to housing for one week and then marked with 2D barcode ear tags. Animal holding rooms temperature ranged from 20-26 °C and humidity ranged from 30-70%. Lighting was on an automated light/dark cycle with lights on between 6:00 AM and 6:00 PM. Mice were provided with Alpha Dri bedding material to just cover the bottoms of cages cage, one Nestlet square, and two 8g Bed-r’Nest “pucks” or similar. Environmental enrichment included a plastic hut, a paper hut, one wood gnawing block, and a tunnel suspended from the top of cages. Mice received a hydrogel cup upon arrival until familiarized with the automatic water system which supplied reverse osmosis purified water via the Scantainer rack system. Standard rodent chow diet [PicoLab Rodent Diet 20 Lab Diet #5R53 (24.5% Protein, 13.1% Fat, 62.4% Carbohydrate)] was provided to the mice upon arrival until diet was switched from chow to high fat.

extract_protocol:
Mice were sacrificed and tissues of interest were extracted and kept at -80 °C until RNA extraction.  RNA isolated from frozen tissue chunks using RNAeasy kit (Qiagen).
Isolated RNA was sent for RNA-sequencing at the Covance Genomics Lab, Redmond, WA. cDNA libraries were prepared with Illumina TruSeq stranded mRNA kit and sequenced on an Illumina HiSeq. 2000 using paired-end, 100 nucleotide reads with an average depth of 20 million reads per sample.

treatment_protocol: At 4 weeks of age mice were placed on a 60% high fat diet (High-Fat Diet #D12492 (20.0% Protein, 60% Fat, 20% Carbohydrate) during 10 weeks and they reached dietary induced obese status (DIO). After this point, mice were moved from group housing to 2 mice per Type IV Scanbur cage, separated by an opaque cage divider. Food and water were provided ad lib.  Transcriptomic profile from 19 tissues, comparing control chow diet and HFD diet interventions were carried out.

tag: status

value: Lean


title: US-1675283_colon_DIO


title: Subject_8_Control [Human postmortem prefrontal cortex]

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

description:
mRNA transcriptome data
Sample_128

data_processing:
The bulk RNA-seq processing pipeline Pipeliner [Federico et al. Front Genet 2019; 10, 614] was utilized to quantitate gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Human postmortem prefrontal cortex

growth_protocol: Not applicable

extract_protocol:
RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.
The KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA, USA) was used to deplete ribosomal RNAs (rRNAs) and construct RNA-seq libraries with 1 ug of total RNAs as the starting material.
Ribosomal RNA depletion RNA-seq

treatment_protocol: Not applicable

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: batch

tag: rin

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Never

tag: liverclass

value: Steatosis


title: Galac_D

tag: strain

tag: sample type

value: pool D

value: Galactose treated (50 mM)


title: Gluc_C

tag: zoospore pool/biological replicate

tag: treatment

value: Glucose treated (50 mM)


title: US-1674393_colon_DIO

tag: status


title: HEPM_11_m: mRNA-SAG-3

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina bcl2fastq (v2.20.0) was used for basecalling and demultiplexing.
Read quality was checked for each sample using FastQC (v0.11.8).
Reads were aligned to Ensemble GRCh38 reference genome using TopHat (v2.1.0).
Read summarization to gene counts was performed using featureCounts (v1.5.1).
Normalized counts were generated using DESeq2 (v1.22.2).
Genome_build: GRCh38/hg38.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

molecule: polyA RNA

growth_protocol: The Daoy medulloblastoma and HEPM (CRL-1486) human embryonic palatal mesenchyme cells were cultured in EMEM medium with L-glutamine (Lonza, Switzerland) and UW-228 cells in DMEM/F12 (1:1) medium with L-glutamine (11320033, Gibco, USA), supplemented with 10 % fetal bovine serum (FBS) (A31608-02, Gibco) and 100 IU/ml penicillin/streptomycin (15140-122, Gibco) and maintained in 5 % CO2 humidified incubator at 37˚C.

extract_protocol:
Total RNA from cell lines or the medulloblastoma tumor sample was isolated with E.Z.N.A total RNA kit I (R6834-02) or total RNA midi kit (R6664-02) (Omega Bio-tek, USA) according to the manufacturer’s instructions. On-column DNA digestion was performed with 40 KU (R6834-02 kit) and 60 KU (R6664-02 kit) of DNase (79254, Qiagen, Germany).
a) Poly(A) enriched fraction: ≈ 100 ng of total RNA was used to generate stranded mRNA libraries with the TruSeq®Stranded mRNA Low Throughput Sample Preparation kit according to the manufacturer’s instructions (15031047, Illumina, USA). This protocol involves a poly(A) selection/enrichment and ribosomal RNA depletion step.
b) circRNA enriched fraction: 5 μg of total RNA was used. First, ribosomal RNA was depleted using the RiboMinusTM Eukaryote System V2 (Ambion) (A15026, ThermoFisher USA), followed by digestion with 5U RNase R for 1 hr to degrade linear RNAs and purification with the RNeasy MinElute Cleanup Kit (74204, Qiagen). The concentration and quality of the enriched circRNA RiboMinus/RNase R preparations were assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). 4.4 ng (for Daoy cells) or 1 ng (for HEPM cells) of RiboMinus/RNase R treated RNA was used for cDNA library generation. Random hexamer primers and Superscript III reverse transcriptase (18080055, Invitrogen, USA) were used for 1st strand synthesis and stranded mRNA library was generated according to the TruSeq®Stranded mRNA Low Throughput Sample Preparation protocol (15031047, Illumina, USA) as described above. The concentration and quality of the cDNA libraries were assessed with Qubit (Life Technologies, USA) and TapeStation, respectively. The cDNA libraries were normalized and pooled for sequencing on the Illumina NextSeq 550 platform using the Illumina NextSeq 500/550 High Output v2 kit (75 cycles; single read).

treatment_protocol: The Smoothened agonist (SAG, 566660) was purchased from Merck (Germany) and the recombinant human Sonic Hedgehog N-terminus ligand (SHH-C24II, 185-SH) was purchased from R&D Systems (USA). SAG was dissolved and diluted in DMSO, and SHH was dissolved and diluted in PBS with 0.1 % BSA. Daoy cells were seeded in 6-well plates at ≈ 30 % confluency in complete medium, then starved in Optimem medium (11058-021, Gibco) for 24 hr and treated with either 200 nM SAG in EMEM medium supplemented with 0.5 % FBS for 72 hr or with 400 ng/ml SHH in Optimem for 72 hr. From each treatment condition two separate wells were combined and processed further for RNA isolation. Similarly, for the control (Ctr) treatments, cells were either starved in Optimem for 24 hr and mock-treated with SAG solvent (DMSO) in EMEM medium supplemented with 0.5 % FBS for 72 hr (SAG_Ctr) or with SHH solvent (0.1 % BSA in PBS) in Optimem for 72 hr (SHH_Ctr). HEPM cells were seeded in 10 cm cell culture dishes at ≈ 40 % confluency in complete medium, then starved in Optimem for 24 hr and treated with either 200 nM SAG or 400 ng/ml SHH in Optimem medium for 72 hr or with DMSO + 0.1 % BSA in PBS as the control treatment.

tag: organ

value: embryonic palatal mesenchyme

tag: tissue type

value: palatal mesenchyme, epithelial morphology

tag: cell line

value: HEPM

tag: molecule

value: mRNA / poly(A)

value: SAG-200 nM


title: HEPM_1_c: circRNA-DMSO/PB-1

source_name: HEPM (CRL-1486) human embryonic palatal mesenchyme cells

value: circRNA / (poly(A-) / RNaseR+)

value: Control-DMSO-PBS/BSA


title: HEPM_12_m: mRNA-SAG-4


title: US-1674706_colon_DIO

value: DIO


title: Subject_11_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_131

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

tag: rin

value: Current

value: Congestion


title: Galac_C

value: zoospores

value: pool C

tag: duration treatment

value: 1 hour


title: US-1674391_ileum__lean

source_name: Ileum

value: Lean


title: Subject_7_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_127

value: AlcoholUseDisorder

value: Female

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Cirrhosis


title: Subject_9_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_129

value: Male

value: Toxicity

tag: liverclass

value: Steatosis


title: H2O_C

tag: strain

tag: sample type

tag: zoospore pool/biological replicate

tag: treatment

value: H2O treated


title: Subject_6_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_126

tag: aud status

value: Respiratory

value: Normal


title: Subject_3_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_123

value: Control

tag: alcoholdailyuse(gram/day)

value: Left

value: Current


title: Subject_4_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_124

tag: Sex


title: Gluc_B

value: zoospores

value: pool B

value: Glucose treated (50 mM)


title: HEPM_8_m: mRNA-SHH-4

tag: organ

value: embryonic palatal mesenchyme

tag: tissue type

value: palatal mesenchyme, epithelial morphology

tag: cell line

value: HEPM

tag: molecule

value: mRNA / poly(A)

value: SHH-400 ng/ml


title: Man_B

value: Mannose treated (50 mM)

tag: duration treatment

value: 1 hour


title: US-1674389_ileum__lean

tag: status

value: Lean


title: HEPM_9_m: mRNA-SAG-1

value: SAG-200 nM


title: Galac_B

value: Galactose treated (50 mM)


title: HEPM_10_m: mRNA-SAG-2


title: Subject_5_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_125

value: AlcoholUseDisorder

value: Female

tag: batch

tag: rin

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Right

value: Respiratory

value: Cirrhosis


title: Subject_2_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_122

value: Control

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Unknown

tag: liverclass

value: Normal


title: HEPM_7_m: mRNA-SHH-3

value: embryonic palatal mesenchyme

value: palatal mesenchyme, epithelial morphology

value: HEPM

tag: treatment


title: Galac_A

tag: strain

tag: sample type

value: zoospores

tag: zoospore pool/biological replicate

value: pool A


title: US-1674387_ileum__lean

value: Lean


title: Man_A

value: Mannose treated (50 mM)

value: 1 hour


title: US-1674390_ileum__lean


title: HEPM_5_m: mRNA-SHH-1

tag: organ

tag: tissue type

tag: cell line

value: mRNA / poly(A)

value: SHH-400 ng/ml


title: US-1674388_ileum__lean

tag: status


title: Subject_24_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_24

source_name: Human postmortem amygdala

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: batch

value: Left

value: Cardiovascular

value: Current

value: Steatosis


title: US-1674392_colon_DIO

value: DIO


title: HEPM_4_m: mRNA-DMSO/PB-4

value: embryonic palatal mesenchyme

tag: molecule

value: Control-DMSO-PBS/BSA


title: Gluc_A

value: Glucose treated (50 mM)

tag: duration treatment


title: US-1674386_ileum_DIO


title: H2O_B

value: zoospores

value: pool B

value: H2O treated


title: HEPM_3_m: mRNA-DMSO/PB-3

value: palatal mesenchyme, epithelial morphology

value: HEPM


title: HEPM_6_m: mRNA-SHH-2

value: mRNA / poly(A)


title: US-1674384_ileum_DIO


title: HEPM_2_m: mRNA-DMSO/PB-2


title: Subject_22_Control [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_22

value: Control

value: Female

tag: rin

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Cardiac

value: Never

value: Normal


title: Subject_1_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_121

value: Male

value: Left

tag: smoking

tag: liverclass

value: MildSteatosis


title: H2O_A

tag: strain

tag: sample type

tag: zoospore pool/biological replicate

value: pool A

tag: treatment

value: 1 hour


title: Subject_21_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_21

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Current

value: Cirrhosis


title: US-1674382_ileum_DIO

tag: status

value: DIO


title: HEPM_1_m: mRNA-DMSO/PB-1

tag: organ

value: embryonic palatal mesenchyme

tag: tissue type

value: palatal mesenchyme, epithelial morphology

tag: cell line

tag: molecule

value: Control-DMSO-PBS/BSA


title: Subject_20_Control [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_20

value: Control

tag: Sex

tag: batch

tag: rin

tag: brainweight

tag: brainph

value: Toxicity

value: Unknown

value: Congestion


title: Subject_19_Control [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_19

value: Female

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Cardiac

tag: smoking

tag: liverclass


title: US-1674383_ileum_DIO


title: US-1674381_jejunum__lean

source_name: Jejunum

value: Lean


title: Daoy_15_c: circRNA-SHH-3

source_name: Daoy medulloblastoma cells

value: brain/cerebelar tumor

value: medulloblastoma

value: Daoy

value: circRNA / (poly(A-) / RNaseR+)

tag: treatment

value: SHH-400 ng/ml


title: US-1674385_ileum_DIO

value: DIO


title: Subject_23_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_23

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Never

value: Steatosis


title: Daoy_14_c: circRNA-SHH-2

tag: organ


title: Subject_18_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_18

value: Male

value: Hepatic

value: Current


title: Subject_17_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_17

value: Control

value: Vascular

value: Normal


title: US-1674379_jejunum__lean

tag: status


title: Daoy_13_c: circRNA-SHH-1

tag: tissue type

tag: cell line


title: Subject_16_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_16

tag: Sex

value: Left

value: Cirrhosis


title: US-1674378_jejunum__lean

value: Lean


title: Daoy_16_c: circRNA-SHH-4

value: brain/cerebelar tumor

value: medulloblastoma

tag: molecule


title: Subject_15_Control [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_15

value: Female

tag: batch

tag: rin

value: Cardiac


title: US-1674377_jejunum__lean


title: Daoy_12_c: circRNA-PB-4

value: Daoy

value: circRNA / (poly(A-) / RNaseR+)

value: Control-PBS/BSA


title: US-1674380_jejunum__lean


title: US-1674376_jejunum_DIO

value: DIO


title: Daoy_11_c: circRNA-PB-3


title: Subject_14_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_14

value: AlcoholUseDisorder

tag: brainweight

tag: brainph

value: Toxicity


title: PUT_96_Control

type: RNA

description: mRNA & lncRNA transcriptome data

hyb_protocol: A “rotisserie” oven was used to carry out the array hybridization at 45°C and 60 rpm for 16 hours.

scan_protocol: The images were analyzed using Affymetrix Command Console Viewer

data_processing: CEL files were processed using the Affymetrix Expression Console (EC) software (v1.4.1)

label: biotin

source_name: Human postmortem putamen

label_protocol: About 500 ng of total RNA was used as starting material to obtain labeled cRNA. cRNA was fragmented in the presence of heat and Mg+2 before hybridization to the the Affymetrix Clariom D human array.

extract_protocol: RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.

value: Male

tag: pmi

tag: leftrightbrain

value: Current

value: Steatosis


title: PUT_95_Control

description: mRNA & lncRNA transcriptome data

value: Control

value: Right

tag: causeofdeathcategory

tag: smoking

value: Never

value: Congestion


title: Daoy_10_c: circRNA-PB-2

value: brain/cerebelar tumor

tag: treatment


title: PUT_94_Case

description: mRNA & lncRNA transcriptome data

tag: aud status

value: Case

tag: liverclass


title: PUT_93_Case

description: mRNA & lncRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Left

value: Normal


title: PUT_90_Control

description: mRNA & lncRNA transcriptome data

value: Cardiac

value: Former


title: Subject_13_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_13


title: US-1674373_jejunum_DIO

tag: status


title: Subject_12_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_12


title: US-1674375_jejunum_DIO


title: Subject_11_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_11


title: Daoy_9_c: circRNA-PB-1

tag: organ

tag: tissue type

value: medulloblastoma

value: Daoy

value: circRNA / (poly(A-) / RNaseR+)

value: Control-PBS/BSA


title: Daoy_8_c: circRNA-SAG-4

tag: cell line

value: SAG-200 nM


title: US-1674374_jejunum_DIO

value: DIO


title: Daoy_6_c: circRNA-SAG-2

tag: molecule


title: PUT_91_Case

description: mRNA & lncRNA transcriptome data

tag: Sex

value: Male

tag: batch

value: Unknown

value: Current


title: Daoy_7_c: circRNA-SAG-3


title: US-1674372_jejunum_DIO


title: PUT_92_Case

description: mRNA & lncRNA transcriptome data

tag: rin

tag: brainweight

value: Steatosis


title: Subject_9_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_9

value: AlcoholUseDisorder

tag: brainph

tag: pmi

value: Right

value: Toxicity


title: Subject_10_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_10

value: Control

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Congestion


title: US-1672860_stomach_lc__lean

source_name: Lesser Curvuture

value: Lean


title: PUT_88_Case

description: mRNA & lncRNA transcriptome data

value: Case

value: Stroke

tag: smoking


title: Subject_8_Control [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_8

tag: aud status

value: Cardiac

value: Never


title: Daoy_5_c: circRNA-SAG-1

value: brain/cerebelar tumor

value: medulloblastoma

value: Daoy

value: circRNA / (poly(A-) / RNaseR+)

tag: treatment

value: SAG-200 nM


title: Subject_15_Control [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_135

tag: alcoholdailyuse(gram/day)

value: Female

value: Current

tag: liverclass

value: Normal


title: PUT_86_Control

description: mRNA & lncRNA transcriptome data

value: Male

value: Steatosis


title: US-1672859_stomach_lc__lean

tag: status


title: Subject_7_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_7

value: AlcoholUseDisorder

value: Right

value: Cirrhosis


title: PUT_83_Case

description: mRNA & lncRNA transcriptome data

value: Case

value: Toxicity


title: Daoy_4_c: circRNA-DMSO-4

tag: organ

tag: tissue type

value: Control-DMSO


title: Subject_5_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_5

value: Respiratory


title: Daoy_1_c: circRNA-DMSO-1

value: brain/cerebelar tumor

tag: cell line

tag: molecule


title: PUT_85_Case

description: mRNA & lncRNA transcriptome data

tag: Sex

tag: batch

value: Never


title: Subject_4_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_4

tag: rin

tag: brainweight


title: US-1672856_stomach_lc__lean

value: Lean


title: Daoy_16_m: mRNA-SHH-4

value: medulloblastoma

value: Daoy

value: mRNA / poly(A)

value: SHH-400 ng/ml


title: PUT_87_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: pmi

value: Cardiac

value: Congestion


title: PUT_84_Control

description: mRNA & lncRNA transcriptome data

value: Male

tag: leftrightbrain

value: Current

value: Normal


title: US-1672858_stomach_lc__lean


title: PFC_80_Control

description: mRNA & lncRNA transcriptome data

value: Left

tag: causeofdeathcategory

value: Steatosis


title: Daoy_2_c: circRNA-DMSO-2

value: circRNA / (poly(A-) / RNaseR+)

value: Control-DMSO


title: US-1672854_stomach_lc_DIO

value: DIO


title: Daoy_13_m: mRNA-SHH-1

value: brain/cerebelar tumor


title: Subject_3_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_3

value: Female

tag: brainph

tag: smoking


title: Subject_6_AlcoholUseDisorder [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_6

tag: aud status

value: AlcoholUseDisorder

value: Right

value: Respiratory


title: US-1672857_stomach_lc__lean

value: Lean


title: US-1672851_stomach_lc_DIO


title: Subject_23_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_71

source_name: Human postmortem cerebellum

tag: alcohol daily use(gram/day)

tag: brain weight

tag: brain ph

tag: brain location (left or rightbrain)

tag: cause of death category

value: Toxicity

value: Never

tag: liver class


title: Subject_24_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_72

value: Cardiovascular


title: US-1672850_adrenal__lean

source_name: Adrenal

tag: status


title: US-1672853_stomach_lc_DIO


title: PFC_79_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

value: Cardiac

tag: liverclass

value: Congestion


title: US-1672852_stomach_lc_DIO


title: Daoy_11_m: mRNA-PB-3

tag: organ

tag: tissue type

value: medulloblastoma

tag: cell line

value: Daoy

tag: molecule

value: mRNA / poly(A)

tag: treatment

value: Control-PBS/BSA


title: PUT_89_Control

description: mRNA & lncRNA transcriptome data

tag: batch

tag: rin

tag: brainweight

tag: pmi

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

tag: smoking

value: Former


title: Subject_22_Control [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_70

tag: aud status

tag: alcohol daily use(gram/day)

value: Female

tag: brain weight

tag: brain ph

tag: brain location (left or rightbrain)

tag: cause of death category

tag: liver class

value: Normal


title: US-1672849_adrenal__lean

tag: status


title: Daoy_14_m: mRNA-SHH-2

tag: organ

value: brain/cerebelar tumor

tag: tissue type

tag: cell line

tag: molecule

value: SHH-400 ng/ml


title: Daoy_3_c: circRNA-DMSO-3

value: circRNA / (poly(A-) / RNaseR+)

tag: treatment

value: Control-DMSO


title: US-1672848_adrenal__lean

value: Lean


title: PUT_81_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

tag: rin

tag: brainweight

tag: pmi

value: Right

value: HepaticBloodLoss

tag: liverclass

value: Steatosis


title: Subject_2_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_2

tag: aud status

value: Control

tag: brainph

tag: leftrightbrain

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Unknown


title: US-1672855_stomach_lc_DIO

tag: status

value: DIO


title: Daoy_9_m: mRNA-PB-1

tag: organ

tag: tissue type

value: medulloblastoma

value: Daoy

value: mRNA / poly(A)

value: Control-PBS/BSA


title: Daoy_15_m: mRNA-SHH-3

value: brain/cerebelar tumor

tag: cell line

tag: molecule


title: Subject_1_Control  [Human postmortem amygdala]

description:
miRNA transcriptome data
Sample_1

tag: alcoholdailyuse(gram/day)

value: Male

value: Left

value: Never

value: MildSteatosis


title: PFC_75_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: Sex

value: Current

value: Normal


title: Daoy_8_m: mRNA-SAG-4

tag: treatment

value: SAG-200 nM


title: Daoy_12_m: mRNA-PB-4


title: PUT_82_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: batch

tag: rin

value: Steatosis


title: US-1672846_adrenal__lean

value: Lean


title: Subject_20_Control [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_68

tag: alcohol daily use(gram/day)

value: Female

tag: brain weight

tag: brain ph

tag: pmi

tag: brain location (left or rightbrain)

tag: cause of death category

value: Toxicity

value: Unknown

tag: liver class

value: Congestion


title: PFC_72_Case

description: mRNA & lncRNA transcriptome data

tag: aud status

tag: brainweight

tag: leftrightbrain

tag: causeofdeathcategory

value: Stroke

tag: smoking

tag: liverclass


title: PFC_77_Case

description: mRNA & lncRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Cardiac


title: Subject_21_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_69

value: AlcoholUseDisorder

value: Male

tag: batch

value: Cirrhosis


title: Subject_18_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_66

tag: rin

value: Right

value: Hepatic


title: Daoy_7_m: mRNA-SAG-3

tag: organ

value: brain/cerebelar tumor

tag: tissue type

value: medulloblastoma

tag: cell line

value: Daoy

tag: molecule

value: mRNA / poly(A)

tag: treatment


title: PFC_78_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: pmi

value: Current

value: Steatosis


title: US-1672845_adrenal_DIO

tag: status

value: DIO


title: Daoy_6_m: mRNA-SAG-2

value: SAG-200 nM


title: Subject_19_Control [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_67

tag: aud status

value: Control

tag: alcohol daily use(gram/day)

value: Female

tag: brain weight

tag: brain ph

tag: brain location (left or rightbrain)

tag: cause of death category

tag: liver class

value: Congestion


title: Subject_17_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_65

tag: Sex

value: Vascular

tag: smoking

value: Normal


title: PFC_73_Control

description: mRNA & lncRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Male

tag: batch

tag: rin

tag: brainweight

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Cardiac

value: Former

tag: liverclass


title: PFC_71_Control

description: mRNA & lncRNA transcriptome data

tag: pmi

value: Right

value: Never


title: Subject_16_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_64

tag: aud status

value: AlcoholUseDisorder

value: Cirrhosis


title: PFC_74_Control

description: mRNA & lncRNA transcriptome data


title: Daoy_4_m: mRNA-DMSO-4

tag: organ

value: brain/cerebelar tumor

tag: tissue type

value: medulloblastoma

tag: cell line

value: Daoy

tag: molecule

value: mRNA / poly(A)

tag: treatment

value: Control-DMSO


title: Subject_15_Control [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_63

value: Control

tag: alcohol daily use(gram/day)

value: Female

tag: brain weight

tag: brain ph

tag: brain location (left or rightbrain)

tag: cause of death category

value: Current

tag: liver class


title: US-1672843_adrenal_DIO

tag: status

value: DIO


title: Daoy_5_m: mRNA-SAG-1

value: SAG-200 nM


title: PFC_70_Control

description: mRNA & lncRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: batch

tag: rin

tag: brainweight

tag: leftrightbrain

value: Left

tag: smoking

value: Steatosis


title: PFC_76_Case

description: mRNA & lncRNA transcriptome data

tag: aud status

value: Case

tag: pmi

tag: causeofdeathcategory

value: Cardiac

value: Former

tag: liverclass


title: US-1672841_adrenal_DIO


title: Daoy_10_m: mRNA-PB-2

tag: organ

tag: tissue type

tag: cell line

tag: molecule

tag: treatment

value: Control-PBS/BSA


title: US-1672842_adrenal_DIO

tag: status


title: Subject_14_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_62

value: AlcoholUseDisorder

tag: alcohol daily use(gram/day)

tag: brain weight

tag: brain ph

tag: brain location (left or rightbrain)

tag: cause of death category

value: Toxicity

tag: liver class

value: Cirrhosis


title: Daoy_3_m: mRNA-DMSO-3

value: brain/cerebelar tumor

value: medulloblastoma

value: Daoy

value: mRNA / poly(A)


title: Daoy_1_m: mRNA-DMSO-1

value: Control-DMSO


title: US-1672839_cerebellum__lean

source_name: Cerebellum

value: Lean


title: US-1672840_cerebellum__lean


title: Subject_13_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_61

value: Control

tag: Sex

tag: batch

tag: rin

tag: smoking

value: Never

value: Normal


title: US-1672838_cerebellum__lean


title: Daoy_2_m: mRNA-DMSO-2


title: Subject_10_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_58

tag: aud status

value: Male

tag: pmi

value: Left

value: Current

value: Congestion


title: Subject_12_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_60

value: Cardiac


title: US-1672837_cerebellum__lean


title: PFC_69_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: alcoholdailyuse(gram/day)

tag: brainweight

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Respiratory

tag: liverclass

value: Steatosis


title: Subject_9_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_57

value: AlcoholUseDisorder

tag: alcohol daily use(gram/day)

value: Toxicity


title: Subject_11_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_59

tag: brain weight


title: Subject_7_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_55

value: Female

tag: brain ph

value: Cirrhosis


title: US-1672836_cerebellum__lean

tag: status

value: Lean


title: HLEC-Control-1

city: Madrid

first: David

last: Olmeda

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina RTA software. Cell Ranger version 3.0.2 software (10x Genomics) pipeline was subsequently used to perform various steps. Conversion of BCL files to FASTQ format was performed with "cellranger mkfastq", a wrapper for "bcl2fastq" (Illumina).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Normalised counts obtained with DESeq2

source_name: HLEC

growth_protocol: Human Lymphatic Microvascular Endothelial Cells (HMVEC-dLy) (Lonza, MD) were grown in EGM™-2 medium supplemented with MV BulletKit (Lonza). SK-Mel-147 melanoma cells were grown in DMEN 10% FBS.

extract_protocol:
Total RNA was purified using RNeasy Mini kit (Qiagen) and digested with DNase (Qiagen).
Total RNA samples (500ng) were processed with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. RNA Quality scores were 8.7 on average (range 7.4-9.5) when assayed on a PerkinElmer LabChip analyzer. Briefly, library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.
Illumina NextSeq 550 (with v2.5 reagent kits)

treatment_protocol: The cells were treated for 10h with 1 µg/ml BO-110 or vehicle control.

tag: cell line

value: HLEC

tag: cell type

value: Human primary Lymphatic Endothelial Cells

tag: treatment

value: Vehicle control


title: HLEC-Control-2


title: HLEC-Control-3


title: US-1672835_cerebellum_DIO

value: DIO


title: HLEC-BO110-1


title: SK-Mel-147-BO110-3

value: Human melanoma cells


title: PFC_68_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: Sex

value: Male

tag: batch

value: Current

value: Normal


title: HLEC-BO110-3


title: US-1672833_cerebellum_DIO


title: HLEC-BO110-2


title: US-1672847_adrenal__lean


title: Subject_6_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_54

tag: rin

tag: brain location (left or rightbrain)

value: Right

tag: cause of death category

tag: smoking

tag: liver class


title: Subject_5_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_53

tag: aud status

tag: pmi

value: Respiratory


title: SK-Mel-147-BO110-2


title: Subject_4_AlcoholUseDisorder [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_52


title: Subject_8_Control [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_56

value: Left

value: Cardiac

value: Never

value: Steatosis


title: US-1672834_cerebellum_DIO


title: SK-Mel-147-Control-3


title: US-1672832_cerebellum_DIO


title: Subject_2_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_50

value: Female

value: Unknown


title: US-1672831_cerebellum_DIO


title: US-1672829_midbrain_stem__lean

source_name: Midbrain/BS

value: Lean


title: SK-Mel-147-Control-2


title: Subject_3_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_51


title: US-1672830_midbrain_stem__lean


title: Subject_1_Control  [Human postmortem cerebellum]

description:
mRNA transcriptome data
Sample_49

value: MildSteatosis


title: SK-Mel-147-BO110-1


title: US-1672828_midbrain_stem__lean


title: SK-Mel-147-Control-1

value: Vehicle control


title: US-1672827_midbrain_stem__lean


title: Subject_24_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_96

source_name: Human postmortem hippocampus

value: AlcoholUseDisorder

tag: location of brain (left or rightbrain)

value: Cardiovascular


title: Lib_P1_CD127p

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

data_processing:
Basecalls performed using RTA v2 version 2.4.11
RNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.5.1b
Differential Gene Expression analysis was performed using EdgeR 3.20.9
Genome_build: GRCh38

source_name: Cells isolated from frozen tumor samples

extract_protocol:
Cells were sorted in 10 µL PBS 1X (Sigma-Aldrich), spun down immediately and stored frozen at -80°C in a maximum volume of 7 µL PBS 1X (Sigma-Aldrich).
Library preparation was performed by starting directly from   ̴500 cells per sample using the SMART-Seq Stranded Kit (Clontech-Takara) and following the manufacturer’s protocol.  Libraries were qualitatively assessed by using TapeStation 4200, quantified by Qubit Fluorimeter, then multiplexed in equimolar pools and sequenced on a NextSeq-550 Illumina Platform, generating on average 32.9 million 75bp-PE reads per sample .

treatment_protocol: Cells from frozen TILs were harvested in R10 culture medium, washed with PBS 1x and immediately proccesed for surface staining for FACS sorting (FACS Aria cell sorter).


title: Lib_3E_mem

value: TMEM CD103-


title: US-1672844_adrenal_DIO

value: DIO


title: PFC_67_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: alcoholdailyuse(gram/day)

value: Male

tag: brainweight

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

value: Current

tag: liverclass


title: HIPPO_61_Case

description: mRNA & lncRNA transcriptome data

value: Left

value: Normal


title: HIPPO_57_Control

description: mRNA & lncRNA transcriptome data

value: Control

value: Cardiac

value: Former

value: Congestion


title: PFC_66_Control

description: mRNA & lncRNA transcriptome data

value: Steatosis


title: HIPPO_64_Control

description: mRNA & lncRNA transcriptome data


title: HIPPO_52_Control

description: mRNA & lncRNA transcriptome data

value: Right


title: HIPPO_56_Case

description: mRNA & lncRNA transcriptome data

value: Stroke


title: US-1672825_midbrain_stem_DIO

tag: status


title: Subject_22_Control [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_94

tag: alcohol daily use(gram/day)

value: Female

tag: brain weight

tag: brain ph

value: Never


title: HIPPO_58_Control

description: mRNA & lncRNA transcriptome data

tag: Sex

tag: batch

tag: rin


title: HIPPO_53_Case

description: mRNA & lncRNA transcriptome data

value: Respiratory

tag: smoking


title: Subject_21_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_93

value: AlcoholUseDisorder

tag: cause of death category

tag: liver class

value: Cirrhosis


title: HIPPO_50_Control

description: mRNA & lncRNA transcriptome data

tag: aud status

value: Male

tag: pmi


title: HIPPO_63_Control

description: mRNA & lncRNA transcriptome data

tag: alcoholdailyuse(gram/day)


title: HIPPO_62_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: brainweight


title: PFC_65_Case

description: mRNA & lncRNA transcriptome data

tag: leftrightbrain

value: HepaticBloodLoss


title: HIPPO_55_Control

description: mRNA & lncRNA transcriptome data

tag: causeofdeathcategory


title: HIPPO_54_Control

description: mRNA & lncRNA transcriptome data

value: Left

tag: liverclass


title: HIPPO_51_Case

description: mRNA & lncRNA transcriptome data

value: Toxicity

value: Current


title: HIPPO_59_Case

description: mRNA & lncRNA transcriptome data

value: Unknown

value: Normal


title: US-1672824_midbrain_stem_DIO

tag: status

value: DIO


title: HIPPO_60_Case

description: mRNA & lncRNA transcriptome data

value: Cardiac

value: Former

value: Steatosis


title: US-1672822_midbrain_stem_DIO


title: US-1672823_midbrain_stem_DIO


title: Subject_18_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_90

tag: alcohol daily use(gram/day)

tag: location of brain (left or rightbrain)

value: Right

value: Hepatic


title: CER_48_Control

description: mRNA & lncRNA transcriptome data

value: Control


title: Lib_1D_CD127p

tag: cell type


title: HIPPO_49_Case

description: mRNA & lncRNA transcriptome data

tag: Sex


title: Subject_23_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_95

value: AlcoholUseDisorder

value: Female

tag: batch

tag: brain weight

tag: brain ph

value: Never


title: US-1672826_midbrain_stem__lean

value: Lean


title: US-1672821_midbrain_stem_DIO


title: US-1672820_cortex__lean

source_name: Cerebral cortex


title: Subject_16_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_88

value: Male

tag: rin

tag: cause of death category

tag: smoking

value: Cirrhosis


title: Lib_2E_CD127n


title: US-1672818_cortex__lean


title: Subject_20_Control [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_92

tag: aud status

tag: pmi

value: Left

value: Toxicity

tag: liver class

value: Congestion


title: CER_45_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: alcoholdailyuse(gram/day)

tag: brainweight

tag: leftrightbrain

value: Current

value: Normal


title: Lib_2B_CD127n


title: CER_42_Control

description: mRNA & lncRNA transcriptome data

tag: causeofdeathcategory

value: Cardiac

value: Former

tag: liverclass


title: CER_47_Control

description: mRNA & lncRNA transcriptome data

value: Right


title: Subject_17_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_89

tag: alcohol daily use(gram/day)

tag: location of brain (left or rightbrain)

value: Vascular


title: Subject_19_Control [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_91

value: Control

tag: Sex


title: Subject_15_Control [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_87

tag: batch


title: Lib_1E_CD127p

tag: cell type


title: miR342-5P+IM, replicate 2

city: Taipei

first: Yilin

last: Chiu

address: No.161, Minquan E. Road 6th Sec., Neihu dist.,

department: Biochemistry

country: Taiwan

institute: National Defense Medical Center

hyb_protocol: According to the manufacturer’s instructions.

growth_protocol: K562 cells were maintained in RPMI-1640 medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNA was isolated from K562 cells and lysis by TRIzol reagent (ThermoFisher Scientific Inc., Waltham, MA, USA) according to the manufacturer's protocol.

treatment_protocol: K562 cells were pre-treated with miR-NEG or miR-342-5P 20nM for 1 day, then followed by IM 0.5μM treatment. Total RNA of each treated cells was extracted 24 hours after IM exposure and gene expressions were compared among 4 groups; control (miR-NEG), miR-342-5P, miR-NEG+IM, and miR-342-5P+IM.

tag: treatment

value: miR-342-5P 20nM+imatinib 0.5μM


title: US-1672817_cortex__lean

tag: status


title: miR342-5P, replicate 1

scan_protocol: According to the manufacturer’s instructions.


title: CER_40_Case

description: mRNA & lncRNA transcriptome data

tag: rin

value: Stroke

value: Steatosis


title: Lib_1B_CD127p


title: US-1672816_cortex__lean

value: Lean


title: miR342-5P+IM, replicate 1

data_processing: According to the manufacturer’s instructions.


title: US-1672767_cortex_DIO

value: DIO


title: US-1671433_cortex_DIO


title: US-1672819_cortex__lean


title: Subject_14_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_86

value: AlcoholUseDisorder

value: Female

tag: brain weight

tag: brain ph

tag: cause of death category

tag: smoking

value: Cirrhosis


title: US-1671432_cortex_DIO


title: CER_41_Control

description: mRNA & lncRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Male

tag: pmi

value: Left

value: Congestion


title: CER_43_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: brainweight

tag: leftrightbrain

tag: causeofdeathcategory

value: Unknown

value: Current

value: Normal


title: Lib_2D_CD127n


title: CER_46_Case

description: mRNA & lncRNA transcriptome data

value: Right

value: Cardiac

tag: liverclass


title: CER_37_Case

description: mRNA & lncRNA transcriptome data

tag: Sex

value: Respiratory

value: Never


title: CER_44_Case

description: mRNA & lncRNA transcriptome data

tag: batch

value: Former

value: Steatosis


title: Subject_13_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_85

value: Control

tag: alcohol daily use(gram/day)

tag: location of brain (left or rightbrain)

tag: liver class


title: US-1659495_kidney__lean

source_name: Kidney

tag: status

value: Lean


title: Subject_7_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_79

value: AlcoholUseDisorder

value: Female

tag: rin

tag: brain weight


title: S65_pMT10_CD4

city: Porto

first: Ana

middle: Raquel

last: Maceiras

address: Rua Alfredo Allen, 208

country: Portugal

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipB_torrent-server_4086.bcmatrix.xls
IonXpress_065

data_processing:
Run metrics on technical reproducibility, read alignment to mm10 reference genome, and detection of on-target transcripts was performed using Torrent Suite Software v5.6, producing a raw count matrix as output.
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: CD4 T cells

growth_protocol: Not applicable - cells were sort-purified prior to RNA extraction

extract_protocol:
Total RNA from the different sorted populations was extracted with RNeasy Micro kit
Sequencing library was obtained using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit; Targeted RNA-seq

treatment_protocol: Mice were fed with zinc-enriched (pMT-10 plus Zn; and BL6 plus Zn) or control (pMT-10 control) water for 30 days.

tag: strain

tag: tissue

value: Bone marrow

tag: cell type

value: CD4 T cells

tag: treatment

tag: cells purification

value: Fluorescence-activated cell sorting (FACS)


title: Subject_12_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_84

tag: aud status

value: Male

tag: brain ph

tag: pmi

value: Left

tag: cause of death category

tag: smoking


title: miRNEG, replicate 1

label_protocol: According to the manufacturer’s instructions.

value: miR-NEG 20nM


title: CER_35_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

tag: brainweight

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

value: Current

tag: liverclass


title: Subject_11_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_83

tag: alcohol daily use(gram/day)

tag: rin

tag: brain weight

tag: location of brain (left or rightbrain)

value: Cardiac

tag: liver class

value: Congestion


title: CER_34_Control

description: mRNA & lncRNA transcriptome data

tag: aud status


title: Subject_5_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_77

tag: brain ph

value: Right

value: Respiratory

value: Cirrhosis


title: S15_pMT10_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipB_torrent-server_4086.bcmatrix.xls
IonXpress_015

tag: strain

tag: tissue

tag: cell type

tag: treatment

tag: cells purification


title: CER_39_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

tag: pmi

tag: smoking

value: Never


title: Subject_10_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_82

tag: alcohol daily use(gram/day)

tag: cause of death category


title: US-1659492_kidney__lean

tag: status

value: Lean


title: US-1672766_cortex_DIO

value: DIO


title: S14_pMT10_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipB_torrent-server_4086.bcmatrix.xls
IonXpress_014

source_name: CD8 T cells

value: Bone marrow

value: CD8 T cells


title: miRNEG+IM, replicate 2

value: miR-NEG 20nM+imatinib 0.5μM


title: US-1659494_kidney__lean


title: CER_38_Control

description: mRNA & lncRNA transcriptome data

value: Male

tag: rin

tag: brainweight

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

tag: liverclass

value: Steatosis


title: Subject_8_Control [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_80

tag: aud status

tag: brain weight

tag: brain ph

tag: location of brain (left or rightbrain)

tag: liver class


title: US-1659491_kidney__lean


title: US-1671431_cortex_DIO


title: miR342-5P, replicate 2

tag: treatment


title: Subject_9_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_81

value: AlcoholUseDisorder

tag: Sex

tag: batch

value: Toxicity


title: miRNEG+IM, replicate 1


title: miRNEG, replicate 2

value: miR-NEG 20nM


title: US-1659493_kidney__lean


title: CAU_31_Control

description: mRNA & lncRNA transcriptome data

source_name: Human postmortem caudate

tag: alcoholdailyuse(gram/day)

tag: pmi

value: Cardiac

tag: smoking

value: Congestion


title: S66_pMT10_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipB_torrent-server_4086.bcmatrix.xls
IonXpress_066

tag: strain

tag: tissue

tag: cell type

tag: cells purification

value: Fluorescence-activated cell sorting (FACS)


title: CER_33_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: rin

tag: brainweight

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: HepaticBloodLoss

value: Former


title: US-1659490_kidney_DIO

tag: status

value: DIO


title: US-1659489_kidney_DIO


title: Subject_4_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_76

tag: aud status

tag: alcohol daily use(gram/day)

value: Female

tag: brain weight

tag: brain ph

tag: location of brain (left or rightbrain)

tag: cause of death category

value: Current

value: Normal


title: Subject_3_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_75

value: Control

tag: Sex

tag: batch

tag: pmi

tag: liver class


title: S12_pMT10plusZn_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_012

tag: strain

tag: tissue

value: Bone marrow

tag: cell type

value: CD8 T cells

tag: treatment

value: Zn in the drinking water for 30 days


title: Subject_1_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_73

value: Male

tag: rin

value: Left

tag: smoking

value: Never

value: MildSteatosis


title: Subject_2_Control  [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_74

value: Cardiac

value: Unknown


title: S13_pMT10_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipB_torrent-server_4086.bcmatrix.xls
IonXpress_013

value: CD4 T cells

tag: cells purification

value: Fluorescence-activated cell sorting (FACS)


title: S16_pMT10_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipB_torrent-server_4086.bcmatrix.xls
IonXpress_016


title: CER_36_Control

description: mRNA & lncRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: brainweight

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

tag: liverclass


title: Subject_6_AlcoholUseDisorder [Human postmortem hippocampus]

description:
mRNA transcriptome data
Sample_78

value: AlcoholUseDisorder

tag: alcohol daily use(gram/day)

tag: Sex

tag: brain weight

tag: brain ph

tag: location of brain (left or rightbrain)

tag: cause of death category

value: Respiratory


title: S10_pMT10plusZn_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_010

tag: strain

tag: tissue

tag: cell type


title: CAU_32_Control

description: mRNA & lncRNA transcriptome data

tag: batch

tag: rin

tag: pmi

tag: smoking

value: Current

value: Steatosis


title: US-1659488_kidney_DIO

tag: status

value: DIO


title: Subject_24_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_48

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: brain location (lef or right)

value: Cardiovascular

tag: liver class


title: Subject_23_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_47

tag: Sex

value: Female

value: Toxicity


title: S9_pMT10plusZn_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_009

value: Bone marrow

tag: treatment

value: Zn in the drinking water for 30 days

tag: cells purification


title: S8_pMT10plusZn_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_008

value: CD8 T cells


title: US-1659487_kidney_DIO


title: S11_pMT10plusZn_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_011


title: Subject_22_Control [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_46

value: Control

tag: brain weight

tag: brain ph

value: Left

value: Never

value: Normal


title: Subject_21_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_45

value: Male

tag: cause of death category

value: Cirrhosis


title: US-1659486_kidney_DIO


title: US-1659485_heart__lean

source_name: Heart

value: Lean


title: S6_BL6plusZn_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_006

tag: strain

tag: tissue

value: Fluorescence-activated cell sorting (FACS)


title: US-1659484_heart__lean


title: S5_BL6plusZn_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_005

tag: cell type

value: CD4 T cells


title: S7_pMT10plusZn_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_007


title: Subject_20_Control [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_44

tag: batch

tag: rin

value: Unknown

value: Congestion


title: Subject_19_Control [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_43

tag: pmi

value: Right

value: Cardiac

tag: smoking

value: Current


title: US-1659483_heart__lean

tag: status


title: S4_BL6plusZn_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_004

value: Bone marrow


title: Subject_18_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_42

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Hepatic

value: Steatosis


title: Subject_17_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_41

value: Control

tag: brain location (lef or right)

value: Vascular

tag: liver class


title: CAU_30_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: Sex

tag: brainweight

tag: leftrightbrain

tag: causeofdeathcategory

tag: liverclass


title: CAU_29_Case

description: mRNA & lncRNA transcriptome data

value: Male

value: Left

value: Normal


title: CAU_26_Control

description: mRNA & lncRNA transcriptome data

value: Former


title: CAU_28_Case

description: mRNA & lncRNA transcriptome data


title: US-1659482_heart__lean

value: Lean


title: US-1659481_heart__lean


title: US-1659480_heart_DIO

value: DIO


title: CAU_25_Control

description: mRNA & lncRNA transcriptome data

value: Congestion


title: S2_BL6plusZn_CD8

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_002

tag: strain

value: CD8 T cells

tag: treatment

value: Zn in the drinking water for 30 days

tag: cells purification

value: Fluorescence-activated cell sorting (FACS)


title: Subject_16_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_40

tag: batch

tag: brain weight

tag: brain ph

tag: cause of death category

value: Cirrhosis


title: CAU_27_Case

description: mRNA & lncRNA transcriptome data

tag: rin

tag: pmi

value: Right

value: Unknown

tag: smoking

value: Current


title: Subject_15_Control [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_39

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

value: Female

tag: brain location (lef or right)

value: Cardiac


title: CAU_24_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: Sex

value: Male

tag: brainweight

value: Stroke

value: Steatosis


title: S1_BL6plusZn_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_001

tag: tissue

value: Bone marrow

tag: cell type

value: CD4 T cells


title: US-1659478_heart_DIO

tag: status

value: DIO


title: BL/6_CMPs_2

description:
Msaraiva_25-04-2019_ChipA_torrent-server_2995.csv
IonXpress_011

data_processing:
Run metrics on technical reproducibility, read alignment to mm10 reference genome, and detection of on-target transcripts was performed usgin Torrent Suite Software v5.6, producing a raw count matrix as output.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Common myeloid progenitors (CMPs)

extract_protocol:
Total RNA from the different sorted populations was extracted with RNeasy Micro kit
Sequencing library was obtained using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit

treatment_protocol: Mice were fed with zinc for 15 days

tag: strain

value: Common myeloid progenitors (CMPs)

tag: treatment

value: Zn in the drinking water for 15 days


title: S3_BL6plusZn_CD4

description:
Auto_CatarinaMartins_TMGE_27-01-2021_ChipA_torrent-server_4084.bcmatrix.xls
IonXpress_003

value: Zn in the drinking water for 30 days

tag: cells purification

value: Fluorescence-activated cell sorting (FACS)


title: CAU_23_Control

description: mRNA & lncRNA transcriptome data

tag: batch

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Never

tag: liverclass

value: Congestion


title: Subject_14_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_38

value: AlcoholUseDisorder

tag: rin

tag: brain weight

tag: brain ph

tag: pmi

value: Left

tag: cause of death category

value: Toxicity

value: Current

tag: liver class

value: Cirrhosis


title: US-1659479_heart_DIO


title: Subject_13_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_37

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: brain location (lef or right)

value: Cardiac

tag: smoking

value: Normal


title: BL/6_CMPs_1

description:
Msaraiva_25-04-2019_ChipA_torrent-server_2995.csv
IonXpress_010

tag: strain

tag: tissue

value: Bone marrow

tag: cell type

tag: treatment


title: US-1659477_heart_DIO

tag: status

value: DIO


title: US-1659476_heart_DIO


title: Subject_12_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_36

tag: batch


title: Subject_10_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_34

tag: rin


title: US-1659475_hypothalamus__lean

source_name: Hypothalamus

value: Lean


title: Subject_11_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_35

tag: brain weight


title: US-1659474_hypothalamus__lean


title: pMT10_CD150+CD48+_1

description:
Msaraiva_16-11-2018_ChipA_torrent-server_2705.csv
IonXpress_009

source_name: Lineage- SCA-1+ c-KIT+ (LSK) CD150+ CD48+

value: Zn in the drinking water for 15 days

tag: cells purification


title: pMT10_HSC

description:
Msaraiva_25-04-2019_ChipA_torrent-server_2995.csv
IonXpress_012

source_name: Hematopoietic stem cells

value: Hematopoietic stem cells

value: Fluorescence-activated cell sorting (FACS)


title: CAU_20_Control

description: mRNA & lncRNA transcriptome data

tag: brainweight

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

tag: liverclass


title: CAU_22_Control

description: mRNA & lncRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Never

value: Steatosis


title: US-1659473_hypothalamus__lean


title: pMT10_CMPs_2

description:
Msaraiva_16-11-2018_ChipA_torrent-server_2705.csv
IonXpress_012

tag: strain

value: Common myeloid progenitors (CMPs)


title: Subject_9_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_33

value: AlcoholUseDisorder

tag: brain ph

tag: brain location (lef or right)

tag: cause of death category

value: Toxicity

tag: smoking

tag: liver class


title: Subject_8_Control [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_32

tag: batch

tag: rin

value: Left


title: pMT10_CD150+CD48+_2

description:
Msaraiva_16-11-2018_ChipA_torrent-server_2705.csv
IonXpress_010

tag: tissue

tag: cell type

value: Lineage- SCA-1+ c-KIT+ (LSK) CD150+ CD48+

tag: treatment

tag: cells purification


title: pMT10_CMPs_1

description:
Msaraiva_16-11-2018_ChipA_torrent-server_2705.csv
IonXpress_011


title: AMY_15_Control

description: mRNA & lncRNA transcriptome data

source_name: Human postmortem amygdala

value: Control

value: Male

tag: brainweight

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Congestion


title: AMY_16_Control

description: mRNA & lncRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Cardiac

value: Current

tag: liverclass


title: CAU_19_Case

description: mRNA & lncRNA transcriptome data

value: Case


title: CAU_21_Case

description: mRNA & lncRNA transcriptome data

value: Respiratory


title: US-1659472_hypothalamus__lean

tag: status

value: Lean


title: AMY_14_Case

description: mRNA & lncRNA transcriptome data

tag: smoking


title: Subject_6_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_30

value: Female

tag: brain weight

tag: brain ph

tag: brain location (lef or right)

tag: cause of death category

tag: liver class

value: Normal


title: CAU_17_Case

description: mRNA & lncRNA transcriptome data

tag: batch

tag: rin

value: Right

value: HepaticBloodLoss

value: Former


title: AMY_13_Case

description: mRNA & lncRNA transcriptome data

tag: brainweight


title: US-1659471_hypothalamus__lean


title: US-1659470_hypothalamus_DIO

value: DIO


title: Subject_5_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_29

value: AlcoholUseDisorder

tag: pmi

value: Cirrhosis


title: Subject_7_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_31


title: P-33

city: Shanghai

first: CHAO

last: LI

address: No. 2699, West GaoKe Road

country: China

institute: Shanghai First Maternity and Infant Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic [[ Bolger AM, Lohse M & Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30(15): 2114-2120.]] and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the human genome (GRCh38) using HISAT2 [[ Kim D, Langmead B & Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015; 12(4): 357-360.]].
FPKM [[ Roberts A, Trapnell C, Donaghey J, et al. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology 2011; 12(3): R22.]] of each gene was calculated using Cufflinks [[ Trapnell C, William BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnolgy 2010; 28(5): 511-515.]], and the read counts of each gene were obtained by HTSeq-count [[ Anders S, Pyl PT & Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 2015; 31(2): 166-169.]].
Genome_build: GRCh38
Supplementary_files_format_and_content: files include FPKM values for each Sample
Supplementary_files_format_and_content: raw gene counts for every gene and every sample

source_name: endometrial tissue

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

tag: tissue

value: paired adjacent nontumor tissue

tag: age

value: 67 years

value: famale


title: US-1659469_hypothalamus_DIO


title: P-32

value: 68 years


title: CAU_18_Control

description: mRNA & lncRNA transcriptome data

tag: aud status

value: Control

value: Male

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Cardiac

value: Steatosis


title: Subject_4_AlcoholUseDisorder [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_28

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Female

value: Toxicity

value: Current


title: AMY_12_Case

description: mRNA & lncRNA transcriptome data

value: Case

tag: smoking

tag: liverclass


title: US-1659468_hypothalamus_DIO

tag: status


title: P-30

value: 55 years


title: P-35

value: 59 years


title: Subject_3_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_27

tag: brain weight

tag: brain ph

tag: brain location (lef or right)

value: Normal


title: AMY_11_Case

description: mRNA & lncRNA transcriptome data

tag: batch

value: Right

value: Unknown


title: P-29

value: paired adjacent nontumor tissue

value: 63 years


title: AMY_8_Case

description: mRNA & lncRNA transcriptome data

tag: rin

value: Stroke


title: AMY_10_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: brainweight

value: Former

value: Congestion


title: P-28

value: 65 years

value: famale


title: US-1659465_duodenum__lean

source_name: Duodenum

value: Lean


title: P-23

value: 49 years


title: US-1659464_duodenum__lean


title: P-27

value: 46 years


title: AMY_9_Control

description: mRNA & lncRNA transcriptome data

value: Male

tag: pmi

value: Left

value: Cardiac


title: P-25

tag: tissue

value: 53 years


title: Subject_24_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

data_processing:
The Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow [BMC Genomics. 2014; 15:423] was used for raw reads (in fastq files) pre-processing, alignment, mature/precursor/novel miRNA qualification and prediction.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.
Small RNA-seq libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1) (NEB, Ipswich, MA, USA) with 250 ng of total RNAs.
RNA libraries were prepared for sequencing using the protocol for use with NEBNext Small RNA Library Prep Set for Illumina

value: Human postmortem ventral tegmental area

value: AlcoholUseDisorder

tag: brainph

value: Cardiovascular

value: Current

value: Steatosis


title: Subject_2_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_26

tag: aud status

value: Control

value: Female

value: Right

tag: cause of death category

value: Unknown

tag: liver class

value: Normal


title: Subject_1_Control  [Human postmortem caudate]

description:
mRNA transcriptome data
Sample_25

tag: alcoholdailyuse(gram/day)

value: Never

value: MildSteatosis


title: US-1659467_hypothalamus_DIO

value: DIO


title: US-1659463_duodenum__lean

value: Lean


title: AMY_7_Control

description: mRNA & lncRNA transcriptome data

tag: Sex

value: Male

tag: leftrightbrain

tag: causeofdeathcategory

value: Congestion


title: US-1659466_hypothalamus_DIO

tag: status


title: US-1659461_duodenum__lean


title: Subject_22_Control; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Left

value: Cardiac

tag: smoking

tag: liverclass


title: AMY_4_Control

description: mRNA & lncRNA transcriptome data


title: AMY_3_Case

description: mRNA & lncRNA transcriptome data

value: Case

value: Toxicity


title: I-KO 2

first: Lin-Juan

last: Du

address: 115 Jinzun Rd

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Clean reads were mapped to mouse genome using HISAT2 2.0 software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using formula: 10^6 * C / [N*L/(10^3)]. C is the number of reads unique mapped to the gene，N is the number of reads unique mapped to the whole genome, L is the base number of CDS region
Genome_build: mm9
Supplementary_files_format_and_content: excel file include FPKM values for each Sample
Supplementary_files_format_and_content: raw counts

source_name: vascular smooth muscle cells

extract_protocol:
Total RNA of VSMCs was exacted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: cell type

value: vascular smooth muscle cells

tag: genotype


title: Subject_21_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

value: AlcoholUseDisorder

tag: batch

tag: rin

tag: brainweight

value: Current

value: Cirrhosis


title: AMY_6_Control

description: mRNA & lncRNA transcriptome data

value: Control

tag: pmi

value: Steatosis


title: Subject_23_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

tag: tissue

tag: aud status

value: Female

tag: brainph

value: Right

value: Never


title: Subject_18_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Hepatic


title: I-KO 3


title: AMY_5_Case

description: mRNA & lncRNA transcriptome data

tag: Sex

value: Male

value: Respiratory


title: US-1659462_duodenum__lean

value: Lean


title: Subject_19_Control; Human postmortem ventral tegmental area

description: miRNA transcriptome data

tag: leftrightbrain

value: Cardiac

value: Congestion


title: Subject_20_Control; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Left

tag: causeofdeathcategory

value: Toxicity

value: Unknown


title: AMY_2_Control

description: mRNA & lncRNA transcriptome data


title: P-20

value: paired adjacent nontumor tissue

tag: age

value: 66 years

value: famale


title: US-1659460_duodenum_DIO

tag: status

value: DIO


title: US-1659459_duodenum_DIO


title: P-19

value: 56 years


title: I-WT 3

value: vascular smooth muscle cells

value: wild type


title: Subject_17_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

value: Control

value: Right

value: Vascular

tag: smoking

tag: liverclass

value: Normal


title: US-1659458_duodenum_DIO


title: P-16

value: 43 years


title: P-17

value: 59 years


title: P-18

value: 57 years


title: I-WT 2

tag: strain

tag: cell type


title: US-1659457_duodenum_DIO


title: P-21

value: 55 years


title: P-14

value: 48 years


title: US-1659455_liver__lean

source_name: Liver

value: Lean


title: US-1659456_duodenum_DIO


title: BTSC349, X+30

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

description: GBM cell line

data_processing:
Data analyses on fastq files were conducted with CLC Genomics Workbench (version 10.1.1, QIAGEN, The Netherlands).
The reads of all probes were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2
Trimmed reads were aligned against the hg38 genome using the STAR v2.4.1d aligner and unaligned reads were further processed using Bowtie 2 v2.2.5 aligner
Genome_build: GRCh38

source_name: human brain

extract_protocol:
Total RNA was extracted from snap-frozen cell pellets using the NucleoSpin RNA extraction kit (Macherey-Nagel, Germany) with DNaseI treatment according to manufactures protocol
Library preparation was performed according to the manufacturer’s protocol using the VAHTS™ Stranded mRNA-Seq Library Prep Kit for Illumina® V2 (Vazyme, China)

tag: gender

value: male

value: brain

tag: disease state

value: glioblastoma


title: Subject_14_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Female

tag: batch

tag: rin

tag: brainweight

value: Left

value: Toxicity

value: Current

value: Cirrhosis


title: I-WT 1

value: vascular smooth muscle cells

tag: genotype

value: wild type


title: Subject_16_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

tag: tissue

value: Human postmortem ventral tegmental area

tag: aud status

value: Male

tag: brainph

tag: pmi


title: P-13

value: paired adjacent nontumor tissue

value: 49 years

tag: Sex

value: famale


title: US-1659454_liver__lean

value: Lean


title: Subject_15_Control; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Control

tag: alcoholdailyuse(gram/day)

tag: leftrightbrain

tag: causeofdeathcategory

value: Cardiac

value: Normal


title: I-KO 1


title: BTSC268, X+0

description: GBM cell line

value: male

value: brain

value: glioblastoma


title: BTSC268, X+30

description: GBM cell line


title: Subject_12_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Left

tag: smoking

tag: liverclass


title: Subject_13_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Never


title: Subject_10_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Current

value: Congestion


title: AMY_1_Case

description: mRNA & lncRNA transcriptome data

value: Case

value: Right

value: HepaticBloodLoss

value: Former

value: Steatosis


title: US-1659451_liver__lean

tag: status

value: Lean


title: BTSC349, X+0

description: GBM cell line

tag: gender

tag: cell type


title: P-10

value: paired adjacent nontumor tissue

tag: age

value: 40 years

value: famale


title: US-1659453_liver__lean


title: BTSC23, X+30

description: GBM cell line

value: male

tag: disease state


title: BTSC233, X+30

description: GBM cell line

value: brain


title: US-1659450_liver_DIO

value: DIO


title: BTSC23, X+0

description: GBM cell line

value: glioblastoma


title: Subject_9_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

value: AlcoholUseDisorder

value: Male

tag: batch

tag: rin

tag: brainweight

value: Toxicity


title: Subject_11_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

tag: tissue

tag: aud status

value: Control

value: Left

value: Cardiac

value: Current

value: Congestion


title: Subject_6_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Female

tag: brainph

tag: pmi

value: Right

value: Respiratory

value: Normal


title: US-1659448_liver_DIO


title: NCH644, X+0

description: GBM cell line

value: male


title: P-6

value: paired adjacent nontumor tissue

value: 65 years

tag: Sex

value: famale


title: BTSC233, X+0

description: GBM cell line

value: brain

value: glioblastoma


title: P-12

value: 54 years


title: US-1659446_liver_DIO

value: DIO


title: Subject_7_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: leftrightbrain

value: Cirrhosis


title: US-1659447_liver_DIO


title: P-7

value: 56 years


title: P-9

value: 69 years


title: P-8

value: 51 years


title: US-1659445_gastrocMusc__lean

source_name: Gastco red muscle

value: Lean


title: P-11

value: 63 years


title: JHH520, X+0

description: GBM cell line


title: P-5

value: 67 years


title: US-1659449_liver_DIO


title: P-3

value: 52 years


title: Subject_3_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Control

value: Female

value: Left

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Current

value: Normal


title: P-2

value: paired adjacent nontumor tissue

value: 60 years

value: famale


title: paired adjacent nontumor tissue

value: 48 years


title: Subject_1_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

value: Male

value: Never

tag: liverclass

value: MildSteatosis


title: Subject_8_Control; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Steatosis


title: US-1659444_gastrocMusc__lean

tag: status

value: Lean


title: P-4


title: C-35

value: Cancer tissue

value: 59 years


title: Subject_23_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: AlcoholUseDisorder

value: Female

value: Right

value: Toxicity


title: C-33

value: 67 years


title: Subject_24_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: Left

value: Cardiovascular

value: Current


title: US-1659440_gastrocMusc_DIO

value: DIO


title: US-1659443_gastrocMusc__lean


title: NCH644, X+30

description: GBM cell line

tag: gender

value: male

tag: cell type

value: brain

value: glioblastoma


title: Control_sample_rep3

city: San Juan

first: Alfredo

last: Ghezzi

state: Puerto Rico

address: PO box 23360

department: Department of Biology

institute: University of Puerto Rico, Rio Piedras

data_processing:
The generated sequencing data was stored in FASTQ format and, the quality of the sequencing reads was assessed using FastQC 0.11.9.
Adapters present in the sequences were eliminated using Trimmomatic 0.39.
Tools from the “new tuxedo suite” were used to process the reads following the protocol by Pertea et al. (2016). Briefly, sequence alignment to the Drosophila dm6 genome assembly was completed using HISAT 2.2.0; SamTools was used to compress, sort, and index transcripts, while merging and quantifying transcripts was done using StringTie 2.1.4.
Calculation of differential expression was achieved using Ballgown (Pertea et al., 2016)
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each transcript in each Sample
Supplementary_files_format_and_content: tab-delimited text files with differential expression values (fold change, p-value, q-value) between Control and Ethanol treated samples calcualated for each transcript

organism: Drosophila melanogaster

growth_protocol: All flies were maintained on a standard cornmeal/molasses/agar medium under 12:12 light:dark conditions

extract_protocol:
Six days after egg-laying, as larvae began to crawl out of the food to proceed with pupae formation, individual third-instar larvae were collected using a needle, transferred to microcentrifuge tubes, and frozen at -80°C for 24 to 48 hours. Freezing was followed by the addition of 200uL of RNAlater-ICE Frozen Tissue Transition Solution (AM7030, Thermo Fisher Scientific) to larvae. Approximately 30 larval brains were dissected per replicate in RNAlater-ICE, for a total of three replicates (~90 larval brains) for each group. Total RNA was extracted from larval brains using EZ1 RNA Tissue mini kit (EZ1 RNA Tissue Mini Kit no. 959034, Qiagen). All samples were treated with DNase I (DNase Set no. 79254, Qiagen). RNA concentration and quality were evaluated using a Qubit 2.0 fluorometer (Life Technologies, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Capture of mRNA (poly-A selection) and library preparation was carried out using the Illumina TruSeq® Stranded mRNA Library Prep kit from 300ng of total RNA. Libraries were sequenced with an Illumina NextSeq 500/550 High Output Kit v2.5 for 80 cycles following manufacturer’s protocol (Illumina, Inc). At least 20 million reads were obtained for each replicate (a pool of 30 brains).

treatment_protocol: Chronic alcohol exposure was performed following the procedure described by Robinson et al. (2012a). Briefly, standard cornmeal food was supplemented with pure alcohol (Ethyl alcohol no. S73985A, Fisher Scientific) to obtain a 5% alcohol concentration in food (alcohol food). After melting the standard fly food for approximately 30 seconds, 2.65 mL of 95% alcohol was added to 50 mL of fly food just before re-solidification. Food was stirred to homogenize the solution and allowed to cool at room temperature for 24 hours. After the 24 hours were through, adult CS files were transferred to each bottle and allowed to lay eggs for 24 hours. At the end of the 24 hours, adult flies were discarded. The alcohol food was supplemented daily by pipetting 0.3 mL with 10% alcohol on the surface of the food until larvae reached the third instar stage, ~5-6 days after eggs had been laid. For control larvae, the food was supplemented with water when melted instead of alcohol (control food). Control food was not supplemented daily.

tag: strain

value: Canton-S

tag: developmental stage

value: Larvae (third instar)

tag: treatment

value: control (grown in regular food)

value: dissected larval brains (pool of ~30 brains)


title: Ethanol-treated_sample_rep3

value: Ethanol (grown in 5% ethanol disloved in regular food (v/v))


title: JHH520, X+30

description: GBM cell line

tag: disease state


title: GBM-1, X+30

description: GBM cell line


title: C-30

tag: tissue

value: Cancer tissue

tag: age

value: 55 years

value: famale


title: Control_sample_rep2


title: Subject_2_Control ; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

tag: aud status

value: Control

value: Female

tag: batch

tag: rin

tag: brainweight

tag: brainph

value: Right

value: Cardiac

value: Unknown

value: Normal


title: US-1659442_gastrocMusc__lean

value: Lean


title: Subject_4_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

value: Current


title: US-1659441_gastrocMusc__lean

tag: status


title: GBM-1, X+0

description: GBM cell line

tag: gender

value: male

tag: cell type

value: brain

value: glioblastoma


title: Subject_21_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: Male

value: Left

tag: smoking

tag: liverclass

value: Cirrhosis


title: Subject_22_Control; Human postmortem putamen

description: miRNA transcriptome data

tag: tissue

value: Control

value: Never


title: C-32

value: Cancer tissue

tag: age

value: 68 years

value: famale


title: Subject_5_AlcoholUseDisorder; Human postmortem ventral tegmental area

description: miRNA transcriptome data

value: Human postmortem ventral tegmental area

tag: aud status

value: Female

value: Right

value: Respiratory


title: Ethanol-treated_sample_rep1

tag: strain

value: Canton-S

tag: developmental stage

value: Larvae (third instar)

tag: treatment

value: Ethanol (grown in 5% ethanol disloved in regular food (v/v))

value: dissected larval brains (pool of ~30 brains)


title: Ethanol-treated_sample_rep2


title: Control_sample_rep1

value: control (grown in regular food)


title: P-15

value: paired adjacent nontumor tissue

value: 50 years


title: C-28

value: 65 years


title: US-1659438_gastrocMusc_DIO

value: DIO


title: US-1659437_gastrocMusc_DIO


title: Subject_20_Control; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: Control

tag: batch

tag: rin

tag: brainweight

tag: brainph

value: Left

value: Toxicity

value: Unknown

value: Congestion


title: C-29

value: Cancer tissue

value: 63 years

tag: Sex

value: famale


title: US-1659439_gastrocMusc_DIO


title: RNAseq.ctrl.unf_egg.rep2

city: Freiburg

first: Michael

last: Rauer

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). RNA-seq was processed using the mRNA-seq workflow(–trim option).
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary file is a featureCounts table of number of reads per genes (stranded)

source_name: unfertilized eggs

extract_protocol:
RNA extraction was performed as in Zenk et al., 2017. Briefly, chloroform extraction was performed followed RNA precipitation with Isopropanol. Samples were then washed twice with 80% EtOH and resuspended in TURBO DNase (Ambion AM2238) reaction mix. Finally, DNase was inactivated.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA protocol

tag: genotype

tag: timepoint

value: unfertilized eggs

tag: assay

value: RNA-seq


title: US-1659434_soleusMusc__lean

source_name: Soleus muscle

tag: status

value: Lean


title: US-1659435_soleusMusc__lean


title: US-1659436_gastrocMusc_DIO


title: C-23

value: 49 years


title: RNAseq.ctrl.unf_egg.rep4


title: C-25

value: 53 years


title: Subject_19_Control; Human postmortem putamen

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Female

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Current


title: C-27

tag: tissue

tag: age

value: 46 years


title: Subject_18_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

tag: aud status

value: AlcoholUseDisorder

value: Male

value: Hepatic

tag: liverclass

value: Steatosis


title: Subject_15_Control; Human postmortem putamen

description: miRNA transcriptome data

value: Control

tag: batch

tag: rin

value: Left

value: Normal


title: US-1659433_soleusMusc__lean


title: RNAseq.ctrl.unf_egg.rep3

value: unfertilized eggs

value: RNA-seq


title: C-19

value: Cancer tissue

value: 56 years

value: famale


title: Subject_16_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

tag: brainweight

tag: brainph

value: Cirrhosis


title: RNAseq.ctrl.unf_egg.rep1

tag: genotype


title: C-21

value: 55 years

tag: Sex


title: Subject_12_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: Cardiac

value: Current


title: Subject_17_Control ; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: Right

value: Vascular


title: C_H3K36me3.ctrl.st5.rep2

description:
processed data file:
h3k36me3.subtract_input.ctrl.mean.bw

library_source: genomic

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). ChIP-seq samples were processed with the DNA-mapping workflow (–trim, --dedup, –properPairs), followed by assay-specific workflow, i.e. ChIP-seq.
Differential Pol II occupancy was determined using the method described in Blythe and Wieschaus, 2015. In brief, reads were countered per transcript using featureCounts (-t transcript -g transcript_id -f -O -Q 3 --primary -s 0). Reads were counted multiple times if they overlap several isoforms. Then, per transcript read counts were processed with edgeR (Robinson et al., 2010) to compute differential Pol2 occupancy. Like in the published method, transcripts spanning less than 125 nucleotides were discarded and only transcripts with read counts across replicates sum more that 10 reads were considered.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs contains library size and input corrected bigwig tracks and the promoter quantification of the Rpb3 (pol2) ChIP-seq.

molecule: genomic DNA

source_name: embryos

extract_protocol:
ChIP-seq experiments were performed as in Zenk et al., 2017. Briefly, nuclei were extracted in lysis buffer (140 mM NaCl, 15 mM HEPES [pH 7.6], 1 mM EDTA, 0.5 mM EGTA, 1 % TritonX100, 0.5 mM DTT, 0.1 % Sodium Deoxycholate, 10 mM Sodium Butyrate, 1X Protease Inhibitors) and subsequent ultrasound treatment (Covaris E220, 45 sec, peak power 75, duty factor 10, cycles burst 200). Fixed chromatin was then sheared using Covaris E220 (900 sec, peak power 140, duty factor 5, cycle burst 200) and precleared overnight. Each sample was incubated with the relevant antibody and concentration for at least 4 hrs at 4°C. Samples were then washed, eluted and decrosslinked overnight by incubation at 65°C. Next, samples were treated with RNaseA(50mg/mL final concentration) for 30min at 37°C and ProteinaseK (200mg/mL, final) for 3 hrs at 56°C.
Libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).

tag: timepoint

tag: assay

value: ChIP-seq

tag: chip antibody

value: H3K36me3 (Abcam, Cat. No. ab9050)


title: US-1659429_soleusMusc_DIO

tag: status

value: DIO


title: Subject_14_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Female

tag: pmi

tag: leftrightbrain

value: Left

value: Toxicity


title: C-20

tag: tissue

value: Cancer tissue

value: 66 years


title: C-17

tag: age

value: 59 years

value: famale


title: A_Input.dom-kd.st5_rep2

description: processed data file:

value: none (input)


title: US-1659452_liver__lean

value: Lean


title: US-1659431_soleusMusc__lean


title: US-1659428_soleusMusc_DIO


title: RNAseq.ctrl.st5.rep3

value: RNA-seq


title: US-1659432_soleusMusc__lean


title: RNAseq.ctrl.st5.rep4


title: Subject_10_Control ; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

tag: aud status

value: Control

value: Male

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Current

value: Congestion


title: A_H2Av.dom-kd.st5_rep2

description:
processed data file:
H2Av.subtract_input.dom-kd.pooled.bw

value: ChIP-seq

value: Histone H2Av antibody (Active Motif, Cat. No. 39715, lot No.00417003)


title: C-18

value: 57 years


title: US-1659427_soleusMusc_DIO

value: DIO


title: Subject_11_Control ; Human postmortem putamen

description: miRNA transcriptome data

tag: batch

tag: rin

value: Left

tag: liverclass


title: US-1659426_soleusMusc_DIO


title: C_H3K36me3.ctrl.st5.rep1

tag: genotype

value: H3K36me3 (Abcam, Cat. No. ab9050)


title: A_Input.dom-kd.st5_rep1

description: processed data file:


title: Subject_13_Control ; Human postmortem putamen

description: miRNA transcriptome data

tag: Sex

tag: brainweight

tag: brainph

value: Never

value: Normal


title: A_H2Av.dom-kd.st5_rep1

tag: timepoint

tag: assay

tag: chip antibody


title: US-1659425_BAT__lean

source_name: BAT

tag: status


title: C-16

value: Cancer tissue

value: 43 years

value: famale


title: US-1659430_soleusMusc_DIO


title: A_Input.ctrl.st5_rep2

description: processed data file:

value: none (input)


title: US-1659424_BAT__lean

value: Lean


title: A_Input.ctrl.st5_rep1

description: processed data file:


title: Subject_7_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Female

tag: pmi

tag: leftrightbrain

value: Right

value: Cirrhosis


title: C-12

tag: tissue

tag: age

value: 54 years


title: C-14

value: 48 years


title: Subject_6_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

tag: aud status

tag: causeofdeathcategory

value: Respiratory

tag: smoking

value: Current


title: Subject_5_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

tag: batch

tag: rin

tag: liverclass


title: Subject_9_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

tag: Sex

value: Male

tag: brainweight

value: Toxicity

value: Steatosis


title: US-1659423_BAT__lean


title: A_H2Av.ctrl.st5_rep1

description:
processed data file:
H2Av.subtract_input.ctrl.pooled.bw

tag: genotype

tag: timepoint

value: ChIP-seq

value: Histone H2Av antibody (Active Motif, Cat. No. 39715, lot No.00417003)


title: C-10

value: Cancer tissue

value: 40 years

value: famale


title: C-9

value: 69 years