title: PRO-seq-20-NELFC-AID-42C-Aux-rep2

description: PRO-seq

data_processing:
Library strategy: PRO-seq
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg19 and mouse mm9 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, plotProfile (Ramírez et al., 2016). ChIP-seq peaks were called using MACS 2.1.0 (Zhang et al., 2008) with a q-value cutoff of 0.05. Peaks were annotated using HOMER 4.10 (Heinz et al., 2010).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg19 and fly dm3 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Protein coding transcripts were chosen from Ensembl version 75 database by R 3.3.3, according to the previously described protocol (Liang et al., 2018) with minor modifications. Briefly, we selected RefSeq-validated transcripts with TSSs that overlapping NELF-C ChIP-seq peaks. We filtered out transcripts that are ≤ 2 kb long and ≤ 2 kb away from the nearest genes. Next, we chose transcripts that have ≥ 2 rpm total PRO-seq coverage at the region between TSS – 100 bp and TSS + 300 bp, using 3 independent PRO-seq data in untreated NELF-C-AID cells. In these selected transcripts, the nucleotide position with maximum PRO-seq coverage in the region between TSS – 100 bp and TSS + 300 bp was assigned to the 1st pause region. Transcripts that have ≤ 0.2 rpm coverage at the 1st pause region nucleotide were excluded. The resulting transcripts with assigned the 1st pause regions were used for further analyses. The nucleotide positions with maximum PRO-seq coverage in 1h auxin-treated NELF-C-AID cells at the region from +10 to +500 bp downstream of the 1st pause region was assigned to the 2nd pause region. For Heat shock experiments, transcripts with ≥ 1.5-fold increase or decrease in PRO-seq coverage at gene bodies (the 1st pause regions +500 to +100kb or to transcription termination sites) upon heat shock were assigned to HS-upregulated or HS-downregulated genes, respectively. Heatmaps and metaplots of PRO-seq signals were generated by deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, and plotProfile (Ramírez et al., 2016). Log2 fold change of PRO-seq signals at nucleotide resolution were calculated by deepTools 3.0.0/3.1.1/3.1.2 bigwigCompare with pseudocount 0.25 rpm.
For PRO-cap, raw reads were processed as described for PRO-seq above, requiring a read length of 18–36 bp. Processed paired-end reads were aligned to a concatenated genome comprised of hg19 and dm3 assemblies using bowtie2 with options (--very-sensitive -X 1000 --no-mixed --no-discordant --no-unal) (Langmead and Salzberg, 2012). The 5’ ends of aligned R2 reads with MAPQ ≥ 40 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options. Read counts were normalized to total reads aligned to the spike-in genome. de novo transcription start sites were identified from PRO-cap data using HOMER 4.11 with findcsRNATSS option (Duttke et al., 2019; Heinz et al., 2010). TSS identified in untreated and auxin-treated samples were merged then defined as TSS regions. Distances between TSS in each sample were measured using HOMER 4.11 annotatePeaks. Raw PRO-cap reads were counted using HOMER 4.11 annotatePeaks. Read counts were normalized to spike-in counts using RUVseq with RUVg option (Risso et al., 2014) in R 3.3.3. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and visualized in R 3.3.3. TSS with significant gain of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Up TSS, while TSS with significant loss of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Down TSS. Metaplots of PRO-cap and PRO-seq at Cap Up TSS or Cap Down TSS were generated using deepTools 3.1.1. For heatmaps of ChIP-seq and MNase-seq at TSS, TSS were first merged with gap of no longer than 600 bp to obtain TSS clusters, heatmaps were then generated at Cap Up TSS clusters and Cap Down TSS clusters.
Genome_build: hg19, dm3, mm9
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

tag: treatment

value: Heat shock and Auxin


title: PRO-cap-03-NELFC-AID-untreated-rep2

status: Public on Mar 09 2020

type: SRA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

country: USA

institute: Northwestern University Feinberg School of Medicine

description: PRO-cap

library_source: transcriptomic

data_processing:
Library strategy: PRO-cap
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg19 and mouse mm9 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, plotProfile (Ramírez et al., 2016). ChIP-seq peaks were called using MACS 2.1.0 (Zhang et al., 2008) with a q-value cutoff of 0.05. Peaks were annotated using HOMER 4.10 (Heinz et al., 2010).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg19 and fly dm3 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Protein coding transcripts were chosen from Ensembl version 75 database by R 3.3.3, according to the previously described protocol (Liang et al., 2018) with minor modifications. Briefly, we selected RefSeq-validated transcripts with TSSs that overlapping NELF-C ChIP-seq peaks. We filtered out transcripts that are ≤ 2 kb long and ≤ 2 kb away from the nearest genes. Next, we chose transcripts that have ≥ 2 rpm total PRO-seq coverage at the region between TSS – 100 bp and TSS + 300 bp, using 3 independent PRO-seq data in untreated NELF-C-AID cells. In these selected transcripts, the nucleotide position with maximum PRO-seq coverage in the region between TSS – 100 bp and TSS + 300 bp was assigned to the 1st pause region. Transcripts that have ≤ 0.2 rpm coverage at the 1st pause region nucleotide were excluded. The resulting transcripts with assigned the 1st pause regions were used for further analyses. The nucleotide positions with maximum PRO-seq coverage in 1h auxin-treated NELF-C-AID cells at the region from +10 to +500 bp downstream of the 1st pause region was assigned to the 2nd pause region. For Heat shock experiments, transcripts with ≥ 1.5-fold increase or decrease in PRO-seq coverage at gene bodies (the 1st pause regions +500 to +100kb or to transcription termination sites) upon heat shock were assigned to HS-upregulated or HS-downregulated genes, respectively. Heatmaps and metaplots of PRO-seq signals were generated by deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, and plotProfile (Ramírez et al., 2016). Log2 fold change of PRO-seq signals at nucleotide resolution were calculated by deepTools 3.0.0/3.1.1/3.1.2 bigwigCompare with pseudocount 0.25 rpm.
For PRO-cap, raw reads were processed as described for PRO-seq above, requiring a read length of 18–36 bp. Processed paired-end reads were aligned to a concatenated genome comprised of hg19 and dm3 assemblies using bowtie2 with options (--very-sensitive -X 1000 --no-mixed --no-discordant --no-unal) (Langmead and Salzberg, 2012). The 5’ ends of aligned R2 reads with MAPQ ≥ 40 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options. Read counts were normalized to total reads aligned to the spike-in genome. de novo transcription start sites were identified from PRO-cap data using HOMER 4.11 with findcsRNATSS option (Duttke et al., 2019; Heinz et al., 2010). TSS identified in untreated and auxin-treated samples were merged then defined as TSS regions. Distances between TSS in each sample were measured using HOMER 4.11 annotatePeaks. Raw PRO-cap reads were counted using HOMER 4.11 annotatePeaks. Read counts were normalized to spike-in counts using RUVseq with RUVg option (Risso et al., 2014) in R 3.3.3. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and visualized in R 3.3.3. TSS with significant gain of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Up TSS, while TSS with significant loss of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Down TSS. Metaplots of PRO-cap and PRO-seq at Cap Up TSS or Cap Down TSS were generated using deepTools 3.1.1. For heatmaps of ChIP-seq and MNase-seq at TSS, TSS were first merged with gap of no longer than 600 bp to obtain TSS clusters, heatmaps were then generated at Cap Up TSS clusters and Cap Down TSS clusters.
Genome_build: hg19, dm3, mm9
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: DLD-1 cells were grown in DMEM (Corning) supplemented with 10% FBS (Corning), 1X GlutaMAX (Gibco), 2 µg/ml puromycin (Gibco), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco).

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014) for NELF-C, NELF-E, SPT5, Pol II CTD Ser2P, Pol II CTD Ser5P, XRN2, DCP2 ChIP-seq in NELF-C-AID cells. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).  PRO-seq sample preparation was performed according to the previously published protocol (Mahat et al., 2016b) with minor modifications. 10 million DLD-1 nuclei were mixed with spike-in Drosophila S2 nuclei. Nuclear run-on assay was performed with 4 biotinylated nucleotides (PerkinElmer). 5’ cap was removed by RppH (NEB).  PRO-cap libraries were prepared as described previously (Kwak et al., 2013; Mahat et al., 2016b) with minor modifications. NELF-C-AID cells were treated with or without 500 µM auxin for 2 h, followed by nuclear extraction. ~10 million NELF-C-AID nuclei with 0.5 million spike-in drosophila S2 nuclei were subjected to nuclear run-on reaction.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. DNA Libraries were size selected by PippinHT (Sage) or AMpure XP (Beckman Coulter) and sequenced on a NextSeq 500 (Illumina). For PRO-cap, PRO-seq adapter sequences were used instead of PRO-cap adapters. Libraries were then sequenced by NextSeq 500 in paired-end sequencing mode.

treatment_protocol: Cells were treated with 500 µM Auxin (3-indole-acetic acid sodium salt, abcam), 1 µM Flavopiridol (Cayman), or 250 nM NVP-2 (MedChemExpress). Heat shock treatment at 42 ˚C for 1 h was carried out as described previously (Mahat et al, 2016)

tag: cell type

value: Colorectal adenocarcinoma

tag: genotype

value: NELF-C-AID OsTIR1

tag: cell line


title: PRO-seq-18-NELFC-AID-37C-rep2

description: PRO-seq

value: Non-heat shock


title: PRO-cap-01-NELFC-AID-untreated-rep1

description: PRO-cap


title: PRO-seq-20-NELFC-AID-42C-Aux-rep1

description: PRO-seq


title: PRO-seq-19-NELFC-AID-42C-rep2

description: PRO-seq

value: Heat shock


title: PRO-seq-17-NELFC-AID-NVP-Aux

description: PRO-seq

value: NVP-2 and Auxin


title: PRO-cap-04-NELFC-AID-treated-rep2

description: PRO-cap

value: Auxin


title: PRO-seq-19-NELFC-AID-42C-rep1

description: PRO-seq


title: small RNA_HRCS_WT_CD_rep3

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

country: Japan

institute: RIKEN

description: small length of RNA

data_processing:
After trimming of adapter sequence, small RNA reads were extracted and counted using CLC Genomics Workbench (version 11.0) with default setting.
Extracted reads were annotated to 28-36 nt of 5' tRNA sequence obtained from GtRNAdb using CLC Genomics Workbench (version 11.0) with default setting..
Counts of tRNA fragments were normalized by read number annotated to tRNA flagment in each sample, using CLC Genomics Workbench (version 11.0).
tRNA fragments with lower read counts (<45 count) in any sample were omitted for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Results of 12 samples were summarized in tab-delimited txt file. The table contains normalized expression values in each sequence that matches 5' terminal of tRNA.

molecule: total RNA

organism: Mus musculus

source_name: HRCS

growth_protocol: Caudal epididymis and vas deferens were incubated in M2 medium for 1 hour at 37C to prepare total sperm fraction. After mild sonication to separate sperm head from the tail, HRCS was isolated from total sperm fraction by 82% Percoll precipitation.

extract_protocol:
Total RNA was extracted from HRCS by treatments with sperm lysis buffer and Trizol.
RNA-seq libraries were prepared by the NEBNext small RNA Library Prep Kit (New England Biolabs), and sequenced on Illumina Nextseq 500 (36-bp paired end).

treatment_protocol: Male mice were fed with control diet or low protein diet at 3-12 weeks age,

tag: diet

value: control diet

value: wild-type

value: histone replacement-completed sperm (HRCS)


title: subject ID 00308-0 at diease time point 3_Male, a T1D case and 4.8268309yrs old_EPIC array [201414140173_R08C01]

type: genomic

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

institute: Colorado School of Public Health

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe (v1.0.0) pipeline was used to normalize data (via Noob), perform dye bias correction and perform probe specific QC (via pOOBAH).
ComBat was used to adjust for batch effects were batch was considered to be plate and row position combination
Filtered probes with a small Beta range (range < 0.05), those with known SNPs in the CpG site, and those located on the sex chromosomes
Mvalues.normalized.*.txt contains methylation M-value

label: cy3, cy5

molecule: genomic DNA

source_name: T1D case_Male_time point 3

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human450K or EPIC Beadchip using standard Illumina protocol

extract_protocol: Standard Illumina Protocol

tag: subject id

tag: disease time point

tag: age

tag: Sex

value: Male

tag: t1d status

value: T1D case

tag: tissue

value: peripheral blood sample


title: subject ID 00308-0 at diease time point 5_Male, a T1D case and 9.6071184yrs old_EPIC array [201414140173_R07C01]

source_name: T1D case_Male_time point 5


title: subject ID 00308-0 at diease time point 4_Male, a T1D case and 5.8425736yrs old_EPIC array [201414140173_R06C01]

source_name: T1D case_Male_time point 4


title: PRO-seq-14-NELFC-AID-FP-Aux

description: PRO-seq

value: Flavopiridol and Auxin


title: ATF7_TGCs_WT_LPD_rep2

library_source: genomic

data_processing:
ChIP-seq and input reads were aligned to the mm9 genome assembly using CLC Genomics Workbench (version 11.0) with default setting, and non-specific reads were ignored.
BAM files were converted to BED files by BED tool, BAMtoBED (v2.27.0).
Length of reads in BED files was adjusted to insert size by extention of the end coordinate by BED tool, slopbed (v2.27.0).
BED files were converted to BedGraph files by BED tool, genomecov (v2.27.0) with normalization by read number mapped to the regions.
BedGraph files were converted to BW files by Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.0).
Genome_build: mm9
Supplementary_files_format_and_content: BW files show read coverage after scaling by read number mapped to 3kb around TSS.

source_name: testicular germ cells

growth_protocol: Testes were collected from each group of mice at 11-12 weeks age. TGCs were prepared from seminiferous tubules by collagenase and trypsin treatment, and cross-linked with 1% FA for 8 min at room temparature.

extract_protocol:
Cell ysates were prepared from sonicated TGCs, and ATF7-DNA complexes were isolated by ATF7 antibody.
ChIP-seq libraries were prepared by the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), and sequenced on Illumina Nextseq (36-bp paired end).

value: low protein diet

value: testicular germ cells

tag: chip antibody

value: ATF7 antibody (prepared in our lab; clone number 2F10)


title: PRO-seq-16-NELFC-AID-NVP

description: PRO-seq


title: PRO-seq-13-NELFC-AID-FP

description: PRO-seq

value: Flavopiridol


title: subject ID 00045-0 at diease time point 5_Female, a T1D case and 6.3025325yrs old_EPIC array [201414140173_R05C01]

source_name: T1D case_Female_time point 5

value: Female


title: PRO-seq-11-NELFC-AID-DMSO

description: PRO-seq

value: Colorectal adenocarcinoma

value: NELF-C-AID OsTIR1

value: DMSO


title: subject ID 00928-0 at diease time point 5_Male, a T1D control and 6.1437372yrs old_EPIC array [201414140173_R04C01]

source_name: T1D control_Male_time point 5

value: T1D control


title: PRO-seq-09-Parental-2h

description: PRO-seq

value: Auxin

tag: time point


title: subject ID 00308-0 at diease time point 2_Male, a T1D case and 1.2511978yrs old_EPIC array [201414140173_R03C01]

source_name: T1D case_Male_time point 2


title: PRO-seq-08-Parental-0h

description: PRO-seq


title: subject ID 00928-0 at diease time point 3_Male, a T1D control and 0.7583847yrs old_EPIC array [201414140173_R02C01]

source_name: T1D control_Male_time point 3


title: PRO-seq-18-NELFC-AID-37C-rep1

description: PRO-seq

value: Non-heat shock


title: subject ID 10690-0 at diease time point 4_Female, a T1D control and 4.2135524yrs old_EPIC array [201414140173_R01C01]

source_name: T1D control_Female_time point 4


title: PRO-seq-07-NELFE-AID-24h

description: PRO-seq

value: NELF-E-AID OsTIR1


title: subject ID 35082-0 at diease time point 4_Female, a T1D case and 14.7132101yrs old_EPIC array [201414140137_R06C01]

source_name: T1D case_Female_time point 4


title: subject ID 00958-0 at diease time point 4_Female, a T1D control and 1.2238193yrs old_EPIC array [201414140137_R08C01]


title: subject ID 35082-0 at diease time point 2_Female, a T1D case and 0.7583847yrs old_EPIC array [201414140137_R05C01]

source_name: T1D case_Female_time point 2


title: PRO-seq-15-NELFC-AID-DMSO

description: PRO-seq


title: PRO-seq-05-NELFE-AID-0h

description: PRO-seq


title: subject ID 35831-0 at diease time point 5_Male, a T1D control and 16.1013005yrs old_EPIC array [201414140137_R04C01]


title: subject ID 35831-0 at diease time point 4_Male, a T1D control and 15.0773443yrs old_EPIC array [201414140137_R03C01]

source_name: T1D control_Male_time point 4


title: PRO-seq-04-NELFC-AID-24h

description: PRO-seq


title: PRO-seq-02-NELFC-AID-1h

description: PRO-seq


title: PRO-seq-03-NELFC-AID-4h

description: PRO-seq


title: PRO-seq-10-Parental-24h

description: PRO-seq


title: subject ID 35082-0 at diease time point 5_Female, a T1D case and 15.9425051yrs old_EPIC array [201414140137_R02C01]


title: PRO-seq-12-NELFC-AID-DMSO-Aux

description: PRO-seq

value: DMSO and Auxin


title: subject ID 00788-0 at diease time point 4_Male, a T1D control and 2.0095825yrs old_EPIC array [201414140129_R07C01]

value: Male


title: PRO-seq-06-NELFE-AID-2h

description: PRO-seq


title: ChIP-seq-input-for-13

description: ChIP-seq input

data_processing:
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg19 and mouse mm9 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, plotProfile (Ramírez et al., 2016). ChIP-seq peaks were called using MACS 2.1.0 (Zhang et al., 2008) with a q-value cutoff of 0.05. Peaks were annotated using HOMER 4.10 (Heinz et al., 2010).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg19 and fly dm3 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Protein coding transcripts were chosen from Ensembl version 75 database by R 3.3.3, according to the previously described protocol (Liang et al., 2018) with minor modifications. Briefly, we selected RefSeq-validated transcripts with TSSs that overlapping NELF-C ChIP-seq peaks. We filtered out transcripts that are ≤ 2 kb long and ≤ 2 kb away from the nearest genes. Next, we chose transcripts that have ≥ 2 rpm total PRO-seq coverage at the region between TSS – 100 bp and TSS + 300 bp, using 3 independent PRO-seq data in untreated NELF-C-AID cells. In these selected transcripts, the nucleotide position with maximum PRO-seq coverage in the region between TSS – 100 bp and TSS + 300 bp was assigned to the 1st pause region. Transcripts that have ≤ 0.2 rpm coverage at the 1st pause region nucleotide were excluded. The resulting transcripts with assigned the 1st pause regions were used for further analyses. The nucleotide positions with maximum PRO-seq coverage in 1h auxin-treated NELF-C-AID cells at the region from +10 to +500 bp downstream of the 1st pause region was assigned to the 2nd pause region. For Heat shock experiments, transcripts with ≥ 1.5-fold increase or decrease in PRO-seq coverage at gene bodies (the 1st pause regions +500 to +100kb or to transcription termination sites) upon heat shock were assigned to HS-upregulated or HS-downregulated genes, respectively. Heatmaps and metaplots of PRO-seq signals were generated by deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, and plotProfile (Ramírez et al., 2016). Log2 fold change of PRO-seq signals at nucleotide resolution were calculated by deepTools 3.0.0/3.1.1/3.1.2 bigwigCompare with pseudocount 0.25 rpm.
For PRO-cap, raw reads were processed as described for PRO-seq above, requiring a read length of 18–36 bp. Processed paired-end reads were aligned to a concatenated genome comprised of hg19 and dm3 assemblies using bowtie2 with options (--very-sensitive -X 1000 --no-mixed --no-discordant --no-unal) (Langmead and Salzberg, 2012). The 5’ ends of aligned R2 reads with MAPQ ≥ 40 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options. Read counts were normalized to total reads aligned to the spike-in genome. de novo transcription start sites were identified from PRO-cap data using HOMER 4.11 with findcsRNATSS option (Duttke et al., 2019; Heinz et al., 2010). TSS identified in untreated and auxin-treated samples were merged then defined as TSS regions. Distances between TSS in each sample were measured using HOMER 4.11 annotatePeaks. Raw PRO-cap reads were counted using HOMER 4.11 annotatePeaks. Read counts were normalized to spike-in counts using RUVseq with RUVg option (Risso et al., 2014) in R 3.3.3. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and visualized in R 3.3.3. TSS with significant gain of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Up TSS, while TSS with significant loss of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Down TSS. Metaplots of PRO-cap and PRO-seq at Cap Up TSS or Cap Down TSS were generated using deepTools 3.1.1. For heatmaps of ChIP-seq and MNase-seq at TSS, TSS were first merged with gap of no longer than 600 bp to obtain TSS clusters, heatmaps were then generated at Cap Up TSS clusters and Cap Down TSS clusters.
Genome_build: hg19, dm3, mm9
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.


title: ChIP-seq-input-for-18_20

description: ChIP-seq input


title: PRO-seq-01-NELFC-AID-0h

description: PRO-seq


title: subject ID 00788-0 at diease time point 3_Male, a T1D control and 0.8049281yrs old_EPIC array [201414140129_R08C01]


title: subject ID 00435-0 at diease time point 5_Male, a T1D case and 14.4065708yrs old_EPIC array [201414140129_R04C01]

value: T1D case


title: subject ID 00435-0 at diease time point 4_Male, a T1D case and 3.0828200yrs old_EPIC array [201414140129_R05C01]

value: peripheral blood sample


title: ChIP-seq-input-for-08_10_12

description: ChIP-seq input


title: ChIP-seq-input-for-06_15

description: ChIP-seq input


title: subject ID 00788-0 at diease time point 5_Male, a T1D control and 12.4188912yrs old_EPIC array [201414140129_R06C01]


title: subject ID 00435-0 at diease time point 3_Male, a T1D case and 1.3032170yrs old_EPIC array [201414140129_R01C01]


title: ChIP-seq-input-for-19_21

description: ChIP-seq input


title: ChIP-seq-input-for-07_09_11

description: ChIP-seq input


title: subject ID 00642-0 at diease time point 4_Male, a T1D case and 3.5263518yrs old_EPIC array [201414140018_R05C01]


title: ChIP-seq-input-for-05_14

description: ChIP-seq input


title: subject ID 01104-0 at diease time point 5_Female, a T1D control and 8.1149897yrs old_EPIC array [201414140018_R04C01]

source_name: T1D control_Female_time point 5


title: ChIP-seq-input-for-02_04_17

description: ChIP-seq input


title: ChIP-seq-input-for-01_03_16

description: ChIP-seq input


title: subject ID 00642-0 at diease time point 5_Male, a T1D case and 8.6433949yrs old_EPIC array [201414140018_R01C01]


title: subject ID 00683-0 at diease time point 5_Female, a T1D case and 12.3367557yrs old_EPIC array [201414140009_R06C01]


title: subject ID 00333-0 at diease time point 4_Female, a T1D control and 3.6550308yrs old_EPIC array [201414140009_R02C01]


title: subject ID 00683-0 at diease time point 4_Female, a T1D case and 2.1629021yrs old_EPIC array [201414140009_R03C01]


title: subject ID 00333-0 at diease time point 5_Female, a T1D control and 14.9185489yrs old_EPIC array [201414140009_R04C01]


title: subject ID 00174-0 at diease time point 5_Male, a T1D case and 22.7926078yrs old_EPIC array [201414140008_R03C01]


title: subject ID 00459-0 at diease time point 4_Female, a T1D control and 0.9253936yrs old_EPIC array [201414140006_R08C01]


title: subject ID 00459-0 at diease time point 5_Female, a T1D control and 3.3018480yrs old_EPIC array [201414140006_R06C01]


title: ChIP-seq-17-NELFC-AID-treated-Pol2-S5P

description: ChIP-seq Pol2-S5P

tag: antibody

value: Pol2-CTD-Ser5P (Millipore, 04-1572)


title: ChIP-seq-19-NELFC-AID-treated-CBP80-rep1

description: ChIP-seq CBP80


title: ChIP-seq-18-NELFC-AID-untreated-CBP80-rep1

description: ChIP-seq CBP80


title: subject ID 00343-0 at diease time point 4_Female, a T1D case and 0.8131417yrs old_EPIC array [201414140006_R02C01]


title: subject ID 00279-0 at diease time point 5_Male, a T1D case and 3.6769336yrs old_EPIC array [201501980034_R08C01]


title: ChIP-seq-14-NELFC-AID-untreated-Pol2-S2P

description: ChIP-seq Pol2-S2P

value: Pol2-CTD-Ser2P (Millipore, 04-1571)


title: subject ID 00773-0 at diease time point 4_Male, a T1D control and 2.2176591yrs old_EPIC array [201501980034_R07C01]


title: ChIP-seq-15-NELFC-AID-treated-Pol2-S2P

description: ChIP-seq Pol2-S2P


title: ChIP-seq-21-NELFC-AID-treated-CBP80-rep2

description: ChIP-seq CBP80


title: ChIP-seq-13-Parental-H3K4me3

description: ChIP-seq H3K4me3

value: H3K4me3 (homemade)


title: ChIP-seq-11-NELFE-AID-untreated-SPT5

description: ChIP-seq SPT5


title: subject ID 00907-0 at diease time point 4_Female, a T1D case and 3.1238877yrs old_EPIC array [201501980034_R06C01]


title: ChIP-seq-12-NELFE-AID-treated-SPT5

description: ChIP-seq SPT5


title: subject ID 00773-0 at diease time point 5_Male, a T1D control and 3.7618070yrs old_EPIC array [201501980034_R05C01]


title: subject ID 00907-0 at diease time point 5_Female, a T1D case and 4.8405202yrs old_EPIC array [201501980034_R04C01]


title: subject ID 01104-0 at diease time point 4_Female, a T1D control and 2.1300479yrs old_EPIC array [201414140018_R02C01]


title: ChIP-seq-20-NELFC-AID-untreated-CBP80-rep2

description: ChIP-seq CBP80


title: ChIP-seq-16-NELFC-AID-untreated-Pol2-S5P

description: ChIP-seq Pol2-S5P


title: ChIP-seq-10-NELFE-AID-treated-NELFE

description: ChIP-seq NELFE

value: NELFE (Abcam, ab170104)


title: ChIP-seq-06-NELFC-AID-treated-SPT5

description: ChIP-seq SPT5


title: ChIP-seq-08-NELFE-AID-treated-NELFC

description: ChIP-seq NELFC

value: NELFC (CST, 12265)


title: ChIP-seq-09-NELFE-AID-untreated-NELFE

description: ChIP-seq NELFE


title: subject ID 00279-0 at diease time point 4_Male, a T1D case and 3.5099247yrs old_EPIC array [201501980034_R01C01]


title: ChIP-seq-05-NELFC-AID-untreated-SPT5

description: ChIP-seq SPT5


title: subject ID 00819-0 at diease time point 5_Female, a T1D control and 4.8186174yrs old_EPIC array [201501980034_R02C01]

value: Female


title: ChIP-seq-04-NELFC-AID-treated-NELFE

description: ChIP-seq NELFE

value: Colorectal adenocarcinoma


title: subject ID 30364-0 at diease time point 5_Male, a T1D control and 6.1492129yrs old_EPIC array [201501980003_R08C01]


title: subject ID 84860-0 at diease time point 5_Female, a T1D case and 8.9144422yrs old_EPIC array [201501980003_R07C01]


title: ChIP-seq-03-NELFC-AID-untreated-NELFE

description: ChIP-seq NELFE

value: NELF-C-AID OsTIR1


title: ChIP-seq-01-NELFC-AID-untreated-NELFC

description: ChIP-seq NELFC


title: ChIP-seq-02-NELFC-AID-treated-NELFC

description: ChIP-seq NELFC


title: subject ID 30364-0 at diease time point 4_Male, a T1D control and 2.0260096yrs old_EPIC array [201501980003_R03C01]


title: subject ID 84860-0 at diease time point 3_Female, a T1D case and 1.2539357yrs old_EPIC array [201501980003_R05C01]

source_name: T1D case_Female_time point 3


title: ChIP-seq-07-NELFE-AID-untreated-NELFC

description: ChIP-seq NELFC


title: subject ID 84860-0 at diease time point 4_Female, a T1D case and 3.0143737yrs old_EPIC array [201501980003_R02C01]


title: subject ID 19829-0 at diease time point 5_Male, a T1D control and 7.5455168yrs old_EPIC array [201501980002_R08C01]


title: subject ID 84002-0 at diease time point 3_Female, a T1D case and 0.9965777yrs old_EPIC array [201501980002_R06C01]


title: cSCC9: cutaneous squamous cell carcinoma biopsy

city: Stockholm

first: Kunal

last: Das Mahaptra

state: Select Option

address: PO BOX 23109

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina integrated software was used for base-calling. Fastq files were generated using bcl2fastq software (Illumina Inc.)
TopHat  was used for subsequent data filtering, read mapping and splice junction detection
Transcript assembly was done using Cufflinks suite
Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression.
When comparing groups with paired samples, featureCounts is used to calculate the counts of mapped reads in specific genes, and generalized linear model likelihood ratio test (glmLRT) implemented by edgeR is used to test for differential expression across the submitted samples using featureCounts output.
Genome_build: genome version: hg19/GrCh37
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized FPKM values for each samples

source_name: 4 mm punch biopsy

extract_protocol:
4 mm punch biopsies were collected from 7 unmatched healthy skin and 9 cSCC samples. Snap frozen punch biopsies were homogenized followed by RNA extraction using the miRNeasey mini kit (Qiagen). RNA concentrations were measured using a Nanodrop  and RNA integrity was assessed on the Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
The library preparation was done using Illumina TruSeq® Stranded Total RNA (with Ribo-Zero Gold) preparation kit. 100 ng of total RNA was depleted of rRNAs using ribo-zero gold magnetic bead based capture-probe system (Illumina Inc.). The remaining RNA (including mRNAs, lincRNAs and other RNA species) was subsequently purified (RNAcleanXP, Beckman Coulter) and fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The stranded libraries were amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer. Sequencing was performed on NextSeq 500 instrument using v2 reagent kits according to the manufacturer instructions (Illumina Inc.).

tag: ethnicity

value: Caucasian

value: Whole skin

tag: gender

tag: disease state

value: cutaneous squamous cell carcinoma


title: cSCC7: cutaneous squamous cell carcinoma biopsy


title: cSCC6: cutaneous squamous cell carcinoma biopsy


title: subject ID 00819-0 at diease time point 4_Female, a T1D control and 3.1841205yrs old_EPIC array [201501980034_R03C01]

value: T1D control


title: cSCC4: cutaneous squamous cell carcinoma biopsy


title: cSCC5: cutaneous squamous cell carcinoma biopsy


title: subject ID 19829-0 at diease time point 4_Male, a T1D control and 2.0095825yrs old_EPIC array [201501980002_R03C01]


title: cSCC3: cutaneous squamous cell carcinoma biopsy


title: subject ID 19829-0 at diease time point 3_Male, a T1D control and 1.2265572yrs old_EPIC array [201501980002_R02C01]


title: subject ID 84002-0 at diease time point 5_Female, a T1D case and 7.8959617yrs old_EPIC array [201501980002_R01C01]


title: subject ID 30364-0 at diease time point 3_Male, a T1D control and 1.2511978yrs old_EPIC array [201501980003_R06C01]


title: subject ID 30305-0 at diease time point 4_Male, a T1D control and 2.1136208yrs old_EPIC array [201501980058_R08C01]


title: cSCC2: cutaneous squamous cell carcinoma biopsy


title: subject ID 26143-0 at diease time point 5_Male, a T1D case and 6.1136208yrs old_EPIC array [201501980058_R07C01]


title: H7: Healthy skin biopsy

value: healthy


title: H6: Healthy skin biopsy


title: H5: Healthy skin biopsy


title: cSCC8: cutaneous squamous cell carcinoma biopsy


title: subject ID 30305-0 at diease time point 3_Male, a T1D control and 1.2265572yrs old_EPIC array [201501980058_R05C01]


title: subject ID 30305-0 at diease time point 5_Male, a T1D control and 5.6563997yrs old_EPIC array [201501980058_R03C01]


title: H4: Healthy skin biopsy


title: subject ID 84002-0 at diease time point 4_Female, a T1D case and 2.3545517yrs old_EPIC array [201501980002_R05C01]


title: H3: Healthy skin biopsy


title: H2: Healthy skin biopsy


title: H1: Healthy skin biopsy


title: subject ID 13386-0 at diease time point 3_Female, a T1D control and 0.7665982yrs old_EPIC array [201501980032_R08C01]

source_name: T1D control_Female_time point 3


title: subject ID 12754-0 at diease time point 3_Male, a T1D case and 0.9062286yrs old_EPIC array [201501980032_R05C01]


title: subject ID 13386-0 at diease time point 4_Female, a T1D control and 2.0451745yrs old_EPIC array [201501980032_R03C01]


title: subject ID 13386-0 at diease time point 5_Female, a T1D control and 4.1697467yrs old_EPIC array [201501980032_R04C01]


title: subject ID 26143-0 at diease time point 3_Male, a T1D case and 3.0061602yrs old_EPIC array [201501980058_R01C01]


title: subject ID 00689-0 at diease time point 5_Male, a T1D control and 7.0143737yrs old_EPIC array [201501980032_R02C01]


title: subject ID 13776-0 at diease time point 4_Male, a T1D case and 1.2566735yrs old_EPIC array [201501980017_R04C01]


title: subject ID 26143-0 at diease time point 4_Male, a T1D case and 3.9972621yrs old_EPIC array [201501980058_R06C01]


title: subject ID 12754-0 at diease time point 4_Male, a T1D case and 2.5352498yrs old_EPIC array [201501980032_R01C01]


title: subject ID 50147-0 at diease time point 4_Female, a T1D control and 2.9869952yrs old_EPIC array [201501980004_R05C01]


title: subject ID 13776-0 at diease time point 5_Male, a T1D case and 8.9609856yrs old_EPIC array [201501980017_R01C01]


title: subject ID 12754-0 at diease time point 5_Male, a T1D case and 5.7741273yrs old_EPIC array [201501980032_R06C01]


title: mouse kidney sample 3

city: Baltimore

first: Theresa

middle: K

last: Hodges

state: MD

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

data_processing:
Illumina reads from Human and Mouse were aligned to their target reference genome using TopHat version 1.4.0.
Gene-level read counts were produced by HTseq (version 0.4.7). DESeq (version 1.1.10) was used to determine gene-level differential expression.
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Expression estimates in the form of Fragments per Kilobase of exon per Million bases mapped (FPKM) were calculated by Cufflinks version 1.3.0. Isoform-level differential expression was determined using Cuffdiff (version 1.3.0).
Genome_build: human build = GRCh37; mouse build = GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts generated for each sample using HTSeq

source_name: kidney

extract_protocol:
Total RNA extracted from samples in RNAlater
RIN = 10
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: tissue section

value: cortex

tag: strain


title: mouse kidney sample 1

extract_protocol:
Total RNA extracted from samples in RNAlater
RIN = 9.5
RNA libraries were prepared for sequencing using standard Illumina protocols


title: mouse kidney sample 2

extract_protocol:
Total RNA extracted from samples in RNAlater
RIN = 9.1
RNA libraries were prepared for sequencing using standard Illumina protocols

value: medulla


title: subject ID 12079-0 at diease time point 5_Male, a T1D case and 13.4565366yrs old_EPIC array [201501980004_R03C01]

value: Male

value: T1D case

value: peripheral blood sample


title: subject ID 50147-0 at diease time point 5_Female, a T1D control and 14.7296372yrs old_EPIC array [201501980004_R02C01]


title: subject ID 12079-0 at diease time point 4_Male, a T1D case and 3.1457906yrs old_EPIC array [201501980004_R01C01]


title: WT_1

type: RNA

city: Tokyo

first: Yu

last: Toyoda

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Pharmacy

institute: The University of Tokyo Hospital

hyb_protocol: Cy3-labeled cRNA was hybridized to the SurePrint G3 Mouse Gene Expression 8 × 60K Microarray (Agilent Technologies).

scan_protocol: The microarray was washed using Gene Expression Wash Pack (Agilent Technologies) and scanned by a DNA Microarray Scanner (G2565CA; Agilent Technologies).

data_processing: Scanner output images were normalized and digitalized by Feature Extraction software (Agilent Technologies) according to the Minimum Information About a Microarray Experiment (MIAME) guidelines.

source_name: Liver from WT mouse

label_protocol: Total RNAs extracted from two or three mice were pooled, reverse-transcribed to double-stranded complementary DNA, and then in vitro transcribed to yield cRNA labeled with the fluorescent dye Cy3 according to the manufacturer’s protocol.

growth_protocol: Transgenic mice expressing human NPC1L1 in hepatocytes (L1-Tg mice) (B6;D2-Tg(APOE-NPC1L1)20Lqyu/J) were purchased from The Jackson Laboratory (Bar Harbor, Maine, USA) and backcrossed at least eight generations to C57BL/6J mice (Japan SLC, Inc., Shizuoka, Japan) before use. Hemizygous positive L1-Tg mice were always crossed to WT C57BL/6J mice to generate hemizygous L1-Tg mice and WT littermate controls for all experiments

extract_protocol: Total RNA was extracted using RNA isoPlus® Reagent (Takara, Shiga, Japan) from the murine liver, according to the manufacturer’s protocol. For microarray analysis, total RNA was purified by RNeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s instruction. The integrity of RNA was evaluated by Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA).

treatment_protocol: The male mice used in this study were maintained on an indicated diet and water ad libitum under a 12 h/12 h light/dark cycle (starting at 7:00), as described previously (DOI: 10.1126/scitranslmed.3010329).

tag: genotype

value: wild type

value: Liver


title: subject ID 85370-0 at diease time point 4_Male, a T1D case and 0.8459959yrs old_EPIC array [201501970048_R07C01]


title: Tg_3

source_name: Liver from Tg mouse

value: Transgenic mice expressing human NPC1L1 in hepatocytes


title: Tg_2


title: WT_3


title: cSCC1: cutaneous squamous cell carcinoma biopsy

value: Female


title: Tg_1


title: WT_2


title: subject ID 36662-0 at diease time point 5_Male, a T1D control and 4.3778234yrs old_EPIC array [201501970048_R06C01]


title: subject ID 85370-0 at diease time point 5_Male, a T1D case and 4.6023272yrs old_EPIC array [201501970048_R03C01]

source_name: T1D case_Male_time point 5


title: mouse kidney sample 4


title: subject ID 36662-0 at diease time point 4_Male, a T1D control and 0.7720739yrs old_EPIC array [201501970048_R01C01]


title: subject ID 11473-0 at diease time point 4_Male, a T1D control and 1.2594114yrs old_EPIC array [201501970051_R04C01]


title: subject ID 35229-0 at diease time point 5_Female, a T1D case and 2.9322382yrs old_EPIC array [201501970051_R07C01]


title: air vapor, nondrinker, mouse 55, bed nucleus of the stria terminalis

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

description: Gene expression data from bed nucleus of the stria terminalis of C57BL6/J mouse under air vapor only

hyb_protocol: Hybridization was performed according to procedures optimized by Affymetrix.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 scanner.

data_processing: Affymetrix GeneChip Mouse Genome 430, type 2 array quality was assessed by RNA degradation, average background, percent present probesets, and multi-dimensional scale plots. Background correction usingRobust Multi-array Average (RMA) and quantile normalization was performed and each brain-region was normalized separately. ComBat by RNA hybridization batch was used to correct for any batch effects present in the data.

label: biotin

source_name: C57BL6/J mouse, air vapor, nondrinker, bed nucleus of the stria terminalis

label_protocol: Labelling was performed according to procedures optimized by Affymetrix.

growth_protocol: Male C57BL/6J mice were purchased from Jackson Laboratories at 10 weeks of age. Mice were kept under a 12-hour light/dark cycle and given free access to water and standard rodent chow. All studies were conducted in an AALAC-accredited animal facility, and approved by the Institutional Animal Care and Use Committee at Medical University of South Carolina (MUSC). All experimental and animal care procedures met guidelines outlined in the NIH Guide for the Care and Use of Laboratory Animals

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: Mice were divided into 4 treatment groups: the CIE-Drinking group received inhaled ethanol in the vapor chambers followed by 2-bottle choice ethanol drinking in between vapor exposure cycles;the Air-Drinking group received only air in the vapor chambers, but had2-bottle choice ethanol drinking between CIE cycles;the CIE-NonDrinking group received inhaled ethanol in the vapor chambers but only water accessin between CIE cycles;and the Air-NonDrinking group remained ethanol naïve with air exposure in vapor chambers and only water consumption between CIE cycles. Following a 2-week acclimation period, mice in the CIE-Drinking and Air-Drinking groups underwent 6-weeks of 2-bottle choice drinking to establish baseline drinking levels.The 2-hr limited access session to ethanol (15 v/v)vs. water started 30 min before lights off. Ethanol and water intake for each individual mouse was measured daily. Following 6-weeks of baseline drinking, mice were placed in Plexiglass inhalation chambers (60x36x60 cm) 16 hours/day for 4 days. Ethanol was volatilized with an air stone submerged in 95% ethanol. Vapor chamber ethanol concentrations were monitored daily and air flow was adjusted to ethanol concentrations within 10-13 mg/l air. Before each vapor chamber session, intoxication was initiated in the CIE group by administration of 1.6 138g/kg ethanol and 1 mmol/kg pyrazole intraperitoneally (i.p.) at a volume of 0.02 ml/g body 139weight. All mice received the same number and timing of pyrazole injections prior to final removal from the inhalation chambers with control mice receiving saline and pyrazole (i.p.), also at a volume of 0.02 ml/g body weight, prior to being placed into control vapor chambers. Control vapor chambers delivered only airwithoutethanol vapor. After 4 days in the inhalation chambers, mice underwent a 72-hour period of total abstinence from ethanol. Following the abstinence period, mice in the CIE-Drinking and Air-Drinking groups were given 2-bottle choice drinking for 2 hours per day for 5 days. A total of 4 cycles of CIE-abstinence-drinking were performed. After the end of the 4th cycle mice were sacrificed on the 5th drinking day before receiving ethanol/water access on that day at the time they received 2-bottle choice drinking all previous drinking days.

tag: vapor treatment

value: Control

tag: drinking treatment

value: Nondrinker

tag: brain region

value: bed nucleus of the stria terminalis

value: male


title: air vapor, nondrinker, mouse 56, bed nucleus of the stria terminalis


title: subject ID 11473-0 at diease time point 5_Male, a T1D control and 4.1149897yrs old_EPIC array [201501970051_R03C01]

tag: subject id

tag: disease time point


title: subject ID 00986-0 at diease time point 2_Female, a T1D control and 1.0759754yrs old_EPIC array [201502810054_R04C01]

source_name: T1D control_Female_time point 2

tag: age

tag: Sex


title: air vapor, nondrinker, mouse 53, bed nucleus of the stria terminalis


title: subject ID 84492-0 at diease time point 5_Male, a T1D control and 6.4312115yrs old_EPIC array [201501970001_R05C01]

source_name: T1D control_Male_time point 5

tag: t1d status

tag: tissue


title: air vapor, nondrinker, mouse 52, bed nucleus of the stria terminalis


title: air vapor, nondrinker, mouse 51, bed nucleus of the stria terminalis


title: subject ID 37240-0 at diease time point 5_Male, a T1D case and 6.8309377yrs old_EPIC array [201502810054_R02C01]


title: subject ID 00986-0 at diease time point 4_Female, a T1D control and 3.1950719yrs old_EPIC array [201502810054_R08C01]


title: subject ID 00732-0 at diease time point 2_Male, a T1D case and 0.8624230yrs old_EPIC array [201502810054_R03C01]

source_name: T1D case_Male_time point 2


title: subject ID 35229-0 at diease time point 4_Female, a T1D case and 0.8076660yrs old_EPIC array [201501970051_R02C01]


title: air vapor, nondrinker, mouse 48, bed nucleus of the stria terminalis


title: CIE vapor, nondrinker, mouse 43, bed nucleus of the stria terminalis

description: Gene expression data from bed nucleus of the stria terminalis of C57BL6/J mouse under chronic intermittent ethanol vapor only

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, nondrinker, bed nucleus of the stria terminalis

value: CIE


title: air vapor, nondrinker, mouse 47, bed nucleus of the stria terminalis


title: air vapor, nondrinker, mouse 49, bed nucleus of the stria terminalis


title: CIE vapor, nondrinker, mouse 44, bed nucleus of the stria terminalis


title: air vapor, nondrinker, mouse 50, bed nucleus of the stria terminalis


title: subject ID 00732-0 at diease time point 5_Male, a T1D case and 9.2594114yrs old_EPIC array [201502810054_R01C01]


title: air vapor, nondrinker, mouse 54, bed nucleus of the stria terminalis


title: subject ID 00986-0 at diease time point 5_Female, a T1D control and 8.8377823yrs old_EPIC array [201502810054_R05C01]

value: T1D control


title: subject ID 13513-0 at diease time point 5_Female, a T1D control and 7.3894593yrs old_EPIC array [201502810023_R06C01]


title: CIE vapor, nondrinker, mouse 42, bed nucleus of the stria terminalis


title: CIE vapor, nondrinker, mouse 40, bed nucleus of the stria terminalis


title: subject ID 16148-0 at diease time point 5_Female, a T1D case and 12.0246407yrs old_EPIC array [201502810023_R02C01]

source_name: T1D case_Female_time point 5


title: CIE vapor, nondrinker, mouse 39, bed nucleus of the stria terminalis


title: CIE vapor, nondrinker, mouse 41, bed nucleus of the stria terminalis


title: CIE vapor, nondrinker, mouse 38, bed nucleus of the stria terminalis


title: subject ID 00732-0 at diease time point 4_Male, a T1D case and 3.9589322yrs old_EPIC array [201502810054_R06C01]

source_name: T1D case_Male_time point 4


title: subject ID 26352-0 at diease time point 5_Male, a T1D control and 12.2272416yrs old_EPIC array [201502810023_R08C01]


title: subject ID 00240-0 at diease time point 5_Female, a T1D case and 10.6940452yrs old_EPIC array [201502810015_R08C01]


title: subject ID 00913-0 at diease time point 5_Male, a T1D control and 9.6481862yrs old_EPIC array [201502810015_R06C01]


title: subject ID 00240-0 at diease time point 3_Female, a T1D case and 1.4729637yrs old_EPIC array [201502810015_R04C01]


title: subject ID 28618-0 at diease time point 4_Male, a T1D control and 1.4072553yrs old_EPIC array [201502810015_R07C01]


title: subject ID 28618-0 at diease time point 5_Male, a T1D control and 2.1218344yrs old_EPIC array [201502810015_R02C01]


title: subject ID 28618-0 at diease time point 3_Male, a T1D control and 0.7501711yrs old_EPIC array [201502810015_R01C01]

source_name: T1D control_Male_time point 3


title: subject ID 00132-0 at diease time point 4_Male, a T1D case and 1.1006160yrs old_EPIC array [201501980055_R06C01]


title: subject ID 00132-0 at diease time point 3_Male, a T1D case and 0.7529090yrs old_EPIC array [201501980055_R05C01]

source_name: T1D case_Male_time point 3


title: subject ID 20615-0 at diease time point 2_Male, a T1D case and 0.7912389yrs old_EPIC array [201501980055_R04C01]


title: subject ID 20615-0 at diease time point 3_Male, a T1D case and 8.0054757yrs old_EPIC array [201501980055_R03C01]


title: CIE vapor, nondrinker, mouse 35, bed nucleus of the stria terminalis


title: subject ID 20615-0 at diease time point 4_Male, a T1D case and 9.9904175yrs old_EPIC array [201501980055_R02C01]


title: air vapor, ethanol drinker, mouse 59, bed nucleus of the stria terminalis

description: Gene expression data from bed nucleus of the stria terminalis of C57BL6/J mouse under air vapor and drinking

source_name: C57BL6/J mouse, air vapor, ethanol drinker, bed nucleus of the stria terminalis

value: Drinker


title: air vapor, ethanol drinker, mouse 60, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 58, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 61, bed nucleus of the stria terminalis


title: subject ID 00913-0 at diease time point 4_Male, a T1D control and 2.0013689yrs old_EPIC array [201502810015_R03C01]

source_name: T1D control_Male_time point 4


title: air vapor, ethanol drinker, mouse 28, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 24, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 25, bed nucleus of the stria terminalis


title: CIE vapor, nondrinker, mouse 34, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 57, bed nucleus of the stria terminalis


title: subject ID 17246-0 at diease time point 5_Male, a T1D control and 10.1273101yrs old_EPIC array [201501980046_R04C01]


title: air vapor, ethanol drinker, mouse 32, bed nucleus of the stria terminalis


title: subject ID 17246-0 at diease time point 2_Male, a T1D control and 0.7912389yrs old_EPIC array [201501980046_R03C01]

source_name: T1D control_Male_time point 2


title: air vapor, ethanol drinker, mouse 31, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 30, bed nucleus of the stria terminalis


title: subject ID 10066-0 at diease time point 3_Male, a T1D control and 0.7583847yrs old_EPIC array [201501980029_R06C01]


title: subject ID 17246-0 at diease time point 4_Male, a T1D control and 8.1177276yrs old_EPIC array [201501980046_R01C01]


title: CIE vapor, nondrinker, mouse 37, bed nucleus of the stria terminalis


title: subject ID 00913-0 at diease time point 3_Male, a T1D control and 1.2648871yrs old_EPIC array [201502810015_R05C01]


title: CIE vapor, nondrinker, mouse 36, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 17, bed nucleus of the stria terminalis

description: Gene expression data from bed nucleus of the stria terminalis of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, bed nucleus of the stria terminalis


title: subject ID 10066-0 at diease time point 4_Male, a T1D control and 1.2813142yrs old_EPIC array [201501980029_R02C01]


title: subject ID 17246-0 at diease time point 3_Male, a T1D control and 7.0335387yrs old_EPIC array [201501980046_R02C01]


title: subject ID 00813-0 at diease time point 4_Female, a T1D case and 1.6043806yrs old_EPIC array [201501980029_R03C01]

source_name: T1D case_Female_time point 4


title: subject ID 10066-0 at diease time point 5_Male, a T1D control and 5.4948665yrs old_EPIC array [201501980029_R01C01]


title: CIE vapor, ethanol drinker, mouse 14, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 21, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 10, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 9, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 12, bed nucleus of the stria terminalis


title: air vapor, ethanol drinker, mouse 23, bed nucleus of the stria terminalis


title: subject ID 00188-0 at diease time point 4_Female, a T1D control and 10.9897331yrs old_EPIC array [201501970050_R07C01]

source_name: T1D control_Female_time point 4


title: subject ID 00492-0 at diease time point 3_Female, a T1D case and 0.7830253yrs old_EPIC array [201501970050_R04C01]

source_name: T1D case_Female_time point 3


title: subject ID 00765-0 at diease time point 4_Male, a T1D control and 1.2238193yrs old_EPIC array [201501970050_R05C01]


title: subject ID 00492-0 at diease time point 5_Female, a T1D case and 6.0424367yrs old_EPIC array [201501970050_R08C01]


title: subject ID 00813-0 at diease time point 5_Female, a T1D case and 5.4647502yrs old_EPIC array [201501980029_R04C01]


title: subject ID 00492-0 at diease time point 4_Female, a T1D case and 1.9383984yrs old_EPIC array [201501970050_R03C01]


title: CIE vapor, ethanol drinker, mouse 5, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 6, bed nucleus of the stria terminalis


title: CIE vapor, ethanol drinker, mouse 4, bed nucleus of the stria terminalis


title: subject ID 00765-0 at diease time point 3_Male, a T1D control and 0.9390828yrs old_EPIC array [201501970050_R02C01]


title: subject ID 00188-0 at diease time point 5_Female, a T1D control and 12.1232033yrs old_EPIC array [201501970050_R01C01]

source_name: T1D control_Female_time point 5


title: subject ID 00891-0 at diease time point 4_Female, a T1D control and 1.2484600yrs old_EPIC array [201501970058_R07C01]


title: subject ID 00451-0 at diease time point 4_Male, a T1D case and 1.5961670yrs old_EPIC array [201501970058_R05C01]


title: subject ID 00451-0 at diease time point 3_Male, a T1D case and 0.8021903yrs old_EPIC array [201501970058_R06C01]


title: subject ID 00765-0 at diease time point 5_Male, a T1D control and 6.5735797yrs old_EPIC array [201501970050_R06C01]


title: subject ID 00891-0 at diease time point 3_Female, a T1D control and 0.7501711yrs old_EPIC array [201501970058_R04C01]

source_name: T1D control_Female_time point 3


title: CIE vapor, ethanol drinker, mouse 2, bed nucleus of the stria terminalis


title: air vapor, nondrinker, mouse 55, central nucleus of the amygdala

description: Gene expression data from central nucleus of the amygdala of C57BL6/J mouse under airl vapor only

source_name: C57BL6/J mouse, air vapor, nondrinker, central nucleus of the amygdala

value: central nucleus of the amygdala


title: subject ID 00158-0 at diease time point 4_Male, a T1D case and 10.4339494yrs old_EPIC array [201501970058_R03C01]


title: air vapor, nondrinker, mouse 53, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 1, bed nucleus of the stria terminalis


title: subject ID 00158-0 at diease time point 5_Male, a T1D case and 11.4360027yrs old_EPIC array [201501970058_R02C01]

source_name: T1D case_Male_time point 5


title: CIE vapor, ethanol drinker, mouse 3, bed nucleus of the stria terminalis


title: air vapor, nondrinker, mouse 52, central nucleus of the amygdala


title: subject ID 00873-0 at diease time point 5_Female, a T1D control and 9.4784394yrs old_EPIC array [201501970049_R05C01]


title: air vapor, nondrinker, mouse 48, central nucleus of the amygdala


title: air vapor, nondrinker, mouse 51, central nucleus of the amygdala


title: air vapor, nondrinker, mouse 49, central nucleus of the amygdala


title: subject ID 00451-0 at diease time point 5_Male, a T1D case and 6.7515400yrs old_EPIC array [201501970058_R01C01]


title: subject ID 00017-0 at diease time point 5_Female, a T1D case and 9.7549624yrs old_EPIC array [201501970018_R08C01]


title: subject ID 00873-0 at diease time point 4_Female, a T1D control and 2.0314853yrs old_EPIC array [201501970049_R01C01]


title: subject ID 00017-0 at diease time point 4_Female, a T1D case and 3.7371663yrs old_EPIC array [201501970018_R04C01]


title: subject ID 31177-0 at diease time point 4_Female, a T1D case and 7.5865845yrs old_EPIC array [201502810053_R08C01]


title: subject ID 31177-0 at diease time point 3_Female, a T1D case and 6.4366872yrs old_EPIC array [201502810053_R05C01]


title: subject ID 20272-0 at diease time point 3_Male, a T1D control and 0.7063655yrs old_EPIC array [201502810053_R04C01]


title: air vapor, nondrinker, mouse 56, central nucleus of the amygdala


title: subject ID 31177-0 at diease time point 5_Female, a T1D case and 10.8993840yrs old_EPIC array [201502810053_R02C01]


title: subject ID 31177-0 at diease time point 2_Female, a T1D case and 1.2840520yrs old_EPIC array [201502810053_R01C01]

source_name: T1D case_Female_time point 2


title: subject ID 20272-0 at diease time point 4_Male, a T1D control and 1.2375086yrs old_EPIC array [201502810053_R03C01]


title: CIE vapor, nondrinker, mouse 43, central nucleus of the amygdala

description: Gene expression data from central nucleus of the amygdala of C57BL6/J mouse under chronic intermittent ethanol vapor only

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, nondrinker, central nucleus of the amygdala


title: subject ID 30425-0 at diease time point 4_Female, a T1D control and 7.3675565yrs old_EPIC array [201502810052_R08C01]


title: subject ID 00379-0 at diease time point 5_Female, a T1D case and 4.9965777yrs old_EPIC array [201502810052_R07C01]

source_name: T1D case_Female_time point 5


title: CIE vapor, nondrinker, mouse 40, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 41, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 34, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 42, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 36, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 44, central nucleus of the amygdala


title: subject ID 00379-0 at diease time point 4_Female, a T1D case and 1.2594114yrs old_EPIC array [201502810052_R02C01]


title: air vapor, nondrinker, mouse 45, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 39, central nucleus of the amygdala


title: subject ID 30425-0 at diease time point 5_Female, a T1D control and 9.7823409yrs old_EPIC array [201502810052_R05C01]


title: subject ID 18471-0 at diease time point 4_Male, a T1D case and 1.3388090yrs old_EPIC array [201502810021_R08C01]

source_name: T1D case_Male_time point 4


title: subject ID 30425-0 at diease time point 2_Female, a T1D control and 0.7939767yrs old_EPIC array [201502810052_R04C01]

source_name: T1D control_Female_time point 2


title: air vapor, ethanol drinker, mouse 59, central nucleus of the amygdala

description: Gene expression data from central nucleus of the amygdala of C57BL6/J mouse under air vapor and drinking

source_name: C57BL6/J mouse, air vapor, ethanol drinker, central nucleus of the amygdala


title: air vapor, ethanol drinker, mouse 62, central nucleus of the amygdala


title: subject ID 00379-0 at diease time point 3_Female, a T1D case and 0.7638604yrs old_EPIC array [201502810052_R01C01]


title: air vapor, ethanol drinker, mouse 28, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 37, central nucleus of the amygdala


title: air vapor, ethanol drinker, mouse 58, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 38, central nucleus of the amygdala


title: subject ID 10561-0 at diease time point 4_Male, a T1D control and 1.2731006yrs old_EPIC array [201502810021_R07C01]


title: air vapor, ethanol drinker, mouse 32, central nucleus of the amygdala


title: air vapor, ethanol drinker, mouse 27, central nucleus of the amygdala


title: CIE vapor, nondrinker, mouse 33, central nucleus of the amygdala


title: air vapor, ethanol drinker, mouse 60, central nucleus of the amygdala


title: air vapor, ethanol drinker, mouse 31, central nucleus of the amygdala


title: subject ID 00082-0 at diease time point 5_Male, a T1D case and 5.5715264yrs old_450K array [3999078162_R03C02]


title: subject ID 00674-0 at diease time point 5_Female, a T1D control and 4.8870637yrs old_450K array [3999078162_R05C02]


title: air vapor, ethanol drinker, mouse 25, central nucleus of the amygdala


title: subject ID 18471-0 at diease time point 3_Male, a T1D case and 0.7501711yrs old_EPIC array [201502810021_R04C01]

source_name: T1D case_Male_time point 3


title: subject ID 00239-0 at diease time point 5_Female, a T1D case and 12.5475702yrs old_450K array [200123460117_R06C02]


title: subject ID 00822-0 at diease time point 5_Male, a T1D control and 13.6317591yrs old_450K array [200123460117_R05C02]

source_name: T1D control_Male_time point 5


title: subject ID 18471-0 at diease time point 5_Male, a T1D case and 3.0609172yrs old_EPIC array [201502810021_R03C01]


title: subject ID 10561-0 at diease time point 3_Male, a T1D control and 0.8268309yrs old_EPIC array [201502810021_R02C01]

source_name: T1D control_Male_time point 3


title: air vapor, ethanol drinker, mouse 23, central nucleus of the amygdala


title: subject ID 00822-0 at diease time point 3_Male, a T1D control and 6.4394251yrs old_450K array [200123460117_R03C02]


title: subject ID 37051-0 at diease time point 3_Female, a T1D control and 0.7802875yrs old_EPIC array [201502810009_R05C01]


title: subject ID 00239-0 at diease time point 3_Female, a T1D case and 4.3586585yrs old_450K array [200123460117_R01C02]


title: subject ID 10561-0 at diease time point 5_Male, a T1D control and 2.1683778yrs old_EPIC array [201502810021_R06C01]


title: air vapor, ethanol drinker, mouse 30, central nucleus of the amygdala


title: subject ID 00787-0 at diease time point 4_Female, a T1D case and 2.2094456yrs old_450K array [200123460117_R04C01]


title: CIE vapor, ethanol drinker, mouse 17, central nucleus of the amygdala

description: Gene expression data from central nucleus of the amygdala of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, central nucleus of the amygdala


title: subject ID 37051-0 at diease time point 5_Female, a T1D control and 2.0342231yrs old_EPIC array [201502810009_R04C01]


title: air vapor, ethanol drinker, mouse 24, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 10, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 21, central nucleus of the amygdala


title: subject ID 00665-0 at diease time point 4_Male, a T1D control and 3.0499658yrs old_450K array [200123460117_R03C01]

source_name: T1D control_Male_time point 4


title: CIE vapor, ethanol drinker, mouse 5, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 14, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 6, central nucleus of the amygdala


title: subject ID 14913-0 at diease time point 5_Female, a T1D case and 3.1348392yrs old_EPIC array [201502810009_R03C01]


title: subject ID 14913-0 at diease time point 3_Female, a T1D case and 0.7392197yrs old_EPIC array [201502810009_R08C01]


title: subject ID 00483-0 at diease time point 4_Male, a T1D case and 2.1902806yrs old_450K array [200123460117_R02C01]


title: subject ID 00522-0 at diease time point 4_Female, a T1D control and 2.1437372yrs old_450K array [200123460117_R01C01]

source_name: T1D control_Female_time point 4


title: CIE vapor, ethanol drinker, mouse 12, central nucleus of the amygdala


title: subject ID 37051-0 at diease time point 4_Female, a T1D control and 1.2292950yrs old_EPIC array [201502810009_R02C01]


title: subject ID 14913-0 at diease time point 4_Female, a T1D case and 1.2457221yrs old_EPIC array [201502810009_R01C01]

source_name: T1D case_Female_time point 4


title: subject ID 28299-0 at diease time point 5_Male, a T1D case and 11.0335387yrs old_450K array [200123460108_R04C02]


title: CIE vapor, ethanol drinker, mouse 1, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 4, central nucleus of the amygdala


title: air vapor, nondrinker, mouse 53, hippocampus

description: Gene expression data from hippocampus of C57BL6/J mouse under air vapor only

source_name: C57BL6/J mouse, air vapor, nondrinker, hippocampus

value: hippocampus


title: air vapor, nondrinker, mouse 55, hippocampus


title: CIE vapor, ethanol drinker, mouse 9, central nucleus of the amygdala


title: CIE vapor, ethanol drinker, mouse 3, central nucleus of the amygdala


title: air vapor, nondrinker, mouse 50, hippocampus


title: air vapor, nondrinker, mouse 45, hippocampus


title: subject ID 12245-0 at diease time point 5_Male, a T1D control and 9.0841889yrs old_EPIC array [201502800045_R08C01]


title: CIE vapor, ethanol drinker, mouse 2, central nucleus of the amygdala


title: air vapor, nondrinker, mouse 52, hippocampus


title: air vapor, nondrinker, mouse 48, hippocampus


title: air vapor, nondrinker, mouse 49, hippocampus


title: subject ID 12245-0 at diease time point 3_Male, a T1D control and 5.0540726yrs old_EPIC array [201502800045_R07C01]


title: air vapor, nondrinker, mouse 51, hippocampus


title: subject ID 28299-0 at diease time point 4_Male, a T1D case and 6.9130732yrs old_450K array [200123460108_R03C02]


title: subject ID 28299-0 at diease time point 3_Male, a T1D case and 4.9472964yrs old_450K array [200123460108_R02C02]


title: subject ID 39200-0 at diease time point 4_Female, a T1D case and 1.2758385yrs old_EPIC array [201502800045_R06C01]


title: subject ID 28299-0 at diease time point 2_Male, a T1D case and 0.8323066yrs old_450K array [200123460108_R01C02]

source_name: T1D case_Male_time point 2


title: subject ID 12245-0 at diease time point 2_Male, a T1D control and 1.2758385yrs old_EPIC array [201502800045_R05C01]

source_name: T1D control_Male_time point 2


title: subject ID 12245-0 at diease time point 4_Male, a T1D control and 6.0068446yrs old_EPIC array [201502800045_R04C01]


title: subject ID 50749-0 at diease time point 5_Male, a T1D control and 11.9014374yrs old_450K array [200123460108_R05C01]


title: subject ID 50749-0 at diease time point 4_Male, a T1D control and 7.4852841yrs old_450K array [200123460108_R04C01]


title: CIE vapor, nondrinker, mouse 42, hippocampus

description: Gene expression data from hippocampus of C57BL6/J mouse under chronic intermittent ethanol vapor only

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, nondrinker, hippocampus


title: CIE vapor, nondrinker, mouse 44, hippocampus


title: CIE vapor, nondrinker, mouse 43, hippocampus


title: subject ID 50749-0 at diease time point 3_Male, a T1D control and 6.2997947yrs old_450K array [200123460108_R03C01]


title: subject ID 39200-0 at diease time point 5_Female, a T1D case and 1.6783025yrs old_EPIC array [201502800045_R03C01]


title: CIE vapor, nondrinker, mouse 39, hippocampus


title: subject ID 39200-0 at diease time point 3_Female, a T1D case and 0.8323066yrs old_EPIC array [201502800045_R02C01]

source_name: T1D case_Female_time point 3


title: subject ID 30425-0 at diease time point 3_Female, a T1D control and 6.3326489yrs old_EPIC array [201502810052_R03C01]

source_name: T1D control_Female_time point 3


title: CIE vapor, nondrinker, mouse 41, hippocampus


title: subject ID 50749-0 at diease time point 2_Male, a T1D control and 1.2429843yrs old_450K array [200123460108_R02C01]


title: subject ID 31924-0 at diease time point 3_Male, a T1D case and 4.0766598yrs old_EPIC array [201502800039_R08C01]


title: CIE vapor, nondrinker, mouse 38, hippocampus


title: CIE vapor, nondrinker, mouse 37, hippocampus


title: CIE vapor, nondrinker, mouse 36, hippocampus


title: CIE vapor, nondrinker, mouse 33, hippocampus


title: subject ID 10208-0 at diease time point 5_Male, a T1D control and 2.9760438yrs old_EPIC array [201502800039_R07C01]


title: subject ID 00731-0 at diease time point 4_Male, a T1D control and 2.8473648yrs old_450K array [200123460097_R05C02]


title: air vapor, ethanol drinker, mouse 62, hippocampus

description: Gene expression data from hippocampus of C57BL6/J mouse under air vapor and drinking

source_name: C57BL6/J mouse, air vapor, ethanol drinker, hippocampus


title: subject ID 31924-0 at diease time point 5_Male, a T1D case and 8.4736482yrs old_EPIC array [201502800039_R06C01]

source_name: T1D case_Male_time point 5


title: subject ID 12443-0 at diease time point 5_Female, a T1D case and 13.5742642yrs old_450K array [200123460097_R04C02]

source_name: T1D case_Female_time point 5


title: subject ID 00364-0 at diease time point 4_Male, a T1D case and 3.7782341yrs old_450K array [200123460097_R06C02]

source_name: T1D case_Male_time point 4


title: subject ID 10208-0 at diease time point 3_Male, a T1D control and 0.8405202yrs old_EPIC array [201502800039_R05C01]


title: air vapor, ethanol drinker, mouse 60, hippocampus


title: air vapor, ethanol drinker, mouse 61, hippocampus


title: air vapor, ethanol drinker, mouse 59, hippocampus


title: air vapor, ethanol drinker, mouse 31, hippocampus


title: air vapor, ethanol drinker, mouse 32, hippocampus


title: air vapor, ethanol drinker, mouse 57, hippocampus


title: CIE vapor, nondrinker, mouse 34, hippocampus


title: subject ID 12443-0 at diease time point 4_Female, a T1D case and 7.9425051yrs old_450K array [200123460097_R03C02]


title: subject ID 12443-0 at diease time point 3_Female, a T1D case and 5.9904175yrs old_450K array [200123460097_R02C02]


title: subject ID 31924-0 at diease time point 2_Male, a T1D case and 1.3169062yrs old_EPIC array [201502800039_R03C01]


title: subject ID 12443-0 at diease time point 2_Female, a T1D case and 0.7611225yrs old_450K array [200123460097_R01C02]

source_name: T1D case_Female_time point 2


title: subject ID 10208-0 at diease time point 4_Male, a T1D control and 1.9657769yrs old_EPIC array [201502800039_R01C01]


title: air vapor, ethanol drinker, mouse 25, hippocampus


title: subject ID 31924-0 at diease time point 4_Male, a T1D case and 6.0205339yrs old_EPIC array [201502800039_R04C01]


title: subject ID 11748-0 at diease time point 5_Female, a T1D control and 11.2498289yrs old_450K array [200123460097_R05C01]

source_name: T1D control_Female_time point 5


title: CIE vapor, ethanol drinker, mouse 21, hippocampus

description: Gene expression data from hippocampus of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, hippocampus


title: CIE vapor, ethanol drinker, mouse 12, hippocampus


title: CIE vapor, ethanol drinker, mouse 10, hippocampus


title: CIE vapor, ethanol drinker, mouse 9, hippocampus


title: air vapor, ethanol drinker, mouse 28, hippocampus


title: CIE vapor, ethanol drinker, mouse 20, hippocampus


title: CIE vapor, ethanol drinker, mouse 17, hippocampus


title: CIE vapor, ethanol drinker, mouse 6, hippocampus


title: subject ID 32018-0 at diease time point 5_Female, a T1D case and 12.0246407yrs old_EPIC array [201502800004_R07C01]


title: subject ID 11748-0 at diease time point 3_Female, a T1D control and 5.1663244yrs old_450K array [200123460097_R03C01]


title: air vapor, ethanol drinker, mouse 24, hippocampus


title: air vapor, ethanol drinker, mouse 30, hippocampus


title: subject ID 00933-0 at diease time point 4_Female, a T1D control and 4.9856263yrs old_EPIC array [201502800004_R08C01]


title: subject ID 00933-0 at diease time point 5_Female, a T1D control and 9.6618754yrs old_EPIC array [201502800004_R06C01]


title: CIE vapor, ethanol drinker, mouse 4, hippocampus


title: subject ID 11748-0 at diease time point 2_Female, a T1D control and 0.7583847yrs old_450K array [200123460097_R02C01]

source_name: T1D control_Female_time point 2


title: CIE vapor, ethanol drinker, mouse 3, hippocampus


title: subject ID 32018-0 at diease time point 4_Female, a T1D case and 3.0225873yrs old_EPIC array [201502800004_R05C01]


title: subject ID 12590-0 at diease time point 5_Female, a T1D case and 13.0184805yrs old_450K array [200123460093_R04C02]


title: CIE vapor, ethanol drinker, mouse 5, hippocampus


title: subject ID 32018-0 at diease time point 3_Female, a T1D case and 1.2758385yrs old_EPIC array [201502800004_R04C01]


title: subject ID 11748-0 at diease time point 4_Female, a T1D control and 6.2258727yrs old_450K array [200123460097_R04C01]


title: air vapor, nondrinker, mouse 56, nucleus accumbens

description: Gene expression data from nucleus accumbens of C57BL6/J mouse under chronic intermittent air vapor only

source_name: C57BL6/J mouse, air vapor, nondrinker, nucleus accumbens

value: nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 2, hippocampus


title: air vapor, nondrinker, mouse 55, nucleus accumbens


title: subject ID 12590-0 at diease time point 3_Female, a T1D case and 5.2156057yrs old_450K array [200123460093_R02C02]


title: subject ID 32018-0 at diease time point 2_Female, a T1D case and 0.7967146yrs old_EPIC array [201502800004_R02C01]


title: subject ID 12590-0 at diease time point 4_Female, a T1D case and 6.3956194yrs old_450K array [200123460093_R03C02]


title: air vapor, nondrinker, mouse 54, nucleus accumbens


title: subject ID 00028-0 at diease time point 4_Female, a T1D case and 5.9603012yrs old_EPIC array [201502800004_R01C01]


title: subject ID 20839-0 at diease time point 5_Female, a T1D control and 13.9329227yrs old_450K array [200123460093_R05C01]


title: subject ID 10141-0 at diease time point 4_Female, a T1D control and 2.0479124yrs old_EPIC array [201502800001_R04C01]

source_name: T1D control_Female_time point 4


title: air vapor, nondrinker, mouse 52, nucleus accumbens


title: subject ID 10141-0 at diease time point 3_Female, a T1D control and 1.2347707yrs old_EPIC array [201502800001_R05C01]


title: subject ID 20839-0 at diease time point 4_Female, a T1D control and 7.0308008yrs old_450K array [200123460093_R04C01]


title: air vapor, nondrinker, mouse 53, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 1, hippocampus


title: subject ID 10141-0 at diease time point 2_Female, a T1D control and 0.8761123yrs old_EPIC array [201502800001_R03C01]


title: air vapor, nondrinker, mouse 51, nucleus accumbens


title: air vapor, nondrinker, mouse 49, nucleus accumbens


title: air vapor, nondrinker, mouse 50, nucleus accumbens


title: subject ID 10141-0 at diease time point 5_Female, a T1D control and 10.7460643yrs old_EPIC array [201502800001_R01C01]


title: subject ID 12590-0 at diease time point 2_Female, a T1D case and 1.2867899yrs old_450K array [200123460093_R01C02]


title: subject ID 84492-0 at diease time point 4_Male, a T1D control and 1.2566735yrs old_EPIC array [201501960024_R07C01]

source_name: T1D control_Male_time point 4

value: Male


title: air vapor, nondrinker, mouse 46, nucleus accumbens


title: air vapor, nondrinker, mouse 47, nucleus accumbens


title: air vapor, nondrinker, mouse 45, nucleus accumbens


title: CIE vapor, nondrinker, mouse 43, nucleus accumbens

description: Gene expression data from nucleus accumbens of C57BL6/J mouse under chronic intermittent ethanol vapor only

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, nondrinker, nucleus accumbens


title: CIE vapor, nondrinker, mouse 44, nucleus accumbens


title: subject ID 20839-0 at diease time point 3_Female, a T1D control and 6.0369610yrs old_450K array [200123460093_R03C01]


title: subject ID 00275-0 at diease time point 3_Female, a T1D case and 3.1430527yrs old_450K array [200123470067_R04C02]

value: T1D case


title: air vapor, nondrinker, mouse 48, nucleus accumbens


title: subject ID 85788-0 at diease time point 3_Female, a T1D case and 0.8651608yrs old_EPIC array [201501960024_R06C01]

value: peripheral blood sample


title: CIE vapor, nondrinker, mouse 40, nucleus accumbens


title: CIE vapor, nondrinker, mouse 41, nucleus accumbens


title: subject ID 00840-0 at diease time point 5_Female, a T1D control and 10.1081451yrs old_450K array [200123470067_R03C02]


title: subject ID 84492-0 at diease time point 3_Male, a T1D control and 0.7638604yrs old_EPIC array [201501960024_R05C01]

source_name: T1D control_Male_time point 3


title: subject ID 00174-0 at diease time point 4_Male, a T1D case and 10.1327858yrs old_EPIC array [201501960024_R08C01]


title: CIE vapor, nondrinker, mouse 39, nucleus accumbens


title: CIE vapor, nondrinker, mouse 42, nucleus accumbens


title: subject ID 00840-0 at diease time point 4_Female, a T1D control and 4.0547570yrs old_450K array [200123470067_R02C02]


title: subject ID 00174-0 at diease time point 3_Male, a T1D case and 8.1834360yrs old_EPIC array [201501960024_R04C01]

source_name: T1D case_Male_time point 3


title: CIE vapor, nondrinker, mouse 37, nucleus accumbens


title: subject ID 00275-0 at diease time point 5_Female, a T1D case and 10.3436003yrs old_450K array [200123470067_R05C02]


title: subject ID 00840-0 at diease time point 3_Female, a T1D control and 3.0636550yrs old_450K array [200123470067_R01C02]


title: CIE vapor, nondrinker, mouse 33, nucleus accumbens


title: CIE vapor, nondrinker, mouse 35, nucleus accumbens


title: CIE vapor, nondrinker, mouse 40, hippocampus

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, nondrinker, hippocampus


title: CIE vapor, nondrinker, mouse 36, nucleus accumbens


title: CIE vapor, nondrinker, mouse 38, nucleus accumbens


title: subject ID 00027-0 at diease time point 5_Male, a T1D case and 14.1355236yrs old_450K array [200123470041_R06C02]


title: CIE vapor, nondrinker, mouse 34, nucleus accumbens


title: subject ID 20968-0 at diease time point 5_Female, a T1D control and 2.2614648yrs old_EPIC array [201501960023_R07C01]


title: subject ID 00290-0 at diease time point 5_Male, a T1D control and 12.9253936yrs old_450K array [200123470041_R04C02]

source_name: T1D control_Male_time point 5


title: subject ID 00027-0 at diease time point 4_Male, a T1D case and 4.6707734yrs old_450K array [200123470041_R05C02]


title: subject ID 25180-0 at diease time point 5_Female, a T1D case and 3.1403149yrs old_EPIC array [201501960023_R06C01]


title: subject ID 30213-0 at diease time point 5_Female, a T1D control and 2.2422998yrs old_EPIC array [201501960002_R04C01]


title: air vapor, ethanol drinker, mouse 62, nucleus accumbens

description: Gene expression data from nucleus accumbens of C57BL6/J mouse under air vapor and drinking

source_name: C57BL6/J mouse, air vapor, ethanol drinker, nucleus accumbens


title: subject ID 00290-0 at diease time point 4_Male, a T1D control and 4.7939767yrs old_450K array [200123470041_R03C02]


title: subject ID 15041-0 at diease time point 5_Male, a T1D case and 2.1765914yrs old_EPIC array [201501960002_R03C01]


title: subject ID 00040-0 at diease time point 4_Male, a T1D case and 6.7159480yrs old_450K array [200090280086_R05C01]


title: air vapor, ethanol drinker, mouse 59, nucleus accumbens


title: subject ID 12262-0 at diease time point 5_Female, a T1D control and 9.7659138yrs old_EPIC array [201501960001_R08C01]


title: subject ID 00018-0 at diease time point 4_Female, a T1D case and 7.0937714yrs old_450K array [200090280086_R04C01]

source_name: T1D case_Female_time point 4


title: subject ID 21936-0 at diease time point 5_Male, a T1D case and 10.8637919yrs old_EPIC array [201501960001_R07C01]

source_name: T1D case_Male_time point 5


title: air vapor, ethanol drinker, mouse 32, nucleus accumbens


title: air vapor, ethanol drinker, mouse 25, nucleus accumbens


title: air vapor, ethanol drinker, mouse 31, nucleus accumbens


title: subject ID 01009-0 at diease time point 4_Female, a T1D control and 6.0150582yrs old_450K array [200090280086_R03C01]


title: air vapor, ethanol drinker, mouse 58, nucleus accumbens


title: air vapor, ethanol drinker, mouse 57, nucleus accumbens


title: air vapor, ethanol drinker, mouse 28, nucleus accumbens


title: air vapor, ethanol drinker, mouse 24, nucleus accumbens


title: air vapor, ethanol drinker, mouse 23, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 21, nucleus accumbens

description: Gene expression data from nucleus accumbens of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, nucleus accumbens


title: subject ID 12262-0 at diease time point 4_Female, a T1D control and 3.1019849yrs old_EPIC array [201501960001_R05C01]


title: subject ID 21936-0 at diease time point 2_Male, a T1D case and 0.7638604yrs old_EPIC array [201501960001_R04C01]

source_name: T1D case_Male_time point 2


title: subject ID 85788-0 at diease time point 4_Female, a T1D case and 1.4565366yrs old_EPIC array [201501960024_R01C01]


title: subject ID 00075-0 at diease time point 5_Male, a T1D case and 13.4428474yrs old_450K array [200123470040_R06C02]


title: subject ID 12262-0 at diease time point 2_Female, a T1D control and 0.7802875yrs old_EPIC array [201501960001_R03C01]


title: subject ID 00075-0 at diease time point 3_Male, a T1D case and 8.9555099yrs old_450K array [200123470040_R05C02]


title: subject ID 21936-0 at diease time point 4_Male, a T1D case and 3.0088980yrs old_EPIC array [201501960001_R01C01]

source_name: T1D case_Male_time point 4


title: air vapor, ethanol drinker, mouse 30, nucleus accumbens


title: subject ID 20839-0 at diease time point 2_Female, a T1D control and 1.2621492yrs old_450K array [200123460093_R02C01]


title: subject ID 00246-0 at diease time point 4_Male, a T1D control and 6.6940452yrs old_450K array [200090280086_R01C01]


title: subject ID 24998-0 at diease time point 5_Female, a T1D case and 17.7357974yrs old_EPIC array [201414140190_R08C01]

source_name: T1D case_Female_time point 5


title: subject ID 24998-0 at diease time point 3_Female, a T1D case and 5.3415469yrs old_EPIC array [201414140190_R07C01]

source_name: T1D case_Female_time point 3


title: CIE vapor, ethanol drinker, mouse 9, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 17, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 5, nucleus accumbens


title: subject ID 00653-0 at diease time point 3_Male, a T1D control and 9.5222450yrs old_450K array [200123470040_R02C02]


title: subject ID 00653-0 at diease time point 4_Male, a T1D control and 10.5982204yrs old_450K array [200123470040_R03C02]


title: CIE vapor, ethanol drinker, mouse 4, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 10, nucleus accumbens


title: subject ID 24998-0 at diease time point 2_Female, a T1D case and 0.7802875yrs old_EPIC array [201414140190_R03C01]

source_name: T1D case_Female_time point 2


title: CIE vapor, ethanol drinker, mouse 20, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 1, nucleus accumbens


title: subject ID 00653-0 at diease time point 5_Male, a T1D control and 12.7912389yrs old_450K array [200123470040_R04C02]


title: CIE vapor, ethanol drinker, mouse 3, nucleus accumbens


title: CIE vapor, ethanol drinker, mouse 6, nucleus accumbens


title: subject ID 00170-0 at diease time point 3_Female, a T1D control and 10.2368241yrs old_450K array [3998909102_R02C02]

source_name: T1D control_Female_time point 3


title: air vapor, nondrinker, mouse 56, medial prefrontal cortex

description: Gene expression data from medial prefrontal cortex of C57BL6/J mouse under air vapor only

source_name: C57BL6/J mouse, air vapor, nondrinker, medial prefrontal cortex

value: prefrontal cortex


title: subject ID 24998-0 at diease time point 4_Female, a T1D case and 6.5927447yrs old_EPIC array [201414140190_R02C01]


title: air vapor, nondrinker, mouse 54, medial prefrontal cortex


title: air vapor, nondrinker, mouse 55, medial prefrontal cortex


title: air vapor, nondrinker, mouse 53, medial prefrontal cortex


title: CIE vapor, ethanol drinker, mouse 12, nucleus accumbens


title: air vapor, nondrinker, mouse 52, medial prefrontal cortex


title: air vapor, nondrinker, mouse 51, medial prefrontal cortex


title: subject ID 00170-0 at diease time point 4_Female, a T1D control and 11.5154004yrs old_450K array [3998909102_R01C02]

source_name: T1D control_Female_time point 4


title: subject ID 10387-0 at diease time point 2_Female, a T1D control and 0.8213552yrs old_EPIC array [201414140103_R07C01]

source_name: T1D control_Female_time point 2


title: subject ID 10387-0 at diease time point 3_Female, a T1D control and 5.6591376yrs old_EPIC array [201414140103_R03C01]


title: subject ID 00448-0 at diease time point 4_Male, a T1D control and 6.4394251yrs old_450K array [3998909156_R06C02]

source_name: T1D control_Male_time point 4


title: air vapor, nondrinker, mouse 48, medial prefrontal cortex


title: subject ID 00667-0 at diease time point 4_Female, a T1D case and 6.0451745yrs old_450K array [3998909156_R04C02]


title: subject ID 10387-0 at diease time point 5_Female, a T1D control and 17.7138946yrs old_EPIC array [201414140103_R02C01]

source_name: T1D control_Female_time point 5


title: air vapor, nondrinker, mouse 49, medial prefrontal cortex


title: air vapor, nondrinker, mouse 46, medial prefrontal cortex


title: air vapor, nondrinker, mouse 47, medial prefrontal cortex


title: subject ID 00667-0 at diease time point 5_Female, a T1D case and 8.2546201yrs old_450K array [3998909156_R03C02]


title: subject ID 10387-0 at diease time point 4_Female, a T1D control and 6.7351129yrs old_EPIC array [201414140103_R01C01]


title: subject ID 37227-0 at diease time point 4_Male, a T1D control and 0.8213552yrs old_EPIC array [201414140072_R07C01]


title: subject ID 30030-0 at diease time point 5_Female, a T1D case and 0.7255305yrs old_EPIC array [201414140025_R05C01]


title: subject ID 39503-0 at diease time point 3_Male, a T1D case and 0.8487337yrs old_450K array [3998909032_R03C01]

source_name: T1D case_Male_time point 3


title: subject ID 39503-0 at diease time point 4_Male, a T1D case and 1.2210815yrs old_450K array [3998909032_R02C01]


title: CIE vapor, nondrinker, mouse 42, medial prefrontal cortex

description: Gene expression data from medial prefrontal cortex of C57BL6/J mouse under chronic intermittent ethanol vapor only

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, nondrinker, medial prefrontal cortex


title: subject ID 00448-0 at diease time point 5_Male, a T1D control and 8.4709103yrs old_450K array [3998909156_R05C02]

source_name: T1D control_Male_time point 5


title: CIE vapor, nondrinker, mouse 43, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 39, medial prefrontal cortex


title: air vapor, nondrinker, mouse 45, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 40, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 41, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 38, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 44, medial prefrontal cortex


title: subject ID 39503-0 at diease time point 5_Male, a T1D case and 5.0595483yrs old_450K array [3998909032_R01C01]


title: subject ID 10686-0 at diease time point 5_Female, a T1D case and 1.2950034yrs old_EPIC array [201414140023_R08C01]


title: subject ID 33007-0 at diease time point 5_Male, a T1D case and 9.7850787yrs old_450K array [3998909132_R05C02]


title: subject ID 13470-0 at diease time point 5_Male, a T1D control and 0.7802875yrs old_EPIC array [201414140023_R03C01]


title: subject ID 10095-0 at diease time point 5_Male, a T1D control and 0.7501711yrs old_EPIC array [201414140023_R02C01]


title: CIE vapor, nondrinker, mouse 37, medial prefrontal cortex


title: subject ID 20792-0 at diease time point 5_Male, a T1D control and 8.6926762yrs old_450K array [3998909132_R02C02]


title: CIE vapor, nondrinker, mouse 36, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 34, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 33, medial prefrontal cortex


title: air vapor, ethanol drinker, mouse 60, medial prefrontal cortex

description: Gene expression data from medial prefrontal cortex of C57BL6/J mouse under air vapor and drinking

source_name: C57BL6/J mouse, air vapor, ethanol drinker, medial prefrontal cortex


title: air vapor, ethanol drinker, mouse 61, medial prefrontal cortex


title: air vapor, ethanol drinker, mouse 59, medial prefrontal cortex


title: CIE vapor, nondrinker, mouse 35, medial prefrontal cortex


title: air vapor, ethanol drinker, mouse 58, medial prefrontal cortex


title: subject ID 20792-0 at diease time point 4_Male, a T1D control and 2.6502396yrs old_450K array [3998909132_R01C02]


title: subject ID 13499-0 at diease time point 5_Male, a T1D control and 9.9958932yrs old_450K array [3998909132_R03C01]


title: air vapor, ethanol drinker, mouse 32, medial prefrontal cortex


title: air vapor, ethanol drinker, mouse 57, medial prefrontal cortex


title: subject ID 26244-0 at diease time point 4_Female, a T1D case and 0.7665982yrs old_EPIC array [201414140025_R03C01]

source_name: T1D case_Female_time point 4


title: air vapor, ethanol drinker, mouse 60, nucleus accumbens

source_name: C57BL6/J mouse, air vapor, ethanol drinker, nucleus accumbens


title: air vapor, nondrinker, mouse 50, medial prefrontal cortex


title: subject ID 33007-0 at diease time point 4_Male, a T1D case and 3.2416153yrs old_450K array [3998909132_R04C02]


title: subject ID 00581-0 at diease time point 5_Female, a T1D case and 10.3627652yrs old_450K array [3998909086_R06C02]


title: TAIL-seq exp #3 siTENT4 72hr

city: Daejeon

first: Young-suk

last: Lee

address: 1113 CMS(E16), 291 Daehak-ro, Yuseong-gu,

department: Department of Bio and Brain Engineering

country: South Korea

institute: KAIST

description: TAIL-seq for TENT4A/B knockdown HFF cells

data_processing:
Library strategy: Tail-seq
TAIL-seq analysis was carried out using Tailseeker 3.1.5. Briefly, Read 1 was used for gene identification, and read 2 was used to detect 3′ end modifications and measure the length of the poly(A) tail. For each TAIL-seq library, read 1 was mapped to human genome GRCh38 with STAR 2.5.2b and HBV genome NCBI:U95551.1 with bowtie2.2.6.
Genome_build: hg38
Supplementary_files_format_and_content: The .all.txt, .mapped.txt and .txt file are output files of tailseeker3 with the untemplated tail informtion of the RNA fragment. The first two columns represent the tile and cluster id of the RNA fragment. The third column of the .txt file is the ensembl gene id. The sixth column of the .all.txt and .mapped.txt file is the estimated poly(A) tail length and the last column is the untemplated tail sequence. The .mapped.txt file only contains RNA fragments from .all.txt that are mapped to the genome.

source_name: HFF

growth_protocol: HepG2.2.15 cells were grown in DMEM (Welgene, LM 001-05) containing 10% FBS (Welgene, S001-01). Primary human foreskin fibroblast (HFF, ATCC SCRC-1041) cells were grown in DMEM (HyClone) containing 10% FBS (HyClone), GlutaMAX-I (Gibco) and penicillin-streptomycin (Gibco). Before transfection, primary HFF were grown in antibiotics-free media.

extract_protocol:
Total RNAs were extracted from HepG2.2.15 cells and HFF cells by TRIzol reagent (Invitrogen, 15596018) and purified with RNeasy MinElute Cleanup Kit (Qiagen) according to manufacturer’s instruction.
TAIL-seq was conducted as previously described. In brief, ~50 μg of DNaseI (Takara, 2270A) treated total RNA (>200 nt) was used to deplete rRNA twice by Ribo-Zero kit (Epicentre, MRZH11124 [discontinued] for primary HFF library or Illumina, TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, 20020596 for HepG2.2.15 library). The rRNA-depleted RNAs were ligated to the 3′ adaptor and partially fragmented by RNase T1 (Ambion). The fragmented RNAs were pulled-down with streptavidin beads (Invitrogen), 5′ phosphorylated and purified by 6% urea-PAGE gel (500–1,000 nt). The purified RNAs were ligated to the 5′ adaptor, reverse-transcribed and amplified by PCR. The libraries were sequenced by paired-end run (51×251 cycles) on Illumina platform (MiSeq) with PhiX control library v3 (Illumina) and spike-in mixture.

treatment_protocol: For TENT4A and TENT4B knockdown, HepG2.2.15 cells were transfected with 100 nM siRNAs by Lipofectamine RNAiMAX (Invitrogen) at Day 0, 2 and 4 and harvested at Day 6. For ZCCHC14 knockdown, HepG2.2.15 cells were transfected with 100 nM siRNAs by Lipofectamine RNAiMAX (Invitrogen) at Day 0 and 2, and harvested at Day 4. Primary HFF cells were transfected with 20 nM siRNAs by DharmaFECT 1 (Dharmacon) at Day 0 and 2 and harvested at Day 5.

tag: cell line

value: HFF

tag: condition


title: subject ID 12478-0 at diease time point 5_Female, a T1D case and 8.6954141yrs old_450K array [3998909132_R05C01]


title: air vapor, ethanol drinker, mouse 62, medial prefrontal cortex


title: TAIL-seq exp #2 siZCCHC14

description: TAIL-seq for ZCCHC14 knockdown HepG2.2.15 cells

source_name: HepG2.2.15 cells


title: subject ID 00581-0 at diease time point 2_Female, a T1D case and 0.9034908yrs old_450K array [3998909086_R04C02]


title: air vapor, ethanol drinker, mouse 30, medial prefrontal cortex


title: TAIL-seq exp #2 siCont

description: TAIL-seq for control knockdown HepG2.2.15 cells

value: siCont


title: air vapor, ethanol drinker, mouse 24, medial prefrontal cortex


title: subject ID 13499-0 at diease time point 4_Male, a T1D control and 3.9780972yrs old_450K array [3998909132_R02C01]


title: CIE vapor, ethanol drinker, mouse 20, medial prefrontal cortex

description: Gene expression data from medial prefrontal cortex of C57BL6/J mouse under chronic intermittent ethanol vapor and drinking

source_name: C57BL6/J mouse, chronic intermittent ethanol vapor, ethanol drinker, medial prefrontal cortex


title: CIE vapor, ethanol drinker, mouse 14, medial prefrontal cortex


title: subject ID 20129-3 at diease time point 5_Female, a T1D control and 9.8261465yrs old_450K array [3998909086_R03C02]

value: Female


title: CIE vapor, ethanol drinker, mouse 17, medial prefrontal cortex


title: TAIL-seq exp #3 siCont 72hr

description: TAIL-seq for control knockdown HFF cells


title: air vapor, ethanol drinker, mouse 31, medial prefrontal cortex

value: Control


title: air vapor, ethanol drinker, mouse 28, medial prefrontal cortex


title: TAIL-seq exp #1 siTENT4 Set2

description: TAIL-seq for TENT4A/B knockdown HepG2.2.15 cells, Set2


title: subject ID 20129-3 at diease time point 4_Female, a T1D control and 3.5318275yrs old_450K array [3998909086_R02C02]


title: CIE vapor, ethanol drinker, mouse 6, medial prefrontal cortex