title: S.cerevisiae EC1118 in FSJ, biological rep1

status: Public on Jul 31 2019

type: RNA

city: Sassari

first: Giacomo

last: Zara

address: v.le Italia, 39

department: Department of Agraria

country: Italy

institute: University of Sassari

scan_protocol: As described by the manufacturer (Eukaryotic Arrays GeneChip Expression Analysis and Technical Manual, Affymetrix, Santa Clara, CA), using an Agilent G2500A GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast cells after 60h fermentation in presence of lipid supplements

label_protocol: Following ethanol precipitation, cRNA was prepared by in vitro transcription of the cDNA using the Enzo BioArray™ HighYield™ RNA Transcript Labeling kit (Farmingdale, NY, USA). The cRNA was purified with RNeasy spin columns (Qiagen, Mississauga, ON, Canada), followed by ethanol precipitation. Then, 20 μg of cRNA (0.5 μg μl-1) was fragmented by incubating at 94°C for 35 min in fragmentation buffer (40 mM Tris–acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate). Further details of procedures can be found in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Extraction of total RNA was done according to (Causton et al., Mol. Biol. Cell 12, 323–337, 2001). Double-stranded cDNA was purified using phenol/chloroform/isoamyl alcohol (25:24:1) saturated with 10 mM Tris–HCl, pH 8.0, 1 mM EDTA (Ambion, Austin, TX, USA) and a Phase Lock Gel prepared according to the manufacturer's instructions (Eppendorf, Hamburg, Germany).

tag: strain

tag: media

value: FSJ


title: si-NC-2

type: SRA

city: Wuhan

first: Libin

last: Yan

state: Hubei

address: No.1095, Jiefang Avenue

department: Urology

country: China

institute: Tongji Hospital,Tongji Medical College, Huazhong University of Science Technology

library_source: transcriptomic

data_processing:
counts
FPKM
Supplementary_files_format_and_content: counts and FPKM

organism: Homo sapiens

extract_protocol: none provided by submitter

tag: cell type

value: clear cell renal cell carcinoma cell line


title: si-NC-1


title: si-NC-3


title: siSETD2-3


title: siSETD2-1


title: S.cerevisiae EC1118 in FSJ, biological rep3

hyb_protocol: 20 μg of cRNA (0.5 μg μl-1) was fragmented by incubating at 94°C for 35 min in fragmentation buffer (40 mM Tris–acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate).


title: S.cerevisiae EC1118 in FSJ, biological rep2


title: S.cerevisiae EC1118 in SJ, biological rep3

source_name: Yeast cells after 60h fermentation in absence of lipid supplements

value: SJ


title: MCF7_polyAenrichedRNAseq_LucKD_rep1

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

description: polyA enriched RNA

data_processing:
FastQC
Two biological replicates from total input RNA were used to generate RNA-seq libraries to serve as a normalization control for the RIP-seq datasets.   The libraries were subjected to QC analyses and sequenced using an Illumina HiSeq instrument.
Alignment to the human reference genome (hg19) and one complete copy of an rDNA repeat (GenBank ID: U13369.1) using the BWA aligner
Genome_build: hg19

molecule: polyA RNA

growth_protocol: MCF-7 cells were purchased from the American Type Culture Collection (ATCC), were maintained in Minimum Essential Medium (MEM) Eagle with Hank’s salts (Sigma, M1018) supplemented with  5% calf serum and 1% penicillin/streptomycin.

extract_protocol:
MCF-7 cells were grown to ~approximately 80% confluency in two 150 mm diameter dishes for each immunoprecipitation, harvested, and then collected by centrifugation. Ten percent of the pre-cleared nuclear extract was saved as input to generate RNA-seq libraries to normalize. Total input RNA were eluted by the addition of Trizol reagent (Sigma)
Two biological replicates from total input RNA were used to generate RNA-seq libraries to serve as a normalization control for the RIP-seq datasets.   The libraries were subjected to QC analyses and sequenced using an Illumina HiSeq instrument.
We performed Total RNA-seq for RIP-seq input. polyA-enriched, polyA-depleted RNA-seq to check the expression of snoRNA and their host genes and LucKD, DDX21 KD polyA enriched RNAseq to check host gene expression upon DDX21 KD.

tag: treatment

value: Doxycycline, 1mg/ml


title: MCF7_polyAenrichedRNAseq_DDX21KD_rep2

description: polyA enriched RNA


title: MCF7_polyAenrichedRNAseq_LucKD_rep2

description: polyA enriched RNA


title: S.cerevisiae M25 in FSJ, biological rep3


title: S.cerevisiae EC1118 in SJ, biological rep1


title: S.cerevisiae EC1118 in SJ, biological rep2


title: S.cerevisiae M25 in SJ, biological rep1


title: HDF_FGF2_3_days_rep1

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Single read was done on Illumina HiSeq 2000 sequencer at the Genomic Technologies Facility of the University of Lausanne (Lausanne, Switzerland). Reads were trimmed by using Trimmomatic (v0.22), followed by mapping to human hg19 reference genome using TopHat2 (v2.0.8b). Gene expression levels were then evaluated using HTSeq package (release 0.5.4p1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM

source_name: Dermal fibroblasts

growth_protocol: Two strains of primary human fibroblasts (GP-HDF, KL-HDF) derived from abdominoplasty samples of adult patients cultured in complete medium (DMEM enriched in Glutamine, Pyruvate and high Glucose level supplemented with 10% FBS and 1% Antibiotic Cocktail).

extract_protocol:
RNA was extracted from HDFs through Direct-zol RNA MiniPrep kit (Zymo Research) with on-column DNase treatment and its quality was verified by a Bioanalyzer (Agilent Technologies).
500 ng of total RNA per sample was used for library preparation using a NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: HDFs were treated with 10 ng/mL FGF2 adding the growth factors in complete DMEM once and collecting RNA samples 72 hours after treatment.

tag: tissue

value: Dermal fibroblasts

value: FGF-2 3 days


title: HDF_FGF2_3_days_rep2


title: HDF_NaAc_3_days_rep2

value: NaAc 3 days


title: S.cerevisiae M25 in FSJ, biological rep1


title: siSETD2-2


title: S.cerevisiae M25 in FSJ, biological rep2


title: S.cerevisiae M25 in SJ, biological rep2


title: MCF7_polyAenriched_RNAseq_replicate2

description: polyA enriched

data_processing:
FastQC
The raw reads were aligned to the human reference genome (hg19/GRCh37) using default parameters in Tophat (v2.0.12)
Genome_build: hg19

source_name: MCF7 polyAenriched

extract_protocol:
MCF-7 cells were grown to ~approximately 80% confluency in two 150 mm diameter dishes for each immunoprecipitation, harvested, and then collected by centrifugation. Ten percent of the pre-cleared nuclear extract was saved as input to generate RNA-seq libraries to normalize. Total input RNA were eluted by the addition of Trizol reagent (Sigma)
Two biological replicates from total input RNA were used to generate RNA-seq libraries to serve as a normalization control for the RIP-seq datasets.   The libraries were subjected to QC analyses and sequenced using an Illumina HiSeq instrument to a depth of x mapped reads.
Total RNA-seq, polyA-enriched RNA-seq, polyA-depleted RNA-seq


title: S.cerevisiae M25 in SJ, biological rep3


title: MCF7_polyAdepleted_RNAseq_replicate2

description: polyA depleted

source_name: MCF7 polyAdepleted


title: MCF7_polyAdepleted_RNAseq_replicate1

description: polyA depleted


title: MCF7_input_RNAseq_replicate1

source_name: MCF7 input


title: MCF7_polyAenriched_RNAseq_replicate1

description: polyA enriched


title: MCF7_RIPseq_Preimmnune_IP_rep2

description: MCF7_RIPseq_Preimmnune_IP_plusStrand.bw,MCF7_RIPseq_Preimmnune_IP_minusStrand.bw

data_processing:
FastQC
RIP-seq reads were aligned to human reference genome (hg19/GRCh37), including autosomes, X chromosome, one complete copy of an rDNA repeat (GenBank ID: U13369.1), and the merged mRNA and lncRNA gene annotations described above. The reads were aligned using the STAR (v2.4.2a) software package (Dobin et al. 2013) using the following parameters: (1) a maximum of 20 multiple alignments (–outFilterMultimapNmax 20); (2) an eight nucleotide overhang was allowed for an unannotated junction (–alignSJoverhangMin 8); (3) a one nucleotide overhang was allowed for an annotated junction (–alignSJDBoverhangMin 1); (4) 20 nucleotides for the minimum intron length (– alignIntronMin 20); and (5) 100,000 nucleotides for maximum intron length (–alignIntronMax 20).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, signal tracks

source_name: Preimmnune IP

extract_protocol:
MCF-7 cells were grown to ~approximately 80% confluency in two 150 mm diameter dishes for each immunoprecipitation, harvested, and then collected by centrifugation. The PARP-1-bound RNAs were eluted from the agarose resin by the addition of Trizol reagent (Sigma)
Two biological replicates of immunoprecipitated PARP-1-bound RNA were used to generate strand-specific RIP-seq libraries as described previously (Sun et al., 2015). The libraries were subjected to QC analyses and sequenced using an Illumina HiSeq instrument to a depth of x mapped reads.


title: MCF7_polyAenrichedRNAseq_DDX21KD_rep1

description: polyA enriched RNA


title: MCF7_RIPseq_PARP1_IP_rep2

description: MCF7_RIPseq_PARP1_IP_plusStrand.bw,MCF7_RIPseq_PARP1_IP_minusStrand.bw

source_name: PARP1 IP


title: MCF7_RIPseq_Preimmnune_IP_rep1


title: MCF7_RIPseq_PARP1_IP_rep1


title: H1.TB.ADS409

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

description:
TB.pp.all.bz2
TB.po.all.bz2

library_source: genomic

data_processing:
Read pairs from Promoter Capture Hi-C library were independently mapped to human genome hg19 using BWA-mem and manually paired with in house script.
Unmapped, non-uniquely mapped, and PCR duplicates were removed.
Trans-chromosomal read pairs and putative self-ligated products (<15kb read pairs) were removed.
Off-target reads were removed when both read pairs did not match to capture probe sequences.
Genome_build: Hg19
Supplementary_files_format_and_content: *.po and *.pp provide interaction frequencies for promoter-promoter interactions or promoter-other interactions, respectively.  We combined multiple donors or replicates according to cell/tissue types.

molecule: genomic DNA

source_name: Human Trophoblast

extract_protocol:
Promoter Capture Hi-C library was constructed by performing a target enrichment protocol (enriching target promoter-centered proximity ligation fragments from Hi-C library using capture RNA probes). Briefly, we incubated 500ng Hi-C library 24h at 65 °C within a humidified hybridization chamber with 2.5ug human Cot-1 DNA (Life Technologies), 2.5ug salmon sperm DNA (Life Technologies), and p5/p7 blocking oligos with hybridization buffer mix (10X SSPE, 10mM EDTA, 10X Denhardts solution, and 0.26% SDS) and 500ng RNA probes. RNA:DNA hybrids were enriched using 50ul T1 streptavidin beads (Invitrogen) with 30min incubation at RT. Next, bead-bound hybrids were washed by a 15min incubation in wash buffer1 (1X SSC and 0.1% SDS) with frequent vortexing, and then washed three times with 500ul of pre-warmed (65 °C) wash buffer2 (0.1X SSC and 0.1% SDS), and resuspended in nuclease-free water. The resulting capture Hi-C libraries were amplified while bound to the T1 beads, and purified using AMPure XP beads, followed by sequencing.
Promoter Capture Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq2500 or HiSeq4000 protocols with minor modifications (Illumina, San Diego, CA).
Capture Hi-C

value: Trophoblast


title: STL001.TH1.ADS424

description:
TH.pp.all.bz2
TH.po.all.bz2

source_name: Human Thymus

value: Thymus


title: STL001.TH1.ADS417

description:
TH.pp.all.bz2
TH.po.all.bz2


title: STL003.SX3.ADS353

description:
SX.pp.all.bz2
SX.po.all.bz2

source_name: Human Spleen

value: Spleen


title: STL001.SX1.ADS296

description:
SX.pp.all.bz2
SX.po.all.bz2


title: STL001.SX1.ADS260

description:
SX.pp.all.bz2
SX.po.all.bz2


title: STL001.SX1.ADS193

description:
SX.pp.all.bz2
SX.po.all.bz2


title: STL001.SX1.ADS272

description:
SX.pp.all.bz2
SX.po.all.bz2


title: STL002.SB2.ADS162

description:
SB.pp.all.bz2
SB.po.all.bz2

source_name: Human Small Bowel

value: Small Bowel


title: STL001.SB1.ADS468

description:
SB.pp.all.bz2
SB.po.all.bz2


title: MCF7_input_RNAseq_replicate2


title: STL002.SB2.ADS173

description:
SB.pp.all.bz2
SB.po.all.bz2


title: STL001.TH1.ADS411

description:
TH.pp.all.bz2
TH.po.all.bz2


title: STL001.SG1.ADS337

description:
SG.pp.all.bz2
SG.po.all.bz2

source_name: Human Sigmoid Colon

value: Sigmoid Colon


title: STL001.SG1.ADS358

description:
SG.pp.all.bz2
SG.po.all.bz2


title: STL001.SG1.ADS325

description:
SG.pp.all.bz2
SG.po.all.bz2


title: STL003.RV3.ADS170

description:
RV.pp.all.bz2
RV.po.all.bz2

source_name: Human Right Ventricle

value: Right Ventricle


title: STL001.RV1.ADS472

description:
RV.pp.all.bz2
RV.po.all.bz2


title: STL001.RV1.ADS413

description:
RV.pp.all.bz2
RV.po.all.bz2


title: STL001.RV1.ADS410

description:
RV.pp.all.bz2
RV.po.all.bz2


title: STL003.RA3.ADS338

description:
RA.pp.all.bz2
RA.po.all.bz2

source_name: Human Right Atrium

value: Right Atrium


title: STL003.RA3.ADS314

description:
RA.pp.all.bz2
RA.po.all.bz2


title: STL001.SG1.ADS174

description:
SG.pp.all.bz2
SG.po.all.bz2


title: STL001.RV1.ADS416

description:
RV.pp.all.bz2
RV.po.all.bz2


title: STL001.SX1.ADS284

description:
SX.pp.all.bz2
SX.po.all.bz2


title: STL003.RA3.ADS326

description:
RA.pp.all.bz2
RA.po.all.bz2


title: STL002.SB2.ADS182

description:
SB.pp.all.bz2
SB.po.all.bz2


title: STL003.RA3.ADS192

description:
RA.pp.all.bz2
RA.po.all.bz2


title: STL003.PO3.ADS464

description:
PO.pp.all.bz2
PO.po.all.bz2

source_name: Human Psoas

value: Psoas


title: STL001.SG1.ADS313

description:
SG.pp.all.bz2
SG.po.all.bz2


title: STL001.RV1.ADS426

description:
RV.pp.all.bz2
RV.po.all.bz2


title: STL003.PO3.ADS335

description:
PO.pp.all.bz2
PO.po.all.bz2


title: STL003.PO3.ADS323

description:
PO.pp.all.bz2
PO.po.all.bz2


title: STL003.PO3.ADS311

description:
PO.pp.all.bz2
PO.po.all.bz2


title: STL003.PO3.ADS346

description:
PO.pp.all.bz2
PO.po.all.bz2


title: STL003.PA3.ADS470

description:
PA.pp.all.bz2
PA.po.all.bz2

source_name: Human Pancreas

value: Pancreas


title: STL003.PO3.ADS167

description:
PO.pp.all.bz2
PO.po.all.bz2


title: STL001.PO3.ADS466

description:
PO.pp.all.bz2
PO.po.all.bz2


title: STL002.PA2.ADS333

description:
PA.pp.all.bz2
PA.po.all.bz2


title: STL002.PA2.ADS321

description:
PA.pp.all.bz2
PA.po.all.bz2


title: STL002.PA2.ADS356

description:
PA.pp.all.bz2
PA.po.all.bz2


title: STL002.PA2.ADS172

description:
PA.pp.all.bz2
PA.po.all.bz2


title: STL002.PA2.ADS191

description:
PA.pp.all.bz2
PA.po.all.bz2


title: STL002.PA2.ADS161

description:
PA.pp.all.bz2
PA.po.all.bz2


title: STL002.OV2.ADS295

description:
OV.pp.all.bz2
OV.po.all.bz2

source_name: Human Ovary

value: Ovary


title: STL002.OV2.ADS259

description:
OV.pp.all.bz2
OV.po.all.bz2


title: STL002.PA2.ADS181

description:
PA.pp.all.bz2
PA.po.all.bz2


title: H1.ME.ADS419

description:
ME.pp.all.bz2
ME.po.all.bz2

source_name: Human Mesendoderm

value: Mesendoderm


title: HDF_NaAc_3_days_rep1

source_name: Dermal fibroblasts


title: H1.NPC.ADS414

description:
npc.pp.all.bz2
npc.po.all.bz2

source_name: Human Neural Prgenitor Cell

value: Neural Prgenitor Cell


title: STL002.OV2.ADS188

description:
OV.pp.all.bz2
OV.po.all.bz2


title: STL002.OV2.ADS271

description:
OV.pp.all.bz2
OV.po.all.bz2


title: STL002.LG2.ADS305

description:
LG.pp.all.bz2
LG.po.all.bz2

source_name: Human Lung

value: Lung


title: STL002.LG2.ADS329

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL002.LG2.ADS317

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL002.PA2.ADS309

description:
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PA.po.all.bz2


title: STL002.LG2.ADS282

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL002.LG2.ADS294

description:
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LG.po.all.bz2


title: STL002.LG2.ADS258

description:
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LG.po.all.bz2


title: STL002.LG2.ADS270

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL002.LG2.ADS190

description:
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LG.po.all.bz2


title: STL002.LG2.ADS175

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS334

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS288

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS310

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS322

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS300

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS276

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL001.LG1.ADS264

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL002.OV2.ADS283

description:
OV.pp.all.bz2
OV.po.all.bz2


title: STL011.LI11.ADS344

description:
LI.pp.all.bz2
LI.po.all.bz2

source_name: Human Liver

value: Liver


title: STL001.LG1.ADS347

description:
LG.pp.all.bz2
LG.po.all.bz2


title: STL011.LI11.ADS275

description:
LI.pp.all.bz2
LI.po.all.bz2


title: STL011.LI11.ADS263

description:
LI.pp.all.bz2
LI.po.all.bz2


title: STL001.LV1.ADS473

description:
LV.pp.all.bz2
LV.po.all.bz2

source_name: Human Left Ventricle

value: Left Ventricle


title: STL001.LV1.ADS425

description:
LV.pp.all.bz2
LV.po.all.bz2


title: STL001.LV1.ADS423

description:
LV.pp.all.bz2
LV.po.all.bz2


title: STL011.LI11.ADS299

description:
LI.pp.all.bz2
LI.po.all.bz2


title: STL011.LI11.ADS287

description:
LI.pp.all.bz2
LI.po.all.bz2


title: STL001.LV1.ADS421

description:
LV.pp.all.bz2
LV.po.all.bz2


title: STL011.LI11.ADS194

description:
LI.pp.all.bz2
LI.po.all.bz2


title: STL001.LV1.ADS418

description:
LV.pp.all.bz2
LV.po.all.bz2


title: H1.ADS180

description:
H1.pp.all.bz2
H1.po.all.bz2

source_name: Human Human ES Cells

value: Human ES Cells


title: H1.ADS171

description:
H1.pp.all.bz2
H1.po.all.bz2


title: H1.ADS187

description:
H1.pp.all.bz2
H1.po.all.bz2


title: hg19.HC.ADS328

description:
HC.pp.all.bz2
HC.po.all.bz2

source_name: Human Hippocampus

value: Hippocampus


title: hg19.HC.ADS316

description:
HC.pp.all.bz2
HC.po.all.bz2


title: hg19.HC.ADS304

description:
HC.pp.all.bz2
HC.po.all.bz2


title: hg19.HC.ADS195

description:
HC.pp.all.bz2
HC.po.all.bz2


title: STL003.GA3.ADS476

description:
GA.pp.all.bz2
GA.po.all.bz2

source_name: Human Gastric

value: Gastric


title: STL003.GA3.ADS339

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL003.GA3.ADS327

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL002.GA2.ADS474

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL003.GA3.ADS315

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL002.GA2.ADS269

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL002.GA2.ADS293

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL002.GA2.ADS281

description:
GA.pp.all.bz2
GA.po.all.bz2


title: H1.ADS160

description:
H1.pp.all.bz2
H1.po.all.bz2


title: STL002.GA2.ADS176

description:
GA.pp.all.bz2
GA.po.all.bz2


title: STL002.GA2.ADS257

description:
GA.pp.all.bz2
GA.po.all.bz2


title: IMR90.ADS186

description:
imr90.pp.all.bz2
imr90.po.all.bz2

source_name: Human Fibroblasts

value: Fibroblasts


title: IMR90.ADS341

description:
imr90.pp.all.bz2
imr90.po.all.bz2


title: STL002.FT2.ADS183

description:
FT.pp.all.bz2
FT.po.all.bz2

source_name: Human Fat

value: Fat


title: STL002.FT2.ADS279

description:
FT.pp.all.bz2
FT.po.all.bz2


title: STL002.FT2.ADS267

description:
FT.pp.all.bz2
FT.po.all.bz2


title: STL002.FT2.ADS303

description:
FT.pp.all.bz2
FT.po.all.bz2


title: STL002.FT2.ADS291

description:
FT.pp.all.bz2
FT.po.all.bz2


title: STL002.EG2.ADS290

description:
EG.pp.all.bz2
EG.po.all.bz2

source_name: Human Esophagus

value: Esophagus


title: STL002.EG2.ADS266

description:
EG.pp.all.bz2
EG.po.all.bz2


title: STL002.EG2.ADS278

description:
EG.pp.all.bz2
EG.po.all.bz2


title: STL002.EG2.ADS302

description:
EG.pp.all.bz2
EG.po.all.bz2


title: hg19.DLPFC.ADS285

description:
DLPFC.pp.all.bz2
DLPFC.po.all.bz2

source_name: Human Dorsolateral Prefrontal Cortex (DLPFC)

value: Dorsolateral Prefrontal Cortex (DLPFC)


title: STL002.EG2.ADS189

description:
EG.pp.all.bz2
EG.po.all.bz2


title: hg19.DLPFC.ADS297

description:
DLPFC.pp.all.bz2
DLPFC.po.all.bz2


title: hg19.DLPFC.ADS273

description:
DLPFC.pp.all.bz2
DLPFC.po.all.bz2


title: hg19.DLPFC.ADS261

description:
DLPFC.pp.all.bz2
DLPFC.po.all.bz2


title: hg19.CM.ADS352

description:
CM.pp.all.bz2
CM.po.all.bz2

source_name: Human Cardiomyocytes

value: Cardiomyocytes


title: hg19.CM.ADS345

description:
CM.pp.all.bz2
CM.po.all.bz2


title: hg19.CM.ADS349

description:
CM.pp.all.bz2
CM.po.all.bz2


title: hg19.CM.ADS163

description:
CM.pp.all.bz2
CM.po.all.bz2


title: hg19.CM.ADS342

description:
CM.pp.all.bz2
CM.po.all.bz2


title: IMR90.ADS179

description:
imr90.pp.all.bz2
imr90.po.all.bz2


title: STL001.BL1.ADS354

description:
BL.pp.all.bz2
BL.po.all.bz2

source_name: Human Bladder

value: Bladder


title: STL001.BL1.ADS336

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL001.BL1.ADS324

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL001.BL1.ADS319

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL001.BL1.ADS312

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL001.BL1.ADS331

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL001.BL1.ADS165

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL001.BL1.ADS307

description:
BL.pp.all.bz2
BL.po.all.bz2


title: STL003.AO3.ADS357

description:
AO.pp.all.bz2
AO.po.all.bz2

source_name: Human Aorta

value: Aorta


title: STL003.AO3.ADS340

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS320

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS332

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS351

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS308

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS265

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS277

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS184

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL002.AO2.ADS298

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS289

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL003.AO3.ADS301

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL002.AO2.ADS262

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL002.AO2.ADS286

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL002.AO2.ADS274

description:
AO.pp.all.bz2
AO.po.all.bz2


title: STL002.AD2.ADS280

description:
AD.pp.all.bz2
AD.po.all.bz2

source_name: Human Adrenal gland

value: Adrenal gland


title: STL002.AD2.ADS292

description:
AD.pp.all.bz2
AD.po.all.bz2


title: STL002.AD2.ADS268

description:
AD.pp.all.bz2
AD.po.all.bz2


title: STL002.AD2.ADS350

description:
AD.pp.all.bz2
AD.po.all.bz2


title: STL002.AD2.ADS256

description:
AD.pp.all.bz2
AD.po.all.bz2


title: STL002.AD2.ADS166

description:
AD.pp.all.bz2
AD.po.all.bz2


title: SerB3

city: Durham

first: Hiroaki

last: Matsunami

state: NC

address: 264 CARL Building

department: Molecular Genetics & Microbiology

institute: Duke University

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_100pTMT.STAR.csv

data_processing:
Library strategy: pS6-IP RNA-Seq
STAR + RSEM were used for read alignment and quantification
Genome_build: Genome version used for read aglignment: Ensembl release 96 (April 2019)
Supplementary_files_format_and_content: Differential expression data based on EdgeR was reported

organism: Mus musculus

source_name: Olfactory epithelium

extract_protocol:
Following odor stimulation, the mouse was sacrificed, and the dissected olfactory epithelium was processed for RNA library in reference to the method described by Jiang et al. with some modifications (Jiang et al., 2015).  Pieces of freshly dissected olfactory epithelium were homogenized and centrifuged. 6 μl of a monoclonal Phospho-S6 Ribosomal Protein (Ser240/244) (D68F8) XP Rabbit mAb (Cell Signaling Technologies) was added to the supernatant, and incubated with rotation for 1.5 hours at 4 °C. Protein A Dynabeads (Invitrogen) were added to the antibody mixture and incubated for another hour with rotation at 4 °C. After incubation and washing, the bead-captured RNA was eluted and purified with RNeasy Micro kit (Qiagen).
10 ng of starting RNA was used to make cDNA libraries with the SMART-Seq v4 kit (Clontech) with 11 cycles of PCR. cDNA was purified with AMPure XP beads (Beckman Coulter) and 0.5 ng was used to make cDNA libraries using the Nextera XT DNA Library Preparation Kit (Illumina). 50 base sequencing was performed on the HiSeq 2500 System (Illumina), obtaining 15-38 million reads per sample.

tag: stimulant

value: Olfactory epithelium

tag: experiment

tag: age

value: p20 to p22


title: YJK4

description:
sample name in processed data file:
Dorsal1
processed data file:
OR_result.DorVen.STAR.csv

data_processing:
STAR + RSEM were used for read alignment and quantification
Genome_build: Genome version used for read aglignment: Ensembl release 96 (April 2019)
Supplementary_files_format_and_content: Differential expression data based on EdgeR was reported

source_name: Dorsal olfactory epithelium

value: No Odor

value: Dorsal olfactory epithelium

value: RNA-Seq


title: SerA9

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_100pTMT.STAR.csv


title: YJK8

description:
sample name in processed data file:
Dorsal3
processed data file:
OR_result.DorVen.STAR.csv


title: YJK7

description:
sample name in processed data file:
Ventral2
processed data file:
OR_result.DorVen.STAR.csv

source_name: Ventral olfactory epithelium

value: Ventral olfactory epithelium


title: SerB2

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_1pTMT.STAR.csv

value: 1% TMT


title: YJK9

description:
sample name in processed data file:
Ventral3
processed data file:
OR_result.DorVen.STAR.csv


title: YJK6

description:
sample name in processed data file:
Dorsal2
processed data file:
OR_result.DorVen.STAR.csv


title: YJK5

description:
sample name in processed data file:
Ventral1
processed data file:
OR_result.DorVen.STAR.csv


title: SerA11

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_1pTMT.STAR.csv


title: SerB1

description:
sample name in processed data file:
no3
processed data file:
NA

value: No odor


title: SerA8

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_1pTMT.STAR.csv


title: SerG11

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_0.1pTMT.STAR.csv


title: SerG9


title: SerA12

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_100pTMT.STAR.csv


title: SerG3


title: SerG1

description:
sample name in processed data file:
no1
processed data file:
NA


title: SerG2

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_0.01pTMT.STAR.csv


title: SerB12

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_100pACT.STAR.csv


title: SerG7

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_0.1pTMT.STAR.csv


title: SerB5

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_1pACT.STAR.csv

value: 1% ACT


title: SerG6

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_0.01pTMT.STAR.csv


title: SerB6

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_100pACT.STAR.csv


title: SerG5

description:
sample name in processed data file:
no2
processed data file:
NA


title: SerA7


title: SerB11

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_1pACT.STAR.csv


title: SerG10

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_0.01pTMT.STAR.csv


title: SerB10

value: No  Odor


title: STL001.TH1.ADS420

description:
TH.pp.all.bz2
TH.po.all.bz2

source_name: Human Thymus

value: Thymus


title: SerA10


title: SerB4


title: SerA6

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_100pACT.STAR.csv


title: SerE9

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_0.1pACT.STAR.csv


title: SerA4


title: SerA5

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_1pACT.STAR.csv


title: Wildtype Sleep deprivation pool [WT SD]

city: Zurich

first: Steven

middle: A

last: Brown

address: Winterthurerstrasse 190

department: Institute of Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

description:
WT SD
Sleep Deprivation ZT4, pool of n=4.
RNAseq total
processed data file: Muheim_et_al_2019_Data_Processed_WT_BLvsWT_SD.xlsx
processed_data_file:_Muheim_et_al_2019_Data_Processed_WT_SDvsKO_SD.xlsx

data_processing:
Raw data was cleaned by removing adaptor sequences and trimming low end quality reads.
Sequence alignment of high end reads to mouse reference genome (build mm10).
Quantification of gene level expression using RSEM (Version 1.2.19).
edgeR (Bioconductor, Version 3.8.2) was used to assess statistical significance.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: xlsx: Excel files includes normalized reads per region.

source_name: Brain

growth_protocol: Animals were housed under standard 12:12 light:dark conditions, standard humidity and temperature.

extract_protocol:
RNA extraction was done using the RNeasy minikit from Qiagen. The protocol was according to Qiagen's recommendations. Samples were treated with DNase I. Samples were sequenced as pools (n=4 per condition).
According to Illumina for HiSeq2500.

treatment_protocol: Animals were housed in their homecages in groups of 2, at light onset half of the animals were sleep deprived via gentle handling for 4h. The control group was left undisturbed for the same time. Brain tissue was harvested immediately after the 4h sleep deprivation at ZT4, the fresh tissue was snap frozen with liquid N2. The following groups were used: Baseline wildtype littermates (WT BL), baseline BK deficient (KO BL), wildtype littermates after 4h sleep deprivation (WT SD) and BK deficient after 4h sleep deprivation (KO SD).

tag: strain/background

value: F1 C57Bl6/J x Sv129

tag: genotype/variation

value: Wildtype

value: Brain cortex

value: Sleep Deprivation

tag: time


title: BK knockout Sleep deprivation pool [KO SD]

description:
KO SD
Sleep Deprivation ZT4, pool of n=4.
RNAseq total
processed data file: Muheim_et_al_2019_Data_Processed_KO_BLvsKO_SD.xlsx
processed_data_file:_Muheim_et_al_2019_Data_Processed_WT_SDvsKO_SD.xlsx

value: BK knockout


title: BK knockout Baseline pool [KO BL]

description:
KO BL
Baseline ZT4, pool of n=4.
RNAseq total
processed data file: Muheim_et_al_2019_Data_Processed_KO_BLvsKO_SD.xlsx
processed_data_file:_Muheim_et_al_2019_Data_Processed_WT_BLvsKO_BL.xlsx

value: Baseline


title: Wildtype Baseline pool [WT BL]

description:
WT BL
Baseline ZT4, pool of n=4.
RNAseq total
processed data file: Muheim_et_al_2019_Data_Processed_WT_BLvsWT_SD.xlsx
processed_data_file:_Muheim_et_al_2019_Data_Processed_WT_BLvsKO_BL.xlsx


title: MIN6 cells, Control-GFP

city: New York

first: Taiyi

middle: Diana

last: Kuo

state: NY

address: 1150 St Nicholas Ave., Ste. 237

department: Medicine

institute: Columbia University

data_processing:
For the analysis, 26 to 35 million read-pairs per sample were used. The reads were mapped to the mouse genome mm10 using STAR (v2.5.2b) algorithm with default settings.
FeatureCounts from the Subread (v1.5.2) package was used to assign concordantly aligned reads pairs to RefSeq genes.
A 25-bp minimum as overlapping bases in a fragment was specified for read assignment.
Raw read counts were used as input for DESeq2 (v1.14.1), which was further used to filter out genes with low counts, normalize the counts using library sizes, and perform statistical tests to find significant differential genes.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_allgenes.xlsx reports raw read counts.  GEO_DESeq2_allgenes_counts.xlsx reports normalized counts.

source_name: MIN6 cell line

growth_protocol: MIN6 cells were maintained in growth media (DMEM supplemented with 15% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin, and fresh 55 μM- final concentration β-mercaptoethanol).

extract_protocol:
After 72 to 96 h of infection, MIN6 cells were washed with PBS three times prior to RNA extraction.
RNA were isolated with Nucleospin RNA kit (Macherey-Nagel) with DNase I treatment.
Directional poly-A RNAseq libraries were prepared and sequenced as PE42 (42 bp paired-end reads) on Illumina Hiseq 2500 in high output mode.

treatment_protocol: We infected MIN6 cells (MOI 100) with adenoviruses carrying C2cd4a-GFP fusion construct. The infection media were composed of DMEM, 8 μg/ml polybrene, and appropriate amount of adenovirus.

tag: cell line

value: MIN6 cell line

tag: expressing

value: Control-GFP


title: BK knockout Sleep Deprivation [SD KO2]

description:
SD KO2
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx

data_processing:
Raw data was cleaned by removing adaptor sequences and trimming low end quality reads.
Sequence alignment of high end reads to mouse reference genome (build mm10).
Quantification of gene level expression using RSEM (Version 1.2.19).
edgeR (Bioconductor, Version 3.8.2) was used to assess statistical significance.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Muheim_et_al_2019_ProcessedData_individuals.xlsx: Excel file includes normalized reads per region.

extract_protocol:
RNA extraction was done using the RNeasy minikit from Qiagen. The protocol was according to Qiagen's recommendations. Samples were treated with DNase I.
According to Illumina for HiSeq2500.


title: SerE8

description:
sample name in processed data file:
st3
processed data file:
OR_result.Ser_0.01pACT.STAR.csv

value: Olfactory epithelium

value: p20 to p22


title: BK knockout Sleep Deprivation [SD KO4]

description:
SD KO4
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: BK knockout Baseline [BL KO1]

description:
BL KO1
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: Wildtype Sleep Deprivation [SD WT4]

description:
SD WT4
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: BK knockout Baseline [BL KO2]

description:
BL KO2
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: SerE4


title: SerE2

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_0.01pACT.STAR.csv


title: SerE5

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_0.01pACT.STAR.csv


title: SerE7

description:
sample name in processed data file:
no3
processed data file:
NA


title: BK knockout Sleep Deprivation [SD KO3]

description:
SD KO3
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: BK knockout Baseline [BL KO4]

description:
BL KO4
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: SerE6

description:
sample name in processed data file:
st2
processed data file:
OR_result.Ser_0.1pACT.STAR.csv


title: SerE1

description:
sample name in processed data file:
no1
processed data file:
NA


title: BK knockout Baseline [BL KO3]

description:
BL KO3
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: MIN6 cells, C2cd4a-GFP


title: Wildtype Sleep Deprivation [SD WT2]

description:
SD WT2
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: Wildtype Sleep Deprivation [SD WT3]

description:
SD WT3
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: SerE3

description:
sample name in processed data file:
st1
processed data file:
OR_result.Ser_0.1pACT.STAR.csv


title: BK knockout Sleep Deprivation [SD KO1]

description:
SD KO1
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: Wildtype Baseline [BL WT2]

description:
BL WT2
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: Wildtype Baseline [BL WT1]

description:
BL WT1
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: EOD_rep5 [EOD_3M5]

city: Singapore

first: Gavin

last: Ng

address: Block MD9, Level 4  2 Medical Drive  117597

department: Physiology

country: Singapore

institute: National University of Singapore

data_processing:
The reference genome for Mus musculus (mm10) and gene model annotation files were downloaded from the National Center for Biotechnology Information (NCBI) genome website browser. Following which, indexes of the reference genome was constructed before the paired-end clean reads were then mapped to the reference genome using STAR (v2.5) [12] for the liver transcriptome.
To count the number of reads mapped onto each gene, HTSeq (v0.6.1) [13] was used to compute such quantification. From there, the Reads Per Kilobase of exon model per Million mapped reads (FPKM) of each gene was then computed using the length of the gene and reads count mapped to this particular gene. The FPKM value was then used for estimation of gene expression levels. 35,275 unique RNA transcripts each were quantified in total for liver datasets.
Differential gene expression analysis between five biological replicates per condition were performed using the DESeq2 R Package (v2_1.6.3). A negative binomial distribution was used to model a statistical analysis for differential gene expression as achieved in DESeq2. The resultant p-values were then adjusted using Benjamini and Hochberg’s test to control false discovery rate (FDR). Genes with adjusted p < 0.05 were assigned as differentially expressed [14]. Principal component plots, venn diagrams and volcano plots in this study were prepared using the ggplot2 R package (v3.0.0) [15].
To allow logarithm adjustment, genes showing FPKM values of zero were assigned a corresponding value of 0.01. Correlation was then determined using the “cor.test” function in R with options set alternative= “greater” and method= “Spearman”. All experiments were performed using at least five biological replicates per condition, and Pearson correlation coefficients obtained of at least 0.9 value demonstrated high coverage and reproducibility. After which, to establish relationship between the different samples, clustering was performed using the FPKM expression level by utilising the hierarchical clustering distance method with the aid of heatmap, self-organisation mapping (SOM) and k-means via silhouette coefficient in order to adapt optimal classification with R’s default parameters imbued. Heatmap illustrated in this manuscript was prepared using pheatmap R package (v1.0.10).
To understand the gene ontology (GO) as well as the pathway association for these differentially expressed genes, gprofile R package (v0.6.7) [17] and clusterProfiler R package (v3.8) [18] were utilised for this function.  After correction of gene length biasness, GO terms with adjusted p-value < 0.05 were assigned as significantly enriched among the pool of differentially expressed genes. Diagrams demonstrating enrichment analysis was plotted using ggplot2 R package (v3.0.0) and Sigmaplot (v1.3).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM and readcounts

extract_protocol:
The left lateral liver lobe was then harvested and immediately flash frozen before being stored at -80°C
RNA samples from the liver was isolated using EZ-10 DNAaway RNA Mini-Preps Kit (Bio Basic, Canada) according to the manufacturers’ protocol. Briefly, frozen liver samples were homogenized and lysed in the provided lysis buffer. Prevention of genomic DNA contamination was achieved using the provided gDNA eliminator column. The RNA’s purity was determined by using the Nanodrop ND-1000 (Thermo Fisher Scientific, USA), whereas the RNA’s integrity was assessed via agarose gel electrophoresis as well as from the Agilent 2100 Bioanalyzer (Agilent, USA). Enrichment of high-quality RNA samples should demonstrate an OD260/OD280 ratio of 1.9-2.0 from Nanodrop readings, two distinct bands indicating 28S and 18S following agarose gel electrophoresis, as well as showing ≥ 6.8 RNA integrity number with a smooth base line using the Agilent 2100 Bioanalyzer.
Following the isolation of these high-quality and pure total RNA samples from the liver tissues, cDNA library construction was mediated using the NEBNext® UltraTM RNA library preparation kit as per the manufacturers’ protocol (New England BioLabs, USA). mRNA was first purified via the addition of poly-T-oligo-attached magnetic beads, before subjecting them to random fragmentation mediated by the usage of a fragmentation buffer. The initial strand of the cDNA is first synthesized through the utilisation of a random hexamer primer and RNase H- (M-MuLV reverse transcriptase). The second strand of cDNA is then synthesized using DNA polymerase I and RNase H, and the resulting double stranded cDNA is then purified using AMPure XP beads. The overhangs of these purified double-stranded cDNA were then processed by exonuclease and polymerase to become blunt ends, before subjecting the 3’ ends of these DNA fragments to adenylation and subsequent ligation of NEBNext hairpin loop structure adaptor on both ends for hybridisation. For optimal isolation of cDNA fragments of approximately 150-200 base pairs in length, DNA fragments were then purified using the AMPure XP system (Beckman Coulter, USA), before utilising both PCR amplification and purification by AMPure XP beads to obtain the completed library DNA fragments. The resultant libraries were then sequenced using HiSeqTM 2500 Illumina platforms to obtain 12GB of raw data per sample (Illumina, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 3M before expt, 6M after expt

value: intermittent fasting (IF) for 24-h (termed as every-other-day (EOD)) for three months

value: liver


title: AL_rep2 [AL_3M2]

value: ad libitum (AL) for three months


title: EOD_rep3 [EOD_3M3]


title: IF16_rep5 [IF_3M5]

value: intermittent fasting (IF) for 16-hr (IF16) for three months


title: Wildtype Baseline [BL WT3]

description:
BL WT3
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx


title: WT control 2

city: Maywood

first: Michael

middle: J

last: Zilliox

state: IL

address: 2160 S. First Ave

department: Ophthalmology

institute: Loyola University Chicago

data_processing:
Remove adaptors with Cutadapt v1.11
Alignment with TopHat v. 2.0.13
Counts with HT-Seq v0.6.1p1
Differential Expression with DESeq2 1.14.1
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts in .txt file.

source_name: gp100 epitope reactive splenic T cells

extract_protocol:
gp100 epitope reactive splenic T cells were obtained from Pmel TCR transgenic mouse and activated with 1 microgram/ml of cognate peptide for 72 hrs. in presence of IL2 (100 u/ml). The cells were harvested after three days and RNA was prepared.
Qiagen RNeasy
TruSeq mRNA Library Prep

value: gp100 epitope reactive splenic T cells

tag: genotype

value: WT control


title: SphK1 -/- 2

extract_protocol:
gp100 epitope reactive splenic T cells were obtained from Sphingosine Kinase-1 deficient Pmel TCR transgenic mouse and activated with 1 microgram/ml of cognate peptide for 72 hrs. in presence of IL2 (100 u/ml). The cells were harvested after three days and RNA was prepared.
Qiagen RNeasy
TruSeq mRNA Library Prep

value: SphK1 -/-


title: Prdm16_3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were aligned to mm9 using STAR pipeline. Number of read aligned to each gene was counted using featureCount in subread package.
Genome_build: mm9
Supplementary_files_format_and_content: Text file containing gene symbol and raw tag counts

growth_protocol: Standard growth media

extract_protocol:
Trizol and PureLink RNA Mini Kit
illumina Truseq RNA Sample Preparation kit

value: Inguinal adipose tissue

value: stromal-vascular cells

value: Prdm16 retrovirus


title: WT control 1


title: IF16_rep4 [IF_3M4]


title: IF16_rep3 [IF_3M3]


title: AL_rep5 [AL_3M5]


title: AL_rep4 [AL_3M4]


title: SphK1 -/- 1


title: IF16_rep2 [IF_3M2]


title: EOD_rep1 [EOD_3M1]


title: Prdm16_1


title: Puro_3

value: control (puro)


title: Wildtype Baseline [BL WT4]

description:
BL WT4
Baseline ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx

value: F1 C57Bl6/J x Sv129

value: Wildtype

value: Brain cortex

value: Baseline


title: Wildtype Sleep Deprivation [SD WT1]

description:
SD WT1
Sleep Deprivation ZT4
RNAseq total
processed data file: Muheim_et_al_2019_ProcessedData_individuals.xlsx

value: Sleep Deprivation


title: EOD_rep2 [EOD_3M2]

value: 3M before expt, 6M after expt


title: EOD_rep4 [EOD_3M4]

value: intermittent fasting (IF) for 24-h (termed as every-other-day (EOD)) for three months


title: IF16_rep1 [IF_3M1]

value: liver


title: AL_rep3 [AL_3M3]

value: ad libitum (AL) for three months


title: Puro_1


title: Prdm16_2


title: AL_rep1 [AL_3M1]


title: mm DC UT PU.1 Rep 1

city: DEBRECEN

first: LAJOS

last: SZELES

address: NAGYERDEI KRT 98

country: Hungary

institute: UNIVERSITY OF DEBRECEN

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
region calling with homer v4.2 findPeaks using -center -size 1000 -minDist 2500 parameters for histone ChIPseq samples
peak calling with MACS2 using -B --SPMR parameters
mm10 ENCODE blacklist were subtracted from the peak list
annotation was created with homer v4.2 annotatePeaks.pl using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: annotation file

source_name: dendritic cells from the spleen

growth_protocol: CD8-positive dendritic cells were cultured in IMDM-glutamax medium supplemented with 10% FCS, β-mercaptoethanol, and penicillin + streptomycin

extract_protocol:
ChIP was performed as previously described (Daniel et al. Genes Dev. 2014)
Indexed cDNA libraries were prepared from 1-10 ng genomic DNA using TruSeq ChIP Sample Preparation kit (Illumina).

treatment_protocol: CD8-positive dendritic cells were left unstimulated or were stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG) for 90 min

value: CD8-positive dendritic cell line

tag: stimulation

tag: chip antibody


title: mm DC CpG STAT1 Rep 1

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: mm DC UT PU.1 Rep 2


title: mm DC pIC PU.1 Rep 2

value: 103 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC CpG PU.1 Rep 1


title: Puro_2


title: mm DC CpG PU.1 Rep 2


title: mm DC pIC STAT1 Rep 1

value: 104 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC pIC PU.1 Rep 1

value: 102 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC UT ATAC Rep 2

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
peak calling with MACS2 using -B --SPMR parameters
mm10 ENCODE blacklist were subtracted from the peak list
annotation was created with homer v4.2 annotatePeaks.pl using default parameters
Genome_build: mm10

extract_protocol:
Mouse bone marrow-derived macrophages were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation.
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol (Illumina).

treatment_protocol: unstimulated CD8-positive dendritic cells were used for ATAC-seq experiments

tag: method

value: ATAC-seq


title: mm DC UT p300 Rep 1


title: mm DC pIC p300 Rep 1

value: 100 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC UT p300 Rep 2


title: mm DC UT JUNB Rep 1

value: JUNB (sc-46x)


title: mm DC pIC JUNB Rep 1

value: 99 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC CpG JUNB Rep 1


title: mm DC UT IRF8 Rep 2


title: mm DC pIC IRF8 Rep 1

value: 97 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC UT IRF8 Rep 1


title: mm DC UT STAT1 Rep 1


title: mm DC UT IRF5 Rep 1

value: IRF5 (Abcam ab21689)


title: mm DC CpG IRF8 Rep 2


title: mm DC pIC IRF5 Rep 1

value: 96 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC pIC p300 Rep 2

value: 101 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC CpG IRF8 Rep 1


title: mm DC pIC IRF8 Rep 2

value: 98 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC CpG IRF5 Rep 1


title: mm DC UT input Rep 2

value: input


title: mm DC UT input Rep 1


title: mm DC UT IRF3 Rep 1

value: IRF3 (Cell Signalling Technology, D83B9, no. 4302)


title: mm DC UT ATAC Rep 1


title: mm DC pIC input Rep 1

value: 93 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC UT H4ac Rep 2

value: CD8-positive dendritic cell line

value: H4ac (Millipore 06-866)


title: mm DC CpG IRF3 Rep 1

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: mm DC CpG H4ac Rep 2


title: mm DC CpG input Rep 2


title: mm DC pIC H4ac Rep 2

value: 92 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC CpG input Rep 1


title: mm DC UT cREL Rep 1

value: cREL (sc-71x)


title: mm DC pIC cREL Rep 1

value: 90 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC pIC input Rep 2

value: 94 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC UT H4ac Rep 1


title: mm DC CpG H4ac Rep 1


title: mm DC CpG cREL Rep 1


title: mm DC pIC RNA Rep 3

data_processing:
alignment with TopHat v2.0.7 using default parameters
RPKM values were calculated by cufflinks v2.0.2 using default parameters
calculating raw count values by HTSeq 0.6.0 using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: raw tag count file

extract_protocol:
Total RNA was isolated from cells using Tri Reagent according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq RNA Sample Preparation Kit (Illumina) protocol.

treatment_protocol: CD8-positive dendritic cells were left unstimulated or were stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG) for 6h

value: 6h; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)

value: RNA-seq


title: mm DC pIC RNA Rep 2


title: mm DC pIC RNA Rep 1


title: mm DC pIC IRF3 Rep 1

value: 95 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC CpG RNA Rep 3

value: 6h; 1 mM class B CpG oligonucleotide (1826)


title: mm DC pIC H4ac Rep 1

value: 91 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: mm DC UT RNA Rep 3


title: mm DC UT RNA Rep 2


title: mm DC CpG RNA Rep 2


title: mm DC UT RNA Rep 1


title: mm DC CpG RNA Rep 1


title: 33T3a

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: Hepatocellular carcinoma tissue

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2

source_name: Hepatocellular carcinoma tissue

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted with the RNeasy Mini Kit(QIAGEN) by following manufacturer's instructions.

value: Hepatocellular carcinoma

tag: Stage


title: 19T3b

description: Hepatocellular carcinoma tissue


title: 26T3b

description: Hepatocellular carcinoma tissue


title: 53T3b

description: Hepatocellular carcinoma tissue


title: 32T3b

description: Hepatocellular carcinoma tissue


title: 20T3b

description: Hepatocellular carcinoma tissue


title: 29T3a

description: Hepatocellular carcinoma tissue


title: 27T3a

description: Hepatocellular carcinoma tissue


title: 30T3a

description: Hepatocellular carcinoma tissue


title: 3T1

description: Hepatocellular carcinoma tissue


title: 48T3b

description: Hepatocellular carcinoma tissue


title: 31T3a

description: Hepatocellular carcinoma tissue


title: 7T1

description: Hepatocellular carcinoma tissue


title: 3T3b

description: Hepatocellular carcinoma tissue


title: 5T1

description: Hepatocellular carcinoma tissue


title: 6T1

description: Hepatocellular carcinoma tissue


title: 8T1

description: Hepatocellular carcinoma tissue


title: 50T3b

description: Hepatocellular carcinoma tissue


title: 9N

description: Normal liver tissue

source_name: Normal liver

value: Normal liver


title: 28T3a

description: Hepatocellular carcinoma tissue


title: 25T3a

description: Hepatocellular carcinoma tissue


title: 4T1

description: Hepatocellular carcinoma tissue


title: 2T1

description: Hepatocellular carcinoma tissue


title: 32T3a

description: Hepatocellular carcinoma tissue


title: MP_I

city: Cambridge

first: Marco

last: Tripodi

address: MRC Laboratory of Molecular Biology, Francis Crick Avenue

department: Neurobiology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

data_processing:
Reads were trimmed using Trim Galore version 0.4.2 with default parameters to remove the standard illumina adapter sequence
Reads were mapped to the GRCm38 assembly using STAR version 907 STAR_2.5.3a_modified
Raw read counts per transcript were calculated using HTSeq version 0.9.1 using non-directional counts
Differential analysis of gene expression performed using the default settings in DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file showing normalised read counts and differential expression results computed by DESeq2 for all samples

source_name: Motor posterior SC

extract_protocol:
RNA extraction using an RNeasy Mini kit (Qiagen, Venlo, Netherlands)
cDNA libraries were generated from total RNA using a TruSeq® Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) and sequenced on an Illumina HiSeq 4000 machine (single read, 50bp read length)

tag: strain

value: wild type

value: Motor posterior SC

value: Post-natal day 7


title: MP_IV


title: MA_I

source_name: Motor anterior SC

value: Motor anterior SC


title: MP_V


title: MP_III


title: MP_II


title: MA_II


title: MA_IV


title: MA_V


title: SP_IV

source_name: Sensory posterior SC

value: Sensory posterior SC


title: SP_V


title: MA_III


title: 1T1

description: Hepatocellular carcinoma tissue


title: 7N

description: Normal liver tissue


title: 2N

description: Normal liver tissue


title: SA_IV

source_name: Sensory anterior SC

value: Sensory anterior SC


title: SP_II


title: SP_III


title: SA_III


title: 3N

description: Normal liver tissue


title: 4N

description: Normal liver tissue


title: 8N

description: Normal liver tissue


title: SA_II


title: iWAT_Old_CL_4

treatment_protocol: ip injection of CL

value: 12 months old

value: Cardiolipin (CL)

value: Inguinal adipose tissue


title: SA_I


title: 1N

description: Normal liver tissue


title: iWAT_Old_Ctrl_1

value: vehicle control


title: iWAT_Young_CL_2

value: 2 months old


title: iWAT_Old_CL_1


title: iWAT_Old_CL_3


title: iWAT_Young_CL_1


title: SA_V


title: iWAT_Young_Ctrl_4


title: iWAT_Old_CL_2


title: iWAT_Young_Ctrl_2


title: iWAT_Young_Ctrl_1


title: iWAT_Young_Ctrl_3


title: iWAT_Old_Ctrl_4


title: iWAT_Young_CL_3


title: iWAT_Young_CL_4


title: IM3_b

city: Ithaca

first: Davide

last: Pisu

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

description:
Mtb_raw_counts_matrix.txt
Mus_musculus_raw_counts.tsv
Mtb_raw_counts_matrix_am_im_only.txt
Mtb_counts_normalized.csv
Mtb_counts_normalized_am_im_only.csv
Mus_musculus_counts_normalized.csv

data_processing:
Flexbar (v. 3.4)  has been used to remove low quality reads and trim Illumina adapters.
rRNA reads have been  removed using Bowtie2 (--sensitive mode)
rRNA filtered fastq files were split using Bowtie2 (--very-sensitive mode) into species-specific  files using the two reference genomes, GRCm38.94 for Mus musculus and NCBI assembly  GCA_00668235.1 for Mtb Erdman
Hisat2 (v. 2.1.0) was used to align reads to the respective transcriptomes
Raw read counts for each sample were obtained using HTSeq (v. 0.11.0)
Genome_build: GRCm38.94 for Mus musculus and NCBI assembly GCA_00668235.1 for Mtb Erdman
Supplementary_files_format_and_content: 1) Mtb_counts_normalized.csv is a comma separated values file, containing the normalized counts from the DESeq2 pipeline for the Mtb transcriptome from the different samples.
2) Mtb_counts_normalized_am_im_only.csv is a comma separated values file, containing the normalized counts from the DESeq2 pipeline for the Mtb transcriptome from the in-vivo samples only.
3) Mtb_raw_counts_matrix.txt is a tabular text file containing the raw reads counts generated by the HTSeq software, for the Mtb transcriptome from each sample.
4) Mtb_raw_counts_matrix_am_im_only is a tabular text file containing the raw reads counts generated by the HTSeq software, for the Mtb transcriptome from the in-vivo samples only.
5) Mus_musculus_counts_normalized.csv is a comma separated values file, containing the normalized counts from the DESeq2 pipeline for the Mus Musculus transcriptome from in-vivo samples.
6) Mus_musculus_raw_counts.tsv is a tabular text file containing the raw reads counts generated by the HTSeq software, for the Mus Musculus transcriptome from in-vivo samples.

source_name: Mtb-infected IM cells from mouse lungs

growth_protocol: C57BL/6J WT mice purchased from the Jackson Laboratory were infected with M.tuberculosis smyc'::mCherry Erdman for 14 days.

extract_protocol:
Flow-sorted
Total mixed RNA enriched for bacterial reads was extracted following the protocol described in the paper.
rRNA removal was performed using 50-100ng total RNA input and a modified protocol for the  Ribo-Zero Epidemiology Gold rRNA removal kit (Illumina). Briefly, 90 μl bead stock was used  per sample, together with 2 μl each of reaction buffer and removal solution in a 20 μl reaction  volume, as detailed in the manufacturer’s protocol. The rRNA-depleted samples were purified by  precipitating the RNA. Sequencing libraries were generated using the NEBNext Ultra™ II  Directional RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced  on a NextSeq500 (Illumina) in multiple rounds until the desired sequencing depth for bacterial  reads was reached (target 1M 85nt reads).
Rna-seq Directional Libraries

tag: host cell type

value: Interstitial Macrophages

tag: infection

tag: sample type

value: Dual-Seq dataset


title: Test Sample 2

source_name: Mtb BMDM-infected macrophages

growth_protocol: Bone marrow was isolated from euthanized C57BL/6J mice. Bone marrow was resuspended in DMEM supplemented with 10% fetal bovine serum (Thermo Scientific), 2 mM  L-glutamine, 1 mM sodium pyruvate, 10% L-cell conditioning media and 1%  penicillin/streptomycin (Corning cellgro). Cells were then grown at 37°C for 7 days in culture  dishes while media was replenished every 3 days. BMDM were infected with Mtb Erdman smyc'::mCherry at a  multiplicity of infection of 2:1 for 4 hours.

value: BMDM

value: test sample_Dual Seq dataset


title: MTB_BMDM1

description:
Mtb_raw_counts_matrix.txt
Mtb_counts_normalized.csv

growth_protocol: Bone marrow was isolated from euthanized C57BL/6J mice. Bone marrow was resuspended in DMEM supplemented with 10% fetal bovine serum (Thermo Scientific), 2 mM  L-glutamine, 1 mM sodium pyruvate, 10% L-cell conditioning media and 1%  penicillin/streptomycin (Corning cellgro). Cells were then grown at 37°C for 7 days in culture  dishes while media was replenished every 3 days. BMDM were infected with Mtb Erdman smyc'::mCherry at a  multiplicity of infection of 2:1 for 6 hours.

extract_protocol:
Bacterial RNA extraction was performed using the protocol previously described (Rohde et al., 2012). See manuscript for reference.
rRNA removal was performed using 50-100ng total RNA input and a modified protocol for the  Ribo-Zero Epidemiology Gold rRNA removal kit (Illumina). Briefly, 90 μl bead stock was used  per sample, together with 2 μl each of reaction buffer and removal solution in a 20 μl reaction  volume, as detailed in the manufacturer’s protocol. The rRNA-depleted samples were purified by  precipitating the RNA. Sequencing libraries were generated using the NEBNext Ultra™ II  Directional RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced  on a NextSeq500 (Illumina) in multiple rounds until the desired sequencing depth for bacterial  reads was reached (target 1M 85nt reads).
Rna-seq Directional Libraries

value: M.tuberculosis (in-vitro infection)


title: IM1_b


title: IM3_a


title: IM1_a


title: Test Sample - Control

extract_protocol:
Flow-sorted
Bacterial RNA extraction was performed using the protocol previously described (Rohde et al., 2012). See manuscript for reference.
rRNA removal was performed using 50-100ng total RNA input and a modified protocol for the  Ribo-Zero Epidemiology Gold rRNA removal kit (Illumina). Briefly, 90 μl bead stock was used  per sample, together with 2 μl each of reaction buffer and removal solution in a 20 μl reaction  volume, as detailed in the manufacturer’s protocol. The rRNA-depleted samples were purified by  precipitating the RNA. Sequencing libraries were generated using the NEBNext Ultra™ II  Directional RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced  on a NextSeq500 (Illumina) in multiple rounds until the desired sequencing depth for bacterial  reads was reached (target 1M 85nt reads).
Rna-seq Directional Libraries

value: test sample_Mtb-only RNA extraction


title: IM2


title: MTB_BMDM2


title: AM3_b

source_name: Mtb-infected AM cells from mouse lungs

value: Alveolar Macrophages


title: C2C12 cells, differentiation for 2 days, si-NC, replicate 3

first: lvwei

middle: jian

last: jun

address: shizishan street, NO.1

department: College of Animal science and technology

institute: huazhong agriculture university

description: gene expression after transfected si-NC in C2C12 cells

hyb_protocol: 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the lncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: Mouse skeletal muscle cells

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, 1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA) according to the manufacture, instructions

treatment_protocol: C2C12 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS), and grown to 80-90% conflunce. Then, cells were transfected si-SYISL to knockdown SYISLand si-NC oligoes. And cells were transferred to DMEM medium contain 2% horse serum (HS), induced cells to differentiate for 2 days.

value: C2C12 cells

tag: treatment

value: si-NC (control)


title: Test Sample 1


title: MTB_BMDM3


title: C2C12 cells, differentiation for 2 days, si-SYISL, replicate 2

description: gene expression after transfected si-SYISL in C2C12 cells

value: si-SYISL


title: AM3_a


title: C2C12 cells, differentiation for 2 days, si-NC, replicate 2


title: mm DC CpG p300 Rep 2

tag: cell type

value: CD8-positive dendritic cell line

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: C2C12 cells, differentiation for 2 days, si-SYISL, replicate 3


title: C2C12 cells, differentiation for 2 days, si-NC, replicate 1


title: mm DC CpG p300 Rep 1


title: Sample Bdkrb2-null UB cells Pool 3

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

description: MUT3 vs. WT1

hyb_protocol: Manufacturer's protocol (Agilent)

scan_protocol: Scan Protocol: GE2_107_Sep09 Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: MUT Pool 3: FACS-sorted Hoxb7+ cells at postnatal day one

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3‐ or 5‐labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent V1 Mouse Whole Genome Oligonucleotide Microarray.

extract_protocol: Total RNA was isolated from GFP+/Tom+ collecting duct cells FACS-sorted from salt‐stressed Day 1 newborn Hoxb7cre+; R26RtdTomato; Bdkrb2f/f and Hoxb7cre+; R26RtdTomato; Bdkrb2+/+kidneys using RNAqueous‐96 Automated Kit (Ambion) and purified by the RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of RNA samples was assessed by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: age

value: postnatal day one

value: FACS-sorted ureteric bud-derivative cells (GFP+ & TdTomato+)

value: MUT

source_name: WT Pool 1: FACS-sorted Hoxb7+ cells at postnatal day one

value: WT


title: Sample Bdkrb2-null UB cells Pool 1

description: MUT1 vs. WT1

source_name: MUT Pool 1: FACS-sorted Hoxb7+ cells at postnatal day one


title: Control wildtype UB cells Pool 1

description: WT1 vs. WT1


title: Control wildtype UB cells Pool 3

description: WT3 vs. WT1

source_name: WT Pool 3: FACS-sorted Hoxb7+ cells at postnatal day one


title: primary aortic Acta2hrGFP+ SMCs GFP+ 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from GFP+ primary aortic smooth muscle cells.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: GFP+ primary aortic smooth muscle cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

extract_protocol: QIAzol extraction of total RNA according to the manufacturer's instructions

value: primary aortic smooth muscle cells

tag: group

value: Aorta GFP+


title: C2C12 cells, differentiation for 2 days, si-SYISL, replicate 1


title: Control wildtype UB cells Pool 2

description: WT2 vs. WT1

source_name: WT Pool 2: FACS-sorted Hoxb7+ cells at postnatal day one

tag: genotype/variation


title: Sample Bdkrb2-null UB cells Pool 2

description: MUT2 vs. WT1

source_name: MUT Pool 2: FACS-sorted Hoxb7+ cells at postnatal day one


title: AM1_b

value: Dual-Seq dataset


title: AM1_a


title: AM2


title: sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (D13) GFP- 6

description: Gene expression data from day 13 GFP- iPSCs.

source_name: day 13 GFP- iPSCs

value: iPSCs

value: D13 GFP-


title: RNASeq_ProB_LN998

city: Linköping

first: Mikael

last: Sigvardsson

address: Campus US

country: Sweden

institute: Linköping University

data_processing:
Quality check was performed on all samples using FastQC (quality control tool for high throughput sequence data, author Simon Andrews). Any overrepresented sequences were excluded and low quality bases were removed by trimmomatic/0.36 using SLIDINGWINDOW 5:20 MINLEN:35
Samples were mapped to mouse genome mm10 (GRCm38.p4) using STAR (Dobin et al, Bioinformatics, 2013) and annotated by featureCounts.
Low expressing genes, MAX<40, across all samples were filtered out and DESeq2 was then used to obtain differential expression data.
Genome_build: mm10 (GRCm38.p4)
Supplementary_files_format_and_content: Processed files include .txt files containing RNAseq expressionmatrix. All genomic coordinates are relative to mm10 mouse assembly.

source_name: lymph node

extract_protocol:
For RNA-seq cells were sorted based on the following surface markers: ProB LIN-(Gr1, Ter119, CD11b, CD11c, CD3, NK1.1)CD19+IgM-IgD-CD43+KIT+, MSC LIN-(Gr1, CD11b, CD19, CD11c, CD3, NK1.1, B220)Ter119-CD31-CD44-CD51+SCA1+, MPC LIN-(Gr1, CD11b, CD19, CD11c, CD3, NK1.1, B220)TER119-CD31-CD44-CD51+SCA1-, CD51/SCA1 LIN-(Gr1, CD11b, CD19, CD11c, CD3, NK1.1, B220)TER119-CD31-CD44-CD51-SCA1-, CD44+ LIN-(Gr1, CD11b, CD19, CD11c, CD3, NK1.1, B220)Ter119-CD31-CD44+.Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA).

value: ProB


title: RNASeq_ProB_LN872


title: RNASeq_ProB_LN885


title: RNASeq_ProB_LN990


title: RNASeq_ProB_LN809


title: RNASeq_ProB_LN834


title: RNASeq_ProB_LN889


title: sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (D13) GFP+ 5

description: Gene expression data from day 13 GFP+ iPSCs.

source_name: day 13 GFP+ iPSCs

value: D13 GFP+


title: JP8b

city: Johnson City

first: Joanna

last: Parkes

address: Pharmacy Building

department: School of Pharmacy and Pharmaceutical Sciences

institute: Binghamton University

description:
microRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls
microRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls
microRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls
microRNA_all_jo1_vs_controls_DESeq2.xls

data_processing:
FastQC was used to produce quality reports for each sample
Reads were trimmed using Trimmomatic
Reads were mapped to the human genome (hg38, gencode v25) using STAR
Reads were counted using htseq
Differential gene expression was analysed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for polymyositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean),  log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description.
Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for dermatomyositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean),  log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description.
Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for inclusion body myositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean),  log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description.
Supplementary_files_format_and_content: Excel file of DESeq2 mRNA output for anti-Jo1 positive polymyositis and dermatomyositis compared to controls.The table columns are gene ids, raw counts, normalised counts, mean values from all normalised samples (baseMean),  log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the gene, strand, gene name and gene description.
Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for polymyositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID.
Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for dermatomyositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID.
Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for inclusion body myositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID.
Supplementary_files_format_and_content: Excel file of DESeq2 microRNA output for anti-Jo1 positive polymyositis and dermatomyositis compared to controls.. The table columns are mature microRNA ids, raw counts, normalised counts, mean values from all normalised samples (baseMean), log2 fold change, standard error for log2 fold change (lfcSE), statistic value for the null hypothesis (stat), p-value, false discovery rate (padj), chromosome name (seqnames), start and end position of the microRNA, microRNA length (width), strand, mature microRNA ID, mature microRNA name and microRNA gene ID.

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from whole blood in Tempus tubes using MagMAX™ for stabilised blood tubes RNA Isolation Kit (Ambion).
1μg of total RNA used with an Illumina TruSeq® Stranded mRNA library preparation kit, 0.5μg total RNA with NEBNext® Multiplex Small RNA Library Prep sets for Illumina with size selection using 6% PolyAcrylamide gel

tag: disease subtype

value: Control

tag: anti-jo1 status

value: Negative


title: JP5b

description: microRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls

value: Inclusion Body Myositis


title: JP6b

description: microRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls

value: Polymyositis


title: primary aortic Acta2hrGFP+ SMCs GFP+ 2


title: sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (D13) GFP+ 3


title: JP4b

description:
microRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls
microRNA_all_jo1_vs_controls_DESeq2.xls

value: Dermatomyositis

value: Positive


title: JP7b

description: microRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls


title: sorted Kdr+ mesodermal progenitors (D5) Flk-1+ 5

description: Gene expression data from day 5 Flk1+ iPSCs.

source_name: day 5 Flk1+ iPSCs

value: D5 Flk-1+


title: sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (D13) GFP- 3


title: sorted Kdr+ mesodermal progenitors (D5) Flk-1+ 6


title: undifferentiated iPSC (D0) 5

description: Gene expression data from day 0 iPSCs.

source_name: day 0 iPSCs


title: sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (D13) GFP+ 6


title: JP9b


title: primary aortic Acta2hrGFP+ SMCs GFP+ 1


title: sorted Acta2hrGFP+ and Acta2hrGFP- candidate SMCs (D13) GFP- 5


title: sorted Kdr+ mesodermal progenitors (D5) Flk-1+ 3


title: RNASeq_ProB_LN828


title: undifferentiated iPSC (D0) 6

description: Gene expression data from day 0 iPSCs.


title: undifferentiated iPSC (D0) 3

description: Gene expression data from day 0 iPSCs.


title: JP3b


title: RNASeq_ProB_LN806


title: JP2b

description:
microRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls
microRNA_all_jo1_vs_controls_DESeq2.xls


title: RNASeq_ProB_LN699


title: JP24b


title: JP23b


title: RNASeq_ProB_LN708


title: RNASeq_ProB_LN697


title: JP1b


title: RNASeq_ProB_LN696


title: JP20b


title: RNASeq_ProB_LN619


title: RNASeq_ProB_LN617


title: JP22b


title: RNASeq_ProB_LN377


title: JP21b


title: JP19b


title: RNASeq_ProB_LN430


title: JP17b


title: RNASeq_ProB_LN292


title: RNASeq_ProB_LN1103


title: JP15b


title: JP14b


title: JP16b


title: RNASeq_ProB_LN686


title: RNASeq_ProB_BMwt713

source_name: bone marrow


title: JP13b


title: RNASeq_ProB_BMwt700


title: JP18b


title: RNASeq_ProB_BMwt674


title: RNASeq_ProB_BM834


title: RNASeq_ProB_BM806


title: RNASeq_ProB_BM708


title: RNASeq_ProB_BM696


title: JP12b


title: JP11b


title: JP10b


title: JP8

description:
mRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls
mRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls
mRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls
mRNA_all_jo1_vs_controls_DESeq2.xls


title: RNASeq_ProB_BM377


title: RNASeq_ProB_BM617


title: RNASeq_ProB_BM699


title: JP7

description: mRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls


title: JP9


title: 10N

description: Normal liver tissue

source_name: Normal liver

tag: tissue

value: Normal liver


title: RNASeq_ProB_BM292

tag: genotype


title: JP4

description:
mRNA_star_DM_vis_CONTROL_Wald_DESeq2.xls
mRNA_all_jo1_vs_controls_DESeq2.xls


title: JP5

description: mRNA_star_IBM_vis_CONTROL_Wald_DESeq2.xls


title: JP3


title: RNASeq_ProB_BMwt720


title: iWAT_Old_Ctrl_3

value: 12 months old

value: vehicle control

value: Inguinal adipose tissue


title: JP6

description: mRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls


title: RNASeq_CD3_LN809


title: RNASeq_CD3_LN686


title: JP2

description:
mRNA_star_PM_vis_CONTROL_Wald_DESeq2.xls
mRNA_all_jo1_vs_controls_DESeq2.xls


title: RNASeq_CD3_BMwt720

value: WT


title: RNASeq_CD3_LN806


title: JP23


title: RNASeq_CD3_BMwt713


title: RNASeq_CD3_BMwt700


title: JP1


title: JP21


title: JP20


title: RNAseq_EXP_MSC_stroma_Day20b

value: MSC


title: RNAseq_EXP_MSC_stroma_Day12


title: RNAseq_EXP_MSC_stroma_Day20


title: JP19


title: RNAseq_ctrl_MSC_stroma_Day7


title: RNAseq_CD3_BMwt674


title: JP15


title: JP24


title: JP14


title: JP16


title: RNAseq_ctrl_MSC_stroma_Day12


title: JP13


title: JP17


title: JP22


title: RNAseq_EXP_MPC_stroma_Day15

value: MPC


title: RNAseq_EXP_MPC_stroma_Day12


title: JP12


title: RNAseq_EXP_MPC_stroma_Day20


title: JP11


title: RNAseq_ctrl_MPC_stroma_Day15b


title: JP10


title: RNAseq_EXP_MPC_stroma_Day7


title: RNAseq_ctrl_MPC_stroma_Day12


title: RNAseq_EXP_CD51-SCA1-_stroma_Day20


title: X5628.DLPFC.HiC

data_processing:
Library strategy: Capture Hi-C
Read pairs from Promoter Capture Hi-C library were independently mapped to human genome hg19 using BWA-mem and manually paired with in house script.
Unmapped, non-uniquely mapped, and PCR duplicates were removed.
Trans-chromosomal read pairs and putative self-ligated products (<15kb read pairs) were removed.
Off-target reads were removed when both read pairs did not match to capture probe sequences.
Raw RNA-seq fastq files were aligned to the reference genome (hg19) using BWA-mem. Duplicate reads were discard with Picard to avoid any artifact caused by amplification step originated from Ovation® RNA-Seq System V2 (NuGEN). Then, FPKM values were calculated using Cufflink with GENCODE v19 annotation.
Genome_build: Hg19
Supplementary_files_format_and_content: *.po and *.pp provide interaction frequencies for promoter-promoter interactions or promoter-other interactions, respectively.  We combined multiple donors or replicates according to cell/tissue types.

source_name: Dorsolateral Prefrontal Cortex (DLPFC)

extract_protocol:
Promoter Capture Hi-C library was constructed by performing a target enrichment protocol (enriching target promoter-centered proximity ligation fragments from Hi-C library using capture RNA probes). Briefly, we incubated 500ng Hi-C library 24h at 65 °C within a humidified hybridization chamber with 2.5ug human Cot-1 DNA (Life Technologies), 2.5ug salmon sperm DNA (Life Technologies), and p5/p7 blocking oligos with hybridization buffer mix (10X SSPE, 10mM EDTA, 10X Denhardts solution, and 0.26% SDS) and 500ng RNA probes. RNA:DNA hybrids were enriched using 50ul T1 streptavidin beads (Invitrogen) with 30min incubation at RT. Next, bead-bound hybrids were washed by a 15min incubation in wash buffer1 (1X SSC and 0.1% SDS) with frequent vortexing, and then washed three times with 500ul of pre-warmed (65 °C) wash buffer2 (0.1X SSC and 0.1% SDS), and resuspended in nuclease-free water. The resulting capture Hi-C libraries were amplified while bound to the T1 beads, and purified using AMPure XP beads, followed by sequencing.
Promoter Capture Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq2500 or HiSeq4000 protocols with minor modifications (Illumina, San Diego, CA). RNA-seq experiments were conducted using Ovation® RNA-Seq System V2 (NuGEN) as previously described (Dahl et al., 2016 Nature).

value: Dorsolateral Prefrontal Cortex (DLPFC)


title: STL003.SX3.TL193

description:
all_interaction.po.txt
all_interaction.pp.txt

source_name: Spleen

value: Spleen


title: RNAseq_EXP_CD51-SCA1-_stroma_Day7b


title: X5628.DLPFC


title: STL003.SX3.TL192


title: STL003.SX3.TL191


title: X5628.HC.HiC

source_name: Hippocampus

value: Hippocampus


title: STL003.SX3.SRC1007


title: RNAseq_EXP_CD51-SCA1-_stroma_Day7


title: X5628.HC


title: RNAseq_ctrl_CD51-SCA1-_stroma_Day12


title: RNAseq_EXP_CD51-SCA1-_stroma_Day12


title: RNAseq_ctrl_CD51-SCA1-_stroma_Day15


title: STL003.SX3.SRC1006


title: RNAseq_EXP_CD44_stroma_Day20


title: STL003.LV3.ADS125_129

source_name: Left Ventricle

value: Left Ventricle


title: RNAseq_EXP_CD44_stroma_Day12


title: hESC.e5.rep2

data_processing:
Read pairs from Promoter Capture Hi-C library were independently mapped to human genome hg19 using BWA-mem and manually paired with in house script.
Unmapped, non-uniquely mapped, and PCR duplicates were removed.
Trans-chromosomal read pairs and putative self-ligated products (<15kb read pairs) were removed.
Off-target reads were removed when both read pairs did not match to capture probe sequences.
Raw RNA-seq fastq files were aligned to the reference genome (hg19) using BWA-mem. Duplicate reads were discard with Picard to avoid any artifact caused by amplification step originated from Ovation® RNA-Seq System V2 (NuGEN). Then, FPKM values were calculated using Cufflink with GENCODE v19 annotation.
Genome_build: Hg19
Supplementary_files_format_and_content: *.po and *.pp provide interaction frequencies for promoter-promoter interactions or promoter-other interactions, respectively.  We combined multiple donors or replicates according to cell/tissue types.


title: STL002.LG2.SRC739

source_name: Lung

value: Lung


title: RNAseq_EXP_CD44_stroma_Day7


title: RNAseq_ctrl_CD44_stroma_Day15


title: hESC.e5.rep1


title: RNAseq_ctrl_CD44_stroma_Day12b


title: STL001.SB1.SRC736

source_name: Small Bowel

value: Small Bowel


title: RNAseq_EXP_CD51-SCA1-_stroma_Day15


title: RNAseq_ctrl_CD44_stroma_Day12


title: STL003.LV3.ADS125_2_129_2


title: hESC.e1.c23.rep2


title: RNAseq_ctrl_CD51-SCA1-_stroma_Day15b


title: RNAseq_EXP_CD44_stroma_Day15


title: hESC.e1.c19.rep2


title: hESC.WA01.WT.rep2


title: hESC.e1.c19.rep1


title: 880

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

address: 120 Mason Farm Rd

department: Genetics

institute: The University of North Carolina at Chapel Hill

data_processing:
Fastx toolkit was used to remove low quality reads; reads with phred quality > 20 for 80% of bases were retained.
Tagdust was used to identify and remove reads containing adapter and linker sequences.
STAR (version 2.4.2a) was used as the aligner, with hg19 and GENCODE v19 as annotation; STAR was run, using a 2-pass strategy, were splice locations from the first pass were used as additional annotation for the second pass.
salmon (version 0.7.2) was used to estimate isoform abundance from aligned BAM files; GENCODE 19 was used as annotation. --gcBias option was used.
tximport (version 1.0.3) was used to collapse isoform abundance estimates from salmon to gene abuddance estimates
Genome_build: hg19
Supplementary_files_format_and_content: Abundance measurements generated using salmon and tximport; values represent the transcripts per million (TPM) estimate of gene abundance.

source_name: subcutaneous adipose tissue

extract_protocol:
Subcutaneous adipose needle biopsies were obtained from near the umbilicus of men from the METSIM cohort. RNA was isolated using the QIAGEN miRNeasy kit.
Libraries were constructed using a polyA+ selection protocol (Illumina TruSeq RNA Sample Preparation Kit v2)

tag: Sex

value: male

tag: sequencing batch

value: batch 4

tag: transcript integrity number

tag: bmi


title: 10510


title: 8302


title: 7624


title: 8075


title: 7930


title: 7791


title: 7431


title: 7384


title: 7381


title: hESC.e1.c16.rep2

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

institute: KAIST


title: 7200


title: hESC.e1.c23.rep1


title: 7033


title: 7362


title: 6855


title: RNAseq_ctrl_MPC_stroma_Day15

tag: strain


title: hESC.e1.c16.rep1


title: 6628


title: 6525


title: 7921


title: 6366


title: 6425


title: 555


title: 6040


title: hESC.WA01.WT.rep1


title: 5006


title: 7462


title: 4123


title: 369


title: 4380


title: 4822


title: 4370


title: 2519


title: 4649


title: 2430


title: 2281


title: 2064


title: 2054


title: 1867


title: 1449


title: 1747


title: 1743


title: 1797


title: 2222


title: 6287


title: 1649


title: 6755


title: 1580


title: 2785


title: 6135


title: 1520


title: 1573


title: 2935


title: 1974


title: 11765


title: 1855


title: Huh7_N_30_3

city: Rotterdam

first: Qiuwei

last: Pan

address: Wytemaweg 80

country: Netherlands

institute: Erasmus University Medical Center

data_processing:
Double- atranded cDNA synthesis
End repair, poly-A & adaptor addition
Fragments selection and PCR
Libary quality assessement
illumina sequencing
Genome_build: mm8

growth_protocol: HCC cell line with DMEM medium

extract_protocol:
RNA isolation kit from thermo fisher
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OPA1 knock down with lentivirus

value: Human hepatocellular carcinoma (HCC) cell line

tag: cell line

value: OPA1 knock-down


title: Huh7_N_30_2


title: Huh7_N_28_3


title: Huh7_N_30_1


title: Huh7_N_28_2


title: 11735


title: Huh7_N_28_1


title: 11658


title: 11724


title: Huh7_ctr3

value: control


title: 1020


title: Huh7_ctr2


title: Huh7_ctr1


title: 5525


title: 1063


title: 1502


title: 10829


title: 6266


title: 1257


title: 7091


title: 10864


title: 11731


title: 422


title: 11132


title: 1803


title: 11102


title: 10940


title: Sample6.G2

city: Woodbury

first: Ashraf

last: Shabaneh

state: MN

address: 2768 Liberty Trail

institute: University of Minnesota

data_processing:
Illumina HiSeq 2500® generates binary base call (BCL) files using Sequencing Analysis Viewer. bcl2fastq was then used to generate FASTQ files to perform alignments.
Alignments were preformed using Tophat.
Assemblies were further proccessed by Cufflinks.
Reads were normalized by FPKM.
Genome_build: Human Genome Reference 19.
Supplementary_files_format_and_content: Gene Annotation on the x axis, samples are on the y axis, with read values normalized by FPKM.

source_name: GVHD Colon Biopsie_Refractory

growth_protocol: biopsie collection didn't involve culturing.

extract_protocol:
PureLink® FFPE RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) was used for RNA extraction.
Libraries were prepared using  Illumina HiSeq 2500® platform.

treatment_protocol: disease stages and survivability were studed rather than treatments.

tag: gvhd stage

value: Refractory

tag: gender

value: Female

tag: survival


title: Sample2.G2


title: Sample23.G2


title: Sample4.G2

value: Male


title: Sample20.G2


title: Sample5.G2


title: Sample22.G2


title: Sample19.G2


title: Sample21.G2


title: Sample7.G2


title: Sample3.G2


title: Sample9.G2


title: 10903


title: Sample18.G2


title: 10715


title: 10697


title: Sample17.G2


title: Sample16.G2


title: 10534


title: 10521


title: 11149


title: Sample15.G2


title: Sample14.G2


title: 10373


title: 11000


title: 10292


title: RNAseq_EXP_MSC_stroma_Day7

value: WT

tag: cell type


title: Sample13.G2

tag: age


title: JP18

value: Inclusion Body Myositis

value: Negative


title: Sample1.G2


title: Sample10.G2


title: Sample9.G1

source_name: GVHD Colon Biopsie_onset

value: Onset


title: Sample11.G2


title: Sample12.G2


title: 10108


title: 10419

value: batch 3


title: 10156


title: 10247


title: 10830


title: Sample5.G1


title: Sample7.G1


title: 10389


title: Sample4.G1


title: Sample23.G1


title: Sample22.G1


title: 10252


title: 10271


title: 10381


title: 10482


title: 10049


title: Sample21.G1


title: 10097


title: Sample18.G1


title: Sample13.G1


title: Sample3.G1


title: Sample11.G1


title: 7897


title: 7343


title: 7611


title: 7421


title: Sample10.G1


title: 7080


title: 6978


title: 7948


title: 10691


title: Sample1.G1


title: Sample6.G1


title: 7436


title: Sample16.G1


title: 7530


title: Sample20.G1


title: Normal9

source_name: Healthy Colon Biopsie

value: Control


title: Sample2.G1


title: Sample19.G1


title: 8067


title: Sample12.G1


title: Sample17.G1


title: Sample14.G1


title: 7954


title: 7927


title: Sample15.G1


title: 6969


title: 7988


title: 6959


title: Normal8


title: 6725


title: Normal5


title: Normal6


title: Normal7


title: Normal4


title: 6781


title: 6835


title: 6684


title: 6675


title: 6671


title: 6589


title: 6680


title: Normal2


title: Normal10


title: Normal1


title: 6419


title: 6484


title: 6183


title: 6200


title: 6517


title: 6101


title: 6283


title: 6433


title: Normal3


title: Input_SynT_MN_rep2

city: Dallas

first: Youn

last: Kwak

address: 5323 Harry Hines Blvd

department: Microbiology

institute: UT-Southwestern Medical Center

data_processing:
The ChIP-seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 75 for R1 for single-end data.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: trophoblast primary culture

growth_protocol: Trophoblasts in primary culture were maintained DMEM/F12 media with 10% FBS and 1% antibiotic and antimycotic.

extract_protocol:
Trophoblasts were crosslinked with 1% formaldehyd and then either treated with Mnase or sheared to 200-500 bp by ultrasonication. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: Trophoblasts were isolated from human mid-gestation placenta by treatment of DNAse I and trypsin followed by Percoll gradient. Cells were harvested either before (0h) and 18h after culture.

value: Mid-gestation placenta

tag: chip antibody

tag: shearing

value: Mnase

tag: cell culture

value: trophoblast primary culture

tag: treatment

value: Synotrophoblast (18h)


title: 6515

value: male


title: Input_SynT_MN_rep1

tag: tissue


title: H3K27me3_SynT_MN_rep1

value: H3K27me3 (CS9733, Cell Signaling)


title: 6051


title: 6083


title: 5935


title: 5901


title: 5951


title: H3K9Ac_SynT_MN_rep2

value: H3K9Ac (ab4441, Abcam)


title: H3K9Ac_SynT_MN_rep1


title: 5859


title: 5571


title: 5530


title: H3K9Ac_CytT_MN_rep2

value: Cytotrophoblast (0h)


title: H3K9Ac_CytT_MN_rep1


title: H3K4me3_SynT_MN_rep2

value: H3K4me3 (39159, Active Motif)


title: H3K27me3_SynT_MN_rep2


title: 5521


title: 5510


title: 5470


title: H3K27Ac_SynT_MN_rep2

value: H3K27Ac (39133, Active Motif)


title: H3K27Ac_SynT_MN_rep1


title: H3K4me3_SynT_MN_rep1


title: H3K27Ac_CytT_MN_rep2


title: 5273


title: 5263


title: 5352


title: 5458


title: 4336


title: H3K27Ac_CytT_MN_rep1


title: Input_SynT_soni_rep2

value: Sonication


title: 4644


title: Input_SynT_soni_rep1


title: 2775


title: 2488


title: Input_CytT_soni_rep2


title: 2655


title: Input_CytT_soni_rep1


title: 2474


title: PolII_SynT_soni_rep2

value: RNA polymerase (sc-899, Santa Cruz)


title: 2338


title: PolII_SynT_soni_rep1


title: 2261


title: PolII_CytT_soni_rep2


title: PolII_CytT_soni_rep1


title: 2165


title: 2057


title: LM2-4175 replicate 2

city: Shanghai

first: Ji

last: Zhang

state: Select a State or Province

address: 197 Ruijin 2nd Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
RNA-Seq reads were mapped to human reference genome (hg19) using Tophat2 with default parameters
FPKM value for each gene was calculated by cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in MDA-MB-231 and LM2-4175 cell lines

source_name: LM2-4175 cell line

growth_protocol: The human breast cancer cell line MDA-MB-231 and LM2-4175 were cultured in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (Gibco BRL, Grand Island, NY, USA) at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Cellular RNA was isolated by Tri-Reagent using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.
RNA sequencing libraries were prepared according to the IlluminaTruseq TM  RNA sample prep Kit

value: breast cancer cell line


title: 2019


title: 1924


title: 1915


title: 1892


title: LM2-4175 replicate 1


title: 1896


title: LM2-H3K27me3

data_processing:
All of the reads were mapped to unmasked human reference genome (hg19) using Bowtie2 with default parameters
Only uniquely mapped reads were retained, and duplicated reads were compressed to single read by samtools
ChIP-seq peak calling was performed using MACS v2.0.10(32), with“–broad” option.
Regions with q-value less than 0.01 were identified as peaks
For each cell line, the respective ChIP inputs were used as control data
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated using bedtools

growth_protocol: The human breast cancer cell line MDA-MB-231 and LM2-4175 were cultured in DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (Gibco BRL, Grand Island, NY, USA) at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
For chromatin immunoprecipitation, MDA-MB-231 and LM2-4175 cells were harvested and performed by ChIP-IT High Sensitivity kit (Active Motif, #53040) according to manufacturer's instructions
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303)

tag: antibody vendorname

value: Abcam

tag: antibody vendorid


title: LM2-input

value: input


title: LM2-Pol-II

value: Pol-II


title: LM2-H3K27ac


title: 1777

tag: Sex

tag: sequencing batch

value: batch 3


title: 1840

tag: transcript integrity number

tag: bmi


title: 1757


title: LM2-H3K4me1

tag: cell line


title: 1768


title: LM2-H3K4me3


title: 1725


title: 1764