title: ATAC.dom-kd.st5.rep1

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). ATAC-seq were processed with the DNA-mapping workflow (–trim, --dedup, –properPairs), followed by assay-specific workflow, i.e. ATAC-seq by the ATAC-seq workflow.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs contains library size corrected bigwig tracks of ATAC fragments

extract_protocol:
ATAC-Seq protocol was performed as described previously by Buenrostro et. al, 2015 with the following modifications in sample preparation: Embryos were dechorionated in 50% bleach for 2 min, and crosslinked with 5mL of fixative. The fixative consisted of bufferA (60 mM KCl, 15 mM NaCl, 15 mM HEPES [pH 7.6], 4 mM MgCl2) supplemented with 1%PFA. Embryos were fixed for 15 min in an orbital shaker at maximum speed. The crosslinking was stopped by adding a final concentration of 225 mM glycine followed by incubation for 5 min in a rotating wheel. After washing with bufferA + 0.1% Triton X100, the embryos were hand-staged on a cooling station under a microscope with transmitted light. 25 embryos were used per replicate. Fixed embryos were then resuspendend in 1ml bufferA (60 mM KCl, 15 mM NaCl, 15 mM HEPES [pH 7.6], 4 mM MgCl2) and crushed with ultrasound (Covaris E220, 45 sec, peak power 75, duty factor 10, cycles burst 200). Nuclei were pelleted by centrifugation (3200g, 10min at 4°C). We proceeded using the protocol of Buenrostro et. al, 2015. Briefly, nuclei were resuspended in transposition reaction. Samples were then incubated at 37°C for 30 min and immediately purified using the Qiagen MinElute PCR Purification Kit, according to manufacturer’s instructions. Transposed DNA was eluted in 10μl of elution buffer (buffer EB, Qiagen MinElute PCR Purification Kit) and amplified as stated in Buenrostro et al., 2015
For library amplification, all the sequences of custom primers were taken from Buenrostro et al., 2013. The number of PCR cycles for each sample was determined using qPCR as recommended by Buenrostro, et al., 2015, and the remaining 45 μl PCR reaction was further amplified. DNA from these libraries was then purified using AMPure beads (Beckman Coulter, A63881) following the manufacturer’s instructions.

tag: assay

value: ATAC-seq


title: Subject_8_Control; Human postmortem putamen

status: Public on Oct 13 2021

type: SRA

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

country: USA

institute: Boston University School of Medicine

description: miRNA transcriptome data

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: tissue

value: Human postmortem putamen

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: C-13

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

molecule: polyA RNA

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.

value: Cancer tissue

tag: age

value: 49 years

value: famale


title: Subject_4_AlcoholUseDisorder; Human postmortem putamen

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Female

value: Right

value: Toxicity

value: Current

value: Normal


title: A_H2Av.ctrl.st5_rep2

city: Freiburg

first: Michael

last: Rauer

address: Breisacherstr. 153

department: Medical Faculty

country: Germany

institute: University of Freiburg

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

organism: Drosophila melanogaster

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: genotype

tag: timepoint

value: ChIP-seq

tag: chip antibody

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


title: C-11

tag: tissue

value: 63 years


title: US-1659422_BAT__lean

city: Seattle

first: Sara

middle: A

last: Murray

state: WA

address: 530 Fairview Ave N

department: Obesity Research Group

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: BAT

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-1659421_BAT__lean


title: C-8

value: 51 years


title: US-1659417_BAT_DIO

value: DIO


title: C-15

value: 50 years


title: US-1659420_BAT_DIO


title: US-1659416_BAT_DIO


title: C-5

value: 67 years


title: Subject_23_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Never

value: Steatosis


title: US-1659415_mesfat__lean

source_name: Mesenteric Fat


title: Subject_3_Control ; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: Control

tag: Sex

tag: batch

value: Left

value: Cardiac


title: PUT_95_Control

type: RNA

description: miRNA transcriptome data

hyb_protocol: A “rotisserie” oven was used to carry out the array hybridization at 48°C and 60 rpm for 16 to 18 hours.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 with Autoloader.

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

label: biotin

source_name: Human postmortem putamen

label_protocol: More than 100 ng of total RNA was used in the Affymetrix miRNA4.0 array assay. RNAs were labeled using the FlashTag Biotin Labeling kit and hybridized to the 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 prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.

value: Male

tag: rin

tag: brainweight

value: Right

value: Congestion


title: US-1659419_BAT_DIO


title: ATAC.ctrl.st5.rep1

tag: assay

value: ATAC-seq


title: US-1659418_BAT_DIO


title: Subject_21_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: brainph

tag: pmi

tag: leftrightbrain

value: Current

value: Cirrhosis


title: Subject_24_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: causeofdeathcategory

value: Cardiovascular

tag: smoking

tag: liverclass


title: C-6

value: Cancer tissue

tag: age

value: 65 years

value: famale


title: C-7

value: 56 years


title: Subject_2_Control ; Human postmortem putamen

description: miRNA transcriptome data

value: Female

value: Unknown

value: Normal


title: US-1659414_mesfat__lean

value: Lean


title: C-2

value: 60 years


title: C-4


title: Subject_20_Control; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: Control

value: Left

value: Toxicity


title: P5-lymph node 2-scRNA

city: Nanjing

first: kun

last: xu

address: 300 Guangzhou Road

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

description:
Patient 5-Sample 15
scRNA-seq

data_processing:
Quality control.
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.6.1a.
Aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.expression_matrix.txt: Expression matrix file using RNA raw counts.

source_name: lymph node

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×10^5 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single-cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

tag: patient id

value: lymph node

tag: treatment

value: untreated

tag: tnm stage

tag: molecular typing


title: PUT_92_Case

description: miRNA transcriptome data

tag: aud status

value: Case

tag: alcoholdailyuse(gram/day)

value: Male

value: Cardiac

value: Former

value: Steatosis


title: C-1

tag: tissue

value: Cancer tissue

value: 48 years

tag: Sex

value: famale


title: Subject_22_Control; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Female

tag: batch

tag: rin

tag: brainweight

value: Never

value: Normal


title: PUT_93_Case

description: miRNA transcriptome data

tag: brainph

tag: pmi

value: Current


title: Subject_19_Control; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: Control

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Congestion


title: US-1659412_mesFat_DIO

tag: status

value: DIO


title: P5-lymph node 1-scRNA

description:
Patient 5-Sample 14
scRNA-seq

value: lymph node

value: untreated


title: US-1659411_mesFat_DIO


title: PUT_91_Case

description: miRNA transcriptome data

value: Case

value: Male

value: Unknown

tag: smoking

tag: liverclass


title: PUT_94_Case

description: miRNA transcriptome data

value: Cardiac

value: Steatosis


title: C-3

value: Cancer tissue

tag: age

value: 52 years

value: famale


title: PUT_90_Control

description: miRNA transcriptome data

value: Left

value: Former


title: P4-lymph node 2-scRNA

description:
Patient 4-Sample 12
scRNA-seq

tag: patient id

tag: treatment

tag: tnm stage

value: TNBC


title: PUT_96_Control

description: miRNA transcriptome data

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

value: Current


title: US-1659410_mesFat_DIO


title: US-1659413_mesfat__lean

value: Lean


title: PUT_88_Case

description: miRNA transcriptome data

tag: Sex

value: Stroke


title: US-1659407_subqFat__lean

source_name: Subcutaneous Fat


title: PUT_89_Control

description: miRNA transcriptome data

tag: batch

value: Congestion


title: P5-primary breast cancer-scRNA

description:
Patient 5-Sample 13
scRNA-seq

source_name: primary breast cancer

tag: tissue

value: primary breast cancer

value: untreated

tag: molecular typing


title: Subject_1_Control ; Human postmortem putamen

description: miRNA transcriptome data

value: Human postmortem putamen

value: Male

tag: rin

tag: brainweight

tag: brainph

value: Never

value: MildSteatosis


title: Subject_14_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: AlcoholUseDisorder

value: Female

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

value: Cirrhosis


title: Subject_13_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Left

value: Cardiac

tag: smoking

tag: liverclass

value: Normal


title: Subject_17_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Control

value: Right

value: Vascular


title: US-1659409_mesFat_DIO

tag: status

value: DIO


title: Subject_18_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Hepatic

value: Current

value: Steatosis


title: P3-lymph node 2-scRNA

description:
Patient 3-Sample 9
scRNA-seq

tag: patient id

value: lymph node

tag: treatment

value: untreated


title: PUT_85_Case

description: miRNA transcriptome data

tag: aud status

value: Case

value: Male

value: Respiratory

value: Never


title: PUT_86_Control

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)


title: P4-primary breast cancer-scRNA

description:
Patient 4-Sample 10
scRNA-seq

value: primary breast cancer

tag: tnm stage

value: TNBC


title: Subject_12_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: AlcoholUseDisorder

tag: Sex

tag: batch

value: Left

value: Cardiac


title: US-1659404_subqFat__lean

value: Lean


title: PUT_83_Case

description: miRNA transcriptome data

value: Right

value: Toxicity


title: PUT_84_Control

description: miRNA transcriptome data

value: Control

value: Current

value: Normal


title: US-1659405_subqFat__lean


title: PUT_82_Control

description: miRNA transcriptome data

value: Steatosis


title: Subject_16_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: tissue

value: Cirrhosis


title: P4-lymph node 1-scRNA

description:
Patient 4-Sample 11
scRNA-seq

value: lymph node

value: untreated

tag: molecular typing


title: US-1659408_subqFat__lean


title: Subject_15_Control; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Female

tag: rin

tag: brainweight


title: PUT_87_Control

description: miRNA transcriptome data

value: Male

tag: brainph

tag: pmi

value: Never

value: Congestion


title: US-1659406_subqFat__lean


title: Subject_7_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: AlcoholUseDisorder

tag: leftrightbrain

tag: causeofdeathcategory


title: P1-lymph node 2-scRNA

description:
Patient 1-Sample 3
scRNA-seq

value: TNBC


title: Subject_11_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Left

value: Cardiac

tag: smoking

tag: liverclass


title: PFC_78_Case

description: miRNA transcriptome data

source_name: Human postmortem prefrontal cortex

value: Case

value: Right


title: P3-primary breast cancer-scRNA

description:
Patient 3-Sample 7
scRNA-seq

tag: patient id

value: primary breast cancer


title: US-1659403_subqFat_DIO

tag: status

value: DIO


title: Subject_9_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: aud status

value: Toxicity

value: Current

value: Steatosis


title: Subject_10_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Control

tag: alcoholdailyuse(gram/day)


title: PFC_77_Case

description: miRNA transcriptome data

value: Normal


title: PUT_81_Case

description: miRNA transcriptome data

value: Male

value: HepaticBloodLoss

value: Former


title: Subject_5_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: Female

value: Respiratory

value: Cirrhosis


title: US-1659400_subqFat_DIO


title: P2-lymph node 1-scRNA

description:
Patient 2-Sample 5
scRNA-seq

value: lymph node

tag: treatment

value: untreated

tag: tnm stage

value: luminal B


title: P3-lymph node 1-scRNA

description:
Patient 3-Sample 8
scRNA-seq


title: P1-primary breast cancer-scRNA

description:
Patient 1-Sample 1
scRNA-seq

value: primary breast cancer

value: TNBC


title: Subject_8_Control; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: Sex

tag: batch

value: Left

value: Cardiac

value: Never


title: RNASeq_preNeu_Rep3

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

data_processing:
Quality control: FastQC v0.11.5 and MultiQC v1.6
Trimming: Trimmomatic v0.36
Alignment (ChIP-Seq, ATAC-Seq): BWA v0.7.17
Peak calling (ChIP-Seq, ATAC-Seq): Macs2 v2.1.0
Pseudoalignment: Kallisto v0.44.0
Genome_build: mm10
Supplementary_files_format_and_content: Xlsx file containing normalized RNA-Seq counts in TPM. Peak calling results in narrowPeak and broadPeak format.

source_name: bone marrow

extract_protocol:
RNA was extracted using MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with RNA 6000 Pico kit (Agilent). RNA-seq libraries were prepared from the RNA extracts using the Illumina TruSeq Stranded mRNA Kit according to the manufacturer’s instructions, and sequenced using the TruSeq PE Clusterkit v3-cBot-HS on an Illumina HiSEq 2000 system. Sequencing reads were aligned to the mm10 genome using Tophat v2.0.10. Reads were processed with Samtools and then mapped to Ensembl transcripts using HTSeq. Differential expression was tested using the DESeq R package (Anders & Huber, 2010)(R Core Team 2015, http://www.r-project.org/). A genome coverage file was generated and scaled to RPM using Bedtools.
ChIPs were performed on 1-20x106 sorted cells. The cells were cross-linked with 1.5mM EGS for 20 minutes and 1% formaldehyde for 8 minutes before quenching with 125mM glycine. Cells were lysed in lysis buffer and sonicated using a Covaris E220 to generate 200-600bp fragments (Lee, Johnstone, & Young, 2006). Samples were immuno-precipitated with 2-5 µg of either anti- GFI1 (AF3540, R&D systems), anti-H3K4me1 (ab8895, Abcam),  anti-H3K4me2 (ab11946; Abcam), anti-H3K4me3 (ab8580; Abcam) or anti-H3K9me2 (ab1220; Abcam). Libraries were generated according to Illumina's instructions. Libraries were sequenced on the Illumina Hi-seq 2000 following the manufacturer's protocols to obtain 50bp paired end reads. External datasets were obtained in the form of .bed files of peaks and .wig visualization tracks, aligned to the mm9 build, with the exception of LSD1, which only included the .bed peak file.

tag: strain

tag: genotype

value: wild type

tag: age

value: adult 6-12 weeks

tag: tissue/cell type

value: GMP


title: PFC_76_Case

description: miRNA transcriptome data

value: Case

value: Male

tag: rin

tag: brainweight

tag: brainph

tag: pmi

value: Steatosis


title: RNASeq_matNeu_Rep2

value: preNeu


title: P2-lymph node 2-scRNA

description:
Patient 2-Sample 6
scRNA-seq

tag: tissue

tag: molecular typing


title: RNASeq_preNeu_Rep2


title: RNASeq_matNeu_Rep1


title: P1-lymph node 1-scRNA

description:
Patient 1-Sample 2
scRNA-seq

tag: patient id


title: P2-primary breast cancer-scRNA

description:
Patient 2-Sample 4
scRNA-seq


title: PFC_79_Control

description: miRNA transcriptome data

tag: aud status

value: Control

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

tag: smoking

tag: liverclass

value: Congestion


title: PFC_80_Control

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

value: Current


title: US-1659402_subqFat_DIO

tag: status

value: DIO


title: Subject_6_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: AlcoholUseDisorder

value: Female

value: Respiratory

value: Normal


title: RNASeq_GMP_Rep3

tag: strain

tag: genotype

value: wild type

tag: age

tag: tissue/cell type

value: matNeu


title: DBM-ECM for 3 days

city: Chongqing

first: Moyuan

last: Deng

state: Chongqing

address: 30 Gao tanyan Street

department: Southwest hospital

institute: Army medical university

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
read counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: macrophages

growth_protocol: Human monocytic cell line THP-1 was maintained in RPMI 1640 medium containing 10% FBS as the previous studies. 5 × 10^5/mL THP-1 cells were differentiated to macrophages with 50 ng/mL of PMA for 48-h and cultured in RPMI 1640 medium containing 10% FBS without PMA.

extract_protocol:
The culture medium were removed, washed with PBS for 3 times, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cells were differentiated to macrophages and cultured in RPMI 1640 medium containing 10% FBS with scaffolds for 3 or 7 days.

tag: cell line

value: Human monocytic cell line THP-1

tag: treatment

value: THP-1 cells were differentiated to macrophages with 50 ng/mL of PMA for 48-h and cultured in RPMI 1640 medium containing 10% FBS with DBM-ECM scaffolds for 3 days.


title: Subject_4_AlcoholUseDisorder; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: tissue

tag: rin

tag: brainweight

tag: brainph

tag: pmi

value: Toxicity


title: PFC_75_Case

description: miRNA transcriptome data

tag: aud status

value: Case

value: Male

tag: leftrightbrain

tag: causeofdeathcategory

value: Unknown

tag: smoking


title: RNASeq_GMP_Rep1

value: adult 6-12 weeks


title: DBM for 7 days

value: THP-1 cells were differentiated to macrophages with 50 ng/mL of PMA for 48-h and cultured in RPMI 1640 medium containing 10% FBS with DBM scaffolds for 7 days.


title: Subject_24_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Human postmortem nucleus accumbens

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

value: Left

value: Cardiovascular

value: Current

tag: liverclass

value: Steatosis


title: Subject_3_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

value: Human postmortem prefrontal cortex

value: Control

value: Female

value: Cardiac


title: RNASeq_matNeu_Rep3

tag: strain

tag: genotype

value: wild type

tag: age

value: preNeu


title: DBM-ECM for 7 days

tag: cell line

value: Human monocytic cell line THP-1

tag: treatment

value: THP-1 cells were differentiated to macrophages with 50 ng/mL of PMA for 48-h and cultured in RPMI 1640 medium containing 10% FBS with DBM-ECM scaffolds for 7 days.


title: RNASeq_preNeu_Rep1

tag: tissue/cell type

value: GMP


title: PFC_73_Control

description: miRNA transcriptome data

value: Male

tag: rin

tag: brainweight

value: Former

value: Congestion


title: DBM for 3 days

value: THP-1 cells were differentiated to macrophages with 50 ng/mL of PMA for 48-h and cultured in RPMI 1640 medium containing 10% FBS with DBM scaffolds for 3 days.


title: Subject_1_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: tissue

tag: brainph

tag: pmi

value: Left

value: Never

value: MildSteatosis


title: Subject_2_Control ; Human postmortem prefrontal cortex

description: miRNA transcriptome data

tag: aud status

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Unknown

value: Normal


title: Subject_20_Control; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Human postmortem nucleus accumbens

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Female

value: Toxicity

tag: smoking


title: PFC_72_Case

description: miRNA transcriptome data

value: Case

tag: batch

value: Stroke

value: Current

tag: liverclass

value: Steatosis


title: PFC_71_Control

description: miRNA transcriptome data

value: Male

value: Cardiac


title: Subject_23_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: AlcoholUseDisorder


title: CutTag.H4k12ac.dom-kd.rep2

data_processing:
Library strategy: Cut&Tag
The Cut&Tag libraries with spike-ins were processed using snakePipes (version 2.4.3) with trimming, aligning to the hybrid genome of dm6 and Lambda phage (Escherichia phage Lambda, NCBI GenBank ID: J02459.1) with the Cut&Tag specific parameters as reported in Kaya-Okur et al. 2019. Alignments with MAPQ below 3 were discarded (DNA-mapping --mapq 3 --trim --properPairs --dedup --alignerOpts=”--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700”).
Spike-in normalization was performed by computing scaling factors using deeptools multiBamSummary with 1 kb bins on the Lambda phage genome. Then the signal tracks were produced with bamCoverage using the scaling factors.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are spike-in corrected bigwig tracks

extract_protocol:
Cut&Tag experiments were performed as in Kaya-Okur, H.S., et al. 2019. Embryos were fixed with 1%PFA. 50 hand-staged embryos were used per sample. DNA was purified and 1pg of tagmented lambda phage genome was added to each sample as spike-in for quantification before library preparation.
Libraries were prepared by amplification of tagmented DNA fragments using NEBNext® Q5® HiFi PCR Master Mix (NEB, Cat. M0543). Primer sequences were taken from Buenrostro et al., 2015. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).

tag: genotype

tag: timepoint

tag: antibody

value: H4K12ac (Merck-Upstate, Cat. No. 07-595, lot No. 3272292)

tag: assay

value: Cut&Tag

tag: spikein

value: lambda phage genome


title: Subject_22_Control; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: rin

tag: brainweight

value: Left

value: Never


title: PFC_67_Case

description: miRNA transcriptome data

tag: brainph

value: Right


title: PFC_69_Case

description: miRNA transcriptome data

tag: pmi

value: Respiratory


title: ATACSeq_Gfi1_WT_matNeu

tag: strain

value: wild type

tag: age

value: adult 6-12 weeks

tag: tissue/cell type

value: preNeu


title: CutTag.H4k12ac.dom-kd.rep1


title: H3K4me3_Gfi1WT_GMP

value: GMP

tag: chip antibody

value: anti H3K4me3 antibodies


title: CutTag.Zelda.dom-kd.rep1

value: Zelda (Kindly provided by Melissa Harrison)


title: PFC_70_Control

description: miRNA transcriptome data

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: leftrightbrain

tag: causeofdeathcategory

value: Steatosis


title: CutTag.H4k12ac.ctrl.rep2

tag: genotype

tag: timepoint


title: Subject_18_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Human postmortem nucleus accumbens

value: Male

tag: batch

value: Hepatic

tag: smoking

value: Current

tag: liverclass


title: RNASeq_GMP_Rep2

value: matNeu


title: PFC_66_Control

description: miRNA transcriptome data

tag: rin

tag: brainweight

tag: brainph

value: Left

value: Cardiac


title: H3K4me2_Gfi1WT_matNeu

tag: strain

tag: age

value: anti H3K4me2 antibodies


title: CHD4_Gfi1KO_GMP

tag: tissue/cell type

tag: chip antibody

value: anti CHD4 antibody


title: Subject_17_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: pmi

value: Right

value: Vascular

value: Normal


title: CutTag.Zelda.dom-kd.rep2

tag: antibody

tag: assay

value: Cut&Tag

tag: spikein

value: lambda phage genome


title: CutTag.H4k12ac.ctrl.rep1

tag: genotype

tag: timepoint

value: H4K12ac (Merck-Upstate, Cat. No. 07-595, lot No. 3272292)


title: H3K4me2_Gfi1WT_GMP

value: wild type

value: adult 6-12 weeks

value: GMP

value: anti H3K4me2 antibody


title: CHD4_Gfi1WT_GMP


title: H3K4me2_Gfi1WT_preNeu


title: PFC_65_Case

description: miRNA transcriptome data

value: Case

tag: Sex

value: Male

tag: batch

tag: leftrightbrain

tag: causeofdeathcategory

value: HepaticBloodLoss

tag: smoking

value: Former

value: Steatosis


title: Subject_21_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Human postmortem nucleus accumbens

value: AlcoholUseDisorder

tag: rin

tag: brainweight

tag: brainph

value: Left

value: Current

tag: liverclass

value: Cirrhosis


title: HIPPO_62_Case

description: miRNA transcriptome data

source_name: Human postmortem hippocampus

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Right

value: Cardiac


title: HIPPO_60_Case

description: miRNA transcriptome data

tag: pmi


title: PFC_68_Control

description: miRNA transcriptome data

value: Control

value: Normal


title: CutTag.Zelda.ctrl.rep2

tag: antibody

value: Zelda (Kindly provided by Melissa Harrison)

tag: assay

value: Cut&Tag

value: lambda phage genome


title: Naïve CD4 T-cells [set2_Naive1]

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description:
set2_Naive1
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

data_processing:
library strategy: tRNA-seq
Read were trimmed using homerTool
Alignment was done to the genome concatenate with mature tRNA (Chan, P.P. & Lowe, T.M. (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucl. Acids Res. 44(Database issue):D184-D189.) using Bowtie2 with parameters --very-sensitive-local. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were assigned by ratio of valid reads of the possible mapping location.
Read count was done using BedTools-coverage count.
Genome_build: mm10
Supplementary_files_format_and_content: read counts of mature tRNA and sum of read per anticodon of all samples

source_name: Naïve CD4 T-cells

growth_protocol: Naïve cells were extracted from six spleens of B6 mice using the StemCell CD62L+CD44+ kit (female, 7 weeks, 6-9% naive). Each two spleens were pooled to a total of 3 samples extracted separately. A portion from the naïve state was taken to FASC sorted for live cells followed by RNA extraction. The remaining naive cells were activated by addition of anti-CD3/anti-CD28 activation bead (1:1 bead:cell ratio, thermoFisher Scientific Cat#11131D)    Cells were grown at 0.25 cell/ml in 24 wells, and were collected at 20h, 48h, and 72h after activation. At 20h only live cells were sorted. At 48 and 72 h cells were sorted into CD62L+CD44+ (memory T-cells) and CD62L-CD44+(effector T-cells). The cells were stained as followed, and analyzed using ARIAIII FACS:

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

treatment_protocol: cells were centrifuged at 12,000 rpm for 1 min, frozen in liquid nitrogen and stored at -80 ̊C until RNA extraction.

tag: strain

tag: activation stage

value: 72 hours

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: tRNA


title: ATACSeq_Gfi1_WT_preNeu

tag: genotype

value: wild type

tag: age

value: adult 6-12 weeks

tag: tissue/cell type

value: GMP


title: Subject_19_Control; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Human postmortem nucleus accumbens

tag: Sex

value: Female

tag: batch

tag: leftrightbrain

tag: causeofdeathcategory

tag: smoking

value: Congestion


title: MNase.st5.dom-kd.rep2

data_processing:
QC, mapping: DNA-mapping pipeline of snakepipes-v2.1.0 (Bhardwaj et al., 2019)
coverage files: deeptools-v 3.4.3 (Ramírez et al., 2016)
Supplementary_files_format_and_content: bigwig files containing read coverage

extract_protocol:
This protocol was modified from the Cut and Run protocol published by Skene and Henikoff, 2017. Embryos were smashed using a pestle in 50µl of the MNase wash buffer (20mM HEPESpH7.5, 150mM NaCl, 0.5mM Spermidine, 1x Protease inhibitor cocktail), then rinsed with 150µl of MNase wash buffer and centrifuged (600g, 3min at room temperature). Cells were wash afterwards in 500µl MNase wash buffer and resuspended in 1ml of MNase wash buffer. For eah sample, 10µl of Concanavalin A (Polyscience, 86057-3) beads were added and incubated for 15min under rotation. The beads were previously equilibrated with binding buffer (20mM HEPES pH7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Afterwards, the beads were resuspended in 1ml permeabilization buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.05% Digitonin, 2mM EDTA, 1x Protease inhibitor cocktail) and incubated for 2hrs under rotation. Beads were washed twice with 1ml digitonin wash Buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5mM Spermidine, 0.05% Digitonin, 1xProtease inhibitor cocktail). Next, 100µl of 37°C preheated digitonin wash buffer + MNase (20U, NEB M0247S) was added to each sample. Immediately after this, 3µl of 100 mM CaCl2 were supplemented to each sample. Samples were then incubated at 37°C for 30 min. To stop the reaction, 100 µl of stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05% digitonin, 50µg/ml RNaseA, 25µg/ml glycogen) was added. Samples were then incubated for another 30 min at 37°C. Chromatin was purified by adding 0.1%SDS and 20mg/ml of Proteinase K to each sample, followed by 1hr incubation at 50°C. DNA was afterwards purified and large fragments (>500bp) were removed using 0.5x volume of NucleoMag® NGS beads (Macherey-Nagel, 744970.50). The ChIP DNA Clean&Concentrator Kit (Zymo Research) was used to concentrate the samples according to manufacturer’s instructions. Digestion efficiency was assessed by capillary electrophoresis on the Fragment Analyzer (Advanced Analytical) before preparing libraries.
Libraries were prepared using the NEB Ultra II DNA Library Prep Kit for Illumina (E7645S and E6440) following the manufacturer’s instructions.

tag: timepoint

value: MNase-seq


title: HIPPO_63_Control

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Male

tag: rin

tag: brainweight

tag: brainph

tag: pmi

value: Right

value: Never

tag: liverclass


title: Naïve CD4 T-cells [set2_Naive3]

description:
set2_Naive3
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

tag: strain

tag: activation stage

tag: cell type

tag: molecule subtype


title: Subject_11_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Control

tag: Sex

value: Left

value: Cardiac

value: Current


title: MNase.st5.ctrl.rep2

tag: genotype

tag: assay


title: HIPPO_61_Case

description: miRNA transcriptome data

value: Case

tag: batch

tag: leftrightbrain

tag: causeofdeathcategory

tag: smoking

value: Normal


title: HIPPO_64_Control

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: rin

value: Steatosis


title: Subject_16_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: brainweight

tag: brainph

tag: pmi

value: Cirrhosis


title: HIPPO_58_Control

description: miRNA transcriptome data

value: Former

tag: liverclass


title: Subject_13_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Human postmortem nucleus accumbens


title: Subject_15_Control; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Female


title: MNase.st5.dom-kd.rep1

tag: timepoint


title: Subject_12_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data


title: Naïve CD4 T-cells [set2_Naive2]

description:
set2_Naive2
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

tag: strain

tag: activation stage

value: 72 hours

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: tRNA


title: activated CD4 T-cells, 72 hours after activation [set2_72h2]

description:
set2_72h2
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

value: 48 hours


title: CutTag.Zelda.ctrl.rep1

tag: genotype

tag: antibody

value: Zelda (Kindly provided by Melissa Harrison)

tag: assay

value: Cut&Tag

tag: spikein

value: lambda phage genome


title: activated CD4 T-cells, 72 hours after activation [set2_72h3]

description:
set2_72h3
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv


title: HIPPO_59_Case

description: miRNA transcriptome data

tag: Sex

value: Male

tag: batch

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Unknown

tag: smoking


title: HIPPO_57_Control

description: miRNA transcriptome data

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: rin

tag: brainweight

tag: brainph

value: Left

value: Cardiac

value: Congestion


title: MNase.st5.ctrl.rep1

tag: timepoint

value: MNase-seq


title: Subject_14_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Human postmortem nucleus accumbens

value: AlcoholUseDisorder

tag: pmi

value: Toxicity

value: Current

tag: liverclass

value: Cirrhosis


title: Rpb3.ctrl.c9-13_rep1

description:
processed data file:
Rpb3.ctrl.c9-13.pooled.bw

tag: genotype

value: ChIP-seq

tag: chip antibody

value: Rpb3 (Kindly provided by Carla Margulies)


title: Subject_7_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Female


title: Subject_10_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data


title: Subject_9_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Steatosis


title: Rbp3.ctrl.c9-13_rep2

tag: assay


title: activated CD4 T-cells, 48 hours after activation [set2_48h1]

description:
set2_48h1
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

tag: strain

tag: activation stage

value: 20 hours

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: tRNA


title: Input.ctrl.c9-13_rep2

description: processed data file:

value: none (input)


title: activated CD4 T-cells, 72 hours after activation [set2_72h1]

description:
set2_72h1
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

value: 48 hours


title: HIPPO_56_Case

description: miRNA transcriptome data

value: Case

tag: Sex

value: Male

tag: batch

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Stroke

tag: smoking


title: activated CD4 T-cells, 48 hours after activation [set2_48h3]

description:
set2_48h3
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv


title: Subject_8_Control; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Human postmortem nucleus accumbens

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: rin

tag: brainweight

tag: brainph

value: Cardiac

value: Never


title: activated CD4 T-cells, 20 hours after activation [set2_20h2]

description:
set2_20h2
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

value: naïve


title: Input.ctrl.c9-13_rep1

description: processed data file:

tag: genotype

tag: timepoint

value: ChIP-seq


title: Subject_5_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: AlcoholUseDisorder

value: Female

tag: pmi

value: Right

value: Respiratory

value: Current

tag: liverclass

value: Cirrhosis


title: Subject_4_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Toxicity

value: Normal


title: HIPPO_54_Control

description: miRNA transcriptome data

value: Male

value: Steatosis


title: HIPPO_55_Control

description: miRNA transcriptome data

value: Congestion


title: H2Av.ctrl.c9-13_rep2

description:
processed data file:
H2Av.subtract_input.ctrl.c9-13.pooled.bw

tag: assay

tag: chip antibody

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


title: activated CD4 T-cells, 48 hours after activation [set2_48h2]

description:
set2_48h2
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv

tag: strain

tag: activation stage

value: 20 hours

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: tRNA


title: Subject_6_AlcoholUseDisorder; Human postmortem nucleus accumbens

description: miRNA transcriptome data

value: Human postmortem nucleus accumbens

tag: Sex

tag: batch

tag: leftrightbrain

tag: causeofdeathcategory

tag: smoking


title: ribo-seq Naïve CD4 T-cells [RPF_NaiveB]

data_processing:
library strategy: ribo-seq
Sequencing reads were aligned as previously described (Tirosh, O. et al. The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions. PLoS Pathog. 11, (2015))
For comparing transcript expression level, mRNA and footprint counts were normalized to units of RPKM in order to normalize for gene length and for sequencing depth, based on the total number reads. Translation efficiency was calculated as the ratio between read counts (RPKM) of ribo-seq protected RNA fragments and mRNA sequencing.
Genome_build: mm10
Supplementary_files_format_and_content: read counts of and RPKM for genes of all samples

source_name: ribo-seq Naïve CD4 T-cells

growth_protocol: Naïve cells were extracted from six spleens of B6 mice using the StemCell CD62L+CD44+ kit (female, 7 weeks, 6-9% naive). Each seven spleens were pooled to a total of 3 samples extracted separately. Cells were activated by addition of anti-CD3/anti-CD28 activation bead (1:1 bead:cell ratio, thermoFisher Scientific Cat#11131D)    Cells were grown at 0.25 cell/ml in 24 wells, and were collected at 0h, 20h, 48h, and 72h after activation.

extract_protocol:
Cells were then placed on ice, washed twice with PBS containing 100µg/mL CHX, and lysed with lysis buffer (1% triton in 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol supplemented with 10 U/ml Turbo DNase and 100µg/ml cycloheximide). After lysis, samples were flash-frozen and stored in -80°C until further processing. mRNA samples were extracted using TRIZOL.
Subsequent, Ribo-seq library generation was performed as previously described (Finkel, Y. et al. Comprehensive Annotations of Human Herpesvirus 6A and 6B Genomes Reveal Novel and Conserved Genomic Features. bioRxiv (2019) doi:10.1101/730028.)

treatment_protocol: cells were treated with 100µg/mL CHX for 1 minute. Cells were then placed on ice, washed twice with PBS containing 100µg/mL CHX, and lysed with lysis buffer (1% triton in 20mM Tris 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol supplemented with 10 U/ml Turbo DNase and 100µg/ml cycloheximide). After lysis, samples were flash-frozen and stored in -80°C until further processing. Subsequent Ribo-seq library generation was performed as previously described

value: naïve

value: Ribosome protected mRNA


title: activated CD4 T-cells, 20 hours after activation [set2_20h3]

description:
set2_20h3
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv


title: H2Av.ctrl.c9-13_rep1

value: ChIP-seq


title: B_Input.dom-kd.st5.rep1

description: processed data file:

value: none (input)


title: HIPPO_53_Case

description: miRNA transcriptome data

tag: aud status

value: Case

tag: alcoholdailyuse(gram/day)

tag: rin

tag: brainweight

tag: brainph

value: Right

value: Respiratory

value: Never


title: B_Input.ctrl.st5.rep2

description: processed data file:

tag: genotype

tag: timepoint


title: activated CD4 T-cells, 20 hours after activation [set2_20h1]

description:
set2_20h1
processed data file:
set2_cytosolictRNAReads_RPM.csv
set2_cytosolictRNA_byAntiCodon_RPM.csv


title: HIPPO_50_Control

description: miRNA transcriptome data

value: Control

tag: pmi

value: Left

value: Cardiac

value: Current

tag: liverclass


title: Subject_3_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Female

value: Normal


title: B_Input.ctrl.st5.rep1

description: processed data file:

tag: assay

tag: chip antibody


title: Subject_2_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: Sex

value: Unknown


title: ribo-seq Naïve CD4 T-cells [RPF_NaiveA]

tag: strain

tag: activation stage

tag: cell type

value: CD4 T-cells

tag: molecule subtype


title: B_Rpb3.dom-kd.st5.rep2

description:
processed data file:
Pol2.subtract_input.dom-kd.pooled.bw
Pol2_ChIP.dom-kd.dm6_ensembl96.transcripts.tsv

value: Rpb3 (Kindly provided by Carla Margulies)


title: HIPPO_51_Case

description: miRNA transcriptome data

tag: aud status

value: Male

tag: batch

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

tag: smoking

value: Steatosis


title: HIPPO_52_Control

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: rin

tag: brainweight

tag: brainph


title: Subject_1_Control ; Human postmortem nucleus accumbens

description: miRNA transcriptome data

tag: tissue

value: Human postmortem nucleus accumbens

tag: pmi

tag: liverclass

value: MildSteatosis


title: Subject_24_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

value: Human postmortem hippocampus

value: AlcoholUseDisorder

tag: Sex

value: Cardiovascular


title: HIPPO_49_Case

description: miRNA transcriptome data

value: Case

value: Right

value: HepaticBloodLoss

value: Former


title: PFC_74_Control

description: miRNA transcriptome data

value: Control

value: Left

value: Cardiac

value: Congestion


title: Subject_23_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

value: Female

value: Never


title: B_Rpb3.dom-kd.st5.rep1

tag: genotype

tag: timepoint

tag: assay

value: ChIP-seq

tag: chip antibody

value: Rpb3 (Kindly provided by Carla Margulies)


title: ribo-seq activated CD4 T-cells, 72 hours after activation [RPF_72hA]

tag: strain

tag: activation stage

value: 72 hours

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: Ribosome protected mRNA


title: B_Rpb3.ctrl.st5.rep2

description:
processed data file:
Pol2.subtract_input.ctrl.pooled.bw
Pol2_ChIP.dom-kd.dm6_ensembl96.transcripts.tsv


title: CER_48_Control

description: miRNA transcriptome data

source_name: Human postmortem cerebellum

tag: aud status

value: Male

tag: batch

tag: leftrightbrain

tag: causeofdeathcategory

tag: smoking

value: Current

value: Steatosis


title: CER_47_Control

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: rin

tag: brainweight

tag: brainph

value: Right


title: ribo-seq activated CD4 T-cells, 48 hours after activation [RPF_48hA]

value: 48 hours


title: ribo-seq activated CD4 T-cells, 48 hours after activation [RPF_48hB]


title: B_Rpb3.ctrl.st5.rep1

tag: genotype


title: Subject_21_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

tag: tissue

value: Human postmortem hippocampus

value: AlcoholUseDisorder

tag: Sex

tag: pmi

tag: liverclass

value: Cirrhosis


title: Subject_20_Control; Human postmortem hippocampus

description: miRNA transcriptome data

value: Control

value: Left

value: Toxicity

value: Unknown


title: ribo-seq activated CD4 T-cells, 72 hours after activation [RPF_72hB]

tag: strain

tag: activation stage


title: Subject_19_Control; Human postmortem hippocampus

description: miRNA transcriptome data

value: Female

value: Cardiac

value: Congestion


title: mRNA-sequencing Naïve CD4 T-cells [mRNA_NaiveB]

source_name: mRNA-sequencing Naïve CD4 T-cells

value: naïve

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: mRNA


title: ribo-seq activated CD4 T-cells, 20 hours after activation [RFP_20hA]

value: 20 hours

value: Ribosome protected mRNA


title: CER_43_Case

description: miRNA transcriptome data

tag: aud status

value: Case

value: Male

tag: batch

value: Right

value: Current

value: Normal


title: CER_45_Case

description: miRNA transcriptome data

tag: leftrightbrain

tag: causeofdeathcategory


title: CER_46_Case

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: smoking

value: Steatosis


title: CD4+ T cells in treatment medium, biological rep3

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

description:
ARG015
Stimulated OVA-specific CD4+ T cells in treatment medium (RPMI-1640 containing 10% dialyzed FBS and only 1% of the normal arginine levels (12uM)), biological rep3.

hyb_protocol: 100ng of total RNA was processed using the Affymetrix Whole Transcript (WT) Plus assay according to the manufacturer's protocol. The resulting cDNA was labeled, fragmented, and hybridized to the Mouse Gene 2.0 assay at 60rpm for 16hr at 45oC. The arrays were then washed and stained using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 7G scanner according to the manufacturer's protocols.

data_processing: Expression measures were background-corrected, normalized, and summarized from scanned intensity (CEL) files using the oligo R package.

label: Biotin

source_name: CD4+ T cells in treatment medium

label_protocol: GeneChip WT Terminal Labeling Kit per manufacturer's protocol.

growth_protocol: Mice were co-housed until 12-16 weeks of age, at which point spleens and non-mesenteric lymph nodes were isolated.

extract_protocol: CD4+ cells were re-purified from the co-cultures, centrifuged, and lysed in TRIzol (Applied Biosystems) for subsequent RNA isolation according to the manufacturer's instructions.

treatment_protocol: 2 × 10e5 APCs were mixed with 5 × 10e5 T cells in medium containing 0.1 μm OVA323-329 peptide. Cells were incubated at 37oC for 72 hours either in control complete RPMI-1640 (containing 10% dialyzed FBS) or in RPMI-1640 (containing 10% dialyzed FBS) containing 1% of the normal arginine levels (12uM).

tag: genotype/variation

value: OT II transgenic

value: Stimulated OVA-specific CD4+ T cells

tag: culture medium

value: Treatment (1% of normal arginine levels)


title: CER_44_Case

description: miRNA transcriptome data

tag: rin

tag: brainweight

tag: brainph

value: Left

value: Former


title: Subject_18_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

tag: tissue

value: Human postmortem hippocampus

value: AlcoholUseDisorder

tag: Sex

tag: pmi

value: Hepatic


title: Subject_22_Control; Human postmortem hippocampus

description: miRNA transcriptome data

value: Control

value: Female

value: Cardiac

value: Never

tag: liverclass


title: ribo-seq activated CD4 T-cells, 20 hours after activation [RPF_20hB]

tag: strain

tag: activation stage

value: 20 hours

tag: cell type

value: CD4 T-cells

value: Ribosome protected mRNA


title: CER_42_Control

description: miRNA transcriptome data

tag: aud status

value: Male

tag: batch

value: Congestion


title: Subject_17_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Vascular

value: Normal


title: Subject_16_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Left

tag: smoking

value: Cirrhosis


title: mRNA-sequencing activated CD4 T-cells, 72 hours after activation [mRNA_72hB]

value: 72 hours

tag: molecule subtype

value: mRNA


title: CD4+ T cells in treatment medium, biological rep2

description:
ARG011
Stimulated OVA-specific CD4+ T cells in treatment medium (RPMI-1640 containing 10% dialyzed FBS and only 1% of the normal arginine levels (12uM)), biological rep2.

tag: genotype/variation

value: OT II transgenic

value: Stimulated OVA-specific CD4+ T cells

tag: culture medium

value: Treatment (1% of normal arginine levels)


title: mRNA-sequencing Naïve CD4 T-cells [mRNA_NaiveA]

value: naïve


title: CD4+ T cells in treatment medium, biological rep1

description:
ARG007
Stimulated OVA-specific CD4+ T cells in treatment medium (RPMI-1640 containing 10% dialyzed FBS and only 1% of the normal arginine levels (12uM)), biological rep1.


title: RNAseq PARP-1 KD E2 rep2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: RNAseq_PARP-1_KD_E2_Plus.bw, RNAseq_PARP-1_KD_E2_Minus.bw

data_processing:
Quality control for the RNA-seq data was performed using the FastQC tool
The reads were then mapped to the human reference genome (GRCh37/hg19) with previously described comprehensive gene annotation using the default parameters in Tophat (v2.0.12) (PMID: 19289445)
Differences in gene expression between RNA-seq datasets were calculated using the cufflinks suite with a statistical threshold of FDR, 0.05 (PMID: 20436464). Gene expression changes were measured by the fold change in each of the treatments and were visualized as box and whisker plots.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: human Estrogen receptor alpha+ breast cancer cells

growth_protocol: MCF-7 cells were kindly provided by Benita S. Katzenellenbogen (University of Illinois, Urbana-Champaign) used for the genomic.  MCF-7 cells were maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum (CS).

extract_protocol:
MCF-7 cells with shRNA-mediated knockdown of luciferase (Luc; as a control) or PARP-1 were isolated and subjected to RNA-seq as described previously (PMID: 21807852, PMID: 26236012).
Estrogen-withdrawn MCF-7 cells were treated with ethanol or 100 nM E2 for 3 hours. Total RNA was isolated MCF-7 cells using the RNeasy kit (Qiagen, 74136) according to the manufacturer’s instructions.  The RNA collected was processed for whole transcriptome polyadenylated RNA sequencing (polyA+ RNA-seq).

treatment_protocol: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum (CDCS). For experiments, cells were treated with 100 nM E2 or vehicle (ethanol) for 3 hours.

tag: cell line

value: PARP-1 KD

tag: treatment


title: mRNA-sequencing activated CD4 T-cells, 72 hours after activation [mRNA_72hA]


title: RNAseq PARP-1 KD E2 rep1


title: Subject_15_Control; Human postmortem hippocampus

description: miRNA transcriptome data

tag: tissue

value: Human postmortem hippocampus

value: Control

tag: Sex

value: Female

tag: rin

tag: brainweight

tag: brainph

value: Cardiac

value: Current


title: Subject_14_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: pmi

value: Toxicity

tag: liverclass


title: mRNA-sequencing activated CD4 T-cells, 48 hours after activation [mRNA_48hA]

tag: strain

tag: activation stage

value: 48 hours

tag: cell type

value: CD4 T-cells


title: CD4+ T cells in control medium, biological rep2

description:
ARG009
Stimulated OVA-specific CD4+ T cells in control medium (complete RPMI-1640 containing 10% dialyzed FBS), biological rep2.

source_name: CD4+ T cells in control medium


title: mRNA-sequencing activated CD4 T-cells, 48 hours after activation [mRNA_48hB]


title: mRNA-sequencing activated CD4 T-cells, 20 hours after activation [mRNA_20hA]

value: 20 hours


title: RNAseq Luc KD E2 rep2

description: RNAseq_LUC_KD_E2_Plus.bw, RNAseq_LUC_KD_E2_Minus.bw

value: Luc KD


title: RNAseq Luc KD E2 rep1


title: RNAseq PARP-1 KD Veh rep1

description: RNAseq_PARP-1_KD_Veh_Plus.bw, RNAseq_PARP-1_KD_Veh_Minus.bw

value: vehicle


title: CER_37_Case

description: miRNA transcriptome data

tag: aud status

value: Case

tag: alcoholdailyuse(gram/day)

value: Male

tag: batch

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Respiratory

value: Never

value: Steatosis


title: RNAseq Luc KD Veh rep2

description: RNAseq_LUC_KD_Veh_Plus.bw, RNAseq_LUC_KD_Veh_Minus.bw

tag: cell line

tag: genotype/variation


title: TECs control batch2

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

data_processing:
Illumina bcl2fastq software was used for generating FASTQ files FASTQ files were processed using Fastp, and reads were demultiplexed and mapped to the mm10 reference genome via Cell Ranger (v3.0.0). Processing data by the Cell Ranger pipeline was performed using the HOKUSAI supercomputer at RIKEN and the NIG supercomputer at ROIS National Institute of Genetics. Expression count matrices were prepared by counting unique molecule identifiers.
Supplementary files format and content are described at http://software.10xgenomics.com/single-cell/overview/welcome
Genome_build: mm10
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices containing all barcodes in MEX format

source_name: thymic epithelial cells

extract_protocol: RNA libraries were prepared for sequencing using Chromium Single Cell 3′ Reagent Kits v2 and v3 Chemistry

tag: age

value: 8 weeks old

tag: tissue

value: thymus

value: thymic epithelial cells

tag: genotype

value: Aire+/+


title: B_Input.dom-kd.st5.rep2

description: processed data file:

source_name: embryos

tag: timepoint

tag: assay

value: ChIP-seq

tag: chip antibody

value: none (input)


title: Subject_11_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

value: Human postmortem hippocampus

value: Control

tag: Sex

tag: rin

tag: brainweight

tag: brainph

tag: pmi

value: Left

value: Cardiac

tag: smoking

value: Current

tag: liverclass

value: Congestion


title: mRNA-sequencing activated CD4 T-cells, 20 hours after activation [mRNA_20hB]

tag: strain

tag: activation stage

value: 20 hours

tag: cell type

value: CD4 T-cells

tag: molecule subtype

value: mRNA


title: RNAseq PARP-1 KD Veh rep2

tag: cell line

tag: genotype/variation

value: PARP-1 KD

tag: treatment

value: vehicle


title: CER_36_Control

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Male

tag: batch

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Normal


title: Subject_10_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

tag: tissue

tag: Sex

tag: rin

tag: brainweight


title: TECs AireKO batch2

tag: age

value: 8 weeks old

value: thymus

value: thymic epithelial cells

tag: genotype

value: Aire-/-


title: CER_38_Control

description: miRNA transcriptome data

value: Control

tag: brainph

tag: pmi

tag: smoking

value: Never

tag: liverclass

value: Steatosis


title: Subject_13_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

value: Human postmortem hippocampus

value: Left

value: Cardiac


title: CER_39_Control

description: miRNA transcriptome data

value: Congestion


title: TECs AireKO batch1

tag: strain

tag: cell type


title: Subject_9_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

tag: aud status

value: AlcoholUseDisorder

value: Toxicity

value: Current


title: Subject_12_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Male


title: Subject_6_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

value: Female

tag: batch

value: Right

value: Respiratory


title: CER_35_Case

description: miRNA transcriptome data

value: Case

tag: leftrightbrain


title: Subject_8_Control; Human postmortem hippocampus

description: miRNA transcriptome data

tag: causeofdeathcategory


title: CER_33_Case

description: miRNA transcriptome data

value: HepaticBloodLoss

value: Former


title: Old24_3

city: Stanford

first: Connie

last: Tsai

address: 1201 Welch Rd

institute: Stanford University

description: oldNorm.txt

data_processing:
Reads were cleaned with Bbduk
Cleaned reads were aligned to the mm10 genome with STAR
Aligned reads were normalized with DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: DESEQ2 normalized counts are saved as text files

source_name: macrophage

extract_protocol:
Cells were lysed with Trizol and RNA was purified with PureLink columns.
Libraries were prepared according to Lexogen Quantseq instructions
3' RNA-seq

tag: tissue

value: macrophage

value: 18-20 month


title: CER_40_Case

description: miRNA transcriptome data

tag: Sex

value: Stroke

value: Steatosis


title: Subject_7_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

value: Human postmortem hippocampus

tag: rin

value: Cirrhosis


title: ChIP-seq PARP-1KD Veh Rep2 H3K27ac

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_PARP-1KD_Veh_H3K27ac.narrowPeak.gz

data_processing:
The ChIP-seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to (1) “bed” files for later Metagene and read-density analyses and (2) “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bed

growth_protocol: MCF-7 cell lines were obtained from the ATCC used for ChIP and proliferation assays described herein. MCF-7 cells were maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum.

extract_protocol:
MCF-7 cells were seeded at ~3 x 106 cells per 15 cm diameter plate and treated as described above.  The cells were cross-linked with 1% paraformaldehyde in PBS for 10 minutes at 37°C and quenched in 125 mM glycine in PBS for 5 minutes at 4°C.  The cells were then collected and lysed in Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and 1x RCPIC).  A crude nuclear pellet was collected by centrifugation, resuspended in lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 7.9, 1 mM DTT, and 1x RCPIC), and incubated on ice for 10 minutes.  The chromatin was sheared at 4°C by sonication using a Bioruptor UC200 at the high setting for four 5-minute cycles of 30 seconds on and 60 seconds off to generate chromatin fragments of ~300 bp in length.  The soluble chromatin was diluted 1:10 with dilution buffer (20 mM Tris-HCl, pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT and 1x RCPIC) and pre-cleared with protein A agarose beads.  The pre-cleared supernatant was used in immunoprecipitation reactions with antibodies against the factor of interest or with rabbit IgG as a control.  The immunoprecipitated material was washed once with low salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM aprotinin, and 1 mM leupetin), once with high-salt wash buffer (20 mM Tris-HCl, pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, 1 mM aprotinin, and 1 mM leupetin), once with LiCl wash buffer (10 mM Tris-HCl, pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM aprotinin, and 1 mM leupetin), and once with 1x Tris-EDTA (TE).  The immunoprecipitated material was eluted in elution buffer (100 mM NaHCO3, 1% SDS) and was then digested with proteinase K and RNase H to remove protein and RNA, respectively.  The immunoprecipitated genomic DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol. The immunoprecipitated DNA was purified further using the MinElute PCR Purification Kit from Qiagen.
After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described  {Robertson, 2007 #41}, with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum (CDCS). For experiments, cells were treated with 100 nM E2 or vehicle (ethanol) for 40 minutes.

tag: cell line

tag: treatment

value: Vehicle

tag: biological replicate

value: Replicate 2

tag: antibody


title: ChIP-seq PARP-1KD E2 Rep1 H3K27ac

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_PARP-1KD_E2_H3K27ac.narrowPeak.gz

tag: genotype


title: CER_41_Control

description: miRNA transcriptome data

value: Control

tag: brainweight

tag: brainph

tag: pmi

value: Left

value: Cardiac

tag: smoking

value: Congestion


title: CER_34_Control

description: miRNA transcriptome data

tag: aud status

value: Male

value: Current

tag: liverclass


title: Subject_5_AlcoholUseDisorder; Human postmortem hippocampus

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: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Female

tag: batch

value: Right

value: Respiratory


title: CD4+ T cells in control medium, biological rep3

description:
ARG013
Stimulated OVA-specific CD4+ T cells in control medium (complete RPMI-1640 containing 10% dialyzed FBS), biological rep3.

tag: genotype/variation

value: OT II transgenic

tag: cell type

value: Stimulated OVA-specific CD4+ T cells

tag: culture medium


title: Old20_3

description: oldNorm.txt

tag: strain

tag: tissue

value: macrophage

tag: age

value: 18-20 month


title: CAU_30_Case

description: miRNA transcriptome data

source_name: Human postmortem caudate

value: Case

tag: Sex

tag: rin

tag: leftrightbrain

tag: causeofdeathcategory

value: Steatosis


title: CAU_31_Control

description: miRNA transcriptome data

tag: brainweight

tag: brainph

value: Never


title: CAU_32_Control

description: miRNA transcriptome data

value: Control

tag: pmi

tag: smoking


title: RNAseq Luc KD Veh rep1

tag: cell line

value: Luc KD

tag: treatment

value: vehicle


title: Old20_2

description: oldNorm.txt


title: CAU_27_Case

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: batch

value: Unknown

tag: liverclass

value: Normal


title: ChIP-seq PARP-1KD Veh Rep1 H3K27ac

tag: genotype

value: Vehicle

tag: biological replicate

tag: antibody


title: CAU_28_Case

description: miRNA transcriptome data

tag: Sex

value: Male

value: Left

value: Cardiac

value: Former


title: CAU_29_Case

description: miRNA transcriptome data

tag: rin

value: Current


title: TECs control batch1

tag: strain

tag: age

value: 8 weeks old

tag: tissue

value: thymus

tag: cell type

value: thymic epithelial cells

value: Aire+/+


title: CD4+ T cells in control medium, biological rep1

description:
ARG005
Stimulated OVA-specific CD4+ T cells in control medium (complete RPMI-1640 containing 10% dialyzed FBS), biological rep1.

tag: genotype/variation

value: OT II transgenic

value: Stimulated OVA-specific CD4+ T cells

tag: culture medium


title: Subject_2_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

value: Human postmortem hippocampus

value: Control

value: Female

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

tag: smoking


title: Old24_2

description: oldNorm.txt

value: macrophage

value: 18-20 month


title: ChIP-seq PARP-1KD E2 Rep2 H3K27ac

tag: cell line

tag: genotype

tag: treatment

value: Replicate 2


title: Subject_1_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: batch

value: Left

value: Never

tag: liverclass

value: MildSteatosis


title: ChIP-seq PARP-1KD E2 Rep2 FOXA1

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_PARP-1KD_E2_FOXA1.narrowPeak.gz

tag: biological replicate

tag: antibody


title: ChIP-seq PARP-1KD Veh Rep1 FOXA1

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_PARP-1KD_Veh_FOXA1.narrowPeak.gz

value: Vehicle


title: Subject_4_AlcoholUseDisorder; Human postmortem hippocampus

description: miRNA transcriptome data

tag: tissue

value: AlcoholUseDisorder

tag: rin

value: Toxicity

value: Current

value: Normal


title: Old16_3

description: oldNorm.txt

tag: strain

tag: age


title: Old16_2

description: oldNorm.txt


title: Old16_1

description: oldNorm.txt


title: ChIP-seq PARP-1KD E2 Rep2 FOXA1 H3K27ac Input

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_PARP-1KD_E2_FOXA1.narrowPeak.gz,ChIP-seq_PARP-1KD_E2_H3K27ac.narrowPeak.gz

value: Input


title: ChIP-seq PARP-1KD E2 Rep1 FOXA1 H3K27ac Input


title: Subject_22_Control; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Cardiac


title: Subject_20_Control; Human postmortem cerebellum

description: miRNA transcriptome data

value: Control

value: Female

tag: causeofdeathcategory

tag: smoking

value: Unknown

value: Congestion


title: Old24_1

description: oldNorm.txt

value: macrophage

value: 18-20 month


title: ChIP-seq PARP-1KD Veh Rep2 FOXA1 H3K27ac Input

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_PARP-1KD_Veh_FOXA1.narrowPeak.gz,ChIP-seq_PARP-1KD_Veh_H3K27ac.narrowPeak.gz

tag: cell line

tag: genotype

tag: treatment

value: Replicate 2


title: CAU_26_Control

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: batch

value: Left

value: Former


title: Old8_3

description: oldNorm.txt

tag: tissue


title: ChIP-seq PARP-1KD E2 Rep1 FOXA1

tag: biological replicate

tag: antibody


title: CAU_19_Case

description: miRNA transcriptome data

value: Case

tag: rin

value: Right

tag: liverclass

value: Steatosis


title: Old20_1

description: oldNorm.txt

tag: strain

tag: age


title: ChIP-seq LucKD E2 Rep1 H3K27ac

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_LucKD_E2_H3K27ac.narrowPeak.gz

value: LucKD


title: CAU_25_Control

description: miRNA transcriptome data

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain


title: CAU_18_Control

description: miRNA transcriptome data

tag: causeofdeathcategory

tag: smoking

value: Current


title: Old8_2

description: oldNorm.txt


title: CAU_17_Case

description: miRNA transcriptome data

tag: aud status

value: HepaticBloodLoss


title: Subject_24_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Cardiovascular


title: ChIP-seq PARP-1KD Veh Rep2 FOXA1

tag: cell line

tag: genotype

tag: treatment

value: Vehicle


title: Subject_3_Control ; Human postmortem hippocampus

description: miRNA transcriptome data

tag: tissue

value: Human postmortem hippocampus

value: Control

tag: Sex

value: Female

tag: batch

value: Cardiac

value: Normal


title: ChIP-seq LucKD Veh Rep2 H3K27ac

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_LucKD_Veh_H3K27ac.narrowPeak.gz

tag: biological replicate

value: Replicate 2

tag: antibody


title: Old8_1

description: oldNorm.txt

tag: strain

value: macrophage

tag: age

value: 18-20 month


title: Old12_3

description: oldNorm.txt


title: AMY_16_Control

description: miRNA transcriptome data

source_name: Human postmortem amygdala

value: Male

tag: rin

tag: brainweight

tag: brainph

value: Left

tag: liverclass


title: CAU_24_Case

description: miRNA transcriptome data

value: Case

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Stroke

tag: smoking

value: Steatosis


title: CAU_23_Control

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Right

value: Never

value: Congestion


title: Old12_1

description: oldNorm.txt

tag: tissue


title: Subject_16_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

value: AlcoholUseDisorder

tag: Sex

value: Cirrhosis


title: Old4_2

description: oldNorm.txt


title: ChIP-seq PARP-1KD Veh Rep1 FOXA1 H3K27ac Input

tag: cell line

tag: genotype

tag: treatment

value: Vehicle

value: Input


title: ChIP-seq LucKD E2 Rep2 FOXA1

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_LucKD_E2_FoxA1.narrowPeak.gz

value: LucKD

tag: biological replicate

tag: antibody


title: AMY_15_Control

description: miRNA transcriptome data

value: Control

tag: batch

tag: rin

value: Cardiac


title: Subject_15_Control; Human postmortem cerebellum

description: miRNA transcriptome data

value: Female

tag: brainweight

tag: brainph

value: Current

value: Normal


title: AMY_14_Case

description: miRNA transcriptome data

value: Case

value: Male

tag: pmi

tag: liverclass


title: CAU_20_Control

description: miRNA transcriptome data

tag: leftrightbrain

tag: causeofdeathcategory


title: Subject_18_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

tag: aud status

value: Hepatic

tag: smoking

value: Steatosis


title: Subject_23_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

tag: tissue

tag: alcoholdailyuse(gram/day)

value: Right

value: Toxicity

value: Never


title: Subject_19_Control; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

tag: Sex

value: Congestion


title: Old4_1

description: oldNorm.txt

tag: strain

value: macrophage

tag: age

value: 18-20 month


title: ChIP-seq LucKD E2 Rep2 H3K27ac

tag: cell line

tag: genotype

value: LucKD

tag: treatment

tag: biological replicate

value: Replicate 2


title: Subject_17_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

value: Control

tag: batch

tag: rin

tag: brainweight

value: Vascular


title: Old12_2

description: oldNorm.txt


title: CAU_21_Case

description: miRNA transcriptome data

tag: brainph

tag: pmi

value: Respiratory

tag: liverclass


title: ChIP-seq LucKD Veh Rep1 H3K27ac

value: Vehicle

tag: antibody


title: AMY_13_Case

description: miRNA transcriptome data

tag: aud status

value: Case

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Current

value: Normal


title: Old4_3

description: oldNorm.txt

tag: strain

tag: tissue


title: Subject_21_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

value: Cirrhosis


title: Old0_3

description: oldNorm.txt

tag: age


title: ChIP-seq LucKD E2 Rep1 FOXA1

tag: cell line

tag: genotype

tag: treatment

tag: biological replicate


title: Subject_13_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

tag: batch

tag: rin

tag: brainweight

tag: brainph

value: Never


title: CAU_22_Control

description: miRNA transcriptome data

tag: aud status

tag: pmi

tag: liverclass

value: Steatosis


title: Subject_14_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

value: Female

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

tag: smoking


title: Subject_11_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

tag: tissue

value: Control

tag: alcoholdailyuse(gram/day)

value: Congestion


title: Old0_1

description: oldNorm.txt

tag: strain

value: macrophage

tag: age

value: 18-20 month


title: Old0_2

description: oldNorm.txt


title: ChIP-seq LucKD Veh Rep1 FOXA1

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_LucKD_Veh_FOXA1.narrowPeak.gz

tag: cell line

tag: genotype

value: LucKD

value: Vehicle

tag: antibody


title: ChIP-seq LucKD Veh Rep2 FOXA1 H3K27ac Input

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_LucKD_Veh_FOXA1.narrowPeak.gz,ChIP-seq_LucKD_Veh_H3K27ac.narrowPeak.gz

tag: treatment

tag: biological replicate

value: Replicate 2

value: Input


title: Subject_9_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

tag: Sex

tag: batch

tag: rin

tag: brainweight

value: Right

value: Current


title: ChIP-seq LucKD E2 Rep1 FOXA1 H3K27ac Input

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_LucKD_E2_FoxA1.narrowPeak.gz,ChIP-seq_LucKD_E2_H3K27ac.narrowPeak.gz


title: Subject_10_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

tag: aud status

value: Male

tag: brainph

tag: pmi

value: Left

value: Cardiac

tag: liverclass


title: AMY_12_Case

description: miRNA transcriptome data

value: Case

tag: leftrightbrain

tag: causeofdeathcategory

tag: smoking

value: Former


title: ChIP-seq LucKD E2 Rep2 FOXA1 H3K27ac Input


title: Subject_8_Control; Human postmortem cerebellum

description: miRNA transcriptome data

tag: tissue

value: Human postmortem cerebellum

tag: alcoholdailyuse(gram/day)

value: Never

value: Steatosis


title: Young24_2

description: youngNorm.txt

tag: strain

tag: age

value: 2-3 month


title: Subject_12_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Normal


title: Young20_3

description: youngNorm.txt

value: macrophage


title: Young24_3

description: youngNorm.txt


title: ChIP-seq LucKD Veh Rep2 FOXA1

tag: cell line

tag: genotype

value: LucKD

tag: treatment

value: Vehicle

tag: antibody


title: AMY_9_Control

description: miRNA transcriptome data

value: Control

tag: Sex

tag: batch

tag: rin

value: Congestion


title: Subject_7_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

tag: aud status

value: Female

tag: brainweight

tag: brainph

value: Right

value: Current

value: Cirrhosis


title: Young24_1

description: youngNorm.txt


title: AMY_8_Case

description: miRNA transcriptome data

value: Case

value: Male

tag: pmi

tag: leftrightbrain

value: Left

value: Stroke

tag: liverclass


title: Young20_2

description: youngNorm.txt

tag: tissue


title: AMY_10_Control

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Former


title: AMY_11_Case

description: miRNA transcriptome data

value: Unknown


title: ChIP-seq PARP-1 KD-E2 Rep2 ER

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_PARP-1KD_E2_ER.narrowPeak.gz

tag: cell line

value: ERa

tag: biological replicate

value: Replicate 2


title: ChIP-seq LucKD Veh Rep1 FOXA1 H3K27ac Input

tag: genotype

value: LucKD

tag: treatment

value: Input


title: AMY_7_Control

description: miRNA transcriptome data

value: Control

tag: Sex

value: Never


title: ChIP-seq PARP-1 KD-E2 Rep1 ER

tag: antibody


title: ChIP-seq PARP-1 KD-E2 Rep2 Input


title: Subject_5_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

value: AlcoholUseDisorder

value: Female

tag: batch

tag: rin

value: Respiratory


title: Subject_6_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

tag: aud status

tag: brainweight

value: Right

value: Current

value: Normal


title: AMY_6_Control

description: miRNA transcriptome data

value: Male

tag: brainph

tag: pmi

value: Left

value: Steatosis


title: Subject_4_AlcoholUseDisorder; Human postmortem cerebellum

description: miRNA transcriptome data

tag: leftrightbrain

value: Toxicity

tag: liverclass


title: ChIP-seq PARP-1 KD-Veh Rep1 ERa

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_PARP-1KD_Veh_ER.narrowPeak.gz

value: ERa


title: Subject_2_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

tag: tissue

value: Cardiac

value: Unknown


title: RNAseq of G-NHX9-DDNA_4 [NHX9_DNAmut_R4]

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

data_processing:
RNA sequencing was performed by the Hartwell Center at St. Jude Children’s Research Hospital. Libraries were prepared using the TruSeq Stranded Total RNA kit (Ilumina). 100 basepair, paired reads were generated by sequencing on the NovaSeq 6000Read alignment to the Mus musculus reference genome (mm10) was performed with STAR software (v2.7.0d). To evaluate gene expression level, the read count for each annotated gene was calculated using HTSeq (version 0.11.2). Differential gene expression and regularized log transformation (rlog) on raw count data were carried out using DESeq2. All the genes were ranked according to the fold-change and significance from differential analysis. GSEA was then performed using molecular signatures database (MSigDB) (version 6.2) C2 genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw read count for each gene across the 35 samples.

source_name: Mouse lineage negative hematopoietic stem and progenitor cells

growth_protocol: Cells were grown in Methocult M3434 with 10 ng/mL GM-CSF for one week

extract_protocol:
RNA was harvested using the Direct-zol RNA MiniPrep or MicroPrep kit and was quantified using the Qubit 2.0 fluorometer prior to library generation
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).
RNAseq: paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

tag: cell surface marker

value: Lineage negative

value: bone marrow

tag: age

value: 8 weeks


title: AMY_5_Case

description: miRNA transcriptome data

value: Case

tag: alcoholdailyuse(gram/day)

tag: causeofdeathcategory

tag: smoking

value: Never


title: Young12_3

description: youngNorm.txt

tag: strain

value: macrophage

value: 2-3 month


title: Subject_1_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

value: Control

tag: Sex

value: MildSteatosis


title: Subject_24_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: Human postmortem caudate

value: AlcoholUseDisorder

value: Male

value: Cardiovascular

value: Current


title: Subject_23_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: Female

value: Right

value: Toxicity

value: Steatosis


title: AMY_1_Case

description: miRNA transcriptome data

value: HepaticBloodLoss

value: Former


title: Young20_1

description: youngNorm.txt


title: RNAseq of G-NHX9-DDNA_2 [NHX9_DNAmut_R2]

value: Lineage negative

value: bone marrow

value: 8 weeks

tag: genotype

tag: cell line

tag: treatment


title: Subject_22_Control; Human postmortem caudate

description: miRNA transcriptome data

tag: aud status

tag: batch

tag: rin

value: Left

value: Cardiac

value: Never

value: Normal


title: Young16_2

description: youngNorm.txt

value: macrophage

value: 2-3 month


title: AMY_4_Control

description: miRNA transcriptome data

value: Control

value: Male

tag: brainweight

tag: brainph

tag: pmi


title: Young16_1

description: youngNorm.txt

tag: tissue


title: AMY_3_Case

description: miRNA transcriptome data

value: Case

tag: leftrightbrain

value: Current

tag: liverclass


title: Subject_21_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: Human postmortem caudate

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Cirrhosis


title: Young16_3

description: youngNorm.txt

tag: age


title: Subject_3_Control ; Human postmortem cerebellum

description: miRNA transcriptome data

value: Human postmortem cerebellum

value: Female

tag: causeofdeathcategory

tag: smoking


title: ChIP-seq Luc KD-E2 Rep2 Input

description:
ChIP-enriched DNA from MCF-7 cells in E2 treated condition
ChIP-seq_LucKD_E2_ER.narrowPeak.gz

value: LucKD

tag: biological replicate

value: Replicate 2

tag: antibody

value: Input


title: ChIP-seq PARP-1 KD-Veh Rep2 Input

tag: cell line

tag: genotype

value: Vehicle


title: ChIP-seq PARP-1 KD-Veh Rep2 ERa

tag: treatment

value: ERa


title: ChIP-seq Luc KD-E2 Rep2 ERa


title: RNAseq of G-NHX9-DDNA_3 [NHX9_DNAmut_R3]

tag: cell surface marker

value: Lineage negative

value: bone marrow

value: 8 weeks


title: ChIP-seq PARP-1 KD-E2 Rep1 Input


title: RNAseq of G-NHX9-DDNA_5 [NHX9_DNAmut_R5]


title: Young12_1

description: youngNorm.txt

tag: strain

value: macrophage

value: 2-3 month


title: Subject_20_Control; Human postmortem caudate

description: miRNA transcriptome data

tag: aud status

value: Control

tag: Sex

tag: batch

tag: rin

tag: brainweight

value: Left

value: Toxicity

value: Unknown

value: Congestion


title: Young12_2

description: youngNorm.txt

tag: tissue


title: Young8_3

description: youngNorm.txt


title: ChIP-seq Luc KD-E2 Rep1 ERa


title: ChIP-seq PARP-1 KD-Veh Rep1 Input


title: RNAseq of G-NHX9-midi-21FGAA_4 [NHX9_midi21FGAA_R4]


title: ChIP-seq Luc KD-Veh Rep1 ERa

description:
ChIP-enriched DNA from MCF-7 cells in vehicle treated condition
ChIP-seq_LucKD_Veh_ER.narrowPeak.gz


title: RNAseq of G-NHX9-midi-21FGAA_5 [NHX9_midi21FGAA_R5]


title: RNAseq of G-NHX9-DDNA_1 [NHX9_DNAmut_R1]


title: Subject_19_Control; Human postmortem caudate

description: miRNA transcriptome data

value: Human postmortem caudate

tag: alcoholdailyuse(gram/day)

tag: brainph

tag: pmi

tag: leftrightbrain

value: Right

value: Cardiac

value: Current

tag: liverclass


title: ChIP-seq Luc KD-E2 Rep1 Input

value: LucKD

tag: biological replicate

tag: antibody

value: Input


title: Subject_18_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Male

tag: causeofdeathcategory

value: Hepatic

tag: smoking

value: Steatosis


title: AMY_2_Control

description: miRNA transcriptome data


title: Young8_2

description: youngNorm.txt

value: macrophage

tag: age


title: ChIP-seq Luc KD-Veh Rep2 ERa

tag: cell line

tag: genotype

tag: treatment

value: Vehicle

value: Replicate 2

value: ERa


title: RNAseq of G-NHX9-midi-21FGAA_2 [NHX9_midi21FGAA_R2]

tag: cell surface marker

value: Lineage negative

value: bone marrow

value: 8 weeks


title: Young8_1

description: youngNorm.txt

tag: strain

value: 2-3 month


title: ChIP-seq Luc KD-Veh Rep2 Input


title: Young4_2

description: youngNorm.txt


title: Subject_17_Control ; Human postmortem caudate

description: miRNA transcriptome data

value: Human postmortem caudate

tag: aud status

value: Control

tag: Sex

tag: batch

tag: rin

tag: brainweight

value: Right

value: Vascular

value: Normal


title: Young4_3

description: youngNorm.txt

tag: tissue


title: Young4_1

description: youngNorm.txt


title: RNAseq of G-NHX9-midi-21FGAA_1 [NHX9_midi21FGAA_R1]


title: Young0_3

description: youngNorm.txt


title: RNAseq of G-NHX9-midi-21FGAA_3 [NHX9_midi21FGAA_R3]


title: Subject_14_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Female

tag: brainph

tag: pmi

tag: leftrightbrain

value: Left

value: Toxicity

value: Current

tag: liverclass

value: Cirrhosis


title: Subject_13_Control ; Human postmortem caudate

description: miRNA transcriptome data

value: Male

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Never


title: Subject_15_Control; Human postmortem caudate

description: miRNA transcriptome data


title: Young0_1

description: youngNorm.txt

value: macrophage

tag: age


title: RNAseq of G-NHX9-midi_4 [NHX9_midi_R4]

value: Lineage negative

value: bone marrow

value: 8 weeks

tag: genotype

tag: cell line

tag: treatment


title: Subject_12_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: Human postmortem caudate

tag: aud status


title: RNAseq of G-NHX9-midi_1 [NHX9_midi_R1]

tag: cell surface marker


title: Subject_11_Control ; Human postmortem caudate

description: miRNA transcriptome data

value: Control

tag: Sex

tag: batch

value: Congestion


title: RNAseq of G-NHX9-midi_5 [NHX9_midi_R5]


title: Subject_16_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

tag: rin

tag: brainweight


title: RNAseq of G-NHX9-midi_2 [NHX9_midi_R2]

tag: tissue


title: RNAseq of G-NHX9-21FGAA_5 [NHX9_21FGAA_R5]


title: ChIP-seq Luc KD-Veh Rep1 Input

value: LucKD

value: Vehicle

tag: biological replicate

tag: antibody

value: Input


title: Subject_10_Control ; Human postmortem caudate

description: miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

tag: brainph

tag: pmi

tag: leftrightbrain

value: Left


title: Subject_9_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Right

tag: causeofdeathcategory

value: Toxicity

tag: smoking

tag: liverclass

value: Steatosis


title: RNAseq of G-NHX9-midi_3 [NHX9_midi_R3]

tag: age

tag: genotype

tag: cell line

tag: treatment


title: Young0_2

description: youngNorm.txt

tag: strain

value: 2-3 month