title: E. coli 102712_LB_0.5_BR2

description: 102712_DMEM_vs_LB.txt,102712_LBB_vs_LB.txt


title: filaments RNA-seq rep2

status: Public on Aug 15 2017

type: SRA

city: Guangzhou

first: chunjie

last: zhu

state: Guangdong

address: 100 xianlie road, yuexiu district

country: China

institute: Guangdong Institute of Microbiology

library_source: transcriptomic

data_processing:
raw sequence data were filtered to remove those containing adapter and reads with more than 10% unknown nucleotides, and reads with more than 40% of low quality base (Qvalue <20)
clean data were align to Lysinibacillus varians genome  and reference genomes using Samtools 0.1.18.0 and tophat 2.0.1
RPKM of each gene was calculated using cufflink 2.0.0
Genome_build: CP006837
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

molecule: total RNA

organism: Lysinibacillus varians

source_name: filamentous cell rep2

growth_protocol: The isolates were inoculated into Luria–Bertani (LB) medium containing yeast extract 5 g l-1 , tryptone 10 g l-1 and NaCl 5 g l-1 (5%, v/v) and incubated on a rotary shaker with 160 rev min-1 at 30 ˚С.

extract_protocol:
the cultures were fixed with 2 vols RNA protect bacteria (Qiagen) and harvested. RNA was isolated from triplicate bacterial pellets with an RNeasy mini kit (Qiagen, USA). Extraction was performed according to manufacturer’s instruction.
Libraries were prepared according to Illumina's instructions

treatment_protocol: 5 h and 10 h culture of the strain were collected and used for RNA extraction

tag: strain

tag: cell type

value: filamentous

tag: growth time

value: 5 hrs


title: Late planula 3, oxidized

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

country: United Kingdom

institute: Marine Biological Association of the UK

description: Barcode: GTAGAG

data_processing:
A minimum of 13 -15 million 50bp sequencing reads were collected from each sample.
The data were pre-processed to remove the adapters using cutadapt
pre-processed reads were analysed using miRDeep2 software (https://www.mdc-berlin.de/8551903/en/)

organism: Nematostella vectensis

source_name: whole animal

extract_protocol:
Total RNA was extracted using Trizol (Life technologies, USA) as instructed in manual, the small (18-30 nt long) RNA were purified on a denaturing 15% acrylamide gel, from 20 μg total RNA per sample. RNAs were eluted from the acrylamide bands overnight in 0.3 M NaCl, then ethanol/glycogen-precipitated. Half of each sample was oxidized (5X borate buffer, ph=8.6; 5 μL freshly prepared 50mM sodium periodate) for 30 minutes at 25 degrees C, then precipitated with sodium acetate, ethanol and glycogen; the other half was not treated.
Small RNA libraries were constructed as described in Phillip Zamore Lab Illumina TruSeq Small RNA Cloning Protocol April, 2014 (http://www.umassmed.edu/zamore/resources/protocols/). Each library was indexed in order to multiplex 30 samples per sequencing run on the Illumina.

treatment_protocol: Half of each sample was treated with periodate (oxidized).

tag: tissue

value: whole animal

tag: developmental stage

value: Late planula

tag: treatment

value: RNA Periodate


title: E. coli HS_LB_0.5_BR2

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

country: USA

institute: University of Maryland School of Medicine

data_processing:
Illumina reads were mapped to the EPEC genomes using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69, HS, H10407, 102651, 102712, 401140, 402290
Supplementary_files_format_and_content: read count, FC, differential expression

organism: Escherichia coli HS

source_name: Escherichia coli cells

growth_protocol: The E. coli strains were grown overnight in LB media and were inoculated 1:100 into 250 ml of fresh LB or DMEM with bile (LBB and DMEMB) or without and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.

extract_protocol:
RNA was isolated from pelleted cells using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HS

tag: growth media

value: LB


title: filaments RNA-seq rep1

source_name: filamentous cell rep1


title: Late planula 2, untreated

description: Barcode: AGTTCC

value: untreated


title: Late planula 2, oxidized

description: Barcode: GTGAAA


title: E. coli 102651_DMEMB_0.5_BR2

description: 102651_DMEMB_vs_LBB.txt,102651_DMEMB_vs_DMEM.txt

organism: Escherichia coli 102651

value: DMEMB


title: E. coli 102651_DMEMB_0.5_BR1


title: E. coli H10407_DMEMB_0.5_BR2

description: H10407_DMEMB_vs_LBB.txt,HS_DMEMB_vs_DMEM.txt

organism: Escherichia coli ETEC H10407


title: E. coli H10407_DMEMB_0.5_BR1


title: Late planula 1, untreated

description: Barcode: AGTCAA


title: Primary polyps 1, untreated

description: Barcode: CAGATC

value: Primary polyps


title: SA_S2

city: Szeged

first: Botond

last: Hegedüs

address: Közép fasor 52.

department: Department of Biotechnology

country: Hungary

institute: University of Szeged

description: SA, stationary phase, rep 2

data_processing:
The reads were trimmed using CLC Genomics Workbench version 7 with the following configurations:  -- Ambiguous trim = Yes  -- Ambiguous limit = 2  -- Quality trim = Yes  -- Quality limit = 0.05  -- Create report = Yes  -- Save discarded sequences = No  -- Remove 5' terminal nucleotides = No  -- Discard short reads = No  -- Remove 3' terminal nucleotides = No  -- Discard long reads = No  -- Save broken pairs = No
The trimmed reads were aligned to the CP017075.1, CP017076.1, CP017077.1, CP017078.1, CP017079.1 genome assembly using CLC Genomics Workbench version 7 with the following configurations:  -- Reference type = Genome annotated with genes only  -- Reference sequence = CP017075-9  -- Gene track = CP017075-9 (CDS)  -- Mapping type = Also map to inter-genic regions  -- Mismatch cost = 2  -- Insertion cost = 3  -- Deletion cost = 3  -- Length fraction = 0.8  -- Similarity fraction = 0.8  -- Global alignment = No  -- Auto-detect paired distances = Yes  -- Strand specific = Both  -- Maximum number of hits for a read = 20  -- Count paired reads as two = No  -- Expression value = Total counts  -- Calculate RPKM for genes without transcripts = No  -- Create report = Yes  -- Create fusion gene table = No  -- Create list of unmapped reads = No
Differential gene expression analysis using EdgeR
Genome_build: CP017075.1, CP017076.1, CP017077.1, CP017078.1, CP017079.1
Supplementary_files_format_and_content: Excel file "Full_Datasets_DEG_Annotations.xlsx" contains the annotation dates, normalized expression values, log2 fold change values, False Discovery Rate adjusted p-values and RPKM values of the genes in the 3 examined conditions: Glc_S vs. Glc_E, SA_E vs. Glc_E, SA_S vs. SA_E.

organism: Novosphingobium resinovorum

source_name: bacterial cell_sulfanilic acid_stationary phase

growth_protocol: N. resinovorum SA1 strain was grown in 250 mL Erlenmeyer flasks in 100 mL minimal salt media (MM) [1], containing 10 mM substrates (either sulfanilic acid (SA), or glucose (Glc)), 25 µg/ml (Sm) and 25 mM MOPS (pH=7.0). Addition of MOPS could stabilize the pH during the cell growth, the pH change/drop was less than 0.2 unit in any cultivation. When glucose was used as carbon source, the medium was supplemented with 10 mM NH4Cl, in the case of SA, the substrate was the sole nitrogen source. The cultures were shaken at 28 °C, 180 rpm and the cell growth was monitored by measuring the OD600nm values. Samples for RNA extraction were taken from exponential and late stationary phase.  1.  Perei K, Rákhely G, Kiss I, Polyák B, Kovács KL. Biodegradation of sulfanilic acid by Pseudomonas paucimobilis. Appl Microbiol Biotechnol. 2001;55(1):101-107. http://www.ncbi.nlm.nih.gov/pubmed/11234949.

extract_protocol:
6 ml samples were taken from exponential and late stationary phase cultures grown on Glc or SA in MM. In each case, two independent biological replicas were used. The samples were harvested (17,226 rcf, 5 min, 4 °C) and immediately frozen in liquid nitrogen and stored at -80°C until RNA isolation.  The frozen samples were resuspended in 350 µl Zymo DNA/RNA Shield. The resuspended cells were mixed with 700 µl RLT buffer (Qiagen) (with β-merkaptoetanol) and were transferred into a new tube containing 0.8 g, 0.5 mm Glass Beads (Scientific Industries, SI-BG05). The cells were vortexed for 5 minutes on maximum speed with a Vortex-Genie 2 (Scientific Industries, SI-0236) supplemented with a TurboMix Attachment (Scientific Industries, SI-0564). Following lysis, the mixtures were centrifuged at 9,600 rcf for 10 seconds to remove the glass beads and cell debris. The supernatants were used for purification of total RNAs with the Qiagen RNeasy Mini Kit protocol (Qiagen) with on-column DNase digestion. Then the Purified RNAs were treated again with RNase free DNase I (Sigma) to remove any residual genomic DNA contamination. Finally, the RNAs obtained were repurified with the RNeasy Mini Kit Clean Up protocol (Qiagen). The integrity of the RNA was checked by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina epicenter ScriptSeq (Bacteria) protocol

tag: carbon source

value: sulfanilic acid

tag: nitrogen source

tag: growth phase

value: stationary phase


title: SA_S1

description: SA, stationary phase, rep 1


title: SA_E2

description: SA, exponential phase, rep 2

source_name: bacterial cell_sulfanilic acid_exponential phase

value: exponential phase


title: E. coli 102651_LBB_0.5_BR2

description: 102651_DMEMB_vs_LBB.txt,102651_LBB_vs_LB.txt

value: LBB


title: E. coli 102651_LBB_0.5_BR1


title: Blastula 3, untreated

description: Barcode: GCCAAT

value: Blastula


title: Blastula 3, oxidized

description: Barcode: GCCAAT


title: SA_E1

description: SA, exponential phase, rep 1


title: filaments RNA-seq rep3

source_name: filamentous cell rep3


title: E. coli H10407_DMEM_0.5_BR2

description: H10407_DMEM_vs_LB.txt,HS_DMEMB_vs_DMEM.txt

value: DMEM


title: E. coli 102651_DMEM_0.5_BR2

description: 102651_DMEM_vs_LB.txt,102651_DMEMB_vs_DMEM.txt


title: Late planula 1, oxidized

description: Barcode: CTTGTA


title: E. coli HS_LB_0.5_BR1


title: E. coli 102712_LB_0.5_BR1

organism: Escherichia coli 102712


title: Blastula 2, untreated

description: Barcode: TGACCA


title: E. coli H10407_DMEM_0.5_BR1


title: Glc_S2

description: Glc, stationary phase, rep 2

source_name: bacterial cell_glucose_stationary phase

value: glucose


title: E. coli H10407_LBB_0.5_BR1

description: H10407_DMEMB_vs_LBB.txt,H10407_LBB_vs_LB.txt


title: Glc_S1

description: Glc, stationary phase, rep 1


title: Blastula 2, oxidized

description: Barcode: TTAGGC


title: E. coli 102651_DMEM_0.5_BR1


title: E. coli 102651_LB_0.5_BR2

description: 102651_DMEM_vs_LB.txt,102651_LBB_vs_LB.txt


title: E. coli 102651_LB_0.5_BR1


title: E. coli H10407_LB_0.5_BR1

description: H10407_DMEM_vs_LB.txt,H10407_LBB_vs_LB.txt


title: Glc_E2

description: Glc, exponential phase, rep 2


title: Blastula 1, untreated

description: Barcode: CGATGT


title: Glc_E1

description: Glc, exponential phase, rep 1


title: E. coli H10407_LBB_0.5_BR2


title: fruR-2

status: Public on Aug 14 2017

city: Gainesville

first: Robert

middle: A

last: Burne

state: Florida

address: 1395 Center Drive

department: Oral BIology

institute: University of Florida

description: repeat 2 of 3

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Genome_build: NC_004350.2
Supplementary_files_format_and_content: Counts obtained from step 6: htseq-count, listed along side each open reading frame

organism: Streptococcus mutans

source_name: fruR:Sp_bacterial batch culture

growth_protocol: Bacterial cells used for extraction of RNA were grown in BHI medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

tag: parental strain

tag: genotype/variation

tag: media

value: BHI


title: fruK-13_3

description: repeat 3 of 3

source_name: fruKM28stop_bacterial batch culture


title: Blastula 1, oxidized

description: Barcode: ATCACG


title: fruK-13_2

description: repeat 2 of 3


title: fruK-13_1

description: repeat 1 of 3


title: UA159_3

description: repeat 3 of 3

source_name: WT_bacterial batch culture

value: Wild type


title: fruR-3

description: repeat 3 of 3


title: DMSO_Zymosan_90min

city: Cambridge

first: Mukund

last: Varma

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Library strategy: TF-seq + 3'DGE
Alignment with BWA
Counting of transcripts with custom python script
QC with custom python script
Differential expression with EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: Tab-seperated values of counts for each gene and each sample
Supplementary_files_format_and_content: tfseq.counts.csv: Comma separated values raw counts matrix for TFSeq
Supplementary_files_format_and_content: tfseq.normalized.csv: Comma separated values normalized counts matrix for TFSeq
Supplementary_files_format_and_content: rnaseq.3dge.totalcounts.csv: Tab separated values total counts matrix for 3'DGE RNASeq
Supplementary_files_format_and_content: rnaseq.3dge.umicounts.csv: Tab separated values UMI (barcode) counts matrix for 3'DGE RNASeq

molecule: polyA RNA

organism: Mus musculus

source_name: BMDM

growth_protocol: Isolated Mouse Bone Marrow, ex vivo differentiated BMDMs using M-CSF-supplemented DMEM with 10% FBS over 7 days.

extract_protocol:
Cells PBS washed, polyA RNA isolated using Dynabeads mRNA DIRECT kit (610-12)
TF-seq + 3'DGE

treatment_protocol: BMDMs were pre-treated with the CDK8 inhibitors dCA (100 nM), or BRD-6989 (1 uM) for 24 hours, then stimulated with a cohort of 11 different TLR ligands for 8 time points from 0-4 hours.

tag: pre-treatment

value: DMSO

tag: nextera barcodes

value: TAAGGCGA

value: ex vivo differentiated BMDMs

tag: age

tag: well tag

value: GCCTTA

tag: sequence to synthesize


title: DMSO_Zymosan_60min

tag: strain

value: CTTCAC


title: UA159_2

description: repeat 2 of 3


title: UA159_1

description: repeat 1 of 3


title: DMSO_Zymosan_30min

value: ATGACC


title: DMSO_Zymosan_150min

value: TCGTGT


title: E. coli H10407_LB_0.5_BR2

value: LB


title: DMSO_Zymosan_180min

value: TTTCCC


title: DMSO_TDB_45min

value: CCCATA


title: DMSO_TDB_60min

value: CTGTCT


title: DMSO_Zymosan_15min

value: ACTCCA


title: DMSO_TDB_30min

value: ATCCTG


title: DMSO_TDB_90min

value: GCATAG


title: DMSO_TDB_180min

value: TTGCAG


title: DMSO_TDB_150min

value: TCGATC


title: fruR-1

description: repeat 1 of 3

value: BHI


title: DMSO_TDB_15min

value: DMSO

value: ACGTCT


title: DMSO_SeV_90min

value: TAAGGCGA

value: ex vivo differentiated BMDMs

value: GAAAGG


title: DMSO_SeV_45min

value: ATTGCC


title: DMSO_SeV_60min

value: CGAATC


title: DMSO_SeV_30min

value: AGACGA


title: DMSO_Zymosan_45min

value: CCGTTA


title: DMSO_SeV_180min

value: TGACAG


title: DMSO_SeV_150min

value: GTTTGG


title: DMSO_SeV_120min

value: GCTGAT


title: DMSO_SeV_15min

value: AACCGT


title: DMSO_R848_90min

value: GAGTTG


title: DMSO_R848_60min

value: CTATGG


title: DMSO_R848_30min

value: AGTCAG


title: DMSO_Poly(I:C)_90min

value: GACACT


title: DMSO_Poly(I:C)_60min

value: DMSO

value: CGGATA


title: DMSO_R848_150min

value: TAAGGCGA

value: TCAGGA


title: DMSO_R848_180min

value: ex vivo differentiated BMDMs

value: TGTGTC


title: DMSO_R848_45min

value: CATCGA


title: DMSO_Poly(I:C)_45min

value: CAAGTC


title: DMSO_Poly(I:C)_180min

value: TGCACA


title: DMSO_Poly(I:C)_15min

value: AAGGAC


title: DMSO_R848_120min

value: GTATGC


title: DMSO_Zymosan_120min

value: GTTACG


title: DMSO_Pam3cys_90min

value: GAACTC


title: DMSO_Pam3cys_60min

value: CGATCA


title: DMSO_Pam3cys_45min

value: CAACGT


title: DMSO_Pam3cys_30min

value: AGAGTC


title: DMSO_R848_15min

value: ACCAGA


title: DMSO_Poly(I:C)_120min

value: DMSO

value: GGATTC


title: DMSO_Pam3cys_180min

value: TAAGGCGA

value: TGAGCA


title: DMSO_Pam3cys_15min

value: ex vivo differentiated BMDMs

value: AACTGG


title: DMSO_Pam3cys_150min

value: TACCGA


title: DMSO_Pam3cys_120min

value: GGAAGT


title: DMSO_NoStim_45min

value: ATGGTG


title: DMSO_NoStim_90min

value: CTTGGA


title: DMSO_NoStim_60min

value: CCTGTT


title: DMSO_NoStim_30min

value: ACTGTC


title: DMSO_Poly(I:C)_150min

value: TACTCG


title: DMSO_MDP_LPS_90min

value: GATTGC


title: DMSO_MDP_LPS_60min

value: CTGAGA


title: DMSO_MDP_LPS_180min

value: TTCGTG


title: DMSO_MDP_LPS_45min

value: CCAGTA


title: DMSO_NoStim_150min

value: DMSO

value: GTTGAC


title: DMSO_NoStim_120min

value: TAAGGCGA

value: GCGTTT


title: DMSO_MDP_LPS_15min

value: ex vivo differentiated BMDMs

value: ACGATG


title: DMSO_NoStim_15min

value: AACACG


title: DMSO_MDP_60min

value: CTCGAT


title: DMSO_MDP_LPS_30min

value: ATAGGC


title: DMSO_MDP_90min

value: GATCTG


title: DMSO_MDP_180min

value: TTCACC


title: DMSO_MDP_45min

value: CATGTG


title: DMSO_MDP_30min

value: AGTGCA


title: DMSO_MDP_15min

value: ACCTTC


title: DMSO_MDP_120min

value: GTCGTA


title: DMSO_MDP_150min

value: TCCATG


title: DMSO_LPS_45min

value: CACGTT


title: DMSO_NoStim_180min

value: DMSO

value: TCTCTG


title: DMSO_LPS_30min

value: TAAGGCGA

value: AGCTAC


title: DMSO_LPS_180min

value: ex vivo differentiated BMDMs

value: TGGAAC


title: DMSO_LPS_150min

value: TAGCGT


title: DMSO_LPS_15min

value: AATCGG


title: DMSO_TDB_120min

value: GTGGTT


title: DMSO_MDP_LPS_150min

value: TCCTCT


title: DMSO_FLA_30min

value: AGGTAG


title: DMSO_FLA_90min

value: GAGGAT


title: DMSO_FLA_180min

value: TGTCAC


title: DMSO_LPS_120min

value: GGGTAT


title: DMSO_MDP_LPS_120min

value: GTGAAC


title: DMSO_FLA_120min

value: GTACGT


title: DMSO_FLA_15min

value: ACAGTG


title: DMSO_FLA_60min

value: DMSO

value: CTACGA


title: DMSO_CpG_60min

value: TAAGGCGA

value: CTAACG


title: DMSO_CpG_90min

value: ex vivo differentiated BMDMs

value: GAGACA


title: DMSO_LPS_90min

value: GACGAA


title: DMSO_CpG_45min

value: CAGATC


title: DMSO_LPS_60min

value: CGTCAT


title: DMSO_FLA_45min

value: CAGTGT


title: DMSO_CpG_180min

value: TGGTCT


title: DMSO_CpG_30min

value: AGGACT


title: dCA1_Zymosan_90min

value: dCA (100 nM) for 24 hours

value: CGTACTAG

value: GCCTTA


title: DMSO_CpG_15min

value: ACACGT


title: DMSO_CpG_120min

value: GGTGTT


title: dCA1_Zymosan_60min

value: CTTCAC


title: DMSO_CpG_150min

value: DMSO

value: TATCGC


title: dCA1_Zymosan_45min

value: CCGTTA


title: dCA1_Zymosan_180min

value: ex vivo differentiated BMDMs

value: TTTCCC


title: dCA1_Zymosan_150min

value: TCGTGT


title: dCA1_Zymosan_15min

value: ACTCCA


title: dCA1_TDB_90min

value: GCATAG


title: dCA1_TDB_30min

value: ATCCTG


title: dCA1_TDB_180min

value: TTGCAG


title: dCA1_TDB_60min

value: CTGTCT


title: dCA1_TDB_15min

value: dCA (100 nM) for 24 hours

value: ACGTCT


title: dCA1_TDB_45min

value: CGTACTAG

value: CCCATA


title: dCA1_Zymosan_120min

value: GTTACG


title: DMSO_FLA_150min

value: TAAGGCGA

value: TCACAC


title: dCA1_TDB_120min

value: GTGGTT


title: dCA1_SeV_90min

value: GAAAGG


title: dCA1_SeV_60min

value: ex vivo differentiated BMDMs

value: CGAATC


title: dCA1_SeV_30min

value: AGACGA


title: dCA1_SeV_45min

value: ATTGCC


title: dCA1_SeV_180min

value: TGACAG


title: dCA1_R848_90min

value: GAGTTG


title: dCA1_SeV_15min

value: AACCGT


title: dCA1_SeV_120min

value: GCTGAT


title: dCA1_R848_60min

value: dCA (100 nM) for 24 hours

value: CTATGG


title: dCA1_R848_45min

value: CGTACTAG

value: CATCGA


title: dCA1_R848_30min

value: AGTCAG


title: dCA1_Zymosan_30min

value: ATGACC


title: dCA1_R848_150min

value: TCAGGA


title: dCA1_R848_180min

value: TGTGTC


title: dCA1_R848_15min

value: ACCAGA


title: dCA1_Poly(I:C)_90min

value: ex vivo differentiated BMDMs

value: GACACT


title: dCA1_R848_120min

value: GTATGC


title: dCA1_Poly(I:C)_60min

value: CGGATA


title: dCA1_Poly(I:C)_180min

value: TGCACA


title: dCA1_Poly(I:C)_45min

value: CAAGTC


title: dCA1_Poly(I:C)_30min

value: AGCCAT


title: dCA1_Poly(I:C)_15min

value: AAGGAC


title: dCA1_TDB_150min

value: dCA (100 nM) for 24 hours

value: TCGATC


title: dCA1_Pam3cys_90min

value: CGTACTAG

value: GAACTC


title: dCA1_Poly(I:C)_150min

value: TACTCG


title: dCA1_Pam3cys_60min

value: CGATCA


title: dCA1_SeV_150min

value: GTTTGG


title: dCA1_Pam3cys_45min

value: CAACGT


title: dCA1_Pam3cys_30min

value: AGAGTC


title: dCA1_Pam3cys_15min

value: ex vivo differentiated BMDMs

value: AACTGG


title: dCA1_NoStim_45min

value: ATGGTG


title: dCA1_NoStim_60min

value: CCTGTT


title: dCA1_Pam3cys_120min

value: GGAAGT


title: dCA1_Pam3cys_150min

value: TACCGA


title: dCA1_NoStim_180min

value: TCTCTG


title: dCA1_NoStim_15min

value: AACACG


title: dCA1_MDP_LPS_60min

value: dCA (100 nM) for 24 hours

value: CTGAGA


title: dCA1_NoStim_150min

value: CGTACTAG

value: GTTGAC


title: dCA1_NoStim_30min

value: ACTGTC


title: dCA1_NoStim_120min

value: GCGTTT


title: dCA1_MDP_LPS_90min

value: GATTGC


title: dCA1_MDP_LPS_45min

value: CCAGTA


title: dCA1_MDP_90min

value: GATCTG


title: dCA1_MDP_LPS_180min

value: ex vivo differentiated BMDMs

value: TTCGTG


title: dCA1_MDP_LPS_120min

value: GTGAAC


title: dCA1_MDP_LPS_15min

value: ACGATG


title: dCA1_MDP_60min

value: CTCGAT


title: dCA1_MDP_LPS_150min

value: TCCTCT


title: dCA1_MDP_45min

value: CATGTG


title: dCA1_MDP_30min

value: AGTGCA


title: dCA1_MDP_150min

value: dCA (100 nM) for 24 hours

value: TCCATG


title: dCA1_MDP_120min

value: CGTACTAG

value: GTCGTA


title: dCA1_Pam3cys_180min

value: TGAGCA


title: dCA1_LPS_90min

value: GACGAA


title: dCA1_MDP_15min

value: ACCTTC


title: dCA1_MDP_180min

value: TTCACC


title: dCA1_NoStim_90min

value: CTTGGA


title: dCA1_LPS_45min

value: ex vivo differentiated BMDMs

value: CACGTT


title: dCA1_LPS_60min

value: CGTCAT


title: dCA1_LPS_30min

value: AGCTAC


title: dCA1_LPS_15min

value: AATCGG


title: dCA1_LPS_180min

value: TGGAAC


title: dCA1_LPS_150min

value: TAGCGT


title: dCA1_LPS_120min

value: GGGTAT


title: dCA1_FLA_60min

value: dCA (100 nM) for 24 hours

value: CTACGA


title: dCA1_FLA_90min

value: CGTACTAG

value: GAGGAT


title: dCA1_FLA_45min

value: CAGTGT


title: dCA1_MDP_LPS_30min

value: ATAGGC


title: dCA1_FLA_30min

value: AGGTAG


title: dCA1_FLA_180min

value: TGTCAC


title: dCA1_FLA_150min

value: TCACAC


title: dCA1_FLA_15min

value: ex vivo differentiated BMDMs

value: ACAGTG


title: dCA1_FLA_120min

value: GTACGT


title: dCA1_CpG_90min

value: GAGACA


title: dCA1_CpG_60min

value: CTAACG


title: dCA1_CpG_45min

value: CAGATC


title: dCA1_CpG_180min

value: TGGTCT


title: dCA1_CpG_120min

value: GGTGTT


title: dCA1_CpG_150min

value: dCA (100 nM) for 24 hours

value: TATCGC


title: dCA1_CpG_15min

value: CGTACTAG

value: ACACGT


title: Brd_Zymosan_90min

value: BRD-6989 (1 uM) for 24 hours

value: AGGCAGAA

value: GCCTTA


title: Brd_Zymosan_60min

value: CTTCAC


title: Brd_Zymosan_45min

value: CCGTTA


title: Brd_Zymosan_30min

value: ex vivo differentiated BMDMs

value: ATGACC


title: Brd_Zymosan_150min

value: TCGTGT


title: Brd_Zymosan_180min

value: TTTCCC


title: Brd_Zymosan_120min

value: GTTACG


title: DMSO_Poly(I:C)_30min

value: DMSO

value: TAAGGCGA

value: AGCCAT


title: Brd_Zymosan_15min

value: ACTCCA


title: dCA1_Poly(I:C)_120min

value: dCA (100 nM) for 24 hours

value: GGATTC


title: Brd_TDB_60min

value: CTGTCT


title: Brd_TDB_150min

value: BRD-6989 (1 uM) for 24 hours

value: TCGATC


title: Brd_TDB_15min

value: AGGCAGAA

value: ACGTCT


title: Brd_TDB_90min

value: GCATAG


title: Brd_TDB_45min

value: ex vivo differentiated BMDMs

value: CCCATA


title: Brd_TDB_120min

value: GTGGTT


title: Brd_TDB_180min

value: TTGCAG


title: Brd_SeV_90min

value: GAAAGG


title: dCA1_CpG_30min

value: CGTACTAG

value: AGGACT


title: Brd_SeV_60min

value: CGAATC


title: Brd_SeV_150min

value: GTTTGG


title: Brd_SeV_30min

value: AGACGA


title: Brd_SeV_180min

value: TGACAG


title: Brd_SeV_15min

value: AACCGT


title: Brd_SeV_45min

value: BRD-6989 (1 uM) for 24 hours

value: ATTGCC


title: Brd_SeV_120min

value: AGGCAGAA

value: GCTGAT


title: Brd_R848_90min

value: GAGTTG


title: Brd_R848_60min

value: ex vivo differentiated BMDMs

value: CTATGG


title: Brd_R848_45min

value: CATCGA


title: Brd_R848_15min

value: ACCAGA


title: Brd_R848_180min

value: TGTGTC


title: Brd_R848_30min

value: AGTCAG


title: Brd_TDB_30min

value: ATCCTG


title: Brd_R848_120min

value: GTATGC


title: Brd_Poly(I:C)_15min

value: AAGGAC


title: Brd_R848_150min

value: TCAGGA


title: Brd_Poly(I:C)_150min

value: TACTCG


title: Brd_Poly(I:C)_45min

value: CAAGTC


title: Brd_Poly(I:C)_30min

value: BRD-6989 (1 uM) for 24 hours

value: AGCCAT


title: Brd_Poly(I:C)_180min

value: AGGCAGAA

value: TGCACA


title: Brd_Poly(I:C)_120min

value: GGATTC


title: Brd_Poly(I:C)_90min

value: ex vivo differentiated BMDMs

value: GACACT


title: Brd_Pam3cys_45min

value: CAACGT


title: Brd_Pam3cys_60min

value: CGATCA


title: Brd_Pam3cys_30min

value: AGAGTC


title: Brd_Pam3cys_15min

value: AACTGG


title: Brd_Pam3cys_150min

value: TACCGA


title: Brd_NoStim_180min

value: TCTCTG


title: Brd_Pam3cys_120min

value: GGAAGT


title: Brd_NoStim_60min

value: CCTGTT


title: Brd_NoStim_45min

value: ATGGTG


title: Brd_NoStim_15min

value: AACACG


title: Brd_NoStim_120min

value: BRD-6989 (1 uM) for 24 hours

value: GCGTTT


title: Brd_MDP_LPS_90min

value: AGGCAGAA

value: GATTGC


title: Brd_NoStim_150min

value: GTTGAC


title: Brd_MDP_LPS_60min

value: ex vivo differentiated BMDMs

value: CTGAGA


title: Brd_Poly(I:C)_60min

value: CGGATA


title: Brd_MDP_LPS_45min

value: CCAGTA


title: Brd_MDP_LPS_30min

value: ATAGGC


title: Brd_MDP_LPS_180min

value: TTCGTG


title: Brd_Pam3cys_90min

value: GAACTC


title: Brd_MDP_LPS_150min

value: TCCTCT


title: Brd_MDP_45min

value: CATGTG


title: Brd_Pam3cys_180min

value: TGAGCA


title: Brd_MDP_15min

value: ACCTTC


title: Brd_MDP_30min

value: AGTGCA


title: Brd_MDP_LPS_15min

value: BRD-6989 (1 uM) for 24 hours

value: ACGATG


title: Brd_MDP_120min

value: AGGCAGAA

value: GTCGTA


title: Brd_MDP_60min

value: CTCGAT


title: Brd_MDP_180min

value: ex vivo differentiated BMDMs

value: TTCACC


title: Brd_MDP_150min

value: TCCATG


title: Brd_MDP_LPS_120min

value: GTGAAC


title: Brd_NoStim_30min

value: ACTGTC


title: Brd_NoStim_90min

value: CTTGGA


title: Brd_LPS_90min

value: GACGAA


title: Brd_LPS_45min

value: CACGTT


title: Brd_LPS_30min

value: AGCTAC


title: Brd_LPS_15min

value: AATCGG


title: Brd_FLA_90min

value: GAGGAT


title: Brd_LPS_180min

value: TGGAAC


title: Brd_LPS_150min

value: BRD-6989 (1 uM) for 24 hours

value: TAGCGT


title: Brd_FLA_45min

value: AGGCAGAA

value: CAGTGT


title: Brd_LPS_120min

value: GGGTAT


title: Brd_FLA_30min

value: ex vivo differentiated BMDMs

value: AGGTAG


title: Brd_FLA_15min

value: ACAGTG


title: Brd_FLA_180min

value: TGTCAC


title: Brd_MDP_90min

value: GATCTG


title: Brd_FLA_150min

value: TCACAC


title: Brd_CpG_60min

value: CTAACG


title: Brd_CpG_90min

value: GAGACA


title: Brd_CpG_45min

value: CAGATC


title: Brd_LPS_60min

value: CGTCAT


title: Brd_CpG_180min

value: TGGTCT


title: Brd_CpG_30min

value: AGGACT


title: Brd_CpG_150min

value: BRD-6989 (1 uM) for 24 hours

value: TATCGC


title: Brd_CpG_120min

value: AGGCAGAA

value: GGTGTT


title: ABA_3d_rep1

city: Shanghai

first: Huang

last: Huan

address: No. 3888 Chenhua Road

institute: Chinese Academy of Sciences

data_processing:
Reads were mapped to TAIR10 using Tophat2
Differetial gene expresssion was analysed by cufflinks
Genome_build: TAIR10
Supplementary_files_format_and_content: abundance measurements

organism: Arabidopsis thaliana

source_name: 3-week-old Arabidopsis_ABA_3d

growth_protocol: 3-week-old Col-0 plants grown in soil

extract_protocol:
Total RNAs were extracted using the TRIzol (Invitrogen) method, and RNase-free Dnase (Qiagen) was used to remove contaminating DNA before RNA-seq.
Total RNAs were sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library preparation and sequencing using standard Illumina protocols.

treatment_protocol: Plants were sprayed with a 10 μM solution of the indicated compound and incubated for 6, 24, or 72 h before RNA extraction.

tag: ecotype

value: ABA

tag: time (after the treatment)

value: 3 day

value: leaf


title: AMF1_3d_rep2

department: Shanghai Center for Plant Stress  Biology

source_name: 3-week-old Arabidopsis_AMF1_3d

tag: tissue


title: AMF4_3d_rep2

source_name: 3-week-old Arabidopsis_AMF4_3d

tag: treatment


title: DMSO_3d_rep1

source_name: 3-week-old Arabidopsis_DMSO_3d

value: DMSO


title: Brd_FLA_60min

value: ex vivo differentiated BMDMs

value: CTACGA


title: AMF1_3d_rep1


title: AMF4_1d_rep2

source_name: 3-week-old Arabidopsis_AMF4_1d

value: 1 day


title: AMF1_1d_rep3

source_name: 3-week-old Arabidopsis_AMF1_1d


title: AMF4_1d_rep1


title: AMF1_1d_rep1


title: DMSO_1d_rep2

source_name: 3-week-old Arabidopsis_DMSO_1d


title: ABA_1d_rep3

source_name: 3-week-old Arabidopsis_ABA_1d


title: ABA_1d_rep2


title: AMF4_6h_rep2

source_name: 3-week-old Arabidopsis_AMF4_6h

value: 6 hr


title: AMF4_6h_rep3


title: AMF4_6h_rep1


title: DMSO_1d_rep1


title: AMF1_6h_rep3

source_name: 3-week-old Arabidopsis_AMF1_6h


title: AMF4_3d_rep1


title: AMF1_1d_rep2


title: Brd_CpG_15min

value: ACACGT


title: DMSO_1d_rep3


title: AMF1_6h_rep2


title: AMF1_6h_rep1


title: ABA_6h_rep3

source_name: 3-week-old Arabidopsis_ABA_6h


title: ABA_6h_rep1


title: DMSO_6h_rep2

source_name: 3-week-old Arabidopsis_DMSO_6h


title: DMSO_6h_rep1


title: Proliferating control (PD34)

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Single-ended, 75bp reads were mildly trimmed using Trimmomatic (version 0.32) to remove leading or trailing nucleotides whose sequencing quality was below 3.
Reads whose length fell below 30bp after trimming were also removed from downstream analysis.
STAR (version 2.3.0e) was using for mapping reads to reference genome (hg19), requiring a minimum alignment score of 10.
The expression level of RefSeq genes was quantified using featureCounts (version 1.5.0) and normalized using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

organism: Homo sapiens

source_name: IMR90 cells

growth_protocol: IMR90 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 μg/ml streptomycin (Invitrogen)

extract_protocol:
Total RNA was isolated from IMR90 cells using RNeasy kit (Qiagen)
The ribo-depleted RNA was then ethanol-precipitated, fragmented, and tagged at both ends for stranded library preparation, using the Scriptseq v2 library preparation protocol.

treatment_protocol: IMR90 cells at ~60-70% confluency were treated with 50 uM etoposide for 48 h. The media were then replaced and cells were harvested at Day 7.

tag: strain background

value: Primary human fibroblasts

tag: mutation

value: Wild-type


title: sh-NTC etoposide-replicate 2

value: Etoposide


title: sh-cGAS etoposide-replicate 1

value: cGAS shRNA knockdown


title: ABA_1d_rep1


title: sh-cGAS etoposide-replicate 2


title: Proliferating control (PD29)


title: sh-NTC etoposide-replicate 1


title: Brd_FLA_120min

value: BRD-6989 (1 uM) for 24 hours

value: GTACGT


title: Dnmt3c rahu/+ mouse y′

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

data_processing:
RNAseq fastq files were aligned using STAR (version 2.4.0f1) to the mouse genome (mm10) using Gencode (version M11) transcriptome assembly for junction points.
Coding genes and transposable elements were quantified using TEToolkit to annotate both uniquely and ambiguously mapped reads. Gencode annotation and Repbase database for repetitive sequences and transposable elements were used during the quantification.
Genome_build: mm10 (NCBIM38)
Supplementary_files_format_and_content: text file with raw counts.

source_name: whole testis

extract_protocol:
Total RNA from one half of a single testis, after removing the tunica albuginea, was extracted using the RNeasy Plus Mini Kit containing a genomic DNA eliminator column (Qiagen). The RNase-Free DNase Set (Qiagen) was used to perform an on-column DNase digestion during RNA purification, as well as an in-solution DNase digestion after RNA purification, followed by RNA cleanup.
RNA-seq libraries were prepared and sequenced by the Integrated Genomics Operation of Memorial Sloan Kettering Cancer Center. 1 μg of total RNA underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT kit (Illumina) with 6 cycles of post-ligation PCR.

value: whole testis

tag: genotype

value: Dnmt3c rahu/+

value: C57BL/6J & FVB/NJ (mixed); derived from ENU mutagenized line

value: 14 days post partum

tag: littermate

value: litter 1


title: Dnmt3c rahu/rahu mouse z

value: Dnmt3c rahu/rahu


title: Dnmt3c rahu/+ mouse z′


title: Dnmt3c rahu/rahu mouse x


title: Dnmt3c rahu/rahu mouse y


title: ABA_6h_rep2

value: ABA

value: leaf


title: DMSO_6h_rep3

value: DMSO


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day7fsk_rep3

city: Tokyo

first: Hironori

last: Waki

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

country: Japan

institute: The University of Tokyo

data_processing:
Demultiplex and basecalling was performed with the CASSAVA 1.8.2 software (Illumina).
The sequence reads were mapped to the mm9 mouse genome using TopHat.
Fragments per kilobase of exon per million fragment mapped (FPKM) values were calculated for each gene using CuffLinks.
Genome_build: mm9
Supplementary_files_format_and_content: txt files showing FPKM value of each samples.

source_name: C2C12 myoblasts

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Techologies) and RNeasy Mini Kit (Qiagen).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

tag: time course

value: 10 uM forskoline for 4 hours


title: RNA-seq_ctrl_C2C12_myoblasts_day7fsk_rep3


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day0_rep3


title: RNA-seq_ctrl_C2C12_myoblasts_day7_rep2


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day7_rep3


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day7_rep2


title: RNA-seq_ctrl_C2C12_myoblasts_day7fsk_rep2


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day0_rep2


title: RNA-seq_ctrl_C2C12_myoblasts_day0_rep3


title: CEBPbeta_ChIP-seq_brown_adipocytes_day6

library_source: genomic

data_processing:
Demultiplex and basecalling was performed with the CASSAVA 1.8.2 software (Illumina).
Sequence reads were aligned to the mm9 genome assembly using ELAND mapping program.
Peak calling were performed using MACS version 1.4 with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph or bigWig files showing the peaks of each samples.

molecule: genomic DNA

source_name: immortalized brown adipocytes

growth_protocol: At the confluence, cells were treated for 48 hours in medium containing 10% FBS, 0.5mM isobuylmethylxanthine, 125nM indomethacin, 1 mM dexamethosone, 850nM insulin, 1nM T3 and 1 mM rosiglitazone. After 48 hours, cells were switched to medium containing 10% FBS, 850nM insulin, 1nM T3 and 1 mM rosiglitazone.

extract_protocol:
Samples were treated by nuclear extraction buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) for 10 minutes and immediately cross-linked with 1% formaldehyde for 7.5 minutes at room temperature. Cross-linking was quenched using 125 mM glycine for 5 minutes. The chromatin was sheared by probe sonicator (Branson) and was spun at 15,000rpm for 5 minutes. Antibodies were added for overnight incubation at 4C. Mix of Protein A and Protein G Sepharose (GE) were added to samples for 4h at 4C. Subsequent procedures were performed as described previously (Waki et.al. 2011).
ChIP-seq libraries were prepared using KAPA hyper prep kit (KAPA Biosystems) according to the manufacturer's instructions.

tag: antibody

value: CEBPbeta


title: CEBPalpha_ChIP-seq_brown_adipocytes_day6

value: CEBPalpha


title: RNA-seq_ctrl_C2C12_myoblasts_day7_rep3


title: H3K27Ac_ChIP-seq_brown_adipocytes_day6


title: H3K27Ac_ChIP-seq_brown_adipocytes_day0


title: CEBPalpha_ChIP-seq_brown_adipocytes_day0


title: ATAC-seq_brown_adipocytes_day0_rep1

description: 50,000 nuclei were transposed using Tn5 transposase as previously described (Buenrostro et al. 2013). Transposed samples were amplified by 15 cycles of PCR. ATAC-seq libraries were prepared using Nextera DNA Library Prep Kit (Illumina) as previously described (Buenrostro et al. 2013).


title: RNA-seq_NFIA_KO_BAT_rep2

source_name: brown adipose tissue

value: NFIA-KO


title: RNA-seq_ctrl_C2C12_myoblasts_day0_rep2


title: CEBPbeta_ChIP-seq_brown_adipocytes_day0


title: Dnmt3c rahu/+ mouse x′


title: RNA-seq_NFIA_KO_BAT_rep3


title: RNA-seq_NFIA_KO_BAT_rep1


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day7fsk_rep2


title: RNA-seq_WT_BAT_rep2

value: wild-type


title: RNA-seq_WT_BAT_rep3


title: RNA-seq_WT_BAT_rep1


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day7fsk


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day7


title: RNA-seq_NFIA-expressing_C2C12_myoblasts_day0


title: RNA-seq_ctrl_C2C12_myoblasts_day0


title: ATAC-seq_brown_adipocytes_day6_rep1

description:
50,000 nuclei were transposed using Tn5 transposase as previously described (Buenrostro et al. 2013). Transposed samples were amplified by 15 cycles of PCR. ATAC-seq libraries were prepared using Nextera DNA Library Prep Kit (Illumina) as previously described (Buenrostro et al. 2013).
ATAC-seq_brown_adipocytes_day6_rep1_2.bigWig


title: ATAC-seq_brown_adipocytes_day6_rep2


description: NFIA_ChIP-seq_NFIA-expressing_C2C12_myoblasts_day7.bigWig

value: FLAG M2


title: RNA-seq_ctrl_C2C12_myoblasts_day7


title: PPARg_ChIP-seq_brown_adipocytes_day6_rep2

description: PPARg_ChIP-seq_brown_adipocytes_day6_rep1_2.bigWig

value: PPARg


title: PPARg_ChIP-seq_brown_adipocytes_day6_rep1


description: PPARg_ChIP-seq_brown_adipocytes_day0_rep1_2.bigWig


title: NFI_ChIP-seq_brown_adipocytes_day6

description: NFI_ChIP-seq_brown_adipocytes_day6.bigWig

value: NFI


description: NFIA_ChIP-seq_NFIA-expressing_C2C12_myoblasts_day0.bigWig


title: FAIRE_eWAT

description:
C57BL/6J male mice were maintained in a 12 hour dark /light cycle and sacrificed when they were 8-weeks old. FAIRE was performed as described previously (Waki et al. 2011), with optimization for experiment using in vivo tissues. Briefly, freshly collected adipose tissues were minced with scissors and cross-linked with 1% formaldehyde for 7 minutes at room temperature, followed by quenching with 125mM glycine for 5 minutes. A Pasteur pipette was used to carefully wash the floating minced samples with cold PBS. The chromatin was sheered by using a homogenizer and then a Branson sonifier. Following procedure was carried out as described previously (Waki et al. 2011).
FAIRE_eWAT.bedgraph

source_name: epididymal WAT


title: NFI_ChIP-seq_brown_adipocytes_day0

description: NFI_ChIP-seq_brown_adipocytes_day0.bigWig


title: 94_healthy_Cerebellum

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Bismark (v0.13.1)
Bowtie 2 (v2.2.3)
MethylKit
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited methylation counts

extract_protocol:
DNA was isolated from 20–40 mg of sampled frontal cortex and cerebellum frozen tissue using the Wizard genomic DNA purification kit (Promega, Madison, WI, USA) as per manufacturers’ instructions, and re-suspended in TE buffer. Concentration was assessed using a Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA), and 50ng/ul of DNA in a 10ul volume was sent to the Mayo Clinic Medical Genome Facility in Rochester (Minnesota, USA) for processing and sequencing.
RRBS library construction and sequencing was conducted at the Mayo Clinic Medical Genome Facility in Rochester (Minnesota, USA). First, the concentration and size distribution of the libraries were determined using Agilent (Santa Clara, CA, USA) Bioanalyzer DNA 1000 chip, Qubit fluorometry (Invitrogen, Carlsbad, CA), and qPCR. Libraries were pooled at equimolar concentrations and loaded onto a paired end flow cell at concentrations of 7-8 pM to generate cluster densities of 600,000-700,000/mm2 following Illumina’s standard protocol, using the Illumina cBot and HiSeq Paired end cluster kit version 3 (San Diego, CA, USA). Because bisulfite treated samples are unbalanced due to an under representation of C bases, a lane of PhiX genomic DNA was run to allow the Illumina data collection software to call bases correctly. Each lane of a HiSeq flow cell produces 21-39 Gbases of sequence. The flow cells were sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 3 and HiSeq data collection version 2.0.12.0 software. Base-calling was performed using Illumina’s RTA version 1.17.21.3.

tag: subject status

value: Healthy

value: brain

tag: tissue subtype

value: Frontal Cortex


title: Triptolide_ATACseq

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

description: ATAC-seq after 10µM triptolide treatment for 3 hours

data_processing:
ChIP-seq and ATAC-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP and ChIAPET reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq or ATAC-seq and .hic containing Hi-C contact matrices.

organism: Drosophila melanogaster

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-CP190 or anti-Pol2phosphoSerine2 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation. For ATAC-seq Kc167 cells grown to exponential stage were treated with DMSO or triptolide as previously described. 200,000 ctrl and treated cells were collected and used for Fast-ATAC protocol. Briefly, cell pellets were resuspened in 50 µl transposes Tn5 mixture (0.01% digitonin for permeabilizing cell membrane, 2.5 µl Tn5, 25 µl TD buffer), and incubated at 30°C for 20 min with occasional shaking. After reaction, cells were cooled on ice and continued with DNA extraction by Minelute Kit (Qiagen).
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

tag: cell type

value: Kc167 Drosophila Embryonic Cell Line


title: H3K27me3_HiChIP_3

description: HiChIP (Hi-C Chromatin immunoprecipitation) for H3K27me3

data_processing:
Library strategy: HiChIP
ChIP-seq and ATAC-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP and ChIAPET reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq or ATAC-seq and .hic containing Hi-C contact matrices.

tag: chip-antibody

value: H3K27me3 (Millipore 07-449)


title: H3K27ac_HiChIP_2

description: HiChIP (Hi-C Chromatin immunoprecipitation) for H3K27ac

value: H3K27ac (Abcam ab4729)


title: 86_healthy_Cerebellum


title: H2Av_ChIPseq

description: ChIP-seq for H2Av

data_processing:
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP and ChIAPET reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-CP190 or anti-Pol2phosphoSerine2 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation.
Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding  adenosine to  the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.


title: PPARg_ChIP-seq_brown_adipocytes_day0_rep2


title: H3.3_ChIPseq

description: ChIP-seq for H3.3


title: FAIRE_BAT

description:
C57BL/6J male mice were maintained in a 12 hour dark /light cycle and sacrificed when they were 8-weeks old. FAIRE was performed as described previously (Waki et al. 2011), with optimization for experiment using in vivo tissues. Briefly, freshly collected adipose tissues were minced with scissors and cross-linked with 1% formaldehyde for 7 minutes at room temperature, followed by quenching with 125mM glycine for 5 minutes. A Pasteur pipette was used to carefully wash the floating minced samples with cold PBS. The chromatin was sheered by using a homogenizer and then a Branson sonifier. Following procedure was carried out as described previously (Waki et al. 2011).
FAIRE_BAT.bedgraph

source_name: BAT


title: FAIRE_iWAT

description:
C57BL/6J male mice were maintained in a 12 hour dark /light cycle and sacrificed when they were 8-weeks old. FAIRE was performed as described previously (Waki et al. 2011), with optimization for experiment using in vivo tissues. Briefly, freshly collected adipose tissues were minced with scissors and cross-linked with 1% formaldehyde for 7 minutes at room temperature, followed by quenching with 125mM glycine for 5 minutes. A Pasteur pipette was used to carefully wash the floating minced samples with cold PBS. The chromatin was sheered by using a homogenizer and then a Branson sonifier. Following procedure was carried out as described previously (Waki et al. 2011).
FAIRE_iWAT.bedgraph

source_name: inguinal WAT


title: DMSO_ATACseq

description: ATAC-seq under normal conditions


title: 94_healthy_Frontal Cortex

source_name: healthy_Frontal Cortex

value: Cerebellum


title: 90_healthy_Cerebellum


title: H4K20me1_ChIPseq

description: ChIP-seq for H4K20me1

value: H4K20me1 (Abcam ab9051)


title: 90_healthy_Frontal Cortex


title: 24_healthy_Cerebellum


title: RNA-seq_ctrl C2C12_myoblasts_day7fsk


title: 86_healthy_Frontal Cortex


title: H3K36me3_ChIPseq

description: ChIP-seq for H3K36me3

value: H3K36me3 (Millipore 05-801)


title: H3K9me3_ChIPseq

description: ChIP-seq for H3K9me3

value: H3K9me3 (Abcam ab8898)


title: 72_sALS_Cerebellum

value: sporadic amyotrophic lateral sclerosis (sALS)


title: 13_sALS_Frontal Cortex

source_name: sALS_Frontal Cortex


title: H3K27me3_HiChIP_1


title: Pol2Ser2_HiChIP_2

description: HiChIP (Hi-C Chromatin immunoprecipitation) for Pol II serine 2

value: RNA Pol II phospho S2 (Abcam ab5095)


title: 13_sALS_Cerebellum


title: H3K27me3_HiChIP_2


title: 12_sALS_Frontal Cortex


title: 24_healthy_Frontal Cortex


title: H3K27ac_HiChIP


title: H2Bub_ChIPseq

description: ChIP-seq for H2B ubiquitinylated

value: H2Bub (Millipore 05-1312)


title: 12_sALS_Cerebellum


title: H4K16ac_ChIPseq

description: ChIP-seq for H4K16ac

value: H4K16ac (Millipore 07-329)


title: 11_sALS_Cerebellum


title: 34_c9ALS_Frontal Cortex

source_name: c9ALS_Frontal Cortex

value: C9orf72-associated amyotrophic lateral sclerosis (c9ALS)


title: 7_b_c9ALS_Cerebellum


title: RDsh ATAC-seq

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description: Untreated

data_processing:
Paired-end reads were first trimmed to 30bp to remove adapter sequences. Then, aligned to the reference genome (hg19) using bowtie software (version 1.1.2).
Duplicated reads and those mapping to the mitochondrial chromosome were removed.
Accessibility peaks were obtained using MACS2 (version 2.1.1.20160309)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format. Accessibility peaks upon multiH1 KD

source_name: Breast cancer cell line

growth_protocol: Breast cancer T47D-MTVL cells (carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) or derivative cells, were grown at 37ºC with 5% CO2 in RPMI 1640 medium

extract_protocol:
75.000 cells were harvested and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen).
All samples were then amplified by PCR using NEBNextHigh-Fidelity 2x PCR Master Mix (New Englands Labs.) and primers containing a barcode to generate the libraries. DNA was again purified using MinElute PCR Purification Kit and samples were sequenced using Illumina HiSeq 2500 system.

treatment_protocol: Stable breast cancer-derived cell lines expressing an shRNA against multiple H1 variants (mainly H1.2 and H1.4 at protein level) or a control/empty shRNA in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox, in duplicate

value: breast cancer

tag: phenotype

value: Control

tag: replicate

value: Replicate 1


title: 2_c9ALS_Frontal Cortex

value: brain


title: multiH1sh_Dox_1 ATAC-seq

description: Dox treated

value: Knock-down


title: CP190_HiChIP

description: HiChIP (Hi-C Chromatin immunoprecipitation) for CP190

data_processing:
Library strategy: HiChIP
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP and ChIAPET reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.

tag: cell line

tag: chip antibody


title: 11_sALS_Frontal Cortex

value: Frontal Cortex


title: PolII_ChIAPET

description: ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing)

data_processing:
Library strategy: ChIAPET
ChIP-seq reads were aligned to the dm6 reference genome using bowtie2 and PCR duplicates were removed. HiChIP and ChIAPET reads were processed using the Juicer pipeline.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig containing coverage of ChIP-seq and .hic containing Hi-C contact matrices.

value: RNA Pol II


title: Epc-KOrep1

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

description: Gene expression of round spermatid of mice deficient for Epc1/2

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Reads were aligned to mm9 genome using tophat2.1.0 and analyzed using cufflinks (version 2.2.1).
Mapped reads were normalized with total mapped reads and exon length.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized read counts (fragment per kilobase exon per million reads) were described as plain text.

source_name: round spermatid

extract_protocol: Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420L).  Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.

tag: genotype/variation

value: Epc-dKO

tag: strain


title: 34_c9ALS_Cerebellum

tag: tissue

value: Cerebellum


title: RDsh_Dox ATAC-seq

description: Dox treated


title: 7_c9ALS_Frontal Cortex


title: Epc-WT

description: Gene expression of round spermatid of WT mice

value: Wild type


title: 2_c9ALS_Cerebellum


title: multiH1sh_1 ATAC-seq

description: Untreated


title: 1_c9ALS_Frontal Cortex


title: Pol2Ser2_HiChIP


title: multiH1sh_2 ATAC-seq

description: Untreated

value: Replicate 2


title: 1_c9ALS_Cerebellum


title: multiH1sh_Dox_2 ATAC-seq

description: Dox treated


title: EBF2_ChIP-seq_brown_adipocytes_day6


title: PPARg_ChIP-seq_white_adipocytes_day7

source_name: 3T3-F442A white adipocytes

value: PPARg


title: 120sh_Dox_3

description:
120sh_Dox replicate 2
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.

data_processing:
Alignment: STAR (version 2.5.1b) with the following configuration --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Quantification: RSEM (version 1.2.28) using default parameters
Differential Expression Analysis: DESeq2 (version 1.10.1) using default parameters. Control samples against H1.4 knock-down (120sh_Dox) or against multiple H1 variants knock-down (225sh_Dox).
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: Matrix showing normalized abundance measurements where columns represent samples and rows transcripts, output from DESeq2 (default parameters) using variance stabilizing transformations

growth_protocol: Cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol:
Total RNA was extracted using High Pure RNA isolation kit (Roche) according to the manufacturer's instructions. cDNA was obtained from 100 ng of total RNA using SuperScript VILO cDNA synthesis (Invitrogen). High RNA integrity was assessed by Bioanalyzer nano 6000 assay with RIN numbers 9.0
TruSeq®Stranded Total Sample Preparation kit (Illumina Inc.,)

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Doxicycline treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated and treated for 6 days

tag: dox

value: Treated

tag: depletion

value: Depletion of histone H1.4

tag: expression

value: Histone H1.4 shRNA vector


title: 120sh_Dox_2

description:
120sh_Dox replicate 1
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.


title: 225sh_Dox_1

description:
225sh_Dox replicate 1
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.

value: Depletion of multiple histone H1 variants

value: Histone H1 shRNA vector


title: 225sh_Dox_3

description:
225sh_Dox replicate 2
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.


title: Rdsh_Dox_2

description:
Rdsh_Dox
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.

value: No depletion

value: Random shRNA vector


title: TRAP_1

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description: TotalBrain

data_processing:
Trimomatic- trim ends and low quality reads
Bowtie2: Ribosomal RNA removed by alignment to rRNA
STAR: Alignment to genome (Ensembl75)
HTseq: Counts calculated
EdgeR: differential expression between fractions was identified
Genome_build: Mouse: Ensembl75
Supplementary_files_format_and_content: Gene Counts .txt file; differential expression .csv files linked to Series record

source_name: This sample is cortex with IP of eGFP ribosomes.

extract_protocol:
SynapTRAP on cortex from SNAP25 bacTRAP mouse.
cDNA created by Nugen V2 Kit. Library preparation was performed by GTAC at Washington University.

tag: age

tag: transgenic line

value: SNAP25 BacTRAP

value: Cortex


title: SynapTRAP_3

description: SN

source_name: This sample is the SN band of a sucrose percoll gradient with IP of eGFP.


title: SynapTRAP_1

description: SN


title: Control_2

description:
120sh
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.

value: Untreated


title: SynapTRAP_2

description: SN


title: Control_1

description:
225sh
T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.


title: TRAP_3

description: TotalBrain


title: EBF2_ChIP-seq_brown_adipocytes_day0

tag: time course

tag: antibody


title: WCH_2

description: TotalBrain

source_name: This sample is a control that is cortex RNA.


title: NFI_ChIP-seq_white_adipocytes_day7

value: NFI


title: WCH_1

description: TotalBrain


title: 1.5M_KO_1

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dymanics Research

description: rep1-3: independent library preparations;

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using TopHat2
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each was counted, which provides the number of molecules detected for each gene
The copy number of RNA moelcules per cell for each gene is calculated based on spike-in RNA detection efficiency
Genome_build: mm10
Supplementary_files_format_and_content: The calculated copy number of RNA moelcules per cell for each gene is listed.

source_name: 1.5M epidermal cell

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction
Libraries were prepared by using molecular barcoding technique. First, for normalization, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: CD45+CD3-CD11b+MHCII+ cells were isolated from epidermal cells using FACS cell sorter

value: epidermal cells

tag: cell markers

tag: developmental stage

value: 1.5 months after birth

value: Cbfbeta2 knockout


title: P5_KO_2

source_name: P5 epidermal cell

tag: cell type


title: P5_KO_1


title: SNF_3

description: SN

source_name: This sample is the SN band of a sucrose percoll gradient without IP.


title: WCH_3

description: TotalBrain


title: P5_KO_3


title: VapC37

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

data_processing:
fastq_quality_filter -q 30 -Q 33 -i NG-8438_HTF_319212927_lib86854_3983_1_1.fastq -o NG-qf.fastq quality filter
fastx_clipper -Q 33 -a TGGAATTCTCGGGTGCCAAGG -l 17 -i NG-qf.fastq -o NG-qf_cl.fastq clip 3' linker
fastx_collapser -Q 33 -i NG-qf_cl.fastq -o NG-qf_cl_col.fasta collapse duplicates
pyBarcodeFilter.py -f NG-qf_cl_col.fasta --file_type=fasta -b barcodes.txt -m 1 demultiplex using pyCRAC software package
novoalign -f FASTA -d M_smeg_MC2_155_NC_008596_1.novoindex -a TGGAATTCTCGGGTGCCAAGG -h 150 -F FA -r Random > NOVO align reads to M_smeg genome NC_008596_1
Genome_build: NC_008596.1
Supplementary_files_format_and_content: mapped read coordinates in GTF format

organism: Mycolicibacterium smegmatis

source_name: tetracylcine induced culture

growth_protocol: M9 medium (Difco) containing 0.1% tween-80 (M9T) with 0.1% Casein hydrolysate, 1ug/mL thiamine and 0.2% glucose as carbon source at 37C. When appropriate, 50 ug/mL kanamycin was added the medium to maintain the plasmid. 20ng/ml of tetracycline was added to induce expression of the fusion protein.

extract_protocol:
The cells were subsequently harvested by centrifugation, washed in ice-cold phosphate buffered saline (PBS) containing 0.1% tween-80 and snap frozen in liquid nitrogen. The pellets were stored at -80C. The HTF tagged proteins were then purified, linkers ligated to crosslinked RNA, cDNA synthesized and DNA libraries generated as described in Tree et al Molecular Cell 2014.
Libraries were constructed as per Tree et al Molecular Cell 2014
OTHER: CRAC

treatment_protocol: Expression of the VapC-HTF fusion was induced with 20ng/ml of tetracylcine before harvesting

tag: construct


title: 1.5M_KO_2


title: 1.5M_wt_3

value: wildtype


title: SNF_2

description: SN


title: TRAP_2

description: TotalBrain


title: VapC30


title: Dnmt3c rahu/rahu mouse w

data_processing:
Adapter sequence were first N-masked from raw FASTQ files using cutadapt v1.9.1.
Short-read alignment was performed with bwa-meth. We modified bwa-meth’s default minimum longest match length for a read (0.44*read-length) to greater than 30 bp (0.2*read-length).
The resulting alignment files were marked for duplicates using Picard v2.4.1.
Methylation levels were calculated using MethylDackel v0.1.13 at cytosines excluding quality control failed, supplemental, duplicate, and MAPQ less than 20 reads (which excluded multi-mapped reads). Additionally, bases with quality less than 20 or within the first 11 bases sequenced on either read pair were also excluded.
Genome_build: mm10 (NCBIM38)
Supplementary_files_format_and_content: text file with methyl call. Headers are: 1. position id (chr.base), 2. chr, 3. position, 4. strand, 5. coverage, 6. C% in bisulfite-seq (methylated read %), 7. T% in bisulfite-seq (unmethylated read %).

source_name: whole testis

extract_protocol:
Genomic DNA was extracted from whole testis by incubating a single testis in 200 μl of DirectPCR lysis reagent (Viagen) containing 1 μl of proteinase K solution (>600 mAU/ml, Qiagen) for 24 hr at 55°. DNA was subsequently RNase A-treated, phenol:chloroform-extracted, and ethanol-precipitated.
Whole-genome bisulfite libraries were prepared and sequenced at the New York Genome Center (NYGC) using a tagmentation-based protocol developed by NYGC and J. Greally. In brief, 100 ng of genomic DNA was fragmented using tagmentation by Tn5 transposase and purified by Silane bead cleanup (Dynabeads MyOne Silane, Thermo Fisher Scientific). End filling was performed using dATP, dGTP, dTTP and methylated dCTP to protect added cytosines from bisulfite treatment. End-repaired DNA was purified by SPRI bead cleanup (Beckman), and subjected to bisulfite treatment and cleanup using EZ DNA Methylation-Gold MagPrep kit (Zymo Research). Illumina sequencing adapters (standard i5 adapter and custom i7 adapter) were added using PCR amplification. Finally, size selection of 300-bp to 800-bp fragments was performed using SPRI bead cleanup (Beckman). Libraries were sequenced with standard Illumina read 1 primer and custom read 2 and i7 index primers. Control library generated from Kineococcus radiotolerans was spiked at 20% to enhance library complexity.

value: whole testis

tag: genotype

value: Dnmt3c rahu/rahu

value: C57BL/6J & FVB/NJ (mixed); derived from ENU mutagenized line

value: 12 days post partum

tag: littermate

value: litter 1


title: 1.5M_wt_1


title: VapC28


title: Dnmt3c rahu/rahu mouse u

value: litter 2


title: P5_wt_1


title: untagged control

value: pMEND-HTF


title: 1.5M_KO_3


title: SNF_1

description: SN


title: Methylated DNA-Seq MRL

status: Public on Aug 13 2017

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

data_processing:
MBD-seq: Base-calling performed using HiSeq Control Software (HCS) v2.0.12, Real Time Analysis (RTA) v1.17.21.3, CASAVA v1.8.2
MBD-seq: Mapping to Mus musculus genome sequence, December. 2011 (GRCm38/mm10) assebly, by Bowtie[1] (version 1.0.0)
MBD-seq: Enrich regions were detected using MACS[2] (version 1.4.2) in Methylated DNA-Seq B6 (DJ0091_A01_annotation.xlsx) comparing with Methylated DNA-Seq MRL as control.
MBD-seq: Enrich regions were detected using MACS[2] (version 1.4.2) in Methylated DNA-Seq MRL (DJ0091_A02_annotation.xlsx) comparing with Methylated DNA-Seq B6 as control.
RNA-seq: Illumina Casava1.8.1 software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.8.
RNA-seq: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.

source_name: Spleen CD4 plus T cells

extract_protocol:
MBD-seq: CD4 plus T cells were negatibely depleted from spleenocyte using magnetic beads, and DNA was harvested using Qiazol reagent. EpiXplore Methylated DNA Enrichment Kit was used for enriching methylated DNA fragments from the whole genome.  Prewash TALON® Magnetic Beads and couple MBD2 protein to magnetic beads. Bind methylated DNA to MBD2 protein/magnetic bead complexes and remove non- and hypomethylated DNA and elute & purify methylated DNA.
RNA-seq: CD4 plus T cells were negatibely depleted from spleenocyte using magnetic beads, and RNA was harvested using Qiazol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
MBD-seq: Total DNA was purified from CD4+ T cells of MRL lupus-prone mice and B6 control mice using an RNeasy Mini Kit (Qiagen). The quality of the total DNA was confirmed by fluorometer using an Qubit® dsDNA BR Assay Kits (Invitrogen). EpiXplore Methylated DNA Enrichment Kit (Clontech) was used for enriching methylated DNA fragments from the total DNA.  First, we prewash TALON® Magnetic Beads and couple MBD2 protein to magnetic beads and bind methylated DNA to MBD2 protein/magnetic bead complexes and remove non- and hypomethylated DNA and elute and purify methylated DNA. Illumina TruSeq ChIP Sample Prep Kit was used for the construction of sequencing libraries. Sequencing was performed using Illumina HiSeq.
RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: spleen

value: Spleen CD4 plus T cells

value: 16 week

tag: gender

value: female


title: VapC29


title: mRNA seq B6-Im830_reanalysis

tag: strain


title: Methylated DNA-Seq B6


title: PMel

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina bcl2fastq version 2.17.1.14 software to generate fastq files.
Tophat software version 2.0.10 was used to align reads to mouse mm10 reference genome
Read counts per exon were calculated over all 628,052 exons in mm10 ensemble GTF (UCSC, December 2011), using bedtools coverage command (version 2.16.2).
Exons annotated as protein coding, pseudogene or lincRNA (n=459,556) were selected for further analysis. Exon counts were normalized by the exon length in Kbp and by million number of aligned reads per sample, to give RPKM values.
Exons with zero counts in all samples were filtered out
Genome_build: mm10

source_name: Primary mouse melaocytes

growth_protocol: Wild type and Mitf knock-in MEFs were plated in a 10cm tissue culture plate, and grown in DMEM (Gibco 41965-039) supplemented with 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 10% FBS (Biological Industries). Primary mouse melanocytes were plated in a 10cm tissue culture plate, and grown in Ham's F10 medium supplemented with 50 ng/ml TPA (Sigma Catalogue No. P-8139) 1% L-Glutamine, 1% Non-essential amino acids, 1% penicillin/streptomycin and 5% FBS.

extract_protocol:
Total RNA was isolated from indicated cell lines, and extracted from Trizol pellets by Direct-zol RNA MiniPrep kit (Zymo) according to manufacturer’s manual.
RNA was extracted from Trizol pellets, and utilized for RNA-Seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

treatment_protocol: Dox was supplamented to the growth media of Mitf knock-in MEFs for the iduction of Mitf for 6 days

value: mouse wild type melanocytes

tag: passages


title: WT Mef

source_name: wild-type mouse embryonic fibroblasts

value: mouse wild type embryonic fibroblasts


title: UM-UC-3_si-PTBP1

city: Guangzhou

first: Xu

last: Chen

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

data_processing:
Base-calling: CASAVA1.8
Data filtering : in house
Read alignment: tophat2.0.12
transcript assemble: cufflink2.2.1
Genome_build: genome build: hg19
Supplementary_files_format_and_content: txt files include normalize values for each Sample

source_name: bladder cancer cell line UM-UC-3

growth_protocol: UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Shanghai ExCell Biology, China) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life technologies) following manufacturer's instructions.

tag: sirna

value: Two different siRNAs targeting PTBP1 were transfected in the cell

tag: sirna sequence

tag: inhibition rate (relative to control sirna) detected by qpcr


title: mRNA seq MRL-Im831_reanalysis

tag: age


title: 1.5M_wt_2

value: epidermal cells

tag: genotype/variation


title: Dnmt3c rahu/rahu mouse v

tag: tissue


title: 72h incubation in the presence of As(III) R3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
cleaning with clean_ngs (v 0.7)
alignment with tophat (v 1.3.2)
counting with htseq-count (v 0.1)
Genome_build: Thiomonas sp. CB2
Supplementary_files_format_and_content: Htseq-count file; txt file with name of gene and corresponding counting

organism: Thiomonas sp. CB2

source_name: Bacterial cells

growth_protocol: biofilms were grown in 6-well plates, 8 plates under each condition, without shaking. After a 24h-hours period of incubation at 30 °C, the mobile phase was gently removed, fresh medium was added and further incubated.

extract_protocol:
enriched mRNA was obtained from total RNA using the rRNA capture hybridization approach from the RiboZero kit
Supernatant was gently removed. 1.5 mL of physiological water at 4°C was added. biofilms were scraped on ice using a cell scraper (Biologix), centrifuged at 8000 x g for 15 min at 4°C. Cell lysis was obtained by shaking the tubes using a Retsch disruptor during three 30-second cycles and centrifuging them at 16 000 x g for 5 minutes at 4°C. The aqueous phases were then transferred to fresh tubes and treated with Trizol
Directional libraries were prepared using the TruSeq Stranded total RNA Sample preparation kit following the manufacturer’s instructions (Illumina). The libraries were quantified by fluorimetric measurements with the Qubit® dsDNA HS Assay Kit (ThermoFisher). 51-bp Single Read sequences were generated on the Hiseq2000 sequencer according to manufacturer’s instructions (Illumina). Sequences were demultiplexed using the Illumina pipeline (Gerald, included in CASAVA version 1.7) giving FASTQ formatted reads.

treatment_protocol: cells were incubated in m126 medium, in the absence or in the presence of 5.33 mM As(III)

tag: biofilm incubation time

tag: treatment

value: incubated in the presence of 5.33 mM As(III)


title: UM-UC-3_si-hnRNPK

value: Two different siRNAs targeting hnRNPK were transfected in the cell


title: 72h incubation in the presence of As(III) R2


title: 48h incubation in the presence of As(III) R3


title: Dnmt3c+/+ mouse v′

value: Dnmt3c +/+


title: 48h incubation in the presence of As(III) R2


title: Mef (-) Dox

source_name: Mitf knock-in mouse embryonic fibroblasts


title: 48h incubation in the presence of As(III) R1


title: 24h incubation in the presence of As(III) R3


title: P5_wt_3

tag: cell markers

tag: developmental stage

value: wildtype


title: Dnmt3c+/+ mouse w′

value: whole testis


title: 72h incubation in the absence of As(III) R2

value: no


title: 48h incubation in the absence of As(III) R3


title: 72h incubation in the absence of As(III) R1


title: 48h incubation in the absence of As(III) R1


title: tg1

city: Beijing

first: Jing-Wei

last: Xiong

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: Institute of Molecular Medicine, Peking University

description: hearts were treated with heat-shock daily from 5 to 14 days post amputation

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Adapter sequence and low-quality sequences were trimmed.
For RNA seq data, TopHat (version 2.0.10) were used for sequence alignment to zebrafish transcriptome (danRer7). Gene expression level (FPKM) were calculated using Cufflinks (version 2.1.1).
Genome_build: danRer7
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Danio rerio

source_name: heart

extract_protocol:
Total RNA was isolated using an RNeasy Mini kit (QIAGEN)
After confirming the quality and integrity of RNA on agarose gels, ~1 μg of total RNA  was used to construct the RNA-Seq libraries by applying a TruSeq RNA Sample Prep kit (Illumina, San Diego, CA)

treatment_protocol: Adult hearts were were amputated. At 5 days post amputation, zebrafish were treated with heat-shock daily untill 14 days post amputation

value: heart

value: 3-6 mothes


title: 24h incubation in the absence of As(III) R2


title: VapC11

tag: construct


title: LeLab_BglII_HiC_ML2413_plus_xylose_1hr_rep2

status: Public on Aug 12 2017

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

data_processing:
For Hi-C, Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Caulobacter CB15N (NA1000) independently by Bowtie version 0.12.7 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, the same mapping procedure was used as for Hi-C but coverage was computed using BEDTools instead (Quinlan and Hall, 2010). Detailed protocols are listed in the Supplementary Materials and Methods.
The two resulting SAM files were then merged together. Unaligned reads were discarded.
The Caulobacter CB15N (NA1000) genome was then divided into restriction fragments (700 BglII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
The genome of Caulobacter CB15N was then divided into bins of 20 kb (for BglII Hi-C) and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID:    22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). Ten iterative normalization rounds were performed. Subsequent analysis and visualisation was done using Perl and R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides

growth_protocol: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290). After synchronization, swarmer cells were fixed formadehyde for chromosome conformation capture and Hi-C analysis. For antibiotic treatments, swarmer cells were incubated with 25 ug/mL rifampicin (final concentration) for 30 minutes before fixing with formadehyde.

extract_protocol:
Hi-C experiments were performed using BglII according to previous publications (Umbarger MA. 2012. Chromosome conformation capture assays in bacteria. PMID: 22776362 and Lieberman-Aiden, E. et al., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. PMID: 19815776). Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2000/Hiseq 2500 sequencing platform

treatment_protocol:
Xylose (final concentration of 0.3%) was added to an exponentially-growing Caulobacter crescentus culture for 1hr. After that, formadehyde is added to a final concentration of 1%.
None

value: 1hr after xylose addition

tag: restriction enzyme

value: BglII


title: LeLab_BglII_HiC_ML2414_plus_xylose_1hr_rep2


title: 247: Subiculum (Sub)

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ and FASTX-toolkit were used to examine the sequencing quality and trim reads. Paired-end reads for the human data were aligned to the HG19 and GENCODE 2014 version of the human genome and annotation using TopHat, using the comprehensive gene annotation on the reference chromosome only.
Reads were counted using HTSeq. A gene was considered the union of all its exons in any known isoforms. Any reads that fell in multiple genes were excluded from the analysis. Threshold for filtering out low expressed genes was set to >5 reads in at least 80% of the samples.
Differentially expressed genes (DEGs) between groups of samples were determined using linear models implemented in the ‘limma’ package of Bioconductor.
Genome_build: hg19
Supplementary_files_format_and_content: text file of fpkm matrix

source_name: postmortem brain

extract_protocol:
RNA was extracted using Trizol Reagents from human postmortem flash-frozen samples. 2.5ug of RNA for human samples was used, every samples got spike-in ERCC control 1. Libraries were created using the Epicenter (Illumina) Gold Kit with ribosomal depletion
Libraries for RNAseq were created using the Epicenter (Illumina) Gold Kit with a ribosomal depletion.

value: Subiculum (Sub)

value: Male

tag: Cause of death

value: Accident

tag: pmi

tag: ph

tag: phenotype

value: CTRL

tag: alcool

tag: drugs

tag: drug type

tag: medication

tag: medication type

tag: smoking

tag: rin


title: 246: Subiculum (Sub)

tag: tissue

tag: gender

value: Female

value: Suicide

tag: age

value: MDD

value: yes

value: AD


title: P5_wt_2

tag: cell type

value: epidermal cells

tag: cell markers

tag: developmental stage

tag: genotype/variation


title: 235: Subiculum (Sub)

tag: Cause of death

tag: pmi

value: yes (heavy)


title: 222: Subiculum (Sub)

tag: ph

tag: phenotype

value: No

value: Lithium

value: yes(moderate)


title: Mef (+) Dox

value: Mitf knock-in mouse embryonic fibroblasts

tag: passages


title: Dnmt3c+/+ mouse u′

value: whole testis

tag: genotype

value: Dnmt3c +/+

tag: strain

value: C57BL/6J & FVB/NJ (mixed); derived from ENU mutagenized line

value: 12 days post partum

tag: littermate

value: litter 2


title: UM-UC-3_si-lncRNA-LBCS

tag: sirna

value: Two different siRNAs targeting lncRNA-LBCS were transfected in the cell

tag: sirna sequence

tag: inhibition rate (relative to control sirna) detected by qpcr


title: UM-UC-3_Control

value: Negetive control

value: UUCUCCGAACGUGUCACGUTT


title: 199: Subiculum (Sub)

tag: tissue

value: Subiculum (Sub)

tag: gender

value: Male

value: Suicide

value: CTRL

tag: alcool

tag: drugs

tag: drug type

tag: medication

tag: medication type

tag: smoking

value: no

tag: rin


title: 72h incubation in the presence of As(III) R1

tag: biofilm incubation time

tag: treatment

value: incubated in the presence of 5.33 mM As(III)


title: 24h incubation in the presence of As(III) R1


title: 183: Subiculum (Sub)

tag: Cause of death

tag: age

tag: pmi

tag: ph

tag: phenotype

value: MDD

value: yes

value: AD


title: 24h incubation in the presence of As(III) R2


title: 72h incubation in the absence of As(III) R3


title: 48h incubation in the absence of As(III) R2


title: tg2

tag: genotype/variation

value: heart

tag: developmental stage

value: 3-6 mothes


title: 120: Subiculum (Sub)

tag: tissue

tag: gender

value: yes (heavy)


title: 124: Subiculum (Sub)

tag: alcool

tag: drugs


title: 24h incubation in the absence of As(III) R3


title: sib2

value: wild-type


title: LeLab_BglII_HiC_TLS1608_swarmer_rep4

treatment_protocol:
Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE and fixed immediately by 1% formadehyde.
None

tag: strain

value: swarmer cells (0 min after synchronization)

tag: restriction enzyme

value: BglII


title: 150: Subiculum (Sub)

value: Natural

tag: drug type

tag: medication

tag: medication type

tag: smoking


title: 24h incubation in the absence of As(III) R1

tag: biofilm incubation time

tag: treatment


title: LeLab_BglII_HiC_ML2414_plus_xylose_1hr_rep3

value: 1hr after xylose addition


title: LeLab_BglII_HiC_ML2413_plus_xylose_1hr_rep3


title: 111: Subiculum (Sub)

value: Subiculum (Sub)

value: Female

tag: Cause of death

tag: age

tag: pmi

tag: rin


title: 249: Subiculum (Sub)

value: Suicide

tag: ph

tag: phenotype


title: 105: Subiculum (Sub)

tag: tissue

tag: gender

value: Male


title: 93: Subiculum (Sub)

tag: alcool

tag: drugs

value: no


title: 238: Subiculum (Sub)

value: CTRL


title: 242: Subiculum (Sub)


title: 236: Subiculum (Sub)


title: sib1

tag: genotype/variation

tag: developmental stage


title: LeLab_BglII_HiC_TLS1608_swarmer_rep3

tag: strain

tag: restriction enzyme


title: 67: Subiculum (Sub)

value: MDD

tag: drug type

tag: medication

tag: medication type

value: anticonvulsivant

tag: smoking


title: 57: Subiculum (Sub)

tag: Cause of death

value: Accident

tag: age

value: yes


title: 205: Subiculum (Sub)

tag: pmi

tag: rin


title: 201: Subiculum (Sub)

tag: ph

tag: phenotype

value: AD


title: 198: Subiculum (Sub)

tag: tissue

tag: gender

value: yes (heavy)


title: 189: Subiculum (Sub)

tag: alcool

tag: drugs


title: 23: Subiculum (Sub)


title: 20: Subiculum (Sub)


title: 153: Subiculum (Sub)

value: No

value: Lithium


title: 32: Subiculum (Sub)


title: 129: Subiculum (Sub)


title: 128: Subiculum (Sub)


title: 117: Subiculum (Sub)


title: 247: Nucleus Accumbens (Nac)

value: Nucleus Accumbens (Nac)


title: 246: Nucleus Accumbens (Nac)


title: 114: Subiculum (Sub)

value: AP


title: 238: Nucleus Accumbens (Nac)


title: 84: Subiculum (Sub)


title: 113: Subiculum (Sub)


title: 74: Subiculum (Sub)


title: 69: Subiculum (Sub)


title: 72: Subiculum (Sub)


title: 61: Subiculum (Sub)


title: 235: Nucleus Accumbens (Nac)


title: 56: Subiculum (Sub)


title: 51: Subiculum (Sub)


title: 212: Nucleus Accumbens (Nac)

value: Natural


title: 45: Subiculum (Sub)

value: Subiculum (Sub)


title: 43: Subiculum (Sub)

value: cannabis


title: 40: Subiculum (Sub)

value: Suicide


title: 17: Subiculum (Sub)

value: Male


title: 242: Nucleus Accumbens (Nac)

value: Female


title: 189: Nucleus Accumbens (Nac)

value: CTRL

value: no


title: 198: Nucleus Accumbens (Nac)

value: MDD


title: 14: Subiculum (Sub)


title: 199: Nucleus Accumbens (Nac)


title: 236: Nucleus Accumbens (Nac)


title: 153: Nucleus Accumbens (Nac)


title: 162: Nucleus Accumbens (Nac)

value: Accident


title: 222: Nucleus Accumbens (Nac)

value: yes

value: yes(moderate)


title: 205: Nucleus Accumbens (Nac)

value: yes (heavy)


title: 129: Nucleus Accumbens (Nac)

value: AD


title: 150: Nucleus Accumbens (Nac)


title: 124: Nucleus Accumbens (Nac)


title: 128: Nucleus Accumbens (Nac)


title: 111: Nucleus Accumbens (Nac)


title: 249: Nucleus Accumbens (Nac)


title: 93: Nucleus Accumbens (Nac)


title: 201: Nucleus Accumbens (Nac)


title: 120: Nucleus Accumbens (Nac)


title: 114: Nucleus Accumbens (Nac)


title: 117: Nucleus Accumbens (Nac)

value: No


title: 183: Nucleus Accumbens (Nac)

value: Nucleus Accumbens (Nac)


title: 113: Nucleus Accumbens (Nac)


title: 68: Nucleus Accumbens (Nac)


title: 69: Nucleus Accumbens (Nac)

value: AP


title: 105: Nucleus Accumbens (Nac)


title: 74: Nucleus Accumbens (Nac)


title: 63: Nucleus Accumbens (Nac)


title: 61: Nucleus Accumbens (Nac)


title: 67: Nucleus Accumbens (Nac)

value: anticonvulsivant


title: 56: Nucleus Accumbens (Nac)


title: 51: Nucleus Accumbens (Nac)


title: 40: Nucleus Accumbens (Nac)


title: 72: Nucleus Accumbens (Nac)


title: 43: Nucleus Accumbens (Nac)


title: 28: Nucleus Accumbens (Nac)

value: Natural


title: 32: Nucleus Accumbens (Nac)


title: 45: Nucleus Accumbens (Nac)


title: 23: Nucleus Accumbens (Nac)


title: 20: Nucleus Accumbens (Nac)


title: 249: Anterior Insula (aINS)

value: Anterior Insula (aINS)


title: 84: Nucleus Accumbens (Nac)

value: Suicide


title: 246: Anterior Insula (aINS)


title: 247: Anterior Insula (aINS)

value: Male


title: 17: Nucleus Accumbens (Nac)


title: 242: Anterior Insula (aINS)

value: Female


title: 235: Anterior Insula (aINS)


title: 57: Nucleus Accumbens (Nac)

value: CTRL


title: 222: Anterior Insula (aINS)

value: no

value: Lithium


title: 205: Anterior Insula (aINS)

value: MDD


title: 199: Anterior Insula (aINS)


title: 198: Anterior Insula (aINS)


title: 183: Anterior Insula (aINS)

value: yes


title: 153: Anterior Insula (aINS)


title: 162: Anterior Insula (aINS)

value: Accident


title: 128: Anterior Insula (aINS)


title: 129: Anterior Insula (aINS)

value: yes (heavy)


title: 150: Anterior Insula (aINS)


title: 120: Anterior Insula (aINS)


title: 124: Anterior Insula (aINS)


title: 14: Nucleus Accumbens (Nac)


title: 117: Anterior Insula (aINS)

value: AD


title: 114: Anterior Insula (aINS)


title: 238: Anterior Insula (aINS)


title: 113: Anterior Insula (aINS)


title: 236: Anterior Insula (aINS)


title: 93: Anterior Insula (aINS)


title: 84: Anterior Insula (aINS)


title: 111: Anterior Insula (aINS)


title: 105: Anterior Insula (aINS)


title: 69: Anterior Insula (aINS)


title: 74: Anterior Insula (aINS)


title: 68: Anterior Insula (aINS)


title: 212: Anterior Insula (aINS)


title: 67: Anterior Insula (aINS)


title: 63: Anterior Insula (aINS)


title: 201: Anterior Insula (aINS)


title: 61: Anterior Insula (aINS)


title: 189: Anterior Insula (aINS)


title: 56: Anterior Insula (aINS)


title: 45: Anterior Insula (aINS)


title: 51: Anterior Insula (aINS)


title: 28: Anterior Insula (aINS)


title: 32: Anterior Insula (aINS)


title: 20: Anterior Insula (aINS)


title: 23: Anterior Insula (aINS)


title: 17: Anterior Insula (aINS)


title: 14: Anterior Insula (aINS)


title: 246: Cingulate gyrus 25 (Cg25)

value: Cingulate gyrus 25 (Cg25)


title: 249: Cingulate gyrus 25 (Cg25)


title: 72: Anterior Insula (aINS)

value: No


title: 247: Cingulate gyrus 25 (Cg25)


title: 236: Cingulate gyrus 25 (Cg25)


title: 242: Cingulate gyrus 25 (Cg25)


title: 238: Cingulate gyrus 25 (Cg25)


title: 205: Cingulate gyrus 25 (Cg25)


title: 235: Cingulate gyrus 25 (Cg25)


title: 198: Cingulate gyrus 25 (Cg25)


title: 189: Cingulate gyrus 25 (Cg25)


title: 201: Cingulate gyrus 25 (Cg25)


title: 43: Anterior Insula (aINS)

value: cannabis


title: 199: Cingulate gyrus 25 (Cg25)


title: 120: Cingulate gyrus 25 (Cg25)


title: 124: Cingulate gyrus 25 (Cg25)


title: 57: Anterior Insula (aINS)


title: 114: Cingulate gyrus 25 (Cg25)

value: AP


title: 153: Cingulate gyrus 25 (Cg25)


title: 212: Cingulate gyrus 25 (Cg25)

value: Natural


title: 222: Cingulate gyrus 25 (Cg25)

value: yes(moderate)


title: 150: Cingulate gyrus 25 (Cg25)


title: 129: Cingulate gyrus 25 (Cg25)

value: Suicide


title: 242: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 17: Cingulate gyrus 25 (Cg25)

value: Male


title: 14: Cingulate gyrus 25 (Cg25)


title: 40: Anterior Insula (aINS)

value: Anterior Insula (aINS)


title: 117: Cingulate gyrus 25 (Cg25)

value: Female


title: 128: Cingulate gyrus 25 (Cg25)

value: CTRL

value: no


title: 113: Cingulate gyrus 25 (Cg25)

value: MDD


title: 222: Dorsolateral prefrontal cortex (dlPFC; BA8/9)

value: yes

value: Lithium


title: 23: Cingulate gyrus 25 (Cg25)


title: 111: Cingulate gyrus 25 (Cg25)


title: 20: Cingulate gyrus 25 (Cg25)

value: Accident

value: yes (heavy)


title: 201: Dorsolateral prefrontal cortex (dlPFC; BA8/9)

value: AD


title: 199: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 212: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 249: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 247: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 162: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 246: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 236: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 235: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 205: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 198: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 238: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 153: Dorsolateral prefrontal cortex (dlPFC; BA8/9)

value: No


title: 129: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 150: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 105: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 93: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 114: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 124: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 120: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 113: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 72: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 183: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 189: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 84: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 69: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 63: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 74: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 68: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 61: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 56: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 67: Dorsolateral prefrontal cortex (dlPFC; BA8/9)

value: anticonvulsivant


title: 128: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 57: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 51: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 40: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 43: Dorsolateral prefrontal cortex (dlPFC; BA8/9)

value: cannabis


title: 32: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 45: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 111: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 28: Dorsolateral prefrontal cortex (dlPFC; BA8/9)

value: Natural


title: 17: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 20: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 23: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 117: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 14: Dorsolateral prefrontal cortex (dlPFC; BA8/9)


title: 242: Orbitofrontal (OFC; BA11)

value: Orbitofrontal (OFC; BA11)


title: 249: Orbitofrontal (OFC; BA11)

value: Suicide


title: 246: Orbitofrontal (OFC; BA11)


title: 247: Orbitofrontal (OFC; BA11)

value: Male


title: 236: Orbitofrontal (OFC; BA11)


title: 235: Orbitofrontal (OFC; BA11)


title: 238: Orbitofrontal (OFC; BA11)